#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Confidence	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_NTotCov	i_NVarCov	i_NVarRat	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_TVarRat	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNP_AF	i_dbSNP_PopFreq	i_dbSNP_Strength	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
KMT2D	8085	hgsc.bcm.edu	37	12	49426385	49426388	+	Frame_Shift_Del	DEL	AAGA	AAGA	-			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	AAGA	AAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr12:49426385_49426388delAAGA	ENST00000301067.7	-	39	12099_12102	c.12100_12103delTCTT	c.(12100-12105)tcttcafs	p.SS4034fs	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	4034	Gln-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										GTGGCCTCTGAAGAAACGGCTGGG	0.569																																					p.4034_4035del		Pindel,Atlas-Indel	.											.	MLL2	1173	.	0			c.12101_12104del						PASS	.																																			SO:0001589	frameshift_variant	8085	exon39			.	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7133	protein-coding gene	gene with protein product		602113	"""trinucleotide repeat containing 21"", ""myeloid/lymphoid or mixed-lineage leukemia 2"""	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.12100_12103delTCTT	12.37:g.49426385_49426388delAAGA	ENSP00000301067:p.Ser4034fs	153.0	0.0	.		71.0	34.0	0.479	NM_003482	O14687	Frame_Shift_Del	DEL	ENST00000301067.7	37	CCDS44873.1																																																																																			.	.	none		0.569	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
HLA-B	3106	hgsc.bcm.edu	37	6	31323097	31323098	+	Frame_Shift_Ins	INS	-	-	T	rs281864645		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr6:31323097_31323098insT	ENST00000412585.2	-	4	919_920	c.891_892insA	c.(889-894)agatggfs	p.W298fs		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	298	Alpha-3.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						TCCTTACCCCATCTCAGGGTGA	0.594									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.W298fs		Atlas-Indel	.											.	HLA-B	54	.	0			c.892_893insA						PASS	.																																			SO:0001589	frameshift_variant	3106	exon4	Familial Cancer Database	;Lichen Sclerosis, Familial	.	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.892dupA	6.37:g.31323098_31323098dupT	ENSP00000399168:p.Trp298fs	65.0	0.0	0		56.0	20.0	0.357143	NM_005514	Q29764	Frame_Shift_Ins	INS	ENST00000412585.2	37	CCDS34394.1																																																																																			.	.	none		0.594	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
MUC2	4583	hgsc.bcm.edu	37	11	1092688	1092689	+	In_Frame_Ins	INS	-	-	CAA			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr11:1092688_1092689insCAA	ENST00000441003.2	+	30	4534_4535	c.4507_4508insCAA	c.(4507-4509)cca>cCAAca	p.1506_1507insT	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_In_Frame_Ins_p.1507_1508insT|MUC2_ENST00000333592.6_5'Flank	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4241	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)	tcccagccctccaacgactacg	0.634																																					p.P1503delinsPT		Atlas-Indel	.											.	MUC2	614	.	0			c.4507_4508insCAA						PASS	.																																			SO:0001652	inframe_insertion	4583	exon30			.	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.4508_4510dupCAA	11.37:g.1092689_1092691dupCAA	ENSP00000415183:p.Thr1506_Thr1506dup	122.0	0.0	0		119.0	13.0	0.109244	NM_002457	Q14878	In_Frame_Ins	INS	ENST00000441003.2	37																																																																																				.	.	none		0.634	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
DMD	1756	hgsc.bcm.edu	37	X	32407663	32407664	+	Frame_Shift_Ins	INS	-	-	T	rs398123957		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chrX:32407663_32407664insT	ENST00000357033.4	-	32	4678_4679	c.4472_4473insA	c.(4471-4473)aagfs	p.K1491fs	DMD_ENST00000378677.2_Frame_Shift_Ins_p.K1487fs	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	1491	Interaction with SYNM. {ECO:0000250}.				cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				GTTCCACACTCTTTGTTTCCAA	0.401																																					p.K1491fs		Pindel,Atlas-Indel	.											.	DMD	2127	.	0			c.4473_4474insA						PASS	.																																			SO:0001589	frameshift_variant	1756	exon32			.	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"""muscular dystrophy, Duchenne and Becker types"""	300377	"""dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272"", ""mental retardation, X-linked 85"""	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.4473dupA	X.37:g.32407666_32407666dupT	ENSP00000354923:p.Lys1491fs	251.0	0.0	.		204.0	44.0	0.216	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Frame_Shift_Ins	INS	ENST00000357033.4	37	CCDS14233.1																																																																																			.	.	none		0.401	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
UBASH3A	53347	hgsc.bcm.edu	37	21	43826425	43826436	+	In_Frame_Del	DEL	CGTTGGCAGCCA	CGTTGGCAGCCA	-			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	CGTTGGCAGCCA	CGTTGGCAGCCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr21:43826425_43826436delCGTTGGCAGCCA	ENST00000319294.6	+	2	153_164	c.122_133delCGTTGGCAGCCA	c.(121-135)gcgttggcagccacg>gcg	p.LAAT42del	UBASH3A_ENST00000398367.1_In_Frame_Del_p.LAAT42del|UBASH3A_ENST00000450356.1_In_Frame_Del_p.LAAT42del|UBASH3A_ENST00000291535.6_In_Frame_Del_p.LAAT42del	NM_018961.3	NP_061834.1	P57075	UBS3A_HUMAN	ubiquitin associated and SH3 domain containing A	42	UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.				negative regulation of T cell receptor signaling pathway (GO:0050860)|regulation of cytokine production (GO:0001817)	cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)	p.A44V(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(9)|lung(12)|ovary(3)	28						AGGCTGAAAGCGTTGGCAGCCACGGGGAGGAA	0.604																																					p.41_44del		Pindel,Atlas-Indel	.											.	UBASH3A	72	.	1	Substitution - Missense(1)	central_nervous_system(1)	c.121_132del						PASS	.																																			SO:0001651	inframe_deletion	53347	exon2			.	AJ277750	CCDS13687.1, CCDS33566.1, CCDS58791.1	21q22.3	2010-04-28	2010-04-28		ENSG00000160185	ENSG00000160185			12462	protein-coding gene	gene with protein product		605736				11281453	Standard	NM_018961		Approved	STS-2, TULA, CLIP4	uc002zbf.3	P57075	OTTHUMG00000086805	ENST00000319294.6:c.122_133delCGTTGGCAGCCA	21.37:g.43826425_43826436delCGTTGGCAGCCA	ENSP00000317327:p.Leu42_Thr45del	77.0	0.0	.		66.0	14.0	0.212	NM_018961	G5E9E4|Q6HA34|Q6HA35|Q6ISI6|Q6ISK3|Q6ISS9	In_Frame_Del	DEL	ENST00000319294.6	37	CCDS13687.1																																																																																			.	.	none		0.604	UBASH3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195382.1	NM_001001895	
MRPL14	64928	hgsc.bcm.edu	37	6	44081581	44081584	+	Stop_Codon_Del	DEL	CACA	CACA	-			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	CACA	CACA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr6:44081581_44081584delCACA	ENST00000372014.3	-	0	565_568					NM_032111.2	NP_115487.2	Q6P1L8	RM14_HUMAN	mitochondrial ribosomal protein L14						translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	12	all_cancers(18;1.66e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00309)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0181)			GGGCTCAACTCACACAAAGTTCTG	0.574																																					p.145_146del		Pindel,Atlas-Indel	.											.	MRPL14	15	.	0			c.435_438del						PASS	.																																			SO:0001567	stop_retained_variant	64928	exon3			.	AB051339	CCDS34460.1	6p21.3	2012-09-13			ENSG00000180992	ENSG00000180992		"""Mitochondrial ribosomal proteins / large subunits"""	14279	protein-coding gene	gene with protein product		611827					Standard	XM_005249300		Approved	RPML32, MRP-L32	uc003owp.3	Q6P1L8	OTTHUMG00000014756	Exception_encountered	6.37:g.44081581_44081584delCACA	Exception_encountered	48.0	0.0	.		62.0	20.0	0.323	NM_032111	B2R575|Q96Q72	Frame_Shift_Del	DEL	ENST00000372014.3	37	CCDS34460.1																																																																																			.	.	none		0.574	MRPL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040707.1	NM_032111	
BFAR	51283	hgsc.bcm.edu	37	16	14738262	14738262	+	Missense_Mutation	SNP	T	T	C			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr16:14738262T>C	ENST00000261658.2	+	2	336	c.59T>C	c.(58-60)cTc>cCc	p.L20P	BFAR_ENST00000426842.2_5'UTR|BFAR_ENST00000563971.1_Missense_Mutation_p.L20P|RNU7-125P_ENST00000458760.1_RNA	NM_016561.2	NP_057645.1	Q9NZS9	BFAR_HUMAN	bifunctional apoptosis regulator	20					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	structural molecule activity (GO:0005198)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|skin(1)	11						GATGAACCTCTCAAAAGCACC	0.458																																					p.L20P		Atlas-SNP	.											.	BFAR	38	.	0			c.T59C						PASS	.						119.0	120.0	120.0					16																	14738262		2197	4300	6497	SO:0001583	missense	51283	exon2			AACCTCTCAAAAG	AF173003	CCDS10554.1	16p13.2	2013-01-10			ENSG00000103429	ENSG00000103429		"""RING-type (C3HC4) zinc fingers"", ""Sterile alpha motif (SAM) domain containing"""	17613	protein-coding gene	gene with protein product						10716992	Standard	NM_016561		Approved	BAR, RNF47	uc002dco.3	Q9NZS9	OTTHUMG00000129848	ENST00000261658.2:c.59T>C	16.37:g.14738262T>C	ENSP00000261658:p.Leu20Pro	106.0	0.0	0		107.0	33.0	0.308411	NM_016561	A8K4Z9|B4DUT0|D3DUG8	Missense_Mutation	SNP	ENST00000261658.2	37	CCDS10554.1	.	.	.	.	.	.	.	.	.	.	T	16.84	3.233880	0.58886	.	.	ENSG00000103429	ENST00000261658	T	0.07688	3.17	5.91	2.28	0.28536	.	1.291620	0.04794	N	0.432159	T	0.07638	0.0192	L	0.29908	0.895	0.09310	N	0.999997	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.06405	0.002;0.001;0.001	T	0.38090	-0.9677	10	0.87932	D	0	.	4.258	0.10726	0.1421:0.2437:0.0:0.6142	.	20;20;20	B2R9R6;Q9NZS9;B4DLM6	.;BFAR_HUMAN;.	P	20	ENSP00000261658:L20P	ENSP00000261658:L20P	L	+	2	0	BFAR	14645763	0.000000	0.05858	0.000000	0.03702	0.207000	0.24258	0.786000	0.26844	0.498000	0.27948	0.533000	0.62120	CTC	.	.	none		0.458	BFAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252088.1	NM_016561	
PIM1	5292	hgsc.bcm.edu	37	6	37138372	37138372	+	Silent	SNP	C	C	T			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr6:37138372C>T	ENST00000373509.5	+	1	394	c.21C>T	c.(19-21)aaC>aaT	p.N7N		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	98					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)	CCAAAATCAACTCGCTTGCCC	0.721			T	BCL6	NHL																																p.N98N		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.C294T						PASS	.						31.0	31.0	31.0					6																	37138372		2202	4298	6500	SO:0001819	synonymous_variant	5292	exon1			AATCAACTCGCTT		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.21C>T	6.37:g.37138372C>T		70.0	0.0	0		54.0	20.0	0.37037	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		
PDE3A	5139	hgsc.bcm.edu	37	12	20787928	20787928	+	Nonsense_Mutation	SNP	A	A	T			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr12:20787928A>T	ENST00000359062.3	+	8	1979	c.1939A>T	c.(1939-1941)Aga>Tga	p.R647*	PDE3A_ENST00000544307.1_3'UTR	NM_000921.4|NM_001244683.1	NP_000912.3|NP_001231612.1	Q14432	PDE3A_HUMAN	phosphodiesterase 3A, cGMP-inhibited	647					blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cGMP (GO:0071321)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cGMP-mediated signaling (GO:0019934)|diterpenoid metabolic process (GO:0016101)|lipid metabolic process (GO:0006629)|negative regulation of apoptotic process (GO:0043066)|negative regulation of vascular permeability (GO:0043116)|oocyte maturation (GO:0001556)|positive regulation of oocyte development (GO:0060282)|positive regulation of vascular permeability (GO:0043117)|regulation of meiosis (GO:0040020)|response to cAMP (GO:0051591)|response to drug (GO:0042493)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|cAMP binding (GO:0030552)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(7)|lung(29)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	58	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Caffeine(DB00201)|Cilostazol(DB01166)|Enoximone(DB04880)|Ibudilast(DB05266)|Levosimendan(DB00922)|Milrinone(DB00235)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Tofisopam(DB08811)	AGAGTGCCTGAGAGAGCCTCT	0.428																																					p.R647X		Atlas-SNP	.											.	PDE3A	184	.	0			c.A1939T						PASS	.						141.0	120.0	127.0					12																	20787928		2203	4300	6503	SO:0001587	stop_gained	5139	exon8			TGCCTGAGAGAGC		CCDS31754.1	12p12.2	2011-04-15			ENSG00000172572	ENSG00000172572	3.1.4.17	"""Phosphodiesterases"""	8778	protein-coding gene	gene with protein product		123805				1315035, 10679291	Standard	NM_000921		Approved	CGI-PDE	uc001reh.2	Q14432	OTTHUMG00000168962	ENST00000359062.3:c.1939A>T	12.37:g.20787928A>T	ENSP00000351957:p.Arg647*	71.0	0.0	0		63.0	21.0	0.333333	NM_000921	O60865|Q13348|Q17RD1	Nonsense_Mutation	SNP	ENST00000359062.3	37	CCDS31754.1	.	.	.	.	.	.	.	.	.	.	A	35	5.494917	0.96339	.	.	ENSG00000172572	ENST00000359062	.	.	.	5.64	3.24	0.37175	.	1.494490	0.03493	N	0.216863	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08837	T	0.75	.	8.1704	0.31252	0.7944:0.1351:0.0705:0.0	.	.	.	.	X	647	.	ENSP00000351957:R647X	R	+	1	2	PDE3A	20679195	0.968000	0.33430	0.004000	0.12327	0.015000	0.08874	2.527000	0.45615	0.405000	0.25532	0.528000	0.53228	AGA	.	.	none		0.428	PDE3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401756.2		
PTPRZ1	5803	hgsc.bcm.edu	37	7	121684560	121684560	+	Missense_Mutation	SNP	T	T	C			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr7:121684560T>C	ENST00000393386.2	+	23	6433	c.6022T>C	c.(6022-6024)Tat>Cat	p.Y2008H	PTPRZ1_ENST00000449182.1_Missense_Mutation_p.Y1141H	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	2008					axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						TATTCATGCCTATGTTAATGC	0.438																																					p.Y2008H		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.T6022C						PASS	.						156.0	142.0	147.0					7																	121684560		2203	4300	6503	SO:0001583	missense	5803	exon23			CATGCCTATGTTA	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.6022T>C	7.37:g.121684560T>C	ENSP00000377047:p.Tyr2008His	123.0	0.0	0		107.0	34.0	0.317757	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	37	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	T	18.34	3.602779	0.66445	.	.	ENSG00000106278	ENST00000393386;ENST00000449182	T;T	0.11169	2.8;2.8	5.5	5.5	0.81552	.	0.000000	0.64402	D	0.000016	T	0.32041	0.0816	M	0.69823	2.125	0.80722	D	1	D;P;D	0.89917	1.0;0.614;1.0	D;P;D	0.91635	0.999;0.517;0.999	T	0.01988	-1.1234	10	0.33141	T	0.24	.	15.6052	0.76664	0.0:0.0:0.0:1.0	.	1147;1141;2008	P23471-2;C9JFM0;P23471	.;.;PTPRZ_HUMAN	H	2008;1141	ENSP00000377047:Y2008H;ENSP00000410000:Y1141H	ENSP00000377047:Y2008H	Y	+	1	0	PTPRZ1	121471796	1.000000	0.71417	0.999000	0.59377	0.512000	0.34134	8.040000	0.89188	2.091000	0.63221	0.533000	0.62120	TAT	.	.	none		0.438	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851	
FAT4	79633	hgsc.bcm.edu	37	4	126370300	126370300	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr4:126370300G>A	ENST00000394329.3	+	9	8142	c.8129G>A	c.(8128-8130)gGc>gAc	p.G2710D	FAT4_ENST00000335110.5_Missense_Mutation_p.G1008D	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	2710	Cadherin 26. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						ATTGTTAATGGCAACATGGAA	0.373																																					p.G2710D		Atlas-SNP	.											.	FAT4	1752	.	0			c.G8129A						PASS	.						103.0	102.0	103.0					4																	126370300		2203	4299	6502	SO:0001583	missense	79633	exon9			TTAATGGCAACAT	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.8129G>A	4.37:g.126370300G>A	ENSP00000377862:p.Gly2710Asp	97.0	0.0	0		81.0	25.0	0.308642	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	18.26	3.584637	0.65992	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.01767	4.65;4.65	5.9	5.9	0.94986	Cadherin (4);Cadherin-like (1);	0.000000	0.35067	U	0.003472	T	0.08268	0.0206	L	0.49513	1.565	0.80722	D	1	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.97110	1.0;0.998;1.0	T	0.49331	-0.8951	10	0.22706	T	0.39	.	20.2789	0.98501	0.0:0.0:1.0:0.0	.	1008;2710;2710	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	D	2710;1008	ENSP00000377862:G2710D;ENSP00000335169:G1008D	ENSP00000335169:G1008D	G	+	2	0	FAT4	126589750	1.000000	0.71417	0.960000	0.40013	0.495000	0.33615	9.666000	0.98612	2.788000	0.95919	0.650000	0.86243	GGC	.	.	none		0.373	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
DLGAP3	58512	hgsc.bcm.edu	37	1	35369943	35369943	+	Missense_Mutation	SNP	C	C	T			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr1:35369943C>T	ENST00000373347.1	-	3	1310	c.1042G>A	c.(1042-1044)Ggg>Agg	p.G348R	DLGAP3_ENST00000495979.1_5'Flank|DLGAP3_ENST00000235180.4_Missense_Mutation_p.G348R			O95886	DLGP3_HUMAN	discs, large (Drosophila) homolog-associated protein 3	348					cell-cell signaling (GO:0007267)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)	beta-amyloid binding (GO:0001540)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(23)|ovary(4)|prostate(3)|skin(3)|urinary_tract(1)	46		Myeloproliferative disorder(586;0.0393)				TTGCCTGGCCCGGCCCCCGGG	0.602																																					p.G348R		Atlas-SNP	.											.	DLGAP3	107	.	0			c.G1042A						PASS	.						40.0	42.0	41.0					1																	35369943		2200	4293	6493	SO:0001583	missense	58512	exon1			CTGGCCCGGCCCC	AF131778	CCDS30670.1	1p35.3-p34.1	2008-02-05			ENSG00000116544	ENSG00000116544			30368	protein-coding gene	gene with protein product		611413				8619474, 9110174	Standard	NM_001080418		Approved	SAPAP3, DAP3	uc001byc.3	O95886	OTTHUMG00000004049	ENST00000373347.1:c.1042G>A	1.37:g.35369943C>T	ENSP00000362444:p.Gly348Arg	15.0	0.0	0		28.0	14.0	0.5	NM_001080418	Q5TDD5|Q9H3X7	Missense_Mutation	SNP	ENST00000373347.1	37	CCDS30670.1	.	.	.	.	.	.	.	.	.	.	C	18.76	3.692621	0.68271	.	.	ENSG00000116544	ENST00000373347;ENST00000235180;ENST00000542913	T;T	0.26373	1.74;1.74	4.49	4.49	0.54785	.	0.164823	0.53938	D	0.000053	T	0.42854	0.1221	L	0.36672	1.1	0.53005	D	0.999961	D	0.89917	1.0	D	0.83275	0.996	T	0.40175	-0.9577	10	0.72032	D	0.01	-16.0127	17.7338	0.88387	0.0:1.0:0.0:0.0	.	348	O95886	DLGP3_HUMAN	R	348;348;31	ENSP00000362444:G348R;ENSP00000235180:G348R	ENSP00000235180:G348R	G	-	1	0	DLGAP3	35142530	0.997000	0.39634	0.961000	0.40146	0.937000	0.57800	3.622000	0.54217	2.492000	0.84095	0.655000	0.94253	GGG	.	.	none		0.602	DLGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011554.1	NM_021234	
C7orf61	402573	hgsc.bcm.edu	37	7	100061611	100061611	+	Missense_Mutation	SNP	C	C	T			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr7:100061611C>T	ENST00000332375.3	-	1	283	c.38G>A	c.(37-39)cGg>cAg	p.R13Q	RN7SL161P_ENST00000582642.1_RNA|TSC22D4_ENST00000496728.1_5'UTR	NM_001004323.1	NP_001004323.1	Q8IZ16	CG061_HUMAN	chromosome 7 open reading frame 61	13						nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|prostate(1)|skin(1)	4						TTGCCAAGCCCGTCTAACCCA	0.532																																					p.R13Q		Atlas-SNP	.											.	C7orf61	12	.	0			c.G38A						PASS	.						60.0	56.0	57.0					7																	100061611		1940	4153	6093	SO:0001583	missense	402573	exon1			CAAGCCCGTCTAA		CCDS47661.1	7q22.1	2013-10-11			ENSG00000185955	ENSG00000185955			22135	protein-coding gene	gene with protein product						12690205	Standard	NM_001004323		Approved	IMAGE:4839025	uc003uuz.1	Q8IZ16	OTTHUMG00000150234	ENST00000332375.3:c.38G>A	7.37:g.100061611C>T	ENSP00000327732:p.Arg13Gln	77.0	0.0	0		82.0	27.0	0.329268	NM_001004323		Missense_Mutation	SNP	ENST00000332375.3	37	CCDS47661.1	.	.	.	.	.	.	.	.	.	.	C	4.827	0.153693	0.09185	.	.	ENSG00000185955	ENST00000332375	.	.	.	2.64	-0.9	0.10544	.	.	.	.	.	T	0.12305	0.0299	N	0.04508	-0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30268	-0.9984	8	0.07030	T	0.85	-2.9938	4.6723	0.12694	0.0:0.5405:0.1821:0.2774	.	13	Q8IZ16	CG061_HUMAN	Q	13	.	ENSP00000327732:R13Q	R	-	2	0	C7orf61	99899547	0.000000	0.05858	0.000000	0.03702	0.379000	0.30106	-0.051000	0.11885	-0.822000	0.04306	-1.401000	0.01141	CGG	.	.	none		0.532	C7orf61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316976.2	NM_001004323	
ANKFN1	162282	hgsc.bcm.edu	37	17	54403699	54403699	+	Silent	SNP	C	C	T			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr17:54403699C>T	ENST00000318698.2	+	3	215	c.180C>T	c.(178-180)gcC>gcT	p.A60A	ANKFN1_ENST00000566473.2_Silent_p.A60A	NM_153228.2	NP_694960.2	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain containing 1	60										NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(11)|lung(27)|ovary(1)|prostate(1)|skin(1)	53						CCTCTGCTGCCTCGAACAGCA	0.373																																					p.A60A		Atlas-SNP	.											.	ANKFN1	115	.	0			c.C180T						PASS	.						132.0	119.0	123.0					17																	54403699		2203	4300	6503	SO:0001819	synonymous_variant	162282	exon3			TGCTGCCTCGAAC	AK095654	CCDS32686.1	17q23.2	2014-02-12	2005-11-15		ENSG00000153930	ENSG00000153930		"""Ankyrin repeat domain containing"", ""Fibronectin type III domain containing"""	26766	protein-coding gene	gene with protein product							Standard	NM_153228		Approved	FLJ38335	uc002iun.1	Q8N957	OTTHUMG00000155010	ENST00000318698.2:c.180C>T	17.37:g.54403699C>T		145.0	0.0	0		118.0	35.0	0.29661	NM_153228		Silent	SNP	ENST00000318698.2	37	CCDS32686.1																																																																																			.	.	none		0.373	ANKFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338043.1	NM_153228	
