#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_ACHILLES_Lineage_Results_Top_Genes	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_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	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_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_Start_position_hg18	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_entrez_gene_id	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
ICA1	3382	hgsc.bcm.edu	37	7	8268281	8268281	+	Missense_Mutation	SNP	G	G	T			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr7:8268281G>T	ENST00000402384.3	-	4	472	c.206C>A	c.(205-207)aCc>aAc	p.T69N	ICA1_ENST00000396675.3_Missense_Mutation_p.T69N|ICA1_ENST00000406470.2_Missense_Mutation_p.T69N|ICA1_ENST00000401396.1_Missense_Mutation_p.T57N|ICA1_ENST00000407906.1_Missense_Mutation_p.T69N|ICA1_ENST00000265577.7_Missense_Mutation_p.T68N|ICA1_ENST00000422063.2_Missense_Mutation_p.T69N			Q05084	ICA69_HUMAN	islet cell autoantigen 1, 69kDa	69	AH. {ECO:0000255|PROSITE- ProRule:PRU00294}.				neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|secretory granule membrane (GO:0030667)|synaptic vesicle membrane (GO:0030672)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(8)|urinary_tract(1)	23		Ovarian(82;0.0612)		UCEC - Uterine corpus endometrioid carcinoma (126;0.246)		GTCCAGACAGGTTCTCTGAAT	0.303																																																	0			7											89.0	84.0	86.0					7																	8268281		2202	4297	6499	8234806	SO:0001583	missense	3382				CCDS34602.1, CCDS64595.1	7p22	2006-12-13	2002-08-29		ENSG00000003147	ENSG00000003147			5343	protein-coding gene	gene with protein product		147625	"""islet cell autoantigen 1 (69kD)"""			7918678, 8777998	Standard	NM_001276478		Approved	ICAp69	uc003srm.3	Q05084	OTTHUMG00000152008	ENST00000402384.3:c.206C>A	7.37:g.8268281G>T	ENSP00000385570:p.Thr69Asn	Somatic		Capture	Illumina HiSeq	Phase_I	8234806	A8K7U1|B3FTQ2|P78506|Q13824|Q96HG3	Missense_Mutation	SNP	ENST00000402384.3	37	CCDS34602.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.049382	0.93740	.	.	ENSG00000003147	ENST00000402384;ENST00000406470;ENST00000265577;ENST00000396675;ENST00000401396;ENST00000422063;ENST00000407906;ENST00000317367;ENST00000447326;ENST00000430867;ENST00000446305	T;T;T;T;T;T;T;T;T;T;T	0.78364	-1.17;-1.17;-1.17;-1.17;-1.17;-1.17;-1.17;-1.17;-1.17;-1.17;-1.17	5.96	5.96	0.96718	Arfaptin-like (3);	0.000000	0.85682	D	0.000000	D	0.88782	0.6530	M	0.76170	2.325	0.80722	D	1	P;D;D;D;D	0.89917	0.933;1.0;0.999;0.999;1.0	P;D;D;D;D	0.87578	0.718;0.99;0.976;0.976;0.998	D	0.88592	0.3144	10	0.72032	D	0.01	-16.0965	20.422	0.99049	0.0:0.0:1.0:0.0	.	69;69;68;69;57	B3FTQ2;E7ENI6;Q96HG3;Q05084;E9PDL4	.;.;.;ICA69_HUMAN;.	N	69;69;68;69;57;69;69;57;69;68;68	ENSP00000385570:T69N;ENSP00000385651:T69N;ENSP00000265577:T68N;ENSP00000379908:T69N;ENSP00000385305:T57N;ENSP00000403982:T69N;ENSP00000386021:T69N;ENSP00000316074:T57N;ENSP00000398435:T69N;ENSP00000397496:T68N;ENSP00000406722:T68N	ENSP00000265577:T68N	T	-	2	0	ICA1	8234806	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.965000	0.93393	2.832000	0.97577	0.655000	0.94253	ACC		ICA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324793.1	NM_004968	
ABCB5	340273	hgsc.bcm.edu	37	7	20768054	20768054	+	Missense_Mutation	SNP	G	G	A	rs200559589		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr7:20768054G>A	ENST00000404938.2	+	23	3495	c.2843G>A	c.(2842-2844)cGa>cAa	p.R948Q	ABCB5_ENST00000258738.6_Missense_Mutation_p.R503Q	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	948	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent (GO:0002485)|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent (GO:0002489)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|cell differentiation (GO:0030154)|compound eye corneal lens development (GO:0048058)|positive regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002591)|regulation of membrane potential (GO:0042391)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|efflux transmembrane transporter activity (GO:0015562)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(1)|pancreas(1)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)	77						CAAGCTGGACGAATGACCCCA	0.473																																																