ETV6	2120	hgsc.bcm.edu	37	12	11803095	11803095	+	Splice_Site	SNP	G	G	A			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr12:11803095G>A	ENST00000396373.4	+	1	307		c.e1+1		ETV6_ENST00000544715.1_Splice_Site	NM_001987.4	NP_001978.1	P41212	ETV6_HUMAN	ets variant 6						cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	protein domain specific binding (GO:0019904)|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)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)		ETV6/JAK2(11)|ETV6/ITPR2(2)|ETV6/NTRK3(238)	breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(15)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(2;1.88e-12)|Acute lymphoblastic leukemia(2;6.91e-39)|all_hematologic(2;2.7e-36)				TAGCATTAAGGTAAAAATCTT	0.532			T	"""NTRK3, RUNX1, PDGFRB, ABL1, MN1, ABL2, FACL6, CHIC2, ARNT, JAK2, EVI1, CDX2, STL, HLXB9, MDS2, PER1, SYK, TTL, FGFR3, PAX5"""	"""congenital fibrosarcoma, multiple leukemia and lymphoma,  secretory breast, MDS, ALL"""																																.		Atlas-SNP	.		Dom	yes		12	12p13	2120	ets variant gene 6 (TEL oncogene)		"""L, E, M"""	.	ETV6	91	.	0			c.33+1G>A						PASS	.						137.0	133.0	134.0					12																	11803095		2203	4300	6503	SO:0001630	splice_region_variant	2120	exon1			ATTAAGGTAAAAA	BC043399	CCDS8643.1	12p13	2014-09-17	2008-09-12		ENSG00000139083	ENSG00000139083			3495	protein-coding gene	gene with protein product	"""TEL oncogene"""	600618	"""ets variant gene 6 (TEL oncogene)"""			7731705	Standard	NM_001987		Approved	TEL	uc001qzz.3	P41212	OTTHUMG00000168538	ENST00000396373.4:c.33+1G>A	12.37:g.11803095G>A		47.0	0.0	0		26.0	16.0	0.615385	NM_001987	A3QVP6|A8K076|Q9UMF6|Q9UMF7|Q9UMG0	Splice_Site	SNP	ENST00000396373.4	37	CCDS8643.1	.	.	.	.	.	.	.	.	.	.	G	14.53	2.561598	0.45590	.	.	ENSG00000139083	ENST00000396373	.	.	.	4.11	3.2	0.36748	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.7932	0.23711	0.1278:0.0:0.8722:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ETV6	11694362	1.000000	0.71417	0.995000	0.50966	0.931000	0.56810	3.784000	0.55416	1.832000	0.53329	0.491000	0.48974	.	.	.	none		0.532	ETV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400130.2	NM_001987	Intron
PIM1	5292	hgsc.bcm.edu	37	6	37139210	37139210	+	Missense_Mutation	SNP	C	C	T	rs200495767	byFrequency	TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr6:37139210C>T	ENST00000373509.5	+	4	923	c.550C>T	c.(550-552)Ctc>Ttc	p.L184F		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	275	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)	CGAGCTCAAGCTCATCGACTT	0.652			T	BCL6	NHL																																p.L275F		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	PIM1,NS,NS,0,1	PIM1	71	1	0			c.C823T						PASS	.						31.0	32.0	31.0					6																	37139210		2203	4300	6503	SO:0001583	missense	5292	exon4			CTCAAGCTCATCG		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.550C>T	6.37:g.37139210C>T	ENSP00000362608:p.Leu184Phe	73.0	0.0	0		70.0	31.0	0.442857	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.926320	0.92319	.	.	ENSG00000137193	ENST00000373509	T	0.26067	1.76	4.36	4.36	0.52297	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000002	T	0.58509	0.2127	H	0.96142	3.775	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.74166	-0.3753	10	0.87932	D	0	.	15.8069	0.78520	0.0:1.0:0.0:0.0	.	275	P11309	PIM1_HUMAN	F	184	ENSP00000362608:L184F	ENSP00000362608:L184F	L	+	1	0	PIM1	37247188	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.611000	0.82962	2.254000	0.74563	0.448000	0.29417	CTC	C|1.000;G|0.000	.	alt		0.652	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1		
MT-CO3	4514	hgsc.bcm.edu	37	M	9445	9445	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chrM:9445G>A	ENST00000362079.2	+	1	239	c.239G>A	c.(238-240)cGa>cAa	p.R80Q	MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-ND3_ENST00000361227.2_5'Flank|MT-TG_ENST00000387429.1_RNA|MT-ND4L_ENST00000361335.1_5'Flank|MT-TS1_ENST00000387416.2_RNA|MT-TH_ENST00000387441.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-ND4_ENST00000361381.2_5'Flank			P00414	COX3_HUMAN	mitochondrially encoded cytochrome c oxidase III	80					aerobic electron transport chain (GO:0019646)|cellular metabolic process (GO:0044237)|respiratory chain complex IV assembly (GO:0008535)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|respiratory chain complex IV (GO:0045277)	cytochrome-c oxidase activity (GO:0004129)			breast(1)|endometrium(10)|kidney(14)|lung(1)|urinary_tract(1)	27						AAAAGGCCTTCGATACGGGAT	0.473																																					p.R80Q		Atlas-SNP	.											.	.	.	.	0			c.G239A						PASS	.																																			SO:0001583	missense	5742	exon1			GCCTTCGATACGG			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198938	ENSG00000198938		"""Mitochondrial respiratory chain complex / Complex IV"""	7422	protein-coding gene	gene with protein product		516050	"""cytochrome c oxidase III"""	MTCO3			Standard			Approved	COX3, COIII, CO3		P00414		ENST00000362079.2:c.239G>A	M.37:g.9445G>A	ENSP00000354982:p.Arg80Gln	43.0	0.0	0		26.0	12.0	0.461538	ENST00000362079	Q14Y83	Missense_Mutation	SNP	ENST00000362079.2	37																																																																																				.	.	none		0.473	MT-CO3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024032	
ZIC3	7547	hgsc.bcm.edu	37	X	136649636	136649636	+	Missense_Mutation	SNP	C	C	G			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chrX:136649636C>G	ENST00000287538.5	+	1	1336	c.786C>G	c.(784-786)agC>agG	p.S262R	ZIC3_ENST00000370606.3_Missense_Mutation_p.S262R	NM_003413.3	NP_003404.1	O60481	ZIC3_HUMAN	Zic family member 3	262					anterior/posterior pattern specification (GO:0009952)|cell differentiation (GO:0030154)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of left/right asymmetry in nervous system (GO:0035545)|determination of left/right symmetry (GO:0007368)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|heart looping (GO:0001947)|lung development (GO:0030324)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|large_intestine(3)|liver(1)|lung(18)|ovary(3)|soft_tissue(2)|urinary_tract(1)	37	Acute lymphoblastic leukemia(192;0.000127)					CTCAGCTGAGCCGGCCCAAGA	0.632																																					p.S262R		Atlas-SNP	.											.	ZIC3	93	.	0			c.C786G						PASS	.						49.0	47.0	47.0					X																	136649636		2203	4300	6503	SO:0001583	missense	7547	exon1			GCTGAGCCGGCCC	AF028706	CCDS14663.1	Xq24-q27.1	2013-01-08	2011-05-19		ENSG00000156925	ENSG00000156925		"""Zinc fingers, C2H2-type"""	12874	protein-coding gene	gene with protein product		300265	"""heterotaxy 1"", ""Zic family member 3 (odd-paired homolog, Drosophila)"""	HTX1		8298651, 7747776	Standard	NM_003413		Approved	HTX, ZNF203	uc004fak.3	O60481	OTTHUMG00000022525	ENST00000287538.5:c.786C>G	X.37:g.136649636C>G	ENSP00000287538:p.Ser262Arg	72.0	0.0	0		73.0	23.0	0.315068	NM_003413	B2CNW4|Q14DE5|Q5JY75	Missense_Mutation	SNP	ENST00000287538.5	37	CCDS14663.1	.	.	.	.	.	.	.	.	.	.	c	13.20	2.165805	0.38217	.	.	ENSG00000156925	ENST00000287538;ENST00000370606	T;T	0.12255	2.7;2.75	4.58	3.65	0.41850	Zinc finger, C2H2-like (1);	0.143603	0.64402	D	0.000008	T	0.10165	0.0249	L	0.27053	0.805	0.39225	D	0.963566	B	0.12630	0.006	B	0.14578	0.011	T	0.09122	-1.0689	10	0.62326	D	0.03	.	9.6292	0.39770	0.0:0.8829:0.0:0.1171	.	262	O60481	ZIC3_HUMAN	R	262	ENSP00000287538:S262R;ENSP00000359638:S262R	ENSP00000287538:S262R	S	+	3	2	ZIC3	136477302	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.318000	0.43779	0.807000	0.34208	0.597000	0.82753	AGC	.	.	none		0.632	ZIC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058526.1		
PIM1	5292	hgsc.bcm.edu	37	6	37138901	37138901	+	Splice_Site	SNP	C	C	T			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr6:37138901C>T	ENST00000373509.5	+	4	614	c.241C>T	c.(241-243)Cct>Tct	p.P81S		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	172					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)	GCCCCTGCAGCCTAATGGCAC	0.667			T	BCL6	NHL																																p.P172S		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.C514T						PASS	.						45.0	52.0	50.0					6																	37138901		2203	4299	6502	SO:0001630	splice_region_variant	5292	exon4			CTGCAGCCTAATG		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.241-1C>T	6.37:g.37138901C>T		33.0	0.0	0		48.0	12.0	0.25	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	C	8.304	0.820601	0.16678	.	.	ENSG00000137193	ENST00000373509	T	0.63096	-0.02	4.28	4.28	0.50868	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.230218	0.35525	N	0.003156	T	0.29882	0.0747	N	0.20610	0.595	0.41234	D	0.98659	B	0.06786	0.001	B	0.09377	0.004	T	0.10823	-1.0613	9	.	.	.	.	15.0358	0.71744	0.0:1.0:0.0:0.0	.	172	P11309	PIM1_HUMAN	S	81	ENSP00000362608:P81S	.	P	+	1	0	PIM1	37246879	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	4.378000	0.59568	2.371000	0.80710	0.549000	0.68633	CCT	.	.	none		0.667	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1		Missense_Mutation
SNX8	29886	hgsc.bcm.edu	37	7	2304007	2304007	+	Silent	SNP	G	G	A			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr7:2304007G>A	ENST00000222990.3	-	6	750	c.708C>T	c.(706-708)cgC>cgT	p.R236R		NM_013321.2	NP_037453.1	Q9Y5X2	SNX8_HUMAN	sorting nexin 8	236					early endosome to Golgi transport (GO:0034498)|intracellular protein transport (GO:0006886)	early endosome membrane (GO:0031901)	identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)	p.R236R(1)		breast(2)|endometrium(5)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(2)|skin(3)	26		Ovarian(82;0.11)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0853)|OV - Ovarian serous cystadenocarcinoma(56;3.79e-14)		CGGCCCTGTCGCGAAGCTTGT	0.552																																					p.R236R		Atlas-SNP	.											SNX8,NS,carcinoma,0,2	SNX8	46	2	1	Substitution - coding silent(1)	ovary(1)	c.C708T						PASS	.						81.0	72.0	75.0					7																	2304007		2203	4300	6503	SO:0001819	synonymous_variant	29886	exon6			CCTGTCGCGAAGC	AF121858	CCDS5331.1	7p22.3	2010-08-05			ENSG00000106266	ENSG00000106266		"""Sorting nexins"""	14972	protein-coding gene	gene with protein product		614905					Standard	NM_013321		Approved	Mvp1	uc003slw.3	Q9Y5X2	OTTHUMG00000151512	ENST00000222990.3:c.708C>T	7.37:g.2304007G>A		29.0	0.0	0		31.0	11.0	0.354839	NM_013321	A4D207|Q96I67	Silent	SNP	ENST00000222990.3	37	CCDS5331.1																																																																																			.	.	none		0.552	SNX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322949.2		
PIM1	5292	hgsc.bcm.edu	37	6	37138765	37138765	+	Silent	SNP	C	C	T			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr6:37138765C>T	ENST00000373509.5	+	3	571	c.198C>T	c.(196-198)atC>atT	p.I66I		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	157					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)	AGGTGGCCATCAAACACGTGG	0.721			T	BCL6	NHL																																p.I157I		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.C471T						PASS	.						53.0	56.0	55.0					6																	37138765		2203	4300	6503	SO:0001819	synonymous_variant	5292	exon3			GGCCATCAAACAC		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.198C>T	6.37:g.37138765C>T		70.0	0.0	0		86.0	21.0	0.244186	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		
ABCA13	154664	hgsc.bcm.edu	37	7	48318518	48318518	+	Nonsense_Mutation	SNP	T	T	A	rs544493291	byFrequency	TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr7:48318518T>A	ENST00000435803.1	+	18	7751	c.7727T>A	c.(7726-7728)tTa>tAa	p.L2576*		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	2576					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						ATAGCTACTTTAAAAAAAATA	0.318													T|||	3	0.000599042	0.0	0.0014	5008	,	,		18836	0.0		0.0	False		,,,				2504	0.002				p.L2576X		Atlas-SNP	.											ABCA13_ENST00000435803,NS,carcinoma,-1,4	ABCA13	1192	4	0			c.T7727A						scavenged	.						55.0	59.0	58.0					7																	48318518		1794	4040	5834	SO:0001587	stop_gained	154664	exon18			CTACTTTAAAAAA	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"""ATP binding cassette transporters / subfamily A"""	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.7727T>A	7.37:g.48318518T>A	ENSP00000411096:p.Leu2576*	120.0	1.0	0.00833333		97.0	32.0	0.329897	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Nonsense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	T	47	13.299669	0.99733	.	.	ENSG00000179869	ENST00000435803	.	.	.	4.93	-0.0604	0.13789	.	1.145970	0.06770	N	0.783306	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	4.0212	0.09667	0.0:0.3009:0.2063:0.4928	.	.	.	.	X	2576	.	ENSP00000411096:L2576X	L	+	2	0	ABCA13	48289064	0.000000	0.05858	0.000000	0.03702	0.088000	0.18126	-1.274000	0.02820	-0.020000	0.14032	-0.331000	0.08364	TTA	.	.	none		0.318	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
PCLO	27445	hgsc.bcm.edu	37	7	82583413	82583413	+	Missense_Mutation	SNP	C	C	A			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr7:82583413C>A	ENST00000333891.9	-	5	7193	c.6856G>T	c.(6856-6858)Gct>Tct	p.A2286S	PCLO_ENST00000423517.2_Missense_Mutation_p.A2286S	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						ACAGTGTCAGCAACTGGCCCT	0.403																																					p.A2286S		Atlas-SNP	.											.	PCLO	1506	.	0			c.G6856T						PASS	.						107.0	106.0	106.0					7																	82583413		1880	4119	5999	SO:0001583	missense	27445	exon5			TGTCAGCAACTGG	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.6856G>T	7.37:g.82583413C>A	ENSP00000334319:p.Ala2286Ser	189.0	0.0	0		166.0	52.0	0.313253	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	C	3.075	-0.190260	0.06299	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.16457	2.35;2.34	5.48	2.37	0.29283	.	.	.	.	.	T	0.09069	0.0224	N	0.12182	0.205	0.22066	N	0.999384	B;B	0.16396	0.017;0.017	B;B	0.12156	0.007;0.007	T	0.27706	-1.0066	9	0.87932	D	0	.	4.8141	0.13358	0.2214:0.5849:0.1068:0.0869	.	2286;2286	Q9Y6V0-5;Q9Y6V0-6	.;.	S	2217;2286;2286	ENSP00000334319:A2286S;ENSP00000388393:A2286S	ENSP00000334319:A2286S	A	-	1	0	PCLO	82421349	0.003000	0.15002	0.589000	0.28718	0.072000	0.16883	-0.115000	0.10741	0.667000	0.31107	-0.230000	0.12252	GCT	.	.	none		0.403	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
ITIH5	80760	hgsc.bcm.edu	37	10	7679231	7679231	+	Silent	SNP	C	C	T			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr10:7679231C>T	ENST00000256861.6	-	5	690	c.612G>A	c.(610-612)ccG>ccA	p.P204P	ITIH5_ENST00000434980.1_5'UTR|ITIH5_ENST00000446830.2_5'UTR|ITIH5_ENST00000397146.2_Silent_p.P204P|ITIH5_ENST00000397145.2_Silent_p.P204P	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	204					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						TGTTGTGAAGCGGCAGCACCT	0.647																																					p.P204P		Atlas-SNP	.											.	ITIH5	343	.	0			c.G612A						PASS	.						83.0	87.0	86.0					10																	7679231		2203	4300	6503	SO:0001819	synonymous_variant	80760	exon5			GTGAAGCGGCAGC			10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"""inter-alpha (globulin) inhibitor H5"""			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000256861.6:c.612G>A	10.37:g.7679231C>T		36.0	0.0	0		33.0	16.0	0.484848	NM_001001851	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Silent	SNP	ENST00000256861.6	37																																																																																				.	.	none		0.647	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569	
BCOR	54880	hgsc.bcm.edu	37	X	39933243	39933243	+	Silent	SNP	A	A	G			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chrX:39933243A>G	ENST00000378444.4	-	4	1584	c.1356T>C	c.(1354-1356)gcT>gcC	p.A452A	BCOR_ENST00000378455.4_Silent_p.A452A|BCOR_ENST00000397354.3_Silent_p.A452A|BCOR_ENST00000342274.4_Silent_p.A452A	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	452					heart development (GO:0007507)|histone H2A monoubiquitination (GO:0035518)|negative regulation of bone mineralization (GO:0030502)|negative regulation of histone H3-K36 methylation (GO:0000415)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|palate development (GO:0060021)|specification of axis polarity (GO:0065001)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	heat shock protein binding (GO:0031072)|histone deacetylase binding (GO:0042826)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(4)|central_nervous_system(11)|cervix(1)|endometrium(24)|eye(6)|haematopoietic_and_lymphoid_tissue(33)|kidney(2)|large_intestine(11)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	126						CAGCTTTGGAAGCATCTACAT	0.498			"""F, N, S, T"""	RARA	"""retinoblastoma, AML, APL(translocation)"""		oculo-facio-cardio-dental genetic																														p.A452A		Atlas-SNP	.		Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		.	BCOR	351	.	0			c.T1356C						PASS	.						82.0	68.0	73.0					X																	39933243		2202	4300	6502	SO:0001819	synonymous_variant	54880	exon4			TTTGGAAGCATCT	AF317391	CCDS14250.1, CCDS48092.1, CCDS48093.1	Xp11.4	2014-09-17	2010-06-10		ENSG00000183337	ENSG00000183337		"""Ankyrin repeat domain containing"""	20893	protein-coding gene	gene with protein product		300485	"""BCL6 co-repressor"""			10898795	Standard	NM_017745		Approved	FLJ20285, KIAA1575	uc004den.4	Q6W2J9	OTTHUMG00000024100	ENST00000378444.4:c.1356T>C	X.37:g.39933243A>G		86.0	0.0	0		97.0	39.0	0.402062	NM_001123385	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Silent	SNP	ENST00000378444.4	37	CCDS48093.1																																																																																			.	.	none		0.498	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745	
EGR1	1958	hgsc.bcm.edu	37	5	137801553	137801553	+	Silent	SNP	C	C	T	rs558452520		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr5:137801553C>T	ENST00000239938.4	+	1	375	c.103C>T	c.(103-105)Ctg>Ttg	p.L35L		NM_001964.2	NP_001955.1	P18146	EGR1_HUMAN	early growth response 1	35					BMP signaling pathway (GO:0030509)|cellular response to antibiotic (GO:0071236)|cellular response to cAMP (GO:0071320)|cellular response to drug (GO:0035690)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to gamma radiation (GO:0071480)|cellular response to gonadotropin stimulus (GO:0071371)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heparin (GO:0071504)|cellular response to hyperoxia (GO:0071455)|cellular response to hypoxia (GO:0071456)|cellular response to insulin stimulus (GO:0032869)|cellular response to isoquinoline alkaloid (GO:0071317)|cellular response to mechanical stimulus (GO:0071260)|cellular response to mycophenolic acid (GO:0071506)|cellular response to steroid hormone stimulus (GO:0071383)|circadian rhythm (GO:0007623)|cytokine-mediated signaling pathway (GO:0019221)|glomerular mesangial cell proliferation (GO:0072110)|interleukin-1-mediated signaling pathway (GO:0070498)|learning or memory (GO:0007611)|long-term synaptic potentiation (GO:0060291)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oligodendrocyte differentiation (GO:0048709)|positive regulation of glomerular metanephric mesangial cell proliferation (GO:0072303)|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 long-term neuronal synaptic plasticity (GO:0048169)|regulation of protein sumoylation (GO:0033233)|response to amphetamine (GO:0001975)|response to carbon monoxide (GO:0034465)|response to cocaine (GO:0042220)|response to electrical stimulus (GO:0051602)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to norepinephrine (GO:0071873)|response to nutrient levels (GO:0031667)|skeletal muscle cell differentiation (GO:0035914)|T cell differentiation (GO:0030217)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|histone acetyltransferase binding (GO:0035035)|metal ion binding (GO:0046872)|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)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|ovary(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			CTACCCTAAGCTGGAGGAGAT	0.667																																					p.L35L		Atlas-SNP	.											.	EGR1	52	.	0			c.C103T						PASS	.						83.0	74.0	77.0					5																	137801553		2203	4300	6503	SO:0001819	synonymous_variant	1958	exon1			CCTAAGCTGGAGG	M62829	CCDS4206.1	5q23-q31	2013-01-08			ENSG00000120738	ENSG00000120738		"""Zinc fingers, C2H2-type"""	3238	protein-coding gene	gene with protein product	"""nerve growth factor-induced protein A"", ""transcription factor ETR103"", ""zinc finger protein 225"", ""early growth response protein 1"""	128990				3127059	Standard	NM_001964		Approved	TIS8, G0S30, NGFI-A, KROX-24, ZIF-268, AT225, ZNF225	uc003ldb.1	P18146	OTTHUMG00000129197	ENST00000239938.4:c.103C>T	5.37:g.137801553C>T		140.0	0.0	0		113.0	48.0	0.424779	NM_001964		Silent	SNP	ENST00000239938.4	37	CCDS4206.1																																																																																			.	.	none		0.667	EGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251274.1	NM_001964	
NEURL1	9148	hgsc.bcm.edu	37	10	105331517	105331517	+	Missense_Mutation	SNP	C	C	T			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr10:105331517C>T	ENST00000369780.4	+	3	996	c.587C>T	c.(586-588)aCg>aTg	p.T196M	NEURL_ENST00000369777.2_Missense_Mutation_p.T179M|NEURL_ENST00000465048.1_3'UTR	NM_004210.4	NP_004201.3	O76050	NEUL1_HUMAN		196	NHR 1. {ECO:0000255|PROSITE- ProRule:PRU00400}.				brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|lactation (GO:0007595)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Notch signaling pathway (GO:0045746)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse maturation (GO:0090129)|protein monoubiquitination (GO:0006513)|skeletal muscle tissue development (GO:0007519)|sperm axoneme assembly (GO:0007288)|sperm motility (GO:0030317)	apical dendrite (GO:0097440)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ligase activity (GO:0016874)|translation factor activity, non-nucleic acid binding (GO:0045183)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.T196M(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	17				Epithelial(162;2.12e-09)|all cancers(201;6.99e-08)|BRCA - Breast invasive adenocarcinoma(275;0.125)		GGGGTCCGCACGGCCGACCCG	0.652																																					p.T196M		Atlas-SNP	.											NEURL,NS,lymphoid_neoplasm,0,1	NEURL	38	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C587T						PASS	.						119.0	83.0	95.0					10																	105331517		2203	4300	6503	SO:0001583	missense	9148	exon3			TCCGCACGGCCGA																												ENST00000369780.4:c.587C>T	10.37:g.105331517C>T	ENSP00000358795:p.Thr196Met	83.0	0.0	0		80.0	30.0	0.375	NM_004210	Q5TDR2|Q5TDR3|Q8TAN0|Q9H463	Missense_Mutation	SNP	ENST00000369780.4	37	CCDS7551.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.034705	0.75617	.	.	ENSG00000107954	ENST00000369780;ENST00000437579;ENST00000369777	T;T	0.30981	1.51;1.51	5.64	5.64	0.86602	NEUZ (1);	0.047098	0.85682	D	0.000000	T	0.35970	0.0950	L	0.38838	1.175	0.53688	D	0.999976	D	0.65815	0.995	P	0.53185	0.72	T	0.07309	-1.0779	10	0.66056	D	0.02	-25.4468	12.0702	0.53611	0.0:0.9218:0.0:0.0782	.	196	O76050	NEU1A_HUMAN	M	196;179;179	ENSP00000358795:T196M;ENSP00000358792:T179M	ENSP00000358792:T179M	T	+	2	0	NEURL	105321507	0.002000	0.14202	0.971000	0.41717	0.856000	0.48823	0.869000	0.27996	2.648000	0.89879	0.561000	0.74099	ACG	.	.	none		0.652	NEURL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050170.1		
TACC2	10579	hgsc.bcm.edu	37	10	123843062	123843062	+	Silent	SNP	C	C	T			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr10:123843062C>T	ENST00000369005.1	+	4	1387	c.1047C>T	c.(1045-1047)ggC>ggT	p.G349G	TACC2_ENST00000513429.1_Intron|TACC2_ENST00000515603.1_Silent_p.G349G|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000515273.1_Silent_p.G349G|TACC2_ENST00000453444.2_Silent_p.G349G|TACC2_ENST00000334433.3_Silent_p.G349G	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	349					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				TGCCCTGGGGCTTGCCAAGTC	0.627																																					p.G349G		Atlas-SNP	.											.	TACC2	271	.	0			c.C1047T						PASS	.						31.0	36.0	34.0					10																	123843062		2203	4298	6501	SO:0001819	synonymous_variant	10579	exon4			CTGGGGCTTGCCA	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.1047C>T	10.37:g.123843062C>T		48.0	0.0	0		52.0	14.0	0.269231	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Silent	SNP	ENST00000369005.1	37	CCDS7626.1																																																																																			.	.	none		0.627	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
NEB	4703	hgsc.bcm.edu	37	2	152432838	152432838	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr2:152432838G>A	ENST00000172853.10	-	78	11779	c.11632C>T	c.(11632-11634)Cgt>Tgt	p.R3878C	NEB_ENST00000603639.1_Missense_Mutation_p.R5579C|NEB_ENST00000604864.1_Missense_Mutation_p.R5579C|NEB_ENST00000409198.1_Missense_Mutation_p.R3878C|NEB_ENST00000397345.3_Missense_Mutation_p.R5579C|NEB_ENST00000427231.2_Missense_Mutation_p.R5579C			P20929	NEBU_HUMAN	nebulin	3878					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		CCAATGCCACGCAACCACTCC	0.473																																					p.R5579C		Atlas-SNP	.											NEB_ENST00000427231,NS,carcinoma,+1,3	NEB	1697	3	0			c.C16735T						PASS	.						97.0	101.0	100.0					2																	152432838		1918	4134	6052	SO:0001583	missense	4703	exon106			TGCCACGCAACCA	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"""nemaline myopathy type 2"""	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.11632C>T	2.37:g.152432838G>A	ENSP00000172853:p.Arg3878Cys	169.0	0.0	0		163.0	63.0	0.386503	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	G	24.6	4.553342	0.86127	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000413693;ENST00000172853	T;T;T;T;T	0.51325	0.71;0.71;0.71;0.71;0.71	6.03	6.03	0.97812	.	0.048446	0.85682	D	0.000000	T	0.70894	0.3276	M	0.71920	2.185	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.71213	-0.4659	10	0.87932	D	0	.	20.5666	0.99351	0.0:0.0:1.0:0.0	.	3878;309	P20929;Q14215	NEBU_HUMAN;.	C	3878;5579;5579;309;3878	ENSP00000386259:R3878C;ENSP00000380505:R5579C;ENSP00000416578:R5579C;ENSP00000410961:R309C;ENSP00000172853:R3878C	ENSP00000172853:R3878C	R	-	1	0	NEB	152141084	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.030000	0.57260	2.854000	0.98071	0.655000	0.94253	CGT	.	.	none		0.473	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
KRIT1	889	hgsc.bcm.edu	37	7	91855062	91855062	+	Missense_Mutation	SNP	T	T	G			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr7:91855062T>G	ENST00000340022.2	-	12	2244	c.1226A>C	c.(1225-1227)aAa>aCa	p.K409T	KRIT1_ENST00000394505.2_Missense_Mutation_p.K409T|KRIT1_ENST00000394507.1_Missense_Mutation_p.K409T|KRIT1_ENST00000394503.2_Missense_Mutation_p.K361T|KRIT1_ENST00000412043.2_Missense_Mutation_p.K409T	NM_004912.3|NM_194455.1	NP_004903.2|NP_919437.1	O00522	KRIT1_HUMAN	KRIT1, ankyrin repeat containing	409					angiogenesis (GO:0001525)|cell redox homeostasis (GO:0045454)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|positive regulation of protein binding (GO:0032092)|regulation of catalytic activity (GO:0050790)|regulation of establishment of cell polarity (GO:2000114)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|microtubule (GO:0005874)|plasma membrane (GO:0005886)	microtubule binding (GO:0008017)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein complex binding (GO:0032403)|small GTPase regulator activity (GO:0005083)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(2)|stomach(1)	22	all_cancers(62;1.04e-09)|all_epithelial(64;5.75e-09)|Breast(17;0.00206)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			CTTCAACAATTTTGCAGCTTC	0.338																																					p.K409T		Atlas-SNP	.											KRIT1,NS,carcinoma,-1,1	KRIT1	66	1	0			c.A1226C						PASS	.						134.0	133.0	133.0					7																	91855062		2202	4300	6502	SO:0001583	missense	889	exon13			AACAATTTTGCAG	AJ294850	CCDS5624.1, CCDS34679.1	7q21.2	2014-09-17	2005-03-15	2005-03-17	ENSG00000001631	ENSG00000001631		"""Ankyrin repeat domain containing"""	1573	protein-coding gene	gene with protein product		604214	"""cerebral cavernous malformations 1"""	CCM1		7604043, 11342228	Standard	NM_194455		Approved	CAM	uc003ulu.1	O00522	OTTHUMG00000131187	ENST00000340022.2:c.1226A>C	7.37:g.91855062T>G	ENSP00000344668:p.Lys409Thr	262.0	0.0	0		252.0	85.0	0.337302	NM_194456	A6NNU0|O43894|Q506L6|Q6U276|Q75N19|Q9H180|Q9H264|Q9HAX5	Missense_Mutation	SNP	ENST00000340022.2	37	CCDS5624.1	.	.	.	.	.	.	.	.	.	.	T	13.90	2.374446	0.42105	.	.	ENSG00000001631	ENST00000394507;ENST00000340022;ENST00000412043;ENST00000394505;ENST00000394503;ENST00000415227	T;T;T;T;T	0.70986	-0.53;-0.53;-0.53;-0.53;1.21	5.74	5.74	0.90152	Ankyrin repeat-containing domain (2);	0.097704	0.64402	D	0.000001	T	0.45418	0.1341	N	0.02539	-0.55	0.48571	D	0.999675	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.43540	-0.9385	10	0.33940	T	0.23	-3.9337	11.9614	0.53011	0.0:0.0:0.1447:0.8553	.	361;409	A6NNU0;O00522	.;KRIT1_HUMAN	T	409;409;409;409;361;409	ENSP00000378015:K409T;ENSP00000344668:K409T;ENSP00000410909:K409T;ENSP00000378013:K409T;ENSP00000378011:K361T	ENSP00000344668:K409T	K	-	2	0	KRIT1	91692998	1.000000	0.71417	0.999000	0.59377	0.973000	0.67179	4.715000	0.61909	2.168000	0.68352	0.533000	0.62120	AAA	.	.	none		0.338	KRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253910.1		
EMC6	83460	hgsc.bcm.edu	37	17	3572623	3572623	+	Silent	SNP	G	G	A			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr17:3572623G>A	ENST00000397133.2	+	2	423	c.183G>A	c.(181-183)ctG>ctA	p.L61L	EMC6_ENST00000248378.5_Silent_p.L61L|P2RX5-TAX1BP3_ENST00000550383.1_3'UTR|TAX1BP3_ENST00000225525.3_5'Flank	NM_001014764.1	NP_001014764.1	Q9BV81	EMC6_HUMAN	ER membrane protein complex subunit 6	61						ER membrane protein complex (GO:0072546)|integral component of membrane (GO:0016021)											CCTCCGTCCTGCTCTCCCTGC	0.607																																					p.L61L		Atlas-SNP	.											.	.	.	.	0			c.G183A						PASS	.						38.0	39.0	38.0					17																	3572623		2202	4300	6502	SO:0001819	synonymous_variant	83460	exon2			CGTCCTGCTCTCC		CCDS11033.1	17p13.2	2012-05-23	2012-05-23	2012-05-23		ENSG00000127774			28430	protein-coding gene	gene with protein product			"""transmembrane protein 93"""	TMEM93		22119785	Standard	NM_001014764		Approved	MGC2963	uc002fwg.1	Q9BV81		ENST00000397133.2:c.183G>A	17.37:g.3572623G>A		120.0	0.0	0		116.0	39.0	0.336207	NM_001014764		Silent	SNP	ENST00000397133.2	37	CCDS11033.1																																																																																			.	.	none		0.607	EMC6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450159.1	NM_031298	
SYNDIG1L	646658	hgsc.bcm.edu	37	14	74874557	74874557	+	Missense_Mutation	SNP	G	G	T			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr14:74874557G>T	ENST00000554823.1	-	2	614	c.553C>A	c.(553-555)Cag>Aag	p.Q185K	SYNDIG1L_ENST00000331628.3_Missense_Mutation_p.Q185K			A6NDD5	SYN1L_HUMAN	synapse differentiation inducing 1-like	185					response to biotic stimulus (GO:0009607)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|lung(8)|pancreas(1)|prostate(1)|skin(1)	14						CTTACCCCCTGGGAGAAGTAG	0.627																																					p.Q185K		Atlas-SNP	.											.	SYNDIG1L	24	.	0			c.C553A						PASS	.						69.0	77.0	74.0					14																	74874557		2203	4300	6503	SO:0001583	missense	646658	exon3			CCCCCTGGGAGAA		CCDS41970.1	14q24.3	2011-06-30	2011-06-30	2011-06-30		ENSG00000183379			32388	protein-coding gene	gene with protein product	"""caudate-and putamen-enriched sequence"", ""interferon induced transmembrane protein domain containing 4"""	609999	"""transmembrane protein 90A"""	TMEM90A		16359841	Standard	NM_001105579		Approved	capucin, IFITMD4	uc001xpx.2	A6NDD5		ENST00000554823.1:c.553C>A	14.37:g.74874557G>T	ENSP00000450439:p.Gln185Lys	78.0	0.0	0		82.0	28.0	0.341463	NM_001105579		Missense_Mutation	SNP	ENST00000554823.1	37	CCDS41970.1	.	.	.	.	.	.	.	.	.	.	G	19.09	3.759026	0.69763	.	.	ENSG00000183379	ENST00000331628;ENST00000554823	D;D	0.85556	-2.0;-2.0	4.85	4.85	0.62838	.	0.077405	0.56097	D	0.000040	D	0.88385	0.6422	L	0.35854	1.095	0.58432	D	0.999999	D	0.64830	0.994	D	0.64506	0.926	D	0.88933	0.3374	10	0.52906	T	0.07	-13.4894	18.1623	0.89712	0.0:0.0:1.0:0.0	.	185	A6NDD5	SYN1L_HUMAN	K	185	ENSP00000331474:Q185K;ENSP00000450439:Q185K	ENSP00000331474:Q185K	Q	-	1	0	SYNDIG1L	73944310	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	9.657000	0.98554	2.498000	0.84270	0.561000	0.74099	CAG	.	.	none		0.627	SYNDIG1L-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412341.1	XM_938515	
FAM124A	220108	hgsc.bcm.edu	37	13	51855115	51855115	+	Missense_Mutation	SNP	C	C	A			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr13:51855115C>A	ENST00000322475.8	+	4	1499	c.1364C>A	c.(1363-1365)gCa>gAa	p.A455E	FAM124A_ENST00000280057.6_Missense_Mutation_p.A491E	NM_001242312.1	NP_001229241.1	Q86V42	F124A_HUMAN	family with sequence similarity 124A	455										breast(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|skin(1)	26		Acute lymphoblastic leukemia(7;0.000334)|Breast(56;0.00156)|Prostate(109;0.00538)|Lung NSC(96;0.0216)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;4.25e-07)		AGCCACTGGGCAGCTCACAAG	0.587																																					p.A491E		Atlas-SNP	.											.	FAM124A	61	.	0			c.C1472A						PASS	.						56.0	54.0	54.0					13																	51855115		2203	4300	6503	SO:0001583	missense	220108	exon5			ACTGGGCAGCTCA	AK096364	CCDS9427.1, CCDS55900.1	13q14.3	2006-08-11			ENSG00000150510	ENSG00000150510			26413	protein-coding gene	gene with protein product						12975309	Standard	NM_145019		Approved	FLJ30707	uc001vff.2	Q86V42	OTTHUMG00000016942	ENST00000322475.8:c.1364C>A	13.37:g.51855115C>A	ENSP00000324625:p.Ala455Glu	48.0	0.0	0		55.0	22.0	0.4	NM_145019	A2A324|Q8N8P9|Q8NE66|Q96NJ9	Missense_Mutation	SNP	ENST00000322475.8	37	CCDS55900.1	.	.	.	.	.	.	.	.	.	.	C	10.99	1.507667	0.27036	.	.	ENSG00000150510	ENST00000322475;ENST00000280057	T;T	0.47528	0.86;0.84	5.07	1.23	0.21249	.	2.466230	0.01371	N	0.012590	T	0.23370	0.0565	N	0.08118	0	0.09310	N	1	B;B	0.27732	0.0;0.187	B;B	0.25140	0.002;0.058	T	0.23511	-1.0186	10	0.02654	T	1	-11.5191	3.6365	0.08151	0.2691:0.3909:0.2621:0.078	.	455;491	Q86V42;Q86V42-2	F124A_HUMAN;.	E	455;491	ENSP00000324625:A455E;ENSP00000280057:A491E	ENSP00000280057:A491E	A	+	2	0	FAM124A	50753116	0.002000	0.14202	0.000000	0.03702	0.007000	0.05969	1.530000	0.36007	-0.100000	0.12241	-0.188000	0.12872	GCA	.	.	none		0.587	FAM124A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045019.3	NM_145019	
GABRP	2568	hgsc.bcm.edu	37	5	170222292	170222292	+	Silent	SNP	G	G	T	rs41315922		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr5:170222292G>T	ENST00000518525.1	+	6	785	c.321G>T	c.(319-321)ctG>ctT	p.L107L	GABRP_ENST00000519598.1_Silent_p.L107L|GABRP_ENST00000519385.1_Silent_p.L107L|GABRP_ENST00000265294.4_Silent_p.L107L			O00591	GBRP_HUMAN	gamma-aminobutyric acid (GABA) A receptor, pi	107					signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(5)|large_intestine(4)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	29	Renal(175;0.000159)|Lung NSC(126;0.0122)|all_lung(126;0.0193)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)		Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	GCTTCACTCTGGATGCCCGCC	0.567																																					p.L107L		Atlas-SNP	.											.	GABRP	65	.	0			c.G321T						PASS	.						124.0	128.0	127.0					5																	170222292		2203	4300	6503	SO:0001819	synonymous_variant	2568	exon5			CACTCTGGATGCC	U95367	CCDS4375.1, CCDS75368.1	5q35.1	2012-06-22			ENSG00000094755	ENSG00000094755		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4089	protein-coding gene	gene with protein product	"""GABA(A) receptor, pi"""	602729				9182563	Standard	NM_014211		Approved		uc003mau.3	O00591	OTTHUMG00000130443	ENST00000518525.1:c.321G>T	5.37:g.170222292G>T		89.0	0.0	0		67.0	23.0	0.343284	NM_014211	A8KA36|D3DQL2|Q32MJ1	Silent	SNP	ENST00000518525.1	37	CCDS4375.1																																																																																			G|1.000;C|0.000	.	alt		0.567	GABRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252834.3	NM_014211	
MYD88	4615	hgsc.bcm.edu	37	3	38182641	38182641	+	Nonstop_Mutation	SNP	T	T	C	rs387907272		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	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	47.0	0.0	0		37.0	29.0	0.783784	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	
PDE3A	5139	hgsc.bcm.edu	37	12	20522715	20522715	+	Missense_Mutation	SNP	C	C	T	rs532703635		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr12:20522715C>T	ENST00000359062.3	+	1	537	c.497C>T	c.(496-498)gCc>gTc	p.A166V	RP11-284H19.1_ENST00000535755.1_RNA	NM_000921.4|NM_001244683.1	NP_000912.3|NP_001231612.1	Q14432	PDE3A_HUMAN	phosphodiesterase 3A, cGMP-inhibited	166					blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cGMP (GO:0071321)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cGMP-mediated signaling (GO:0019934)|diterpenoid metabolic process (GO:0016101)|lipid metabolic process (GO:0006629)|negative regulation of apoptotic process (GO:0043066)|negative regulation of vascular permeability (GO:0043116)|oocyte maturation (GO:0001556)|positive regulation of oocyte development (GO:0060282)|positive regulation of vascular permeability (GO:0043117)|regulation of meiosis (GO:0040020)|response to cAMP (GO:0051591)|response to drug (GO:0042493)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|cAMP binding (GO:0030552)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(7)|lung(29)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	58	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Caffeine(DB00201)|Cilostazol(DB01166)|Enoximone(DB04880)|Ibudilast(DB05266)|Levosimendan(DB00922)|Milrinone(DB00235)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Tofisopam(DB08811)	CTGCTGGCCGCCTGCTGCGGG	0.692													C|||	1	0.000199681	0.0008	0.0	5008	,	,		12966	0.0		0.0	False		,,,				2504	0.0				p.A166V		Atlas-SNP	.											.	PDE3A	184	.	0			c.C497T						PASS	.						14.0	18.0	17.0					12																	20522715		2086	4148	6234	SO:0001583	missense	5139	exon1			TGGCCGCCTGCTG		CCDS31754.1	12p12.2	2011-04-15			ENSG00000172572	ENSG00000172572	3.1.4.17	"""Phosphodiesterases"""	8778	protein-coding gene	gene with protein product		123805				1315035, 10679291	Standard	NM_000921		Approved	CGI-PDE	uc001reh.2	Q14432	OTTHUMG00000168962	ENST00000359062.3:c.497C>T	12.37:g.20522715C>T	ENSP00000351957:p.Ala166Val	102.0	0.0	0		104.0	35.0	0.336538	NM_000921	O60865|Q13348|Q17RD1	Missense_Mutation	SNP	ENST00000359062.3	37	CCDS31754.1	.	.	.	.	.	.	.	.	.	.	C	12.90	2.076391	0.36662	.	.	ENSG00000172572	ENST00000359062	T	0.62941	-0.01	5.21	3.38	0.38709	.	1.056470	0.07230	N	0.862436	T	0.43612	0.1255	N	0.12182	0.205	0.32681	N	0.515452	B	0.06786	0.001	B	0.06405	0.002	T	0.47522	-0.9111	10	0.41790	T	0.15	.	6.6969	0.23203	0.0:0.6939:0.1471:0.159	.	166	Q14432	PDE3A_HUMAN	V	166	ENSP00000351957:A166V	ENSP00000351957:A166V	A	+	2	0	PDE3A	20413982	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.008000	0.40893	1.196000	0.43129	0.555000	0.69702	GCC	.	.	none		0.692	PDE3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401756.2		
NKD2	85409	hgsc.bcm.edu	37	5	1036421	1036421	+	Missense_Mutation	SNP	G	G	A	rs376557535		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr5:1036421G>A	ENST00000296849.5	+	9	938	c.709G>A	c.(709-711)Gtg>Atg	p.V237M	NKD2_ENST00000382730.2_5'Flank|NKD2_ENST00000274150.4_Missense_Mutation_p.V237M|NKD2_ENST00000537972.1_Missense_Mutation_p.V237M	NM_033120.3	NP_149111.1	Q969F2	NKD2_HUMAN	naked cuticle homolog 2 (Drosophila)	237					exocytosis (GO:0006887)|Golgi vesicle fusion to target membrane (GO:0048210)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein processing (GO:0010954)|protein targeting to plasma membrane (GO:0072661)|Wnt signaling pathway (GO:0016055)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cytoplasmic vesicle (GO:0031410)	calcium ion binding (GO:0005509)|growth factor binding (GO:0019838)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(3)|large_intestine(1)|lung(8)|pancreas(1)	14	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09)		Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165)			GCCCTACTGCGTGGACGAGAA	0.657																																					p.V237M		Atlas-SNP	.											.	NKD2	39	.	0			c.G709A						PASS	.						87.0	70.0	76.0					5																	1036421		2203	4299	6502	SO:0001583	missense	85409	exon9			TACTGCGTGGACG	AF358137	CCDS3859.1, CCDS59486.1	5p15.3	2013-01-10			ENSG00000145506	ENSG00000145506		"""EF-hand domain containing"""	17046	protein-coding gene	gene with protein product	"""naked cuticle-2"", ""Dvl-binding protein NKD2"""	607852				11356022, 11604995	Standard	NM_033120		Approved	Naked2	uc003jbt.2	Q969F2	OTTHUMG00000090348	ENST00000296849.5:c.709G>A	5.37:g.1036421G>A	ENSP00000296849:p.Val237Met	50.0	0.0	0		37.0	15.0	0.405405	NM_001271082	Q96EK8|Q9BSN0	Missense_Mutation	SNP	ENST00000296849.5	37	CCDS3859.1	.	.	.	.	.	.	.	.	.	.	G	17.73	3.461936	0.63513	.	.	ENSG00000145506	ENST00000296849;ENST00000274150;ENST00000537972	T;T;T	0.76060	0.11;-0.99;-0.99	4.39	4.39	0.52855	.	0.000000	0.64402	D	0.000004	D	0.84884	0.5571	M	0.79123	2.44	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77004	0.975;0.989	D	0.86862	0.2030	10	0.87932	D	0	-14.8057	12.4572	0.55710	0.0:0.0:1.0:0.0	.	237;237	Q969F2-2;Q969F2	.;NKD2_HUMAN	M	237	ENSP00000296849:V237M;ENSP00000274150:V237M;ENSP00000440925:V237M	ENSP00000274150:V237M	V	+	1	0	NKD2	1089421	1.000000	0.71417	0.977000	0.42913	0.845000	0.48019	5.412000	0.66392	1.979000	0.57680	0.491000	0.48974	GTG	.	.	weak		0.657	NKD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206720.2	NM_033120	
CACNG7	59284	hgsc.bcm.edu	37	19	54445378	54445378	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr19:54445378G>A	ENST00000391767.1	+	6	871	c.659G>A	c.(658-660)cGt>cAt	p.R220H	CACNG7_ENST00000222212.2_Missense_Mutation_p.R220H			P62955	CCG7_HUMAN	calcium channel, voltage-dependent, gamma subunit 7	220				GAGVMSVYLFTKRYAEEEMYRPHPAFYRPRLSDCSDYSGQF LQPEAWRRGRSPSDISSDVSIQMTQNYPPAIKYPDHLHIST SPC -> VTSVGPRL (in Ref. 1; AAK20030). {ECO:0000305}.	calcium ion transport (GO:0006816)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0711)		TACCGCCCGCGTCTCAGCGAC	0.687																																					p.R220H		Atlas-SNP	.											.	CACNG7	58	.	0			c.G659A						PASS	.						67.0	60.0	62.0					19																	54445378		2203	4300	6503	SO:0001583	missense	59284	exon5			GCCCGCGTCTCAG	AF288387	CCDS12868.1	19q13.4	2008-05-02			ENSG00000105605	ENSG00000105605		"""Calcium channel subunits"""	13626	protein-coding gene	gene with protein product		606899				11170751	Standard	NM_031896		Approved		uc002qcr.2	P62955	OTTHUMG00000064852	ENST00000391767.1:c.659G>A	19.37:g.54445378G>A	ENSP00000375647:p.Arg220His	103.0	0.0	0		153.0	41.0	0.267974	NM_031896	Q52LL8|Q8VBX3|Q8WXS6|Q9BXT1	Missense_Mutation	SNP	ENST00000391767.1	37	CCDS12868.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.682057	0.88542	.	.	ENSG00000105605	ENST00000391767;ENST00000222212	T;T	0.66995	-0.24;-0.24	4.18	1.96	0.26148	.	0.000000	0.85682	D	0.000000	T	0.67401	0.2889	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.62751	-0.6788	10	0.40728	T	0.16	-5.531	7.6938	0.28583	0.0953:0.1645:0.7402:0.0	.	220	P62955	CCG7_HUMAN	H	220	ENSP00000375647:R220H;ENSP00000222212:R220H	ENSP00000222212:R220H	R	+	2	0	CACNG7	59137190	1.000000	0.71417	0.738000	0.30950	0.997000	0.91878	9.011000	0.93618	0.343000	0.23821	0.491000	0.48974	CGT	.	.	none		0.687	CACNG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139240.2		
ASXL3	80816	hgsc.bcm.edu	37	18	31324989	31324989	+	Missense_Mutation	SNP	C	C	A	rs369543627		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr18:31324989C>A	ENST00000269197.5	+	12	5177	c.5177C>A	c.(5176-5178)gCc>gAc	p.A1726D		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	1726					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						GCTACCGATGCCCTGAAGAGA	0.557																																					p.A1726D		Atlas-SNP	.											.	ASXL3	405	.	0			c.C5177A						PASS	.						73.0	76.0	75.0					18																	31324989		2031	4190	6221	SO:0001583	missense	80816	exon12			CCGATGCCCTGAA	AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"""KIAA1713"", ""additional sex combs like 3 (Drosophila)"""	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.5177C>A	18.37:g.31324989C>A	ENSP00000269197:p.Ala1726Asp	57.0	0.0	0		61.0	15.0	0.245902	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	ENST00000269197.5	37	CCDS45847.1	.	.	.	.	.	.	.	.	.	.	C	3.427	-0.116888	0.06838	.	.	ENSG00000141431	ENST00000269197	T	0.14022	2.54	5.86	2.87	0.33458	.	.	.	.	.	T	0.08044	0.0201	N	0.08118	0	0.09310	N	1	B	0.15141	0.012	B	0.14023	0.01	T	0.33240	-0.9876	9	0.56958	D	0.05	.	10.7813	0.46379	0.431:0.4524:0.1166:0.0	.	1726	Q9C0F0	ASXL3_HUMAN	D	1726	ENSP00000269197:A1726D	ENSP00000269197:A1726D	A	+	2	0	ASXL3	29578987	0.378000	0.25114	0.916000	0.36221	0.018000	0.09664	1.299000	0.33424	0.249000	0.21456	0.655000	0.94253	GCC	.	.	alt		0.557	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2		
SYNE1	23345	hgsc.bcm.edu	37	6	152763351	152763351	+	Missense_Mutation	SNP	C	C	A	rs371765451		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr6:152763351C>A	ENST00000367255.5	-	31	4468	c.3867G>T	c.(3865-3867)aaG>aaT	p.K1289N	SYNE1_ENST00000341594.5_Missense_Mutation_p.K1355N|SYNE1_ENST00000413186.2_Missense_Mutation_p.K1289N|SYNE1_ENST00000265368.4_Missense_Mutation_p.K1289N|SYNE1_ENST00000423061.1_Missense_Mutation_p.K1296N|SYNE1_ENST00000367253.4_Missense_Mutation_p.K1289N|SYNE1_ENST00000448038.1_Missense_Mutation_p.K1296N|SYNE1_ENST00000367248.3_Missense_Mutation_p.K1279N	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1289					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GCACATCTCTCTTCTTTGCTG	0.527										HNSCC(10;0.0054)																											p.K1296N		Atlas-SNP	.											.	SYNE1	3227	.	0			c.G3888T						PASS	.						80.0	70.0	73.0					6																	152763351		2203	4300	6503	SO:0001583	missense	23345	exon31			ATCTCTCTTCTTT	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.3867G>T	6.37:g.152763351C>A	ENSP00000356224:p.Lys1289Asn	108.0	0.0	0		90.0	29.0	0.322222	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	14.12	2.441045	0.43326	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000367253;ENST00000367248;ENST00000413186	T;T;T;T;T;D;D;D	0.88818	0.54;0.54;0.45;0.54;0.63;-2.39;-2.43;-2.43	5.41	2.67	0.31697	.	0.096661	0.44902	D	0.000408	D	0.85678	0.5752	L	0.56769	1.78	0.80722	D	1	P;P;P;D;P;P	0.56287	0.932;0.745;0.835;0.975;0.745;0.835	B;B;B;P;B;P	0.53185	0.341;0.276;0.39;0.72;0.276;0.466	D	0.84040	0.0364	10	0.48119	T	0.1	.	10.4617	0.44583	0.0:0.7281:0.0:0.2719	.	1272;1289;1279;1289;1289;1296	B3W695;Q8NF91;F5GXQ8;Q8NF91-6;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.;.;.	N	1289;1296;1289;1296;1355;1289;1279;1289	ENSP00000356224:K1289N;ENSP00000396024:K1296N;ENSP00000265368:K1289N;ENSP00000390975:K1296N;ENSP00000341887:K1355N;ENSP00000356222:K1289N;ENSP00000356217:K1279N;ENSP00000414510:K1289N	ENSP00000265368:K1289N	K	-	3	2	SYNE1	152805044	1.000000	0.71417	0.550000	0.28217	0.423000	0.31445	1.782000	0.38654	0.350000	0.24002	-0.142000	0.14014	AAG	.	.	none		0.527	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
MUC16	94025	hgsc.bcm.edu	37	19	8962366	8962366	+	Missense_Mutation	SNP	T	T	G			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr19:8962366T>G	ENST00000397910.4	-	82	43536	c.43333A>C	c.(43333-43335)Act>Cct	p.T14445P	MUC16_ENST00000380951.5_Missense_Mutation_p.T1086P	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	22090	SEA 16. {ECO:0000255|PROSITE- ProRule:PRU00188}.			Missing (in Ref. 3; AAK74120). {ECO:0000305}.	cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GAATTCCCAGTTAAGGGCTCA	0.473																																					p.T14445P		Atlas-SNP	.											.	MUC16	4315	.	0			c.A43333C						PASS	.						26.0	26.0	26.0					19																	8962366		1790	3970	5760	SO:0001583	missense	94025	exon82			TCCCAGTTAAGGG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.43333A>C	19.37:g.8962366T>G	ENSP00000381008:p.Thr14445Pro	103.0	0.0	0		133.0	41.0	0.308271	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.69|11.69	1.715233|1.715233	0.30413|0.30413	.|.	.|.	ENSG00000181143|ENSG00000181143	ENST00000397910;ENST00000380951|ENST00000542240	T|.	0.02103|.	4.45|.	3.79|3.79	1.64|1.64	0.23874|0.23874	.|.	.|.	.|.	.|.	.|.	T|.	0.47173|.	0.1431|.	M|M	0.66939|0.66939	2.045|2.045	.|.	.|.	.|.	P;D|.	0.69078|.	0.838;0.997|.	B;P|.	0.62184|.	0.367;0.899|.	T|.	0.52358|.	-0.8586|.	8|.	0.62326|.	D|.	0.03|.	.|.	3.1914|3.1914	0.06618|0.06618	0.2051:0.1125:0.0:0.6824|0.2051:0.1125:0.0:0.6824	.|.	22090;14445|.	Q8WXI7;B5ME49|.	MUC16_HUMAN;.|.	P|Y	14445;1086|1267	ENSP00000381008:T14445P|.	ENSP00000370338:T1086P|.	T|X	-|-	1|3	0|2	MUC16|MUC16	8823366|8823366	0.001000|0.001000	0.12720|0.12720	0.004000|0.004000	0.12327|0.12327	0.011000|0.011000	0.07611|0.07611	0.642000|0.642000	0.24735|0.24735	0.284000|0.284000	0.22305|0.22305	0.454000|0.454000	0.30748|0.30748	ACT|TAA	.	.	none		0.473	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
TRIM29	23650	hgsc.bcm.edu	37	11	120008144	120008144	+	Missense_Mutation	SNP	A	A	G			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr11:120008144A>G	ENST00000341846.5	-	1	1017	c.596T>C	c.(595-597)cTc>cCc	p.L199P		NM_012101.3	NP_036233.2	Q14134	TRI29_HUMAN	tripartite motif containing 29	199					negative regulation of protein localization to nucleus (GO:1900181)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(17)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	30		Breast(109;0.00117)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)		GTGGGGCTTGAGATGCAGCTC	0.652																																					p.L199P		Atlas-SNP	.											.	TRIM29	78	.	0			c.T596C						PASS	.						33.0	34.0	34.0					11																	120008144		2203	4300	6503	SO:0001583	missense	23650	exon1			GGCTTGAGATGCA	AF230388	CCDS8428.1	11q23.3	2011-04-20	2011-01-25		ENSG00000137699	ENSG00000137699		"""Tripartite motif containing / Tripartite motif containing"""	17274	protein-coding gene	gene with protein product	"""tripartite motif protein TRIM29"", ""ataxia-telangiectasia group D-associated protein"""	610658	"""tripartite motif-containing 29"""			11331580	Standard	NM_012101		Approved	ATDC, FLJ36085	uc001pwz.3	Q14134	OTTHUMG00000140377	ENST00000341846.5:c.596T>C	11.37:g.120008144A>G	ENSP00000343129:p.Leu199Pro	23.0	0.0	0		26.0	14.0	0.538462	NM_012101	Q96AA9|Q9BZY7	Missense_Mutation	SNP	ENST00000341846.5	37	CCDS8428.1	.	.	.	.	.	.	.	.	.	.	A	26.8	4.773588	0.90108	.	.	ENSG00000137699	ENST00000341846	T	0.55760	0.5	5.91	5.91	0.95273	.	0.000000	0.64402	D	0.000007	T	0.79522	0.4460	M	0.92317	3.295	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.84585	0.0663	9	.	.	.	.	16.3483	0.83171	1.0:0.0:0.0:0.0	.	199	Q14134	TRI29_HUMAN	P	199	ENSP00000343129:L199P	.	L	-	2	0	TRIM29	119513354	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.326000	0.96389	2.254000	0.74563	0.533000	0.62120	CTC	.	.	none		0.652	TRIM29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277108.2	NM_012101	
AGAP6	414189	hgsc.bcm.edu	37	10	51769455	51769455	+	Missense_Mutation	SNP	T	T	C			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr10:51769455T>C	ENST00000374056.4	+	7	1899	c.1501T>C	c.(1501-1503)Tgg>Cgg	p.W501R	AGAP6_ENST00000412531.3_Missense_Mutation_p.W524R			Q5VW22	AGAP6_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 6	501	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(1)|lung(8)|prostate(3)|skin(1)|stomach(2)	29						GCTGGATGACTGGCCAGTTGA	0.522																																					p.W524R		Atlas-SNP	.											.	AGAP6	53	.	0			c.T1570C						PASS	.																																			SO:0001583	missense	414189	exon8			GATGACTGGCCAG		CCDS44397.1	10q11.23	2013-01-10	2008-09-22	2008-09-22	ENSG00000204149	ENSG00000204149		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	23466	protein-coding gene	gene with protein product			"""centaurin, gamma-like family, member 3"""	CTGLF3			Standard	NM_001077665		Approved	bA324H6.1	uc001jix.4	Q5VW22	OTTHUMG00000018220	ENST00000374056.4:c.1501T>C	10.37:g.51769455T>C	ENSP00000363168:p.Trp501Arg	38.0	0.0	0		39.0	11.0	0.282051	NM_001077665		Missense_Mutation	SNP	ENST00000374056.4	37		.	.	.	.	.	.	.	.	.	.	.	13.13	2.145491	0.37825	.	.	ENSG00000204149	ENST00000374056;ENST00000412531	.	.	.	0.0465	0.0465	0.14256	.	0.000000	0.85682	D	0.000000	D	0.86439	0.5933	H	0.99746	4.745	0.53005	D	0.999966	D	0.89917	1.0	D	0.79108	0.992	T	0.81400	-0.0950	9	0.87932	D	0	.	4.565	0.12180	0.0:6.0E-4:0.0:0.9994	.	524	C9IYN2	.	R	524;501	.	ENSP00000363168:W524R	W	+	1	0	AGAP6	51439461	1.000000	0.71417	0.073000	0.20177	0.073000	0.16967	5.349000	0.66010	0.115000	0.18071	0.113000	0.15668	TGG	.	.	none		0.522	AGAP6-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_001077665	
ITGA6	3655	hgsc.bcm.edu	37	2	173368882	173368882	+	Missense_Mutation	SNP	C	C	T	rs370676535		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr2:173368882C>T	ENST00000264106.6	+	26	3498	c.3295C>T	c.(3295-3297)Cgg>Tgg	p.R1099W	ITGA6_ENST00000264107.7_3'UTR|ITGA6_ENST00000375221.2_3'UTR|AC093818.1_ENST00000450443.1_RNA|ITGA6_ENST00000409080.1_Missense_Mutation_p.R1060W|ITGA6_ENST00000409532.1_3'UTR|ITGA6_ENST00000343713.4_3'UTR|AC093818.1_ENST00000442417.1_RNA			P23229	ITA6_HUMAN	integrin, alpha 6	1099					amelogenesis (GO:0097186)|blood coagulation (GO:0007596)|brown fat cell differentiation (GO:0050873)|cell adhesion mediated by integrin (GO:0033627)|cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|cellular response to extracellular stimulus (GO:0031668)|cellular response to organic cyclic compound (GO:0071407)|digestive tract development (GO:0048565)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|nail development (GO:0035878)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|renal system development (GO:0072001)|single organismal cell-cell adhesion (GO:0016337)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|external side of plasma membrane (GO:0009897)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integrin alpha6-beta4 complex (GO:0034676)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	44			OV - Ovarian serous cystadenocarcinoma(117;0.0979)			TGTAAGGATCCGGAAAGAAGA	0.388																																					p.R1060W		Atlas-SNP	.											.	ITGA6	171	.	0			c.C3178T						PASS	.	C	,TRP/ARG	0,3728		0,0,1864	57.0	53.0	54.0		,3178	5.9	1.0	2		54	1,8205		0,1,4102	no	utr-3,missense	ITGA6	NM_000210.2,NM_001079818.1	,101	0,1,5966	TT,TC,CC		0.0122,0.0,0.0084	,probably-damaging	,1060/1092	173368882	1,11933	1864	4103	5967	SO:0001583	missense	3655	exon25			AGGATCCGGAAAG		CCDS2249.1, CCDS46451.1	2q31.1	2010-09-20			ENSG00000091409	ENSG00000091409		"""CD molecules"", ""Integrins"""	6142	protein-coding gene	gene with protein product		147556					Standard	NM_001079818		Approved	CD49f	uc002uhp.1	P23229	OTTHUMG00000132277	ENST00000264106.6:c.3295C>T	2.37:g.173368882C>T	ENSP00000264106:p.Arg1099Trp	217.0	0.0	0		181.0	76.0	0.41989	NM_001079818	B2RMU9|B4DG69|B4DKB8|C4AM96|G5E9H1|Q08443|Q0MRC7|Q14646|Q16508|Q53RX7|Q59HB7|Q86VL6|Q9UCT1|Q9UN03	Missense_Mutation	SNP	ENST00000264106.6	37		.	.	.	.	.	.	.	.	.	.	C	23.1	4.372286	0.82573	0.0	1.22E-4	ENSG00000091409	ENST00000264106;ENST00000409080;ENST00000442250;ENST00000458358;ENST00000416789	T;T;T;T;T	0.24151	1.87;1.87;1.87;1.87;1.87	5.87	5.87	0.94306	.	0.456524	0.24256	N	0.040127	T	0.36771	0.0979	L	0.43152	1.355	0.80722	D	1	D	0.64830	0.994	P	0.55965	0.788	T	0.03394	-1.1041	10	0.66056	D	0.02	.	13.4186	0.60982	0.0:0.9286:0.0:0.0714	.	1060	G5E9H1	.	W	1099;1060;1099;1055;227	ENSP00000264106:R1099W;ENSP00000386896:R1060W;ENSP00000406694:R1099W;ENSP00000394169:R1055W;ENSP00000388435:R227W	ENSP00000264106:R1099W	R	+	1	2	ITGA6	173077128	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.754000	0.62191	2.785000	0.95823	0.655000	0.94253	CGG	.	.	weak		0.388	ITGA6-201	KNOWN	basic	protein_coding	protein_coding			
TACC2	10579	hgsc.bcm.edu	37	10	123987498	123987498	+	Missense_Mutation	SNP	G	G	A	rs114249776	byFrequency	TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr10:123987498G>A	ENST00000369005.1	+	14	8211	c.7871G>A	c.(7870-7872)gGc>gAc	p.G2624D	TACC2_ENST00000513429.1_Missense_Mutation_p.G770D|TACC2_ENST00000515603.1_Missense_Mutation_p.G2579D|TACC2_ENST00000369000.1_Missense_Mutation_p.G324D|TACC2_ENST00000358010.1_Missense_Mutation_p.G770D|TACC2_ENST00000369001.1_Missense_Mutation_p.G328D|TACC2_ENST00000360561.3_Missense_Mutation_p.G702D|TACC2_ENST00000515273.1_Missense_Mutation_p.G2628D|TACC2_ENST00000368999.1_Missense_Mutation_p.G714D|TACC2_ENST00000369004.3_Missense_Mutation_p.G714D|TACC2_ENST00000260733.3_Missense_Mutation_p.G702D|TACC2_ENST00000453444.2_Missense_Mutation_p.G2628D|TACC2_ENST00000334433.3_Missense_Mutation_p.G2624D	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	2624					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				ATGGGCTTGGGCACCCCTTCA	0.572													G|||	3	0.000599042	0.0023	0.0	5008	,	,		18322	0.0		0.0	False		,,,				2504	0.0				p.G2624D		Atlas-SNP	.											.	TACC2	271	.	0			c.G7871A						PASS	.	G	ASP/GLY,ASP/GLY,ASP/GLY,ASP/GLY	6,4400	11.4+/-27.6	0,6,2197	77.0	81.0	80.0		2105,2105,2309,7871	5.2	1.0	10	dbSNP_132	80	0,8600		0,0,4300	yes	missense,missense,missense,missense	TACC2	NM_006997.2,NM_206860.1,NM_206861.1,NM_206862.2	94,94,94,94	0,6,6497	AA,AG,GG		0.0,0.1362,0.0461	probably-damaging,probably-damaging,probably-damaging,probably-damaging	702/1027,702/997,770/1095,2624/2949	123987498	6,13000	2203	4300	6503	SO:0001583	missense	10579	exon14			GCTTGGGCACCCC	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.7871G>A	10.37:g.123987498G>A	ENSP00000358001:p.Gly2624Asp	48.0	0.0	0		52.0	20.0	0.384615	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	37	CCDS7626.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	15.95	2.983285	0.53827	0.001362	0.0	ENSG00000138162	ENST00000369005;ENST00000513429;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000358010;ENST00000453444;ENST00000340076;ENST00000369001;ENST00000369000;ENST00000360561;ENST00000368999;ENST00000369004;ENST00000260733;ENST00000496913	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.18657	3.71;3.4;4.04;4.01;3.71;3.4;4.04;2.2;2.2;3.23;3.27;3.22;3.27;2.4	5.25	5.25	0.73442	.	0.000000	0.37623	N	0.002017	T	0.33235	0.0856	L	0.29908	0.895	0.53688	D	0.999977	D;D;D;D;D;D;D;D;D	0.89917	0.999;1.0;0.999;0.999;0.998;0.999;0.982;0.999;1.0	D;D;D;D;D;D;P;D;D	0.97110	0.986;1.0;0.986;0.986;0.966;0.973;0.881;0.973;0.995	T	0.02553	-1.1142	10	0.15066	T	0.55	-21.8403	17.3979	0.87451	0.0:0.0:1.0:0.0	.	2628;714;2579;2628;702;702;324;770;2624	E9PBC6;D6RAA5;E7EMZ9;B7ZMJ9;O95359-6;O95359-1;O95359-2;O95359-5;O95359	.;.;.;.;.;.;.;.;TACC2_HUMAN	D	2624;770;2628;2579;2624;770;2628;2614;328;324;702;714;714;702;359	ENSP00000358001:G2624D;ENSP00000425062:G770D;ENSP00000424467:G2628D;ENSP00000427618:G2579D;ENSP00000334280:G2624D;ENSP00000350701:G770D;ENSP00000395048:G2628D;ENSP00000357997:G328D;ENSP00000357996:G324D;ENSP00000353763:G702D;ENSP00000357995:G714D;ENSP00000422815:G714D;ENSP00000260733:G702D;ENSP00000422725:G359D	ENSP00000260733:G702D	G	+	2	0	TACC2	123977488	1.000000	0.71417	0.974000	0.42286	0.024000	0.10985	4.505000	0.60421	2.618000	0.88619	0.655000	0.94253	GGC	G|0.999;A|0.001	0.001	strong		0.572	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
AAGAB	79719	hgsc.bcm.edu	37	15	67528329	67528329	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr15:67528329G>A	ENST00000261880.5	-	4	543	c.439C>T	c.(439-441)Cct>Tct	p.P147S	AAGAB_ENST00000542650.1_Missense_Mutation_p.P38S|AAGAB_ENST00000561452.1_Missense_Mutation_p.P38S	NM_001271885.1|NM_001271886.1|NM_024666.3	NP_001258814.1|NP_001258815.1|NP_078942.3	Q6PD74	AAGAB_HUMAN	alpha- and gamma-adaptin binding protein	147					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)	9						TCCTCCTCAGGCAACTCCTCT	0.353																																					p.P147S		Atlas-SNP	.											.	AAGAB	24	.	0			c.C439T						PASS	.						173.0	151.0	158.0					15																	67528329		1865	4113	5978	SO:0001583	missense	79719	exon4			CCTCAGGCAACTC	AL136715	CCDS42050.1, CCDS61679.1	15q22.33-q23	2014-02-12	2009-07-20		ENSG00000103591	ENSG00000103591			25662	protein-coding gene	gene with protein product		614888				11230166, 10477754	Standard	NM_024666		Approved	FLJ11506, p34	uc002aqk.5	Q6PD74	OTTHUMG00000172246	ENST00000261880.5:c.439C>T	15.37:g.67528329G>A	ENSP00000261880:p.Pro147Ser	138.0	0.0	0		143.0	42.0	0.293706	NM_024666	B4DG44|Q6FI86|Q7Z5X9|Q9H0P1|Q9HAK0	Missense_Mutation	SNP	ENST00000261880.5	37	CCDS42050.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.425846	0.83667	.	.	ENSG00000103591	ENST00000261880;ENST00000542650	T;T	0.42900	0.96;0.98	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.42607	0.1210	L	0.52573	1.65	0.80722	D	1	P	0.49862	0.929	P	0.46389	0.515	T	0.30090	-0.9990	10	0.05525	T	0.97	-18.439	19.702	0.96059	0.0:0.0:1.0:0.0	.	147	Q6PD74	AAGAB_HUMAN	S	147;38	ENSP00000261880:P147S;ENSP00000440735:P38S	ENSP00000261880:P147S	P	-	1	0	AAGAB	65315383	1.000000	0.71417	0.995000	0.50966	0.996000	0.88848	9.055000	0.93873	2.738000	0.93877	0.591000	0.81541	CCT	.	.	none		0.353	AAGAB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417472.1	NM_024666	
LRRK2	120892	hgsc.bcm.edu	37	12	40704416	40704416	+	Missense_Mutation	SNP	C	C	T			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr12:40704416C>T	ENST00000298910.7	+	31	4559	c.4501C>T	c.(4501-4503)Cgg>Tgg	p.R1501W		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	1501	Roc. {ECO:0000255|PROSITE- ProRule:PRU00758}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				GGCAAAACTTCGGAAAACCAT	0.408																																					p.R1501W		Atlas-SNP	.											LRRK2_ENST00000298910,NS,carcinoma,0,3	LRRK2	763	3	0			c.C4501T						PASS	.						167.0	164.0	165.0					12																	40704416		2203	4300	6503	SO:0001583	missense	120892	exon31			AAACTTCGGAAAA	AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"""Parkinson disease"""	18618	protein-coding gene	gene with protein product		609007	"""Parkinson disease (autosomal dominant) 8"""	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.4501C>T	12.37:g.40704416C>T	ENSP00000298910:p.Arg1501Trp	90.0	0.0	0		101.0	5.0	0.049505	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	37	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.623937	0.87460	.	.	ENSG00000188906	ENST00000298910	T	0.75367	-0.93	5.53	4.63	0.57726	ROC GTPase (1);	0.000000	0.85682	D	0.000000	D	0.84705	0.5531	M	0.70595	2.14	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.86135	0.1577	10	0.72032	D	0.01	.	14.7522	0.69533	0.0:0.9292:0.0:0.0708	.	1501;1501	Q17RV3;Q5S007	.;LRRK2_HUMAN	W	1501	ENSP00000298910:R1501W	ENSP00000298910:R1501W	R	+	1	2	LRRK2	38990683	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.294000	0.59043	2.597000	0.87782	0.650000	0.86243	CGG	.	.	none		0.408	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513	
SLC44A2	57153	hgsc.bcm.edu	37	19	10738451	10738451	+	Missense_Mutation	SNP	A	A	C			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr19:10738451A>C	ENST00000335757.5	+	3	516	c.140A>C	c.(139-141)tAc>tCc	p.Y47S	SLC44A2_ENST00000407327.4_Missense_Mutation_p.Y45S|SLC44A2_ENST00000586078.1_Missense_Mutation_p.Y47S			Q8IWA5	CTL2_HUMAN	solute carrier family 44 (choline transporter), member 2	47					choline transport (GO:0015871)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	choline transmembrane transporter activity (GO:0015220)|signal transducer activity (GO:0004871)			NS(1)|breast(3)|endometrium(5)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	27			Epithelial(33;8.7e-06)|all cancers(31;2.77e-05)		Choline(DB00122)	ATTGTGGGCTACGTGGCTGTA	0.592																																					p.Y47S		Atlas-SNP	.											.	SLC44A2	56	.	0			c.A140C						PASS	.						191.0	148.0	163.0					19																	10738451		2203	4300	6503	SO:0001583	missense	57153	exon3			TGGGCTACGTGGC	AF070636	CCDS12245.1, CCDS54216.1	19p13.2	2014-08-12	2013-07-17		ENSG00000129353	ENSG00000129353		"""Solute carriers"""	17292	protein-coding gene	gene with protein product		606106				10677542, 15715662	Standard	NM_001145056		Approved	CTL2	uc002mpf.3	Q8IWA5	OTTHUMG00000180585	ENST00000335757.5:c.140A>C	19.37:g.10738451A>C	ENSP00000336888:p.Tyr47Ser	73.0	0.0	0		86.0	26.0	0.302326	NM_020428	B2RBB1|B3KNH3|B4DFJ0|F2Q9D7|Q658V1|Q658Z2|Q6PJV7|Q8N2F0|Q9NY68	Missense_Mutation	SNP	ENST00000335757.5	37	CCDS12245.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.321334	0.81580	.	.	ENSG00000129353	ENST00000407327;ENST00000335757;ENST00000380614	T;T	0.42900	0.96;0.96	4.68	4.68	0.58851	.	0.136380	0.50627	D	0.000101	T	0.65544	0.2701	M	0.82923	2.615	0.58432	D	0.999995	D;D	0.62365	0.967;0.991	P;D	0.71184	0.852;0.972	T	0.71702	-0.4513	10	0.87932	D	0	.	13.2377	0.59979	1.0:0.0:0.0:0.0	.	47;45	Q8IWA5;Q8IWA5-3	CTL2_HUMAN;.	S	45;47;47	ENSP00000385135:Y45S;ENSP00000336888:Y47S	ENSP00000336888:Y47S	Y	+	2	0	SLC44A2	10599451	1.000000	0.71417	0.967000	0.41034	0.911000	0.54048	8.419000	0.90253	1.957000	0.56846	0.379000	0.24179	TAC	.	.	none		0.592	SLC44A2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452045.1		
GRHL3	57822	hgsc.bcm.edu	37	1	24690825	24690825	+	Silent	SNP	C	C	T			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr1:24690825C>T	ENST00000350501.5	+	16	1972	c.1845C>T	c.(1843-1845)acC>acT	p.T615T	STPG1_ENST00000468303.1_Intron|STPG1_ENST00000440416.1_Intron|STPG1_ENST00000003583.8_Intron|STPG1_ENST00000374409.1_Intron|STPG1_ENST00000337248.4_Intron	NM_198174.2	NP_937817.3	Q8TE85	GRHL3_HUMAN	grainyhead-like 3 (Drosophila)	615					central nervous system development (GO:0007417)|cochlea morphogenesis (GO:0090103)|ectoderm development (GO:0007398)|epidermis development (GO:0008544)|establishment of planar polarity (GO:0001736)|eyelid development in camera-type eye (GO:0061029)|pattern specification process (GO:0007389)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of actin cytoskeleton organization (GO:0032956)|wound healing (GO:0042060)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.00171)|all_lung(284;0.00226)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;8.72e-25)|Colorectal(126;4.38e-08)|COAD - Colon adenocarcinoma(152;1.84e-06)|GBM - Glioblastoma multiforme(114;0.000132)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00151)|KIRC - Kidney renal clear cell carcinoma(1967;0.00377)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.143)		gccccaccacCGTCAACAGCC	0.537																																					p.T615T		Atlas-SNP	.											.	GRHL3	69	.	0			c.C1845T						PASS	.																																			SO:0001819	synonymous_variant	57822	exon16			CACCACCGTCAAC	AY231161	CCDS251.1, CCDS252.1, CCDS44088.1, CCDS252.2, CCDS53284.1	1p36	2008-02-05	2005-07-11	2005-07-11	ENSG00000158055	ENSG00000158055			25839	protein-coding gene	gene with protein product		608317	"""transcription factor CP2-like 4"""	TFCP2L4		12549979	Standard	NM_021180		Approved	SOM	uc021oiw.1	Q8TE85	OTTHUMG00000003040	ENST00000350501.5:c.1845C>T	1.37:g.24690825C>T		76.0	0.0	0		57.0	25.0	0.438596	NM_198174	A2A297|B2RCL1|G3XAF0|Q5TH78|Q86Y06|Q8N407	Silent	SNP	ENST00000350501.5	37	CCDS252.2																																																																																			.	.	none		0.537	GRHL3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000009047.2	NM_021180	
ZFP92	139735	hgsc.bcm.edu	37	X	152686543	152686543	+	Silent	SNP	C	C	T			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chrX:152686543C>T	ENST00000338647.5	+	4	709	c.708C>T	c.(706-708)ttC>ttT	p.F236F	U82695.10_ENST00000569962.1_lincRNA	NM_001136273.1	NP_001129745.1	A6NM28	ZFP92_HUMAN	ZFP92 zinc finger protein	236					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(4)	6						AGCGGCCCTTCGCCTGCGGCG	0.701																																					p.F236F		Atlas-SNP	.											.	ZFP92	26	.	0			c.C708T						PASS	.						20.0	20.0	20.0					X																	152686543		692	1591	2283	SO:0001819	synonymous_variant	139735	exon4			GCCCTTCGCCTGC	U82695	CCDS59177.1	Xq28	2013-01-08	2012-11-27		ENSG00000189420	ENSG00000189420		"""Zinc fingers, C2H2-type"", ""-"""	12865	protein-coding gene	gene with protein product			"""zinc finger protein homologous to Zfp92 in mouse"", ""zinc finger protein 92 homolog (mouse)"""				Standard	NM_001136273		Approved	ZNF897	uc011myo.2	A6NM28	OTTHUMG00000024198	ENST00000338647.5:c.708C>T	X.37:g.152686543C>T		90.0	0.0	0		101.0	33.0	0.326733	NM_001136273		Silent	SNP	ENST00000338647.5	37	CCDS59177.1																																																																																			.	.	none		0.701	ZFP92-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332220.2		
SHISA7	729956	hgsc.bcm.edu	37	19	55954006	55954006	+	Silent	SNP	C	C	T			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr19:55954006C>T	ENST00000376325.4	-	1	224	c.225G>A	c.(223-225)gcG>gcA	p.A75A		NM_001145176.1	NP_001138648.1	A6NL88	SHSA7_HUMAN	shisa family member 7	75						integral component of membrane (GO:0016021)				skin(1)	1						cgggagggggcgcccgggccg	0.771																																					p.A75A		Atlas-SNP	.											.	SHISA7	14	.	0			c.G225A						PASS	.						11.0	15.0	14.0					19																	55954006		684	1580	2264	SO:0001819	synonymous_variant	729956	exon1			AGGGGGCGCCCGG		CCDS46193.1	19q13.42	2013-07-31	2013-07-31					"""Shisa homologs"""	35409	protein-coding gene	gene with protein product			"""shisa homolog 7 (Xenopus laevis)"""				Standard	NM_001145176		Approved		uc002qkz.3	A6NL88		ENST00000376325.4:c.225G>A	19.37:g.55954006C>T		39.0	0.0	0		25.0	8.0	0.32	NM_001145176		Silent	SNP	ENST00000376325.4	37	CCDS46193.1																																																																																			.	.	none		0.771	SHISA7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334533.2	NM_001145176	
VWF	7450	hgsc.bcm.edu	37	12	6076733	6076733	+	Silent	SNP	G	G	T			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr12:6076733G>T	ENST00000261405.5	-	47	8060	c.7806C>A	c.(7804-7806)acC>acA	p.T2602T		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	2602	VWFC 3. {ECO:0000255|PROSITE- ProRule:PRU00220}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	TGCAGCGGCAGGTCGTGCACA	0.627																																					p.T2602T		Atlas-SNP	.											.	VWF	338	.	0			c.C7806A						PASS	.						147.0	136.0	139.0					12																	6076733		2203	4300	6503	SO:0001819	synonymous_variant	7450	exon47			GCGGCAGGTCGTG		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"""Endogenous ligands"""	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.7806C>A	12.37:g.6076733G>T		44.0	0.0	0		31.0	18.0	0.580645	NM_000552	Q8TCE8|Q99806	Silent	SNP	ENST00000261405.5	37	CCDS8539.1																																																																																			.	.	none		0.627	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552	
PAQR7	164091	hgsc.bcm.edu	37	1	26189430	26189430	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr1:26189430G>A	ENST00000374296.3	-	2	1567	c.901C>T	c.(901-903)Cgg>Tgg	p.R301W	RP1-125I3.2_ENST00000455431.1_RNA	NM_178422.5	NP_848509.1	Q86WK9	MPRA_HUMAN	progestin and adipoQ receptor family member VII	301					multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|response to steroid hormone (GO:0048545)|steroid hormone mediated signaling pathway (GO:0043401)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)			breast(3)|endometrium(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	9		Colorectal(325;3.46e-05)|Lung NSC(340;0.00038)|all_lung(284;0.00051)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0505)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;2.16e-25)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000724)|BRCA - Breast invasive adenocarcinoma(304;0.000965)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0136)|READ - Rectum adenocarcinoma(331;0.0649)		TAGATGGGCCGTCGGGCCTCA	0.597																																					p.R301W	Esophageal Squamous(111;1206 1556 18433 19151 38418)	Atlas-SNP	.											.	PAQR7	23	.	0			c.C901T						PASS	.						60.0	60.0	60.0					1																	26189430		2203	4300	6503	SO:0001583	missense	164091	exon2			TGGGCCGTCGGGC		CCDS267.1	1p35.3	2012-08-10			ENSG00000182749	ENSG00000182749			23146	protein-coding gene	gene with protein product	"""membrane progestin receptor alpha"""	607779					Standard	NM_178422		Approved	mSR, MPRA	uc001bkx.3	Q86WK9	OTTHUMG00000007373	ENST00000374296.3:c.901C>T	1.37:g.26189430G>A	ENSP00000363414:p.Arg301Trp	143.0	0.0	0		110.0	47.0	0.427273	NM_178422	A2A2D3|Q5XKF9|Q86VE4	Missense_Mutation	SNP	ENST00000374296.3	37	CCDS267.1	.	.	.	.	.	.	.	.	.	.	G	17.86	3.491875	0.64074	.	.	ENSG00000182749	ENST00000374296	T	0.26810	1.71	5.07	3.16	0.36331	.	0.070365	0.56097	D	0.000026	T	0.39200	0.1069	M	0.62723	1.935	0.49687	D	0.999819	D	0.76494	0.999	P	0.57846	0.828	T	0.19745	-1.0296	10	0.87932	D	0	-16.9133	9.4892	0.38948	0.0:0.1248:0.5385:0.3366	.	301	Q86WK9	MPRA_HUMAN	W	301	ENSP00000363414:R301W	ENSP00000363414:R301W	R	-	1	2	PAQR7	26062017	0.767000	0.28508	0.997000	0.53966	0.992000	0.81027	1.262000	0.32992	0.687000	0.31509	0.563000	0.77884	CGG	.	.	none		0.597	PAQR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019312.1	NM_178422	
KRT6A	3853	hgsc.bcm.edu	37	12	52886934	52886934	+	Missense_Mutation	SNP	G	G	T			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr12:52886934G>T	ENST00000330722.6	-	1	107	c.39C>A	c.(37-39)agC>agA	p.S13R		NM_005554.3	NP_005545.1	P02538	K2C6A_HUMAN	keratin 6A	13	Head.				cell differentiation (GO:0030154)|positive regulation of cell proliferation (GO:0008284)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|liver(1)|lung(14)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	39				BRCA - Breast invasive adenocarcinoma(357;0.189)		CCCGGCGGCTGCTGCTGTGGC	0.642																																					p.S13R		Atlas-SNP	.											.	KRT6A	89	.	0			c.C39A						PASS	.						17.0	21.0	20.0					12																	52886934		2153	4212	6365	SO:0001583	missense	3853	exon1			GCGGCTGCTGCTG	BC014152, L42593, L42610	CCDS41786.1	12q13.13	2013-01-16			ENSG00000205420	ENSG00000205420		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6443	protein-coding gene	gene with protein product		148041	"""keratin 6C"", ""keratin 6D"""	KRT6C, KRT6D		1713141, 16831889	Standard	NM_005554		Approved	CK6C, K6C, CK6D, K6D	uc001sam.3	P02538	OTTHUMG00000169597	ENST00000330722.6:c.39C>A	12.37:g.52886934G>T	ENSP00000369317:p.Ser13Arg	102.0	0.0	0		136.0	31.0	0.227941	NM_005554	A4QPC1|P48667|Q08AR4|Q6NT67|Q96CL4	Missense_Mutation	SNP	ENST00000330722.6	37	CCDS41786.1	.	.	.	.	.	.	.	.	.	.	G	12.92	2.081166	0.36758	.	.	ENSG00000205420	ENST00000330722	T	0.58940	0.3	4.68	2.81	0.32909	.	0.556998	0.17430	N	0.174498	T	0.39572	0.1083	N	0.25380	0.74	0.09310	N	0.999998	B	0.02656	0.0	B	0.01281	0.0	T	0.25187	-1.0139	10	0.49607	T	0.09	.	5.6256	0.17480	0.2612:0.1981:0.5407:0.0	.	13	P02538	K2C6A_HUMAN	R	13	ENSP00000369317:S13R	ENSP00000369317:S13R	S	-	3	2	KRT6A	51173201	0.000000	0.05858	0.903000	0.35520	0.870000	0.49936	-0.124000	0.10595	1.140000	0.42260	0.549000	0.68633	AGC	.	.	none		0.642	KRT6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404978.2	NM_005554	
PIM1	5292	hgsc.bcm.edu	37	6	37138309	37138309	+	5'UTR	SNP	C	C	T			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr6:37138309C>T	ENST00000373509.5	+	0	331					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)	CCTGCGGCAGCTCCTCTGGGC	0.697			T	BCL6	NHL																																p.S77S		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.C231T						PASS	.						13.0	14.0	14.0					6																	37138309		2186	4281	6467	SO:0001623	5_prime_UTR_variant	5292	exon1			CGGCAGCTCCTCT		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.-43C>T	6.37:g.37138309C>T		37.0	0.0	0		48.0	14.0	0.291667	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Silent	SNP	ENST00000373509.5	37	CCDS4830.1																																																																																			.	.	none		0.697	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1		
YTHDF2	51441	hgsc.bcm.edu	37	1	29070284	29070284	+	Missense_Mutation	SNP	T	T	C			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr1:29070284T>C	ENST00000373812.3	+	4	1864	c.1502T>C	c.(1501-1503)tTt>tCt	p.F501S	YTHDF2_ENST00000478283.1_3'UTR|YTHDF2_ENST00000542507.1_Missense_Mutation_p.F501S|YTHDF2_ENST00000541996.1_Missense_Mutation_p.F451S	NM_016258.2	NP_057342.2	Q9Y5A9	YTHD2_HUMAN	YTH domain family, member 2	501	Interaction with m6A-containing mRNAs.|YTH. {ECO:0000255|PROSITE- ProRule:PRU00225}.				humoral immune response (GO:0006959)|regulation of mRNA stability (GO:0043488)	cytoplasmic mRNA processing body (GO:0000932)	N6-methyladenosine-containing RNA binding (GO:1990247)|poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Colorectal(325;3.46e-05)|Lung NSC(340;0.000601)|all_lung(284;0.000771)|Breast(348;0.00502)|Renal(390;0.00758)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;5.46e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0221)|KIRC - Kidney renal clear cell carcinoma(1967;0.0296)|READ - Rectum adenocarcinoma(331;0.0649)		AGGTGGATTTTTGTGAAGGAC	0.493																																					p.F501S		Atlas-SNP	.											.	YTHDF2	47	.	0			c.T1502C						PASS	.						84.0	83.0	84.0					1																	29070284		1925	4136	6061	SO:0001583	missense	51441	exon4			GGATTTTTGTGAA	AF155095	CCDS41296.1, CCDS53287.1	1p35	2008-02-05	2004-11-16		ENSG00000198492	ENSG00000198492			31675	protein-coding gene	gene with protein product		610640	"""YTH domain family 2"""			10508479	Standard	NM_016258		Approved	HGRG8, NY-REN-2	uc021okf.1	Q9Y5A9	OTTHUMG00000003648	ENST00000373812.3:c.1502T>C	1.37:g.29070284T>C	ENSP00000362918:p.Phe501Ser	129.0	0.0	0		155.0	64.0	0.412903	NM_016258	A6NKG4|A8K966|B4E1G7|D3DPM8|Q5VSZ9|Q8TDH0|Q9BUJ5	Missense_Mutation	SNP	ENST00000373812.3	37	CCDS41296.1	.	.	.	.	.	.	.	.	.	.	T	13.12	2.140965	0.37825	.	.	ENSG00000198492	ENST00000542507;ENST00000373812;ENST00000541996;ENST00000396232	T;T;T	0.26660	1.72;1.72;1.72	5.93	4.79	0.61399	YTH domain (2);	0.097053	0.64402	D	0.000001	T	0.40694	0.1127	L	0.45352	1.415	0.58432	D	0.999999	D;D	0.67145	0.996;0.996	D;D	0.75020	0.985;0.985	T	0.09015	-1.0694	9	.	.	.	-12.236	12.402	0.55418	0.0:0.0:0.1409:0.8591	.	501;501	B5BU99;Q9Y5A9	.;YTHD2_HUMAN	S	501;501;451;501	ENSP00000444660:F501S;ENSP00000362918:F501S;ENSP00000439394:F451S	.	F	+	2	0	YTHDF2	28942871	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.062000	0.71155	1.048000	0.40298	0.523000	0.50628	TTT	.	.	none		0.493	YTHDF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010335.1	NM_016258	
ELAVL2	1993	hgsc.bcm.edu	37	9	23762079	23762079	+	Nonsense_Mutation	SNP	G	G	A			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr9:23762079G>A	ENST00000397312.2	-	2	428	c.154C>T	c.(154-156)Cag>Tag	p.Q52*	ELAVL2_ENST00000380110.4_Nonsense_Mutation_p.Q81*|ELAVL2_ENST00000462649.1_5'Flank|ELAVL2_ENST00000223951.6_Nonsense_Mutation_p.Q52*|ELAVL2_ENST00000380117.1_Nonsense_Mutation_p.Q52*|ELAVL2_ENST00000544538.1_Nonsense_Mutation_p.Q52*	NM_004432.3	NP_004423.2	Q12926	ELAV2_HUMAN	ELAV like neuron-specific RNA binding protein 2	52	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				regulation of transcription, DNA-templated (GO:0006355)		mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(20)|ovary(2)|skin(1)|stomach(1)|urinary_tract(1)	39				GBM - Glioblastoma multiforme(1;2.18e-156)|Lung(42;2.15e-28)|LUSC - Lung squamous cell carcinoma(38;1.02e-19)		AGTTCCTCCTGTGTCATGTTC	0.403																																					p.Q52X		Atlas-SNP	.											ELAVL2,colon,carcinoma,+1,1	ELAVL2	80	1	0			c.C154T						PASS	.						253.0	231.0	238.0					9																	23762079		2203	4300	6503	SO:0001587	stop_gained	1993	exon2			CCTCCTGTGTCAT	BC030692	CCDS6515.1, CCDS55298.1	9p21	2013-10-03	2013-10-03		ENSG00000107105	ENSG00000107105		"""RNA binding motif (RRM) containing"""	3313	protein-coding gene	gene with protein product	"""Hu antigen B"""	601673	"""ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2"", ""ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B)"""			8812435	Standard	NM_004432		Approved	HuB, HEL-N1	uc003zpu.3	Q12926	OTTHUMG00000019700	ENST00000397312.2:c.154C>T	9.37:g.23762079G>A	ENSP00000380479:p.Gln52*	227.0	0.0	0		233.0	63.0	0.270386	NM_001171195	D3DRK3|Q13235|Q59G15|Q8NEM4|Q9H1Q8	Nonsense_Mutation	SNP	ENST00000397312.2	37	CCDS6515.1	.	.	.	.	.	.	.	.	.	.	G	39	7.566914	0.98361	.	.	ENSG00000107105	ENST00000223951;ENST00000397312;ENST00000544538;ENST00000380110;ENST00000380117;ENST00000359598;ENST00000440102	.	.	.	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	20.33	0.98713	0.0:0.0:1.0:0.0	.	.	.	.	X	52;52;52;52;52;80;52	.	ENSP00000223951:Q52X	Q	-	1	0	ELAVL2	23752079	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.993000	0.88291	2.810000	0.96702	0.585000	0.79938	CAG	.	.	none		0.403	ELAVL2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051943.2	NM_004432	
NOP2	4839	hgsc.bcm.edu	37	12	6672843	6672843	+	Missense_Mutation	SNP	C	C	T			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr12:6672843C>T	ENST00000322166.5	-	7	746	c.625G>A	c.(625-627)Ggc>Agc	p.G209S	NOP2_ENST00000541778.1_Missense_Mutation_p.G205S|NOP2_ENST00000545200.1_Missense_Mutation_p.G205S|NOP2_ENST00000542015.1_Intron|NOP2_ENST00000537442.1_Missense_Mutation_p.G209S|NOP2_ENST00000399466.2_Missense_Mutation_p.G205S|NOP2_ENST00000382421.3_Missense_Mutation_p.G242S	NM_001258308.1|NM_006170.3	NP_001245237.1|NP_006161.2	P46087	NOP2_HUMAN	NOP2 nucleolar protein	209					positive regulation of cell proliferation (GO:0008284)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			breast(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	19						ATCTGCAGGCCCCCATCTGCC	0.562											OREG0021630	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G242S		Atlas-SNP	.											.	NOP2	44	.	0			c.G724A						PASS	.						46.0	49.0	48.0					12																	6672843		1952	4122	6074	SO:0001583	missense	4839	exon8			GCAGGCCCCCATC		CCDS44811.1, CCDS58202.1, CCDS58203.1, CCDS58204.1	12p13	2012-12-10	2012-12-10	2008-10-13	ENSG00000111641	ENSG00000111641		"""NOP2/Sun domain containing"""	7867	protein-coding gene	gene with protein product	"""NOP2/Sun domain family, member 1"""	164031	"""nucleolar protein 1 (120kD)"", ""nucleolar protein 1, 120kDa"", ""nucleolar protein 2 homolog (yeast)"", ""NOP2 nucleolar protein homolog (yeast)"""	NOL1		8088812	Standard	NM_006170		Approved	NOP120, NSUN1, p120	uc021qtz.2	P46087	OTTHUMG00000169163	ENST00000322166.5:c.625G>A	12.37:g.6672843C>T	ENSP00000313272:p.Gly209Ser	71.0	0.0	0	635	68.0	27.0	0.397059	NM_001258309	A1A4Z3|B3KPD6|Q05BA7|Q0P5S5|Q3KQS4|Q58F30	Missense_Mutation	SNP	ENST00000322166.5	37	CCDS58203.1	.	.	.	.	.	.	.	.	.	.	C	11.37	1.619302	0.28801	.	.	ENSG00000111641	ENST00000537442;ENST00000382421;ENST00000545200;ENST00000399466;ENST00000322166;ENST00000541778;ENST00000542944;ENST00000542867	T;T;T;T;T;T;T;T	0.41400	2.53;2.56;2.57;2.53;2.53;2.53;1.0;1.0	5.71	3.86	0.44501	.	0.749013	0.13235	N	0.403359	T	0.27866	0.0686	L	0.33485	1.01	0.22354	N	0.999173	B;B	0.16603	0.01;0.018	B;B	0.12837	0.005;0.008	T	0.20538	-1.0272	10	0.14252	T	0.57	-1.761	6.8458	0.23987	0.0:0.6965:0.1459:0.1576	.	242;205	Q3KQS4;P46087-2	.;.	S	209;242;205;205;209;205;85;205	ENSP00000444437:G209S;ENSP00000371858:G242S;ENSP00000439422:G205S;ENSP00000382392:G205S;ENSP00000313272:G209S;ENSP00000443150:G205S;ENSP00000440754:G85S;ENSP00000443035:G205S	ENSP00000313272:G209S	G	-	1	0	NOP2	6543104	0.000000	0.05858	0.073000	0.20177	0.978000	0.69477	0.508000	0.22692	1.395000	0.46643	0.462000	0.41574	GGC	.	.	none		0.562	NOP2-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402614.1	NM_006170	
FGF3	2248	hgsc.bcm.edu	37	11	69625283	69625283	+	Silent	SNP	G	G	A			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr11:69625283G>A	ENST00000334134.2	-	3	600	c.510C>T	c.(508-510)cgC>cgT	p.R170R		NM_005247.2	NP_005238.1	P11487	FGF3_HUMAN	fibroblast growth factor 3	170					anatomical structure morphogenesis (GO:0009653)|cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of cardiac muscle tissue development (GO:0055026)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|otic vesicle formation (GO:0030916)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|post-anal tail morphogenesis (GO:0036342)|semicircular canal morphogenesis (GO:0048752)|signal transduction (GO:0007165)|thymus development (GO:0048538)	extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)	growth factor activity (GO:0008083)	p.R170R(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|urinary_tract(1)	13			LUSC - Lung squamous cell carcinoma(11;5.05e-15)|STAD - Stomach adenocarcinoma(18;0.0278)			TCTGTGTGCGGCGGGTCTTGA	0.682																																					p.R170R		Atlas-SNP	.											FGF3,NS,carcinoma,0,1	FGF3	27	1	1	Substitution - coding silent(1)	ovary(1)	c.C510T						PASS	.						21.0	24.0	23.0					11																	69625283		2193	4270	6463	SO:0001819	synonymous_variant	2248	exon3			TGTGCGGCGGGTC		CCDS8195.1	11q13	2010-06-25	2010-06-25		ENSG00000186895	ENSG00000186895			3681	protein-coding gene	gene with protein product	"""INT-2 proto-oncogene protein"", ""oncogene INT2"", ""V-INT2 murine mammary tumor virus integration site oncogene homolog"", ""murine mammary tumor virus integration site 2, mouse"""	164950	"""fibroblast growth factor 3 (murine mammary tumor virus integration site (v-int-2) oncogene homolog)"""	INT2			Standard	NM_005247		Approved	HBGF-3	uc001oph.3	P11487	OTTHUMG00000167888	ENST00000334134.2:c.510C>T	11.37:g.69625283G>A		144.0	0.0	0		99.0	7.0	0.0707071	NM_005247	Q0VG69	Silent	SNP	ENST00000334134.2	37	CCDS8195.1																																																																																			.	.	none		0.682	FGF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396835.1	NM_005247	
PIM1	5292	hgsc.bcm.edu	37	6	37139042	37139042	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr6:37139042G>A	ENST00000373509.5	+	4	755	c.382G>A	c.(382-384)Gat>Aat	p.D128N		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	219					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)	GCCGGTGCAAGATCTCTTCGA	0.622			T	BCL6	NHL																																p.D219N		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.G655A						PASS	.						81.0	95.0	91.0					6																	37139042		2203	4300	6503	SO:0001583	missense	5292	exon4			GTGCAAGATCTCT		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.382G>A	6.37:g.37139042G>A	ENSP00000362608:p.Asp128Asn	78.0	0.0	0		86.0	38.0	0.44186	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.857582	0.91433	.	.	ENSG00000137193	ENST00000373509	T	0.15603	2.41	4.28	4.28	0.50868	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.24005	0.0581	L	0.42008	1.315	0.80722	D	1	D	0.53745	0.962	P	0.62885	0.908	T	0.02081	-1.1217	10	0.87932	D	0	.	16.8746	0.86048	0.0:0.0:1.0:0.0	.	219	P11309	PIM1_HUMAN	N	128	ENSP00000362608:D128N	ENSP00000362608:D128N	D	+	1	0	PIM1	37247020	1.000000	0.71417	1.000000	0.80357	0.773000	0.43773	9.149000	0.94659	2.371000	0.80710	0.549000	0.68633	GAT	.	.	none		0.622	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1		
TENM4	26011	hgsc.bcm.edu	37	11	78516504	78516504	+	Missense_Mutation	SNP	C	C	A			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr11:78516504C>A	ENST00000278550.7	-	15	2474	c.2012G>T	c.(2011-2013)gGt>gTt	p.G671V		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	671	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										CACGCAGACACCCCGGCCTGA	0.572																																					p.G671V		Atlas-SNP	.											.	.	.	.	0			c.G2012T						PASS	.						34.0	39.0	37.0					11																	78516504		2136	4245	6381	SO:0001583	missense	26011	exon15			CAGACACCCCGGC	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"""odz, odd Oz/ten-m homolog 4 (Drosophila)"""	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.2012G>T	11.37:g.78516504C>A	ENSP00000278550:p.Gly671Val	23.0	0.0	0		24.0	11.0	0.458333	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Missense_Mutation	SNP	ENST00000278550.7	37	CCDS44688.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.929751	0.92389	.	.	ENSG00000149256	ENST00000278550	T	0.14516	2.5	5.1	5.1	0.69264	Epidermal growth factor-like (1);	0.000000	0.85682	D	0.000000	T	0.56455	0.1986	H	0.98111	4.15	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.74654	-0.3593	9	.	.	.	.	18.7262	0.91714	0.0:1.0:0.0:0.0	.	671	Q6N022	TEN4_HUMAN	V	671	ENSP00000278550:G671V	.	G	-	2	0	ODZ4	78194152	1.000000	0.71417	0.980000	0.43619	0.958000	0.62258	7.651000	0.83577	2.644000	0.89710	0.563000	0.77884	GGT	.	.	none		0.572	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2		
MTMR8	55613	hgsc.bcm.edu	37	X	63568661	63568661	+	Missense_Mutation	SNP	C	C	T	rs201816063		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chrX:63568661C>T	ENST00000374852.3	-	6	678	c.611G>A	c.(610-612)cGc>cAc	p.R204H	MTMR8_ENST00000453546.1_Missense_Mutation_p.R204H	NM_017677.3	NP_060147.2	Q96EF0	MTMR8_HUMAN	myotubularin related protein 8	204	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.					nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)	p.0?(1)		breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|skin(3)	37						CTGGCTACAGCGGCAAATGGC	0.453													C|||	1	0.000264901	0.0	0.0	3775	,	,		12545	0.001		0.0	False		,,,				2504	0.0				p.R204H		Atlas-SNP	.											.	MTMR8	178	.	1	Whole gene deletion(1)	ovary(1)	c.G611A						PASS	.	C	HIS/ARG	1,3834		0,0,1,1632,570	80.0	64.0	69.0		611	-0.4	1.0	X		69	0,6728		0,0,0,2428,1872	yes	missense	MTMR8	NM_017677.3	29	0,0,1,4060,2442	TT,TC,T,CC,C		0.0,0.0261,0.0095	probably-damaging	204/705	63568661	1,10562	2203	4300	6503	SO:0001583	missense	55613	exon6			CTACAGCGGCAAA	AK000133	CCDS14379.1	Xq11.2-q12	2013-01-11			ENSG00000102043	ENSG00000102043		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	16825	protein-coding gene	gene with protein product						11275328	Standard	NM_017677		Approved	FLJ20126	uc004dvs.3	Q96EF0	OTTHUMG00000021707	ENST00000374852.3:c.611G>A	X.37:g.63568661C>T	ENSP00000363985:p.Arg204His	77.0	0.0	0		90.0	31.0	0.344444	NM_017677	Q5JT99|Q9NXP6	Missense_Mutation	SNP	ENST00000374852.3	37	CCDS14379.1	.	.	.	.	.	.	.	.	.	.	C	13.15	2.150406	0.37923	2.61E-4	0.0	ENSG00000102043	ENST00000453546;ENST00000374852	D;D	0.98164	-4.76;-4.76	2.68	-0.425	0.12317	Myotubularin phosphatase domain (1);Myotubularin-related (1);	0.000000	0.49305	U	0.000148	D	0.99208	0.9725	H	0.99312	4.51	0.49798	D	0.99982	B;D	0.89917	0.086;1.0	B;D	0.91635	0.022;0.999	D	0.97436	1.0018	10	0.87932	D	0	.	7.0652	0.25147	0.0:0.6388:0.0:0.3612	.	204;204	B4DQL0;Q96EF0	.;MTMR8_HUMAN	H	204	ENSP00000394003:R204H;ENSP00000363985:R204H	ENSP00000363985:R204H	R	-	2	0	MTMR8	63485386	0.995000	0.38212	0.991000	0.47740	0.994000	0.84299	1.318000	0.33643	-0.414000	0.07495	0.506000	0.49869	CGC	.	.	weak		0.453	MTMR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056949.2	NM_017677	
DHX38	9785	hgsc.bcm.edu	37	16	72137944	72137944	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr16:72137944G>A	ENST00000268482.3	+	14	2433	c.1924G>A	c.(1924-1926)Gac>Aac	p.D642N	DHX38_ENST00000536867.1_Intron	NM_014003.3	NP_054722.2	Q92620	PRP16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 38	642	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(1)|large_intestine(16)|lung(15)|pancreas(1)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	48		Ovarian(137;0.125)				CCGGGAAGCCGACCTGGATCA	0.582																																					p.D642N	Melanoma(97;711 1442 7855 13832 28836)	Atlas-SNP	.											DHX38,NS,carcinoma,0,1	DHX38	91	1	0			c.G1924A						PASS	.						117.0	104.0	108.0					16																	72137944		2198	4300	6498	SO:0001583	missense	9785	exon14			GAAGCCGACCTGG	AF038391	CCDS10907.1	16q22	2008-02-05	2003-06-13	2003-06-20	ENSG00000140829	ENSG00000140829		"""DEAH-boxes"""	17211	protein-coding gene	gene with protein product		605584	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 38"""	DDX38		9524131, 9039502	Standard	NM_014003		Approved	PRP16, KIAA0224, hPrp16, PRPF16	uc002fcb.3	Q92620	OTTHUMG00000137596	ENST00000268482.3:c.1924G>A	16.37:g.72137944G>A	ENSP00000268482:p.Asp642Asn	96.0	0.0	0		66.0	23.0	0.348485	NM_014003	B4DVG8|D3DWS7|O75212|Q96HN7	Missense_Mutation	SNP	ENST00000268482.3	37	CCDS10907.1	.	.	.	.	.	.	.	.	.	.	G	36	5.786051	0.96937	.	.	ENSG00000140829	ENST00000268482	T	0.07688	3.17	5.49	5.49	0.81192	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.114937	0.64402	D	0.000020	T	0.20700	0.0498	L	0.42529	1.33	0.80722	D	1	D	0.58620	0.983	P	0.58820	0.846	T	0.00063	-1.2154	10	0.51188	T	0.08	.	19.7433	0.96241	0.0:0.0:1.0:0.0	.	642	Q92620	PRP16_HUMAN	N	642	ENSP00000268482:D642N	ENSP00000268482:D642N	D	+	1	0	DHX38	70695445	1.000000	0.71417	0.967000	0.41034	0.915000	0.54546	7.954000	0.87848	2.733000	0.93635	0.655000	0.94253	GAC	.	.	none		0.582	DHX38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269004.3	NM_014003	
KRT3	3850	hgsc.bcm.edu	37	12	53185490	53185490	+	Silent	SNP	C	C	T	rs369576134		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr12:53185490C>T	ENST00000417996.2	-	6	1373	c.1299G>A	c.(1297-1299)gaG>gaA	p.E433E	KRT3_ENST00000309505.3_Silent_p.E433E	NM_057088.2	NP_476429.2	P12035	K2C3_HUMAN	keratin 3	433	Coil 2.|Rod.				epithelial cell differentiation (GO:0030855)|intermediate filament cytoskeleton organization (GO:0045104)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|prostate(2)|skin(1)	23						TCTTGACACCCTCGATCTCTG	0.567																																					p.E433E		Atlas-SNP	.											.	KRT3	65	.	0			c.G1299A						PASS	.	C		0,4404		0,0,2202	107.0	108.0	108.0		1299	4.0	0.5	12		108	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KRT3	NM_057088.2		0,1,6501	TT,TC,CC		0.0116,0.0,0.0077		433/629	53185490	1,13003	2202	4300	6502	SO:0001819	synonymous_variant	3850	exon6			GACACCCTCGATC		CCDS44895.1	12q13.13	2013-01-16			ENSG00000186442	ENSG00000186442		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6440	protein-coding gene	gene with protein product	"""keratin, type II cytoskeletal 3"", ""cytokeratin 3"""	148043				7510223, 16831889	Standard	NM_057088		Approved	CK3, K3	uc001say.3	P12035	OTTHUMG00000169799	ENST00000417996.2:c.1299G>A	12.37:g.53185490C>T		154.0	0.0	0		178.0	99.0	0.55618	NM_057088	A6NIS2|Q701L8	Silent	SNP	ENST00000417996.2	37	CCDS44895.1																																																																																			.	.	weak		0.567	KRT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405930.1	NM_057088	
KLHL17	339451	hgsc.bcm.edu	37	1	898557	898557	+	Missense_Mutation	SNP	G	G	A	rs201246933		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr1:898557G>A	ENST00000338591.3	+	7	1218	c.1111G>A	c.(1111-1113)Gtg>Atg	p.V371M		NM_198317.2	NP_938073.1	Q6TDP4	KLH17_HUMAN	kelch-like family member 17	371	Interaction with F-actin. {ECO:0000250}.				actin cytoskeleton organization (GO:0030036)|brain development (GO:0007420)|protein ubiquitination (GO:0016567)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|dendrite cytoplasm (GO:0032839)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	protein complex scaffold (GO:0032947)			central_nervous_system(1)|kidney(2)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.52e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.59e-23)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.000469)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		CCGCTGGCACGTGGTGGCCTC	0.701																																					p.V371M		Atlas-SNP	.											.	KLHL17	31	.	0			c.G1111A						PASS	.						35.0	38.0	37.0					1																	898557		2195	4292	6487	SO:0001583	missense	339451	exon7			TGGCACGTGGTGG	AY423763	CCDS30550.1	1p36	2013-01-30	2013-01-30		ENSG00000187961	ENSG00000187961		"""Kelch-like"", ""BTB/POZ domain containing"""	24023	protein-coding gene	gene with protein product	"""actinfilin"""		"""kelch-like 17 (Drosophila)"""			12063253	Standard	NM_198317		Approved		uc001aca.2	Q6TDP4	OTTHUMG00000040721	ENST00000338591.3:c.1111G>A	1.37:g.898557G>A	ENSP00000343930:p.Val371Met	57.0	0.0	0		48.0	23.0	0.479167	NM_198317	Q5SV94	Missense_Mutation	SNP	ENST00000338591.3	37	CCDS30550.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	13.33	2.204611	0.38905	.	.	ENSG00000187961	ENST00000338591;ENST00000455747;ENST00000540863	T	0.73789	-0.78	5.52	2.27	0.28462	Galactose oxidase, beta-propeller (1);	0.158567	0.53938	D	0.000052	T	0.49813	0.1579	N	0.11870	0.19	0.39807	D	0.972655	B	0.06786	0.001	B	0.04013	0.001	T	0.29458	-1.0011	10	0.25106	T	0.35	.	5.4008	0.16295	0.5559:0.0:0.4441:0.0	.	371	Q6TDP4	KLH17_HUMAN	M	371;247;94	ENSP00000343930:V371M	ENSP00000343930:V371M	V	+	1	0	KLHL17	888420	1.000000	0.71417	0.995000	0.50966	0.986000	0.74619	4.929000	0.63455	0.711000	0.32018	-0.480000	0.04831	GTG	G|0.999;A|0.001	0.001	strong		0.701	KLHL17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097875.3	NM_198317	
OR4K5	79317	hgsc.bcm.edu	37	14	20388876	20388876	+	Silent	SNP	C	C	A			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr14:20388876C>A	ENST00000315915.4	+	1	136	c.111C>A	c.(109-111)gtC>gtA	p.V37V		NM_001005483.1	NP_001005483.1	Q8NGD3	OR4K5_HUMAN	olfactory receptor, family 4, subfamily K, member 5	37						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V37V(1)		central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(6)|liver(1)|lung(27)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	47	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TGTATACAGTCATTGTGCTGG	0.408																																					p.V37V		Atlas-SNP	.											OR4K5,NS,carcinoma,0,1	OR4K5	111	1	1	Substitution - coding silent(1)	lung(1)	c.C111A						PASS	.						202.0	210.0	207.0					14																	20388876		2203	4300	6503	SO:0001819	synonymous_variant	79317	exon1			TACAGTCATTGTG	BK004355	CCDS32024.1	14q11.22	2012-08-09				ENSG00000176281		"""GPCR / Class A : Olfactory receptors"""	14745	protein-coding gene	gene with protein product						14983052	Standard	NM_001005483		Approved		uc010tkw.2	Q8NGD3		ENST00000315915.4:c.111C>A	14.37:g.20388876C>A		182.0	0.0	0		177.0	56.0	0.316384	NM_001005483	Q6IFA7	Silent	SNP	ENST00000315915.4	37	CCDS32024.1																																																																																			.	.	none		0.408	OR4K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409867.1	NM_001005483	
ZDHHC14	79683	hgsc.bcm.edu	37	6	158074641	158074641	+	Silent	SNP	G	G	A	rs35358008	byFrequency	TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr6:158074641G>A	ENST00000359775.5	+	8	1939	c.1050G>A	c.(1048-1050)acG>acA	p.T350T	ZDHHC14_ENST00000341375.8_3'UTR|ZDHHC14_ENST00000414563.2_Silent_p.T350T			Q8IZN3	ZDH14_HUMAN	zinc finger, DHHC-type containing 14	350					protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|skin(1)	17		Breast(66;0.00586)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.9e-17)|BRCA - Breast invasive adenocarcinoma(81;5.8e-05)		ACGGGGCCACGCAGTCACAGA	0.592																																					p.T350T		Atlas-SNP	.											.	ZDHHC14	39	.	0			c.G1050A						PASS	.						69.0	58.0	62.0					6																	158074641		2203	4300	6503	SO:0001819	synonymous_variant	79683	exon8			GGCCACGCAGTCA	AF542388	CCDS5252.1, CCDS47510.1	6q25.3	2008-05-02			ENSG00000175048	ENSG00000175048		"""Zinc fingers, DHHC-type"""	20341	protein-coding gene	gene with protein product							Standard	NM_024630		Approved	FLJ20984, NEW1CP	uc003qqt.3	Q8IZN3	OTTHUMG00000015896	ENST00000359775.5:c.1050G>A	6.37:g.158074641G>A		22.0	0.0	0		33.0	13.0	0.393939	NM_024630	A6NDB7|Q5JS07|Q5JS08|Q6PHS4|Q8IZN2|Q9H7F1	Silent	SNP	ENST00000359775.5	37	CCDS5252.1																																																																																			G|0.959;T|0.041	.	alt		0.592	ZDHHC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042841.2	NM_153746	
SERPINH1	871	hgsc.bcm.edu	37	11	75277917	75277917	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr11:75277917G>A	ENST00000524558.1	+	2	1958	c.523G>A	c.(523-525)Gag>Aag	p.E175K	SERPINH1_ENST00000530284.1_Missense_Mutation_p.E175K|SERPINH1_ENST00000358171.3_Missense_Mutation_p.E175K|SERPINH1_ENST00000525876.1_5'Flank|SERPINH1_ENST00000533603.1_Missense_Mutation_p.E175K			P50454	SERPH_HUMAN	serpin peptidase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)	175					chondrocyte development involved in endochondral bone morphogenesis (GO:0003433)|collagen biosynthetic process (GO:0032964)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|protein maturation (GO:0051604)|regulation of proteolysis (GO:0030162)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(4)|large_intestine(3)|liver(1)|lung(4)|ovary(2)|stomach(1)	15	Ovarian(111;0.11)					GTCCATCAACGAGTGGGCCGC	0.627																																					p.E175K		Atlas-SNP	.											.	SERPINH1	33	.	0			c.G523A						PASS	.						42.0	43.0	43.0					11																	75277917		2200	4293	6493	SO:0001583	missense	871	exon2			ATCAACGAGTGGG	X61598	CCDS8239.1	11q13.5	2014-02-18	2005-08-18		ENSG00000149257	ENSG00000149257		"""Serine (or cysteine) peptidase inhibitors"""	1546	protein-coding gene	gene with protein product		600943	"""serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 2"", ""serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)"""	CBP1, CBP2, SERPINH2		7656593, 9533029, 24172014	Standard	NM_001207014		Approved	HSP47, colligen	uc001owr.3	P50454	OTTHUMG00000165362	ENST00000524558.1:c.523G>A	11.37:g.75277917G>A	ENSP00000434412:p.Glu175Lys	39.0	0.0	0		58.0	22.0	0.37931	NM_001235	B3KVJ3|P29043|Q5XPB4|Q6NSJ6|Q8IY96|Q9NP88	Missense_Mutation	SNP	ENST00000524558.1	37	CCDS8239.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.694570	0.88830	.	.	ENSG00000149257	ENST00000533603;ENST00000358171;ENST00000526397;ENST00000421448;ENST00000525492;ENST00000530284;ENST00000532356;ENST00000524558;ENST00000525611;ENST00000528760	D;D;D;T;D;D;D;D;D	0.87491	-2.26;-2.26;-2.26;-0.84;-2.26;-2.26;-2.26;-2.26;-2.26	4.66	4.66	0.58398	Serpin domain (3);	0.000000	0.85682	D	0.000000	D	0.86981	0.6064	L	0.32530	0.975	0.80722	D	1	D;D	0.63880	0.988;0.993	P;P	0.56216	0.752;0.794	D	0.86178	0.1604	10	0.34782	T	0.22	.	15.0624	0.71964	0.0:0.0:1.0:0.0	.	175;175	E9PPV6;P50454	.;SERPH_HUMAN	K	175;175;175;154;128;175;175;175;175;175	ENSP00000434657:E175K;ENSP00000350894:E175K;ENSP00000434964:E175K;ENSP00000434482:E128K;ENSP00000436305:E175K;ENSP00000436040:E175K;ENSP00000434412:E175K;ENSP00000435452:E175K;ENSP00000437108:E175K	ENSP00000350894:E175K	E	+	1	0	SERPINH1	74955565	1.000000	0.71417	0.999000	0.59377	0.927000	0.56198	7.850000	0.86915	2.140000	0.66376	0.563000	0.77884	GAG	.	.	none		0.627	SERPINH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383610.1	NM_004353	
ZFPM2	23414	hgsc.bcm.edu	37	8	106815063	106815063	+	Missense_Mutation	SNP	A	A	C			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr8:106815063A>C	ENST00000407775.2	+	8	3003	c.2753A>C	c.(2752-2754)aAa>aCa	p.K918T	RP11-152P17.2_ENST00000520433.1_RNA|RP11-152P17.2_ENST00000518932.1_RNA|RP11-152P17.2_ENST00000524045.2_RNA|RP11-152P17.2_ENST00000509144.2_RNA|RP11-152P17.2_ENST00000520594.1_RNA|ZFPM2_ENST00000517361.1_Missense_Mutation_p.K786T|ZFPM2_ENST00000378472.4_Missense_Mutation_p.K649T|ZFPM2_ENST00000522296.1_3'UTR|RP11-152P17.2_ENST00000521622.1_RNA|ZFPM2_ENST00000520492.1_Missense_Mutation_p.K786T	NM_012082.3	NP_036214.2	Q8WW38	FOG2_HUMAN	zinc finger protein, FOG family member 2	918					blood coagulation (GO:0007596)|embryonic organ development (GO:0048568)|gonadal mesoderm development (GO:0007506)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|negative regulation of cell death (GO:0060548)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of female gonad development (GO:2000195)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.K918I(1)		NS(4)|breast(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(11)|liver(2)|lung(48)|ovary(4)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	99			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			AAATGTGAGAAAAATGGGAAT	0.458																																					p.K918T		Atlas-SNP	.											ZFPM2,colon,carcinoma,0,1	ZFPM2	219	1	1	Substitution - Missense(1)	large_intestine(1)	c.A2753C						PASS	.						40.0	39.0	39.0					8																	106815063		1886	4115	6001	SO:0001583	missense	23414	exon8			GTGAGAAAAATGG	AF119334	CCDS47908.1	8q23	2013-01-10	2012-11-27		ENSG00000169946	ENSG00000169946		"""Zinc fingers, C2H2-type"", ""Zinc fingers, C2HC-type containing"""	16700	protein-coding gene	gene with protein product		603693	"""zinc finger protein, multitype 2"""			9927675, 10438528	Standard	NM_012082		Approved	FOG2, hFOG-2, ZNF89B, ZC2HC11B	uc003ymd.3	Q8WW38	OTTHUMG00000164818	ENST00000407775.2:c.2753A>C	8.37:g.106815063A>C	ENSP00000384179:p.Lys918Thr	61.0	0.0	0		62.0	21.0	0.33871	NM_012082	Q32MA6|Q9NPL7|Q9NPS4|Q9UNI5	Missense_Mutation	SNP	ENST00000407775.2	37	CCDS47908.1	.	.	.	.	.	.	.	.	.	.	A	16.53	3.150059	0.57151	.	.	ENSG00000169946	ENST00000407775;ENST00000520492;ENST00000517361;ENST00000378472	T;T;T;T	0.24723	1.84;2.34;2.34;3.54	5.76	5.76	0.90799	.	0.042154	0.85682	D	0.000000	T	0.34221	0.0890	L	0.29908	0.895	0.80722	D	1	D	0.60575	0.988	P	0.57204	0.815	T	0.03555	-1.1025	10	0.42905	T	0.14	.	16.0709	0.80928	1.0:0.0:0.0:0.0	.	918	Q8WW38	FOG2_HUMAN	T	918;786;786;649	ENSP00000384179:K918T;ENSP00000430757:K786T;ENSP00000428720:K786T;ENSP00000367733:K649T	ENSP00000367733:K649T	K	+	2	0	ZFPM2	106884239	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.339000	0.96797	2.198000	0.70561	0.528000	0.53228	AAA	.	.	none		0.458	ZFPM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380614.1		
FCRL5	83416	hgsc.bcm.edu	37	1	157516959	157516959	+	Silent	SNP	G	G	A			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr1:157516959G>A	ENST00000361835.3	-	3	238	c.81C>T	c.(79-81)ctC>ctT	p.L27L	FCRL5_ENST00000356953.4_Silent_p.L27L|FCRL5_ENST00000368188.2_Silent_p.L27L|FCRL5_ENST00000368190.3_Silent_p.L27L|FCRL5_ENST00000368191.3_Intron|FCRL5_ENST00000368189.3_Silent_p.L27L	NM_001195388.1|NM_031281.2	NP_001182317.1|NP_112571.2	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	27	Ig-like C2-type 1.				negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of release of sequestered calcium ion into cytosol (GO:0051280)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(45)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	85	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)				ATGGAGGCTGGAGGAAAATAA	0.537																																					p.L27L		Atlas-SNP	.											FCRL5,mouth,carcinoma,-1,1	FCRL5	177	1	0			c.C81T						PASS	.						119.0	113.0	115.0					1																	157516959		2203	4300	6503	SO:0001819	synonymous_variant	83416	exon3			AGGCTGGAGGAAA	AF369794	CCDS1165.1	1q21	2013-01-11			ENSG00000143297	ENSG00000143297		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18508	protein-coding gene	gene with protein product		605877				11027651, 11290337	Standard	NM_031281		Approved	FCRH5, IRTA2, BXMAS1, CD307e	uc009wsm.3	Q96RD9	OTTHUMG00000017481	ENST00000361835.3:c.81C>T	1.37:g.157516959G>A		113.0	0.0	0		121.0	48.0	0.396694	NM_031281	A0N0M2|B7WNT9|B7WP94|Q495Q2|Q495Q4|Q5VYK9|Q6UY46	Silent	SNP	ENST00000361835.3	37	CCDS1165.1																																																																																			.	.	none		0.537	FCRL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046263.1	NM_031281	
ZNF112	7771	hgsc.bcm.edu	37	19	44832834	44832834	+	Silent	SNP	T	T	A			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr19:44832834T>A	ENST00000337401.4	-	5	1582	c.1494A>T	c.(1492-1494)ccA>ccT	p.P498P	ZNF112_ENST00000536500.1_Silent_p.P515P|ZNF112_ENST00000354340.4_Silent_p.P492P	NM_001083335.1	NP_001076804.1	Q9UJU3	ZN112_HUMAN	zinc finger protein 112	498					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										GCTCCTTACGTGGTTTCTCTC	0.403																																					p.P498P		Atlas-SNP	.											.	ZFP112	219	.	0			c.A1494T						PASS	.						134.0	130.0	132.0					19																	44832834		2203	4300	6503	SO:0001819	synonymous_variant	7771	exon5			CTTACGTGGTTTC	AF198358		19q13.2	2014-02-06	2012-11-27		ENSG00000062370	ENSG00000062370		"""Zinc fingers, C2H2-type"""	12892	protein-coding gene	gene with protein product		603994	"""zinc finger protein 112 homolog (mouse)"", ""zinc finger protein 228"""	ZFP112, ZNF228			Standard	NM_013380		Approved			Q9UJU3	OTTHUMG00000182357	ENST00000337401.4:c.1494A>T	19.37:g.44832834T>A		142.0	0.0	0		138.0	46.0	0.333333	NM_001083335	A4FU53|Q9HCA7	Silent	SNP	ENST00000337401.4	37	CCDS54276.1																																																																																			.	.	none		0.403	ZNF112-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460744.1	NM_013380	
ALDH1B1	219	hgsc.bcm.edu	37	9	38397089	38397089	+	Silent	SNP	G	G	A			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr9:38397089G>A	ENST00000377698.3	+	2	1497	c.1344G>A	c.(1342-1344)gtG>gtA	p.V448V		NM_000692.4	NP_000683.3	P30837	AL1B1_HUMAN	aldehyde dehydrogenase 1 family, member B1	448					carbohydrate metabolic process (GO:0005975)|ethanol catabolic process (GO:0006068)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	aldehyde dehydrogenase (NAD) activity (GO:0004029)			NS(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(1)|stomach(2)|urinary_tract(2)	32				GBM - Glioblastoma multiforme(29;0.043)|Lung(182;0.115)		CTGCGGCTGTGTTCACCCGGG	0.577																																					p.V448V		Atlas-SNP	.											.	ALDH1B1	50	.	0			c.G1344A						PASS	.						65.0	63.0	64.0					9																	38397089		2203	4300	6503	SO:0001819	synonymous_variant	219	exon2			GGCTGTGTTCACC	M63967	CCDS6615.1	9p13	2008-02-05			ENSG00000137124	ENSG00000137124	1.2.1.3	"""Aldehyde dehydrogenases"""	407	protein-coding gene	gene with protein product		100670		ALDH5		2061311	Standard	NM_000692		Approved	ALDHX	uc004aay.3	P30837	OTTHUMG00000019938	ENST00000377698.3:c.1344G>A	9.37:g.38397089G>A		68.0	0.0	0		65.0	22.0	0.338462	NM_000692	B2R8F0|Q8WX76|Q9BV45	Silent	SNP	ENST00000377698.3	37	CCDS6615.1																																																																																			.	.	none		0.577	ALDH1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052492.1		
LCN15	389812	hgsc.bcm.edu	37	9	139651501	139651501	+	IGR	SNP	A	A	C			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr9:139651501A>C	ENST00000316144.5	-	0	762				LCN8_ENST00000482893.1_5'UTR|LCN15_ENST00000482511.1_5'Flank|LCN8_ENST00000371688.3_Silent_p.V48V	NM_203347.1	NP_976222.1	Q6UWW0	LCN15_HUMAN	lipocalin 15						lipid metabolic process (GO:0006629)	extracellular region (GO:0005576)	small molecule binding (GO:0036094)|transporter activity (GO:0005215)			endometrium(1)|lung(1)	2						TGTTATATGCAACCTTCACGG	0.632																																					p.V48V		Atlas-SNP	.											.	LCN8	14	.	0			c.T144G						PASS	.						45.0	40.0	42.0					9																	139651501		2203	4300	6503	SO:0001628	intergenic_variant	138307	exon2			ATATGCAACCTTC		CCDS7006.1	9q34.3	2011-10-24			ENSG00000177984	ENSG00000177984		"""Lipocalins"""	33777	protein-coding gene	gene with protein product							Standard	NM_203347		Approved	UNQ2541, PRO6093	uc004cjd.3	Q6UWW0	OTTHUMG00000020943		9.37:g.139651501A>C		53.0	0.0	0		50.0	19.0	0.38	NM_178469		Silent	SNP	ENST00000316144.5	37	CCDS7006.1																																																																																			.	.	none		0.632	LCN15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055114.2	NM_203347	
ETV6	2120	hgsc.bcm.edu	37	12	11803094	11803094	+	Splice_Site	SNP	G	G	C	rs547638904		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr12:11803094G>C	ENST00000396373.4	+	1	307	c.33G>C	c.(31-33)aaG>aaC	p.K11N	ETV6_ENST00000544715.1_3'UTR	NM_001987.4	NP_001978.1	P41212	ETV6_HUMAN	ets variant 6	11		Breakpoint for translocation to form CHIC2-ETV6 in AML.			cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	protein domain specific binding (GO:0019904)|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)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)		ETV6/JAK2(11)|ETV6/ITPR2(2)|ETV6/NTRK3(238)	breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(15)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(2;1.88e-12)|Acute lymphoblastic leukemia(2;6.91e-39)|all_hematologic(2;2.7e-36)				GTAGCATTAAGGTAAAAATCT	0.537			T	"""NTRK3, RUNX1, PDGFRB, ABL1, MN1, ABL2, FACL6, CHIC2, ARNT, JAK2, EVI1, CDX2, STL, HLXB9, MDS2, PER1, SYK, TTL, FGFR3, PAX5"""	"""congenital fibrosarcoma, multiple leukemia and lymphoma,  secretory breast, MDS, ALL"""																																p.K11N		Atlas-SNP	.		Dom	yes		12	12p13	2120	ets variant gene 6 (TEL oncogene)		"""L, E, M"""	.	ETV6	91	.	0			c.G33C						PASS	.						136.0	133.0	134.0					12																	11803094		2203	4300	6503	SO:0001630	splice_region_variant	2120	exon1			CATTAAGGTAAAA	BC043399	CCDS8643.1	12p13	2014-09-17	2008-09-12		ENSG00000139083	ENSG00000139083			3495	protein-coding gene	gene with protein product	"""TEL oncogene"""	600618	"""ets variant gene 6 (TEL oncogene)"""			7731705	Standard	NM_001987		Approved	TEL	uc001qzz.3	P41212	OTTHUMG00000168538	ENST00000396373.4:c.33+1G>C	12.37:g.11803094G>C		47.0	0.0	0		25.0	16.0	0.64	NM_001987	A3QVP6|A8K076|Q9UMF6|Q9UMF7|Q9UMG0	Missense_Mutation	SNP	ENST00000396373.4	37	CCDS8643.1	.	.	.	.	.	.	.	.	.	.	G	12.63	1.995060	0.35226	.	.	ENSG00000139083	ENST00000396373	T	0.09255	3.0	4.11	3.2	0.36748	.	0.964265	0.08491	N	0.937964	T	0.07954	0.0199	L	0.27053	0.805	0.80722	D	1	B	0.23650	0.089	B	0.22152	0.038	T	0.24154	-1.0168	10	0.22706	T	0.39	.	6.7932	0.23711	0.1278:0.0:0.8722:0.0	.	11	P41212	ETV6_HUMAN	N	11	ENSP00000379658:K11N	ENSP00000379658:K11N	K	+	3	2	ETV6	11694361	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	3.784000	0.55416	1.832000	0.53329	0.491000	0.48974	AAG	.	.	none		0.537	ETV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400130.2	NM_001987	Missense_Mutation
PIM1	5292	hgsc.bcm.edu	37	6	37138951	37138951	+	Silent	SNP	C	C	T			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr6:37138951C>T	ENST00000373509.5	+	4	664	c.291C>T	c.(289-291)agC>agT	p.S97S		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	188					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)	AGAAGGTGAGCTCGGGTTTCT	0.647			T	BCL6	NHL																																p.S188S		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	PIM1,NS,lymphoid_neoplasm,+1,5	PIM1	71	5	0			c.C564T						PASS	.						82.0	92.0	89.0					6																	37138951		2203	4300	6503	SO:0001819	synonymous_variant	5292	exon4			GGTGAGCTCGGGT		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.291C>T	6.37:g.37138951C>T		48.0	0.0	0		50.0	28.0	0.56	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Silent	SNP	ENST00000373509.5	37	CCDS4830.1																																																																																			.	.	none		0.647	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1		
PPEF1	5475	hgsc.bcm.edu	37	X	18824536	18824536	+	Missense_Mutation	SNP	T	T	C			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chrX:18824536T>C	ENST00000361511.4	+	15	1761	c.1267T>C	c.(1267-1269)Tct>Cct	p.S423P	PPEF1_ENST00000544635.1_Missense_Mutation_p.S358P|PPEF1_ENST00000359763.6_Missense_Mutation_p.S370P|PPEF1_ENST00000349874.5_Missense_Mutation_p.S361P|PPEF1_ENST00000543630.1_Intron	NM_006240.2|NM_152224.1	NP_006231.2|NP_689410.1	O14829	PPE1_HUMAN	protein phosphatase, EF-hand calcium binding domain 1	423	Catalytic.				detection of stimulus involved in sensory perception (GO:0050906)|phototransduction, visible light (GO:0007603)|protein dephosphorylation (GO:0006470)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|manganese ion binding (GO:0030145)|protein serine/threonine phosphatase activity (GO:0004722)			breast(3)|endometrium(6)|kidney(2)|large_intestine(8)|lung(19)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	43	Hepatocellular(33;0.183)					GACTATATTTTCTGCTTCTAA	0.368																																					p.S423P		Atlas-SNP	.											.	PPEF1	89	.	0			c.T1267C						PASS	.						130.0	129.0	129.0					X																	18824536		2203	4300	6503	SO:0001583	missense	5475	exon15			ATATTTTCTGCTT	BC036026	CCDS14188.1, CCDS43920.1	Xp22	2013-01-10			ENSG00000086717	ENSG00000086717		"""Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"", ""EF-hand domain containing"""	9243	protein-coding gene	gene with protein product	"""protein phosphatase 7, catalytic subunit, alpha isozyme"""	300109		PPEF		9215685, 9326663	Standard	NM_152224		Approved	PPP7CA	uc004cyq.3	O14829	OTTHUMG00000021219	ENST00000361511.4:c.1267T>C	X.37:g.18824536T>C	ENSP00000354871:p.Ser423Pro	185.0	0.0	0		152.0	54.0	0.355263	NM_006240	A6NHP4|A8K348|O15253|Q9NU21|Q9UJH0	Missense_Mutation	SNP	ENST00000361511.4	37	CCDS14188.1	.	.	.	.	.	.	.	.	.	.	t	16.53	3.150243	0.57151	.	.	ENSG00000086717	ENST00000361511;ENST00000359763;ENST00000349874;ENST00000544635	T;T;T;T	0.28895	1.59;1.59;1.59;1.59	5.57	5.57	0.84162	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (2);	0.397724	0.23189	N	0.050933	T	0.65281	0.2676	M	0.92122	3.275	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.74386	-0.3682	10	0.72032	D	0.01	-7.5314	14.7291	0.69368	0.0:0.0:0.0:1.0	.	361;423;395	O14829-5;O14829;O14829-3	.;PPE1_HUMAN;.	P	423;370;361;358	ENSP00000354871:S423P;ENSP00000352806:S370P;ENSP00000341892:S361P;ENSP00000441289:S358P	ENSP00000341892:S361P	S	+	1	0	PPEF1	18734457	1.000000	0.71417	0.999000	0.59377	0.181000	0.23173	7.563000	0.82314	1.859000	0.53934	0.414000	0.27820	TCT	.	.	none		0.368	PPEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055953.3	NM_006240	
NXF3	56000	hgsc.bcm.edu	37	X	102338561	102338561	+	Silent	SNP	G	G	A			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chrX:102338561G>A	ENST00000395065.3	-	4	512	c.411C>T	c.(409-411)tgC>tgT	p.C137C	NXF3_ENST00000425644.1_5'UTR|NXF3_ENST00000425463.2_Silent_p.C48C	NM_022052.1	NP_071335.1	Q9H4D5	NXF3_HUMAN	nuclear RNA export factor 3	137	RRM.				mRNA export from nucleus (GO:0006406)|poly(A)+ mRNA export from nucleus (GO:0016973)	cytoplasm (GO:0005737)|nuclear RNA export factor complex (GO:0042272)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)			NS(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(15)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26						AGGGTACACTGCATTCATTCT	0.473																																					p.C137C		Atlas-SNP	.											.	NXF3	81	.	0			c.C411T						PASS	.						148.0	135.0	139.0					X																	102338561		2203	4300	6503	SO:0001819	synonymous_variant	56000	exon4			TACACTGCATTCA	AJ277527	CCDS14503.1	Xq22	2008-02-05			ENSG00000147206	ENSG00000147206			8073	protein-coding gene	gene with protein product		300316				11073998	Standard	NM_022052		Approved		uc004eju.3	Q9H4D5	OTTHUMG00000022088	ENST00000395065.3:c.411C>T	X.37:g.102338561G>A		235.0	0.0	0		226.0	75.0	0.331858	NM_022052	B4DYS7|Q5H9I1|Q9H1A9	Silent	SNP	ENST00000395065.3	37	CCDS14503.1	.	.	.	.	.	.	.	.	.	.	G	0.023	-1.405290	0.01155	.	.	ENSG00000147206	ENST00000427570	.	.	.	3.78	2.03	0.26663	.	.	.	.	.	.	.	.	.	.	.	0.31288	N	0.689788	.	.	.	.	.	.	.	.	.	.	.	.	.	-2.3248	5.4863	0.16751	0.2605:0.0:0.7395:0.0	.	.	.	.	X	14	.	.	Q	-	1	0	NXF3	102225217	0.513000	0.26194	0.027000	0.17364	0.003000	0.03518	0.488000	0.22371	0.428000	0.26173	-0.176000	0.13171	CAG	.	.	none		0.473	NXF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057684.1	NM_022052	
PIM1	5292	hgsc.bcm.edu	37	6	37138549	37138549	+	Splice_Site	SNP	G	G	A	rs377274719		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr6:37138549G>A	ENST00000373509.5	+	2	456	c.83G>A	c.(82-84)gGc>gAc	p.G28D		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	119					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)	CCTTTCCTAGGCAAGGAGAAG	0.721			T	BCL6	NHL																																p.G119D		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	PIM1,NS,lymphoid_neoplasm,0,3	PIM1	71	3	0			c.G356A						PASS	.	G	ASP/GLY	1,4257		0,1,2128	18.0	26.0	23.0		83	3.8	1.0	6		23	0,8506		0,0,4253	no	missense-near-splice	PIM1	NM_002648.3	94	0,1,6381	AA,AG,GG		0.0,0.0235,0.0078	probably-damaging	28/314	37138549	1,12763	2129	4253	6382	SO:0001630	splice_region_variant	5292	exon2			TCCTAGGCAAGGA		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.83-1G>A	6.37:g.37138549G>A		65.0	0.0	0		47.0	24.0	0.510638	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	G	13.37	2.215565	0.39102	2.35E-4	0.0	ENSG00000137193	ENST00000373509	T	0.69306	-0.39	3.83	3.83	0.44106	Protein kinase-like domain (1);	0.187844	0.33772	N	0.004562	T	0.23330	0.0564	N	0.08118	0	0.30455	N	0.774827	P	0.42827	0.791	B	0.36719	0.231	T	0.07083	-1.0791	9	.	.	.	.	9.7286	0.40348	0.0983:0.0:0.9017:0.0	.	119	P11309	PIM1_HUMAN	D	28	ENSP00000362608:G28D	.	G	+	2	0	PIM1	37246527	0.119000	0.22226	0.998000	0.56505	0.963000	0.63663	-0.036000	0.12185	2.138000	0.66242	0.549000	0.68633	GGC	.	.	weak		0.721	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1		Missense_Mutation
PIM1	5292	hgsc.bcm.edu	37	6	37140894	37140894	+	Missense_Mutation	SNP	C	C	T			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr6:37140894C>T	ENST00000373509.5	+	5	1103	c.730C>T	c.(730-732)Cat>Tat	p.H244Y	PIM1_ENST00000468243.1_3'UTR	NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	335	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)	TCCTTTCGAGCATGACGAAGA	0.537			T	BCL6	NHL																																p.H335Y		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.C1003T						PASS	.						131.0	123.0	126.0					6																	37140894		2203	4300	6503	SO:0001583	missense	5292	exon5			TTCGAGCATGACG		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.730C>T	6.37:g.37140894C>T	ENSP00000362608:p.His244Tyr	112.0	0.0	0		133.0	44.0	0.330827	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.475129	0.84640	.	.	ENSG00000137193	ENST00000373509	T	0.65916	-0.18	5.35	5.35	0.76521	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.182235	0.48767	D	0.000170	T	0.45155	0.1328	L	0.45422	1.42	0.54753	D	0.999983	P	0.45957	0.869	B	0.37731	0.257	T	0.55036	-0.8203	10	0.56958	D	0.05	.	18.1853	0.89791	0.0:1.0:0.0:0.0	.	335	P11309	PIM1_HUMAN	Y	244	ENSP00000362608:H244Y	ENSP00000362608:H244Y	H	+	1	0	PIM1	37248872	1.000000	0.71417	0.998000	0.56505	0.484000	0.33280	5.755000	0.68750	2.660000	0.90430	0.591000	0.81541	CAT	.	.	none		0.537	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1		
GPR50	9248	hgsc.bcm.edu	37	X	150348670	150348670	+	Silent	SNP	T	T	A			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chrX:150348670T>A	ENST00000218316.3	+	2	684	c.615T>A	c.(613-615)ggT>ggA	p.G205G	GPR50-AS1_ENST00000454196.1_RNA|AF003625.3_ENST00000602313.1_lincRNA	NM_004224.3	NP_004215.2	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50	205					cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|identical protein binding (GO:0042802)|melatonin receptor activity (GO:0008502)			breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(6)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	38	Acute lymphoblastic leukemia(192;6.56e-05)					TCATCGTGGGTTTCTGCTACG	0.527																																					p.G205G		Atlas-SNP	.											.	GPR50	195	.	0			c.T615A						PASS	.						235.0	207.0	216.0					X																	150348670		2123	4223	6346	SO:0001819	synonymous_variant	9248	exon2			CGTGGGTTTCTGC	U52219	CCDS44012.1	Xq28	2012-08-21			ENSG00000102195	ENSG00000102195		"""GPCR / Class A : Orphans"""	4506	protein-coding gene	gene with protein product		300207				9933574, 18400093	Standard	NM_004224		Approved	H9, Mel1c	uc010ntg.2	Q13585	OTTHUMG00000024166	ENST00000218316.3:c.615T>A	X.37:g.150348670T>A		27.0	0.0	0		25.0	10.0	0.4	NM_004224	Q0VGG3|Q3ZAR0	Silent	SNP	ENST00000218316.3	37	CCDS44012.1																																																																																			.	.	none		0.527	GPR50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060874.1	NM_004224	
HLA-C	3107	hgsc.bcm.edu	37	6	31239047	31239047	+	Missense_Mutation	SNP	G	G	A	rs281860470		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr6:31239047G>A	ENST00000376228.5	-	3	436	c.422C>T	c.(421-423)gCc>gTc	p.A141V	HLA-C_ENST00000383329.3_Missense_Mutation_p.A141V	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	141	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						GCCGTCGTAGGCGGACTGGTC	0.706													g|||	1	0.000199681	0.0	0.0	5008	,	,		12845	0.0		0.0	False		,,,				2504	0.001				p.A141V		Atlas-SNP	.											.	HLA-C	92	.	0			c.C422T						PASS	.						35.0	27.0	30.0					6																	31239047		2182	4253	6435	SO:0001583	missense	3107	exon3			TCGTAGGCGGACT	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.422C>T	6.37:g.31239047G>A	ENSP00000365402:p.Ala141Val	114.0	0.0	0		56.0	22.0	0.392857	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	.	.	.	.	.	.	.	.	.	.	.	13.97	2.394451	0.42410	.	.	ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	T;T	0.00018	9.08;9.08	2.59	2.59	0.31030	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.229535	0.21218	U	0.078193	T	0.00328	0.0010	H	0.99914	4.94	0.20196	N	0.999921	D;P;P;P	0.58970	0.984;0.878;0.878;0.939	P;P;P;P	0.58391	0.838;0.482;0.61;0.662	T	0.46830	-0.9163	10	0.87932	D	0	.	7.4947	0.27481	0.0:0.2697:0.7303:0.0	.	141;141;141;141	A2AEA4;A6H578;A2AEA2;P10321	.;.;.;1C07_HUMAN	V	141;141;141;178	ENSP00000365402:A141V;ENSP00000372819:A141V	ENSP00000365402:A141V	A	-	2	0	HLA-C	31347026	0.028000	0.19301	0.011000	0.14972	0.023000	0.10783	0.934000	0.28910	1.768000	0.52137	0.305000	0.20034	GCC	.	.	weak		0.706	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
TNS4	84951	hgsc.bcm.edu	37	17	38645133	38645133	+	Silent	SNP	G	G	A			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr17:38645133G>A	ENST00000254051.6	-	3	686	c.528C>T	c.(526-528)ttC>ttT	p.F176F		NM_032865.5	NP_116254.4	Q8IZW8	TENS4_HUMAN	tensin 4	176	Ser-rich.				apoptotic process (GO:0006915)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	30		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(5;5.91e-05)			GAAGGGAGCCGAAGGGCGGGG	0.622																																					p.F176F		Atlas-SNP	.											.	TNS4	72	.	0			c.C528T						PASS	.						51.0	63.0	59.0					17																	38645133		2200	4299	6499	SO:0001819	synonymous_variant	84951	exon3			GGAGCCGAAGGGC	AF417488	CCDS11368.1	17q21.2	2013-02-14			ENSG00000131746	ENSG00000131746		"""SH2 domain containing"""	24352	protein-coding gene	gene with protein product	"""C terminal tensin like"""	608385				12154022, 12711115	Standard	NM_032865		Approved	CTEN	uc010cxb.3	Q8IZW8	OTTHUMG00000133330	ENST00000254051.6:c.528C>T	17.37:g.38645133G>A		70.0	0.0	0		77.0	34.0	0.441558	NM_032865	A6NMJ7|Q71RB7|Q8WV64|Q96JV4	Silent	SNP	ENST00000254051.6	37	CCDS11368.1																																																																																			.	.	none		0.622	TNS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257154.3	NM_032865	
HIST1H4H	8365	hgsc.bcm.edu	37	6	26285531	26285531	+	Missense_Mutation	SNP	A	A	T			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr6:26285531A>T	ENST00000377727.1	-	1	206	c.197T>A	c.(196-198)gTg>gAg	p.V66E	HIST1H4H_ENST00000289352.1_Missense_Mutation_p.V66E	NM_003543.3	NP_003534.1	P62805	H4_HUMAN	histone cluster 1, H4h	66					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			lung(2)|ovary(2)|upper_aerodigestive_tract(3)	7						GTCACGAATCACGTTCTCCAG	0.557										HNSCC(76;0.23)																											p.V66E		Atlas-SNP	.											.	HIST1H4H	16	.	0			c.T197A						PASS	.						182.0	149.0	160.0					6																	26285531		2203	4300	6503	SO:0001583	missense	8365	exon1			CGAATCACGTTCT	X60487	CCDS4604.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000158406	ENSG00000158406		"""Histones / Replication-dependent"""	4788	protein-coding gene	gene with protein product		602828	"""H4 histone family, member H"", ""histone 1, H4h"""	H4FH		9119399, 12408966	Standard	NM_003543		Approved	H4/h	uc003nhm.2	P62805	OTTHUMG00000014454	ENST00000377727.1:c.197T>A	6.37:g.26285531A>T	ENSP00000366956:p.Val66Glu	102.0	0.0	0		72.0	29.0	0.402778	NM_003543	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000377727.1	37	CCDS4604.1	.	.	.	.	.	.	.	.	.	.	.	17.24	3.340399	0.60963	.	.	ENSG00000158406	ENST00000289352;ENST00000377727	T;T	0.70631	-0.5;-0.5	4.4	4.4	0.53042	.	0.000000	0.45606	U	0.000344	T	0.72326	0.3446	.	.	.	0.44194	D	0.997011	.	.	.	.	.	.	T	0.77389	-0.2606	7	0.87932	D	0	.	11.8938	0.52646	1.0:0.0:0.0:0.0	.	.	.	.	E	66	ENSP00000289352:V66E;ENSP00000366956:V66E	ENSP00000289352:V66E	V	-	2	0	HIST1H4H	26393510	1.000000	0.71417	1.000000	0.80357	0.156000	0.22039	9.196000	0.94978	1.770000	0.52166	0.402000	0.26972	GTG	.	.	none		0.557	HIST1H4H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040119.1	NM_003543	
PIM1	5292	hgsc.bcm.edu	37	6	37139203	37139203	+	Missense_Mutation	SNP	G	G	C			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	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						scavenged	.						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	75.0	1.0	0.0133333		67.0	31.0	0.462687	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		
ZNF814	730051	hgsc.bcm.edu	37	19	58385790	58385790	+	Missense_Mutation	SNP	G	G	T	rs111727691		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr19:58385790G>T	ENST00000435989.2	-	3	1202	c.968C>A	c.(967-969)cCt>cAt	p.P323H	ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000600634.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	323					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						ACATTCATAAGGTCTTTTCCC	0.358																																					p.P323H		Atlas-SNP	.											.	ZNF814	93	.	0			c.C968A						PASS	.						15.0	12.0	13.0					19																	58385790		688	1563	2251	SO:0001583	missense	730051	exon3			TCATAAGGTCTTT		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"""Zinc fingers, C2H2-type"", ""-"""	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.968C>A	19.37:g.58385790G>T	ENSP00000410545:p.Pro323His	168.0	0.0	0		253.0	23.0	0.0909091	NM_001144989	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	37	CCDS46212.1	.	.	.	.	.	.	.	.	.	.	.	8.139	0.784825	0.16189	.	.	ENSG00000204514	ENST00000435989	T	0.29397	1.57	2.27	1.18	0.20946	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.57080	0.2029	M	0.90019	3.08	0.20764	N	0.999853	D	0.89917	1.0	D	0.67231	0.95	T	0.46247	-0.9205	9	0.66056	D	0.02	.	9.258	0.37595	0.0:0.0:0.7811:0.2189	.	323	B7Z6K7	ZN814_HUMAN	H	323	ENSP00000410545:P323H	ENSP00000410545:P323H	P	-	2	0	ZNF814	63077602	0.000000	0.05858	0.028000	0.17463	0.016000	0.09150	-0.439000	0.06897	0.330000	0.23485	-1.407000	0.01130	CCT	G|0.500;T|0.500	0.500	weak		0.358	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708	
ZNF630	57232	hgsc.bcm.edu	37	X	47919314	47919314	+	Missense_Mutation	SNP	G	G	T			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chrX:47919314G>T	ENST00000409324.3	-	5	743	c.517C>A	c.(517-519)Caa>Aaa	p.Q173K	ZNF630_ENST00000442455.3_Missense_Mutation_p.Q159K|ZNF630_ENST00000276054.4_Missense_Mutation_p.Q49K|ZNF630-AS1_ENST00000436124.1_RNA	NM_001037735.2	NP_001032824.2	Q2M218	ZN630_HUMAN	zinc finger protein 630	173					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(6)|lung(11)|ovary(1)	19						TGGAATTTTTGACTTAAAGGA	0.383																																					p.Q173K		Atlas-SNP	.											.	ZNF630	71	.	0			c.C517A						PASS	.						66.0	56.0	59.0					X																	47919314		2194	4286	6480	SO:0001583	missense	57232	exon5			ATTTTTGACTTAA	AK000580	CCDS35237.2, CCDS75971.1	Xp11.3-p11.1	2013-01-08			ENSG00000221994	ENSG00000221994		"""Zinc fingers, C2H2-type"", ""-"""	28855	protein-coding gene	gene with protein product		300819					Standard	NM_001037735		Approved	BC037316, dJ54B20.2, FLJ20573, MGC138344	uc004div.4	Q2M218	OTTHUMG00000021463	ENST00000409324.3:c.517C>A	X.37:g.47919314G>T	ENSP00000386393:p.Gln173Lys	145.0	0.0	0		140.0	46.0	0.328571	NM_001037735	F8WAG4|Q5H8Z5	Missense_Mutation	SNP	ENST00000409324.3	37	CCDS35237.2	.	.	.	.	.	.	.	.	.	.	.	0	-2.628014	0.00115	.	.	ENSG00000221994	ENST00000442455;ENST00000276054;ENST00000409324;ENST00000428686	T;T;T;T	0.07216	3.4;3.21;3.46;5.37	1.47	-1.99	0.07457	.	.	.	.	.	T	0.04543	0.0124	N	0.11724	0.165	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39187	-0.9626	9	0.49607	T	0.09	.	7.9755	0.30153	0.0:0.0:0.712:0.288	.	173	Q2M218	ZN630_HUMAN	K	159;49;173;173	ENSP00000393163:Q159K;ENSP00000354683:Q49K;ENSP00000386393:Q173K;ENSP00000407278:Q173K	ENSP00000354683:Q49K	Q	-	1	0	ZNF630	47804258	0.003000	0.15002	0.001000	0.08648	0.006000	0.05464	-0.458000	0.06737	-0.541000	0.06257	-0.760000	0.03462	CAA	.	.	none		0.383	ZNF630-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327254.1	NM_001037735	
MT-CYB	4519	hgsc.bcm.edu	37	M	15785	15785	+	Missense_Mutation	SNP	T	T	C			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chrM:15785T>C	ENST00000361789.2	+	1	1039	c.1039T>C	c.(1039-1041)Ttt>Ctt	p.F347L	MT-ND6_ENST00000361681.2_5'Flank|MT-TP_ENST00000387461.2_RNA|MT-TE_ENST00000387459.1_RNA|MT-TT_ENST00000387460.2_RNA			P00156	CYB_HUMAN	mitochondrially encoded cytochrome b	347					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(6)|endometrium(25)|kidney(33)|prostate(1)	65						TAAGCTACCCTTTTACCATCA	0.403																																					p.F347L		Atlas-SNP	.											.	.	.	.	0			c.T1039C						PASS	.																																			SO:0001583	missense	0	exon1			TACCCTTTTACCA			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198727	ENSG00000198727		"""Cytochrome b genes"", ""Mitochondrial respiratory chain complex / Complex III"""	7427	protein-coding gene	gene with protein product		516020	"""cytochrome b"""	MTCYB			Standard			Approved	COB, CYTB, UQCR3		P00156		ENST00000361789.2:c.1039T>C	M.37:g.15785T>C	ENSP00000354554:p.Phe347Leu	44.0	0.0	0		17.0	12.0	0.705882	ENST00000361789	Q34786|Q8HBR6|Q8HNQ0|Q8HNQ1|Q8HNQ9|Q8HNR4|Q8HNR7|Q8W7V8|Q8WCV9|Q8WCY2|Q8WCY7|Q8WCY8|Q9B1A6|Q9B1B6|Q9B1B8|Q9B1D4|Q9B1X6|Q9B2V0|Q9B2V8|Q9B2W0|Q9B2W3|Q9B2W8|Q9B2X1|Q9B2X7|Q9B2X9|Q9B2Y3|Q9B2Z0|Q9B2Z4|Q9T6H6|Q9T9Y0|Q9TEH4	Missense_Mutation	SNP	ENST00000361789.2	37																																																																																				T|0.936;C|0.064	0.064	strong		0.403	MT-CYB-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024038	
ALLC	55821	hgsc.bcm.edu	37	2	3745027	3745027	+	Missense_Mutation	SNP	T	T	G			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr2:3745027T>G	ENST00000252505.3	+	10	993	c.831T>G	c.(829-831)atT>atG	p.I277M	ALLC_ENST00000471711.1_3'UTR	NM_018436.3	NP_060906.3	Q8N6M5	ALLC_HUMAN	allantoicase	296					allantoin catabolic process (GO:0000256)		allantoicase activity (GO:0004037)			breast(4)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	30	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.088)	all_cancers(51;0.24)		OV - Ovarian serous cystadenocarcinoma(76;0.088)|all cancers(51;0.151)|Epithelial(75;0.206)		GAATTGAAATTGACACAAAAT	0.388										HNSCC(21;0.051)																											p.I277M		Atlas-SNP	.											ALLC,rectum,carcinoma,0,1	ALLC	61	1	0			c.T831G						PASS	.						127.0	122.0	124.0					2																	3745027		1836	4088	5924	SO:0001583	missense	55821	exon10			TGAAATTGACACA	AF215924	CCDS46223.1	2p25.3	2008-02-05			ENSG00000151360	ENSG00000151360			17377	protein-coding gene	gene with protein product		612396				11054555	Standard	NM_018436		Approved	ALC	uc010ewt.3	Q8N6M5	OTTHUMG00000151485	ENST00000252505.3:c.831T>G	2.37:g.3745027T>G	ENSP00000252505:p.Ile277Met	102.0	0.0	0		100.0	42.0	0.42	NM_018436	Q53T95|Q5RL81|Q96RE6|Q9NZA7	Missense_Mutation	SNP	ENST00000252505.3	37	CCDS46223.1	.	.	.	.	.	.	.	.	.	.	T	5.479	0.273460	0.10403	.	.	ENSG00000151360	ENST00000252505	.	.	.	5.47	-10.9	0.00192	Allantoicase domain (1);Galactose-binding domain-like (1);	0.502623	0.22475	N	0.059570	T	0.35128	0.0921	M	0.82323	2.585	0.24126	N	0.995782	P	0.37548	0.599	B	0.39503	0.301	T	0.41270	-0.9518	9	0.87932	D	0	-5.9914	5.0435	0.14471	0.2651:0.4858:0.1398:0.1093	.	296	Q8N6M5	ALLC_HUMAN	M	277	.	ENSP00000252505:I277M	I	+	3	3	ALLC	3722902	0.000000	0.05858	0.001000	0.08648	0.014000	0.08584	-3.876000	0.00344	-3.622000	0.00131	-1.381000	0.01174	ATT	.	.	none		0.388	ALLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322855.1		
HCN4	10021	hgsc.bcm.edu	37	15	73617312	73617312	+	Silent	SNP	G	G	A			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr15:73617312G>A	ENST00000261917.3	-	6	2955	c.1962C>T	c.(1960-1962)gaC>gaT	p.D654D		NM_005477.2	NP_005468.1	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 4	654					blood circulation (GO:0008015)|cation transport (GO:0006812)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)	cAMP binding (GO:0030552)|cation channel activity (GO:0005261)|identical protein binding (GO:0042802)|intracellular cAMP activated cation channel activity (GO:0005222)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(13)|liver(1)|lung(18)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				COAD - Colon adenocarcinoma(1;0.142)		AGTAGGAGCCGTCGGCCAGCT	0.617																																					p.D654D		Atlas-SNP	.											.	HCN4	150	.	0			c.C1962T						PASS	.						66.0	57.0	60.0					15																	73617312		2198	4297	6495	SO:0001819	synonymous_variant	10021	exon6			GGAGCCGTCGGCC	AJ132429	CCDS10248.1	15q24.1	2011-07-05			ENSG00000138622	ENSG00000138622		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	16882	protein-coding gene	gene with protein product		605206				10228147, 10430953, 16382102	Standard	NM_005477		Approved		uc002avp.3	Q9Y3Q4	OTTHUMG00000137563	ENST00000261917.3:c.1962C>T	15.37:g.73617312G>A		43.0	0.0	0		46.0	17.0	0.369565	NM_005477	Q9UMQ7	Silent	SNP	ENST00000261917.3	37	CCDS10248.1																																																																																			.	.	none		0.617	HCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268900.2	NM_005477	
DAPK1	1612	hgsc.bcm.edu	37	9	90219907	90219907	+	Missense_Mutation	SNP	G	G	T			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr9:90219907G>T	ENST00000408954.3	+	3	436	c.101G>T	c.(100-102)aGc>aTc	p.S34I	DAPK1_ENST00000469640.2_Missense_Mutation_p.S34I|DAPK1_ENST00000358077.5_Missense_Mutation_p.S34I|DAPK1_ENST00000491893.1_Missense_Mutation_p.S34I|DAPK1_ENST00000472284.1_Missense_Mutation_p.S34I	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	34	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(27)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(3)|stomach(1)	72						CGTGAGAAAAGCACCGGCCTC	0.498									Chronic Lymphocytic Leukemia, Familial Clustering of																												p.S34I		Atlas-SNP	.											DAPK1_ENST00000408954,NS,carcinoma,-1,1	DAPK1	329	1	0			c.G101T						PASS	.						35.0	36.0	36.0					9																	90219907		2039	4222	6261	SO:0001583	missense	1612	exon3	Familial Cancer Database	Familial CLL	AGAAAAGCACCGG	X76104	CCDS43842.1	9q34.1	2013-01-10			ENSG00000196730	ENSG00000196730		"""Ankyrin repeat domain containing"""	2674	protein-coding gene	gene with protein product		600831				8530096	Standard	XM_005251757		Approved	DAPK	uc004apd.3	P53355	OTTHUMG00000020150	ENST00000408954.3:c.101G>T	9.37:g.90219907G>T	ENSP00000386135:p.Ser34Ile	78.0	0.0	0		80.0	24.0	0.3	NM_004938	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Missense_Mutation	SNP	ENST00000408954.3	37	CCDS43842.1	.	.	.	.	.	.	.	.	.	.	G	16.67	3.187348	0.57909	.	.	ENSG00000196730	ENST00000358077;ENST00000472284;ENST00000469640;ENST00000408954;ENST00000491893	T;T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.26;-0.26	5.04	5.04	0.67666	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.56097	D	0.000022	T	0.69993	0.3173	L	0.37507	1.11	0.58432	D	0.999999	D;P;D	0.58620	0.983;0.598;0.977	P;B;P	0.54431	0.744;0.248;0.752	T	0.73522	-0.3956	10	0.72032	D	0.01	.	17.55	0.87873	0.0:0.0:1.0:0.0	.	34;34;34	B7ZLE7;B7Z454;P53355	.;.;DAPK1_HUMAN	I	34	ENSP00000350785:S34I;ENSP00000417076:S34I;ENSP00000418885:S34I;ENSP00000386135:S34I;ENSP00000419026:S34I	ENSP00000350785:S34I	S	+	2	0	DAPK1	89409727	1.000000	0.71417	0.993000	0.49108	0.814000	0.46013	3.649000	0.54417	2.628000	0.89032	0.511000	0.50034	AGC	.	.	none		0.498	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938	
MUC5B	727897	hgsc.bcm.edu	37	11	1260239	1260239	+	Silent	SNP	C	C	A	rs374136981	byFrequency	TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr11:1260239C>A	ENST00000529681.1	+	26	3494	c.3436C>A	c.(3436-3438)Cgg>Agg	p.R1146R	MUC5B_ENST00000447027.1_Silent_p.R1149R	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1146	Cys-rich.				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)		TGTGTCCTGGCGGACTCCGGA	0.687													C|||	3	0.000599042	0.0	0.0014	5008	,	,		14063	0.0		0.001	False		,,,				2504	0.001				p.R1146R		Atlas-SNP	.											.	MUC5B	473	.	0			c.C3436A						PASS	.	C		0,4268		0,0,2134	11.0	16.0	14.0		3436	-7.6	0.6	11		14	1,8413		0,1,4206	no	coding-synonymous	MUC5B	NM_002458.2		0,1,6340	AA,AC,CC		0.0119,0.0,0.0079		1146/5763	1260239	1,12681	2134	4207	6341	SO:0001819	synonymous_variant	727897	exon26			TCCTGGCGGACTC	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.3436C>A	11.37:g.1260239C>A		94.0	0.0	0		77.0	26.0	0.337662	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			.	.	weak		0.687	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
ANKK1	255239	hgsc.bcm.edu	37	11	113264381	113264381	+	Missense_Mutation	SNP	C	C	T	rs370146394		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr11:113264381C>T	ENST00000303941.3	+	2	458	c.364C>T	c.(364-366)Cgc>Tgc	p.R122C		NM_178510.1	NP_848605.1	Q8NFD2	ANKK1_HUMAN	ankyrin repeat and kinase domain containing 1	122	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> H (in dbSNP:rs35877321). {ECO:0000269|PubMed:17344846}.				ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|stomach(1)	29		all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194)		BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238)		GCTCAGGTTCCGCATCATCCA	0.582													C|||	1	0.000199681	0.0	0.0	5008	,	,		18780	0.0		0.0	False		,,,				2504	0.001				p.R122C		Atlas-SNP	.											ANKK1,NS,carcinoma,0,1	ANKK1	83	1	0			c.C364T						PASS	.	C	CYS/ARG	1,4287		0,1,2143	56.0	59.0	58.0		364	0.9	0.2	11		58	1,8545		0,1,4272	no	missense	ANKK1	NM_178510.1	180	0,2,6415	TT,TC,CC		0.0117,0.0233,0.0156	probably-damaging	122/766	113264381	2,12832	2144	4273	6417	SO:0001583	missense	255239	exon2			AGGTTCCGCATCA	AJ541797	CCDS44734.1	11q23.2	2013-01-10			ENSG00000170209	ENSG00000170209		"""Ankyrin repeat domain containing"""	21027	protein-coding gene	gene with protein product		608774				15146457	Standard	NM_178510		Approved	X-kinase	uc001pny.3	Q8NFD2	OTTHUMG00000167715	ENST00000303941.3:c.364C>T	11.37:g.113264381C>T	ENSP00000306678:p.Arg122Cys	76.0	0.0	0		81.0	27.0	0.333333	NM_178510		Missense_Mutation	SNP	ENST00000303941.3	37	CCDS44734.1	.	.	.	.	.	.	.	.	.	.	C	9.604	1.129502	0.21041	2.33E-4	1.17E-4	ENSG00000170209	ENST00000303941	D	0.83075	-1.68	4.84	0.896	0.19253	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.234553	0.29172	N	0.012939	T	0.80939	0.4720	M	0.84511	2.7	0.49299	D	0.999779	B	0.15930	0.015	B	0.19148	0.024	T	0.72567	-0.4254	10	0.54805	T	0.06	-4.813	5.6091	0.17396	0.1376:0.6401:0.0:0.2223	.	122	Q8NFD2	ANKK1_HUMAN	C	122	ENSP00000306678:R122C	ENSP00000306678:R122C	R	+	1	0	ANKK1	112769591	0.939000	0.31865	0.191000	0.23289	0.100000	0.18952	0.838000	0.27572	0.006000	0.14734	-0.379000	0.06801	CGC	.	.	weak		0.582	ANKK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395830.1	NM_178510	
ZFP37	7539	hgsc.bcm.edu	37	9	115818843	115818843	+	Silent	SNP	G	G	A			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr9:115818843G>A	ENST00000374227.3	-	1	153	c.126C>T	c.(124-126)agC>agT	p.S42S	ZFP37_ENST00000555206.1_Silent_p.S42S|ZFP37_ENST00000553380.1_Silent_p.S42S	NM_001282515.1|NM_001282518.1	NP_001269444.1|NP_001269447.1	Q9Y6Q3	ZFP37_HUMAN	ZFP37 zinc finger protein	42	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	38						TCACCGCGGCGCTGGCCTCGG	0.592																																					p.S42S		Atlas-SNP	.											.	ZFP37	93	.	0			c.C126T						PASS	.						169.0	180.0	176.0					9																	115818843		2203	4300	6503	SO:0001819	synonymous_variant	7539	exon1			CGCGGCGCTGGCC	AF022158	CCDS6787.1, CCDS65109.1, CCDS65110.1	9q32	2013-01-08	2012-11-27		ENSG00000136866	ENSG00000136866		"""Zinc fingers, C2H2-type"", ""-"""	12863	protein-coding gene	gene with protein product		602951	"""zinc finger protein homologous to Zfp37 in mouse"", ""zinc finger protein 37 homolog (mouse)"""				Standard	NM_001282515		Approved	ZNF906	uc004bgm.1	Q9Y6Q3	OTTHUMG00000021019	ENST00000374227.3:c.126C>T	9.37:g.115818843G>A		65.0	0.0	0		69.0	24.0	0.347826	NM_003408	A0AVJ9|B4DVX4|G3V3L7|Q5T7Q4	Silent	SNP	ENST00000374227.3	37	CCDS6787.1																																																																																			.	.	none		0.592	ZFP37-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055439.1	NM_003408	
HLA-C	3107	hgsc.bcm.edu	37	6	31239416	31239416	+	Silent	SNP	G	G	A	rs281860412		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr6:31239416G>A	ENST00000376228.5	-	2	317	c.303C>T	c.(301-303)agC>agT	p.S101S	HLA-C_ENST00000383329.3_Silent_p.S101S	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	101	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						GGTTCCGCAGGCTCACTCGGT	0.711																																					p.S101S		Atlas-SNP	.											.	HLA-C	92	.	0			c.C303T						PASS	.						42.0	43.0	42.0					6																	31239416		1511	2709	4220	SO:0001819	synonymous_variant	3107	exon2			CCGCAGGCTCACT	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.303C>T	6.37:g.31239416G>A		88.0	0.0	0		74.0	50.0	0.675676	NM_002117	O02864|O02958|Q29643|Q9MY30	Silent	SNP	ENST00000376228.5	37	CCDS34393.1	.	.	.	.	.	.	.	.	.	.	N	6.547	0.469265	0.12461	.	.	ENSG00000204525	ENST00000415537	.	.	.	2.81	1.92	0.25849	.	.	.	.	.	T	0.15435	0.0372	.	.	.	0.19945	N	0.999941	.	.	.	.	.	.	T	0.21381	-1.0247	4	.	.	.	.	7.0143	0.24879	0.0:0.0:0.7285:0.2715	.	.	.	.	S	101	.	.	P	-	1	0	HLA-C	31347395	0.986000	0.35501	0.023000	0.16930	0.010000	0.07245	2.812000	0.47994	0.735000	0.32537	0.305000	0.20034	CCT	.	.	weak		0.711	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
RP1L1	94137	hgsc.bcm.edu	37	8	10467580	10467580	+	Missense_Mutation	SNP	T	T	G	rs143686100		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr8:10467580T>G	ENST00000382483.3	-	4	4251	c.4028A>C	c.(4027-4029)gAa>gCa	p.E1343A		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1359	8 X 16 AA approximate tandem repeats of T-E-E-G-L-Q-E-E-G-V-Q-L-E-E-T-K.		Missing (in allele RP1L1-1).|Missing (in allele RP1L1-2).		cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		tccttctgtttctttagtttc	0.488																																					p.E1343A		Atlas-SNP	.											.	RP1L1	453	.	0			c.A4028C						PASS	.						88.0	79.0	82.0					8																	10467580		1936	4125	6061	SO:0001583	missense	94137	exon4			TCTGTTTCTTTAG	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.4028A>C	8.37:g.10467580T>G	ENSP00000371923:p.Glu1343Ala	207.0	0.0	0		206.0	21.0	0.101942	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	.	.	.	.	.	.	.	.	.	.	T	0.992	-0.693556	0.03303	.	.	ENSG00000183638	ENST00000382483	T	0.04862	3.54	1.84	-3.69	0.04450	.	.	.	.	.	T	0.02929	0.0087	N	0.08118	0	0.09310	N	1	B	0.21225	0.053	B	0.13407	0.009	T	0.44982	-0.9292	9	0.25751	T	0.34	.	8.9452	0.35753	0.0:0.1894:0.0:0.8106	.	1343	A6NKC6	.	A	1343	ENSP00000371923:E1343A	ENSP00000371923:E1343A	E	-	2	0	RP1L1	10504990	0.002000	0.14202	0.001000	0.08648	0.157000	0.22087	-0.507000	0.06352	-1.515000	0.01784	-1.216000	0.01612	GAA	.	.	none		0.488	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
KIAA1731	85459	hgsc.bcm.edu	37	11	93462694	93462694	+	Missense_Mutation	SNP	C	C	T			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr11:93462694C>T	ENST00000325212.6	+	26	7559	c.7397C>T	c.(7396-7398)aCa>aTa	p.T2466I	SNORD6_ENST00000365444.1_RNA|SNORA1_ENST00000384107.1_RNA|SNORA25_ENST00000384384.1_RNA|KIAA1731_ENST00000531700.1_Missense_Mutation_p.T646I|SNORA32_ENST00000384072.1_RNA|SNORA8_ENST00000384574.1_RNA|TAF1D_ENST00000546088.1_5'Flank|KIAA1731_ENST00000411936.1_Missense_Mutation_p.T2466I|KIAA1731_ENST00000344196.4_Missense_Mutation_p.T646I			Q9C0D2	K1731_HUMAN	KIAA1731	2466						centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)	11		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				ACAGCATCTACAGGTAAGCCT	0.448																																					p.T2466I		Atlas-SNP	.											.	KIAA1731	173	.	0			c.C7397T						PASS	.						105.0	87.0	92.0					11																	93462694		692	1591	2283	SO:0001583	missense	85459	exon26			CATCTACAGGTAA	AB051518	CCDS44708.1	11q21	2014-03-11			ENSG00000166004	ENSG00000166004			29366	protein-coding gene	gene with protein product						20844083	Standard	NM_033395		Approved		uc009ywb.1	Q9C0D2	OTTHUMG00000167449	ENST00000325212.6:c.7397C>T	11.37:g.93462694C>T	ENSP00000316681:p.Thr2466Ile	83.0	0.0	0		86.0	26.0	0.302326	NM_033395	C9J5H9|C9JQY8|Q8N7L4|Q8N919|Q8N9B0|Q96LT8	Missense_Mutation	SNP	ENST00000325212.6	37	CCDS44708.1	.	.	.	.	.	.	.	.	.	.	C	14.37	2.516127	0.44763	.	.	ENSG00000166004	ENST00000325212;ENST00000411936;ENST00000344196;ENST00000531700;ENST00000531404	T;T	0.11169	2.83;2.8	3.86	1.97	0.26223	.	.	.	.	.	T	0.07638	0.0192	L	0.29908	0.895	0.19300	N	0.999975	B;B;B	0.24368	0.021;0.102;0.102	B;B;B	0.21151	0.015;0.033;0.033	T	0.32161	-0.9917	9	0.52906	T	0.07	.	5.1584	0.15048	0.0:0.6721:0.2134:0.1145	.	2466;2466;646	Q9C0D2;Q9C0D2-3;Q9C0D2-2	K1731_HUMAN;.;.	I	2466;2466;646;646;478	ENSP00000316681:T2466I;ENSP00000406505:T2466I	ENSP00000316681:T2466I	T	+	2	0	KIAA1731	93102342	0.415000	0.25416	0.341000	0.25589	0.035000	0.12851	0.459000	0.21908	0.590000	0.29694	0.655000	0.94253	ACA	.	.	none		0.448	KIAA1731-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000394640.1	NM_033395	
SECISBP2L	9728	hgsc.bcm.edu	37	15	49338480	49338480	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr15:49338480G>A	ENST00000559471.1	-	1	280	c.17C>T	c.(16-18)aCg>aTg	p.T6M	SECISBP2L_ENST00000261847.3_Missense_Mutation_p.T6M	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	6							poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(5)|kidney(8)|large_intestine(12)|lung(11)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	46						TACCTGCTCCGTGGGGGCTCG	0.731																																					p.T6M		Atlas-SNP	.											.	SECISBP2L	118	.	0			c.C17T						PASS	.						6.0	9.0	8.0					15																	49338480		2064	4063	6127	SO:0001583	missense	9728	exon1			TGCTCCGTGGGGG	BC033001	CCDS32234.1, CCDS53942.1	15q21.1	2014-02-12				ENSG00000138593			28997	protein-coding gene	gene with protein product		615756					Standard	NM_001193489		Approved	KIAA0256	uc001zxe.2	Q93073		ENST00000559471.1:c.17C>T	15.37:g.49338480G>A	ENSP00000453854:p.Thr6Met	146.0	0.0	0		134.0	42.0	0.313433	NM_001193489	Q8N767	Missense_Mutation	SNP	ENST00000559471.1	37	CCDS53942.1	.	.	.	.	.	.	.	.	.	.	G	10.28	1.305656	0.23736	.	.	ENSG00000138593	ENST00000261847;ENST00000380927	T	0.72725	-0.68	4.77	2.78	0.32641	.	1.298010	0.04854	N	0.442829	T	0.54581	0.1867	N	0.08118	0	0.09310	N	1	B;B	0.30914	0.199;0.3	B;B	0.28011	0.039;0.085	T	0.51903	-0.8646	10	0.72032	D	0.01	.	11.1726	0.48579	0.0:0.3605:0.6395:0.0	.	6;6	Q93073;Q93073-2	SBP2L_HUMAN;.	M	6	ENSP00000261847:T6M	ENSP00000261847:T6M	T	-	2	0	SECISBP2L	47125772	0.492000	0.26027	0.023000	0.16930	0.141000	0.21300	2.234000	0.43035	0.660000	0.30964	0.655000	0.94253	ACG	.	.	none		0.731	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417277.1	NM_014701	
ERBB4	2066	hgsc.bcm.edu	37	2	212522545	212522545	+	Missense_Mutation	SNP	C	C	G			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr2:212522545C>G	ENST00000342788.4	-	16	2190	c.1880G>C	c.(1879-1881)gGt>gCt	p.G627A	ERBB4_ENST00000436443.1_Missense_Mutation_p.G627A|ERBB4_ENST00000402597.1_Intron	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	627	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)	ACTAGTGGGACCGTTACACCT	0.473										TSP Lung(8;0.080)																											p.G627A		Atlas-SNP	.											ERBB4,NS,malignant_melanoma,0,1	ERBB4	480	1	0			c.G1880C						PASS	.						284.0	216.0	239.0					2																	212522545		2203	4300	6503	SO:0001583	missense	2066	exon16			GTGGGACCGTTAC	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.1880G>C	2.37:g.212522545C>G	ENSP00000342235:p.Gly627Ala	78.0	0.0	0		73.0	39.0	0.534247	NM_001042599	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	37	CCDS2394.1	.	.	.	.	.	.	.	.	.	.	C	15.51	2.856348	0.51376	.	.	ENSG00000178568	ENST00000342788;ENST00000436443	D;D	0.87412	-2.25;-2.25	5.14	5.14	0.70334	Growth factor, receptor (1);	0.099233	0.64402	D	0.000001	D	0.87661	0.6233	M	0.77486	2.375	0.80722	D	1	B;P;P	0.51057	0.167;0.941;0.902	B;P;B	0.44447	0.076;0.45;0.263	D	0.88473	0.3063	10	0.52906	T	0.07	.	12.3529	0.55159	0.0:0.9224:0.0:0.0776	.	486;627;627	Q53QS8;Q15303-3;Q15303	.;.;ERBB4_HUMAN	A	627	ENSP00000342235:G627A;ENSP00000403204:G627A	ENSP00000342235:G627A	G	-	2	0	ERBB4	212230790	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	3.010000	0.49559	2.557000	0.86248	0.650000	0.86243	GGT	.	.	none		0.473	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599	
PIM1	5292	hgsc.bcm.edu	37	6	37138577	37138577	+	Silent	SNP	G	G	A			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr6:37138577G>A	ENST00000373509.5	+	2	484	c.111G>A	c.(109-111)caG>caA	p.Q37Q		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	128					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.Q37H(2)		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)	TGGAGTCGCAGTACCAGGTGG	0.706			T	BCL6	NHL																																p.Q128Q		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	PIM1,NS,lymphoid_neoplasm,0,2	PIM1	71	2	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	c.G384A						PASS	.						22.0	32.0	28.0					6																	37138577		2167	4268	6435	SO:0001819	synonymous_variant	5292	exon2			GTCGCAGTACCAG		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.111G>A	6.37:g.37138577G>A		79.0	0.0	0		52.0	28.0	0.538462	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Silent	SNP	ENST00000373509.5	37	CCDS4830.1																																																																																			.	.	none		0.706	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1		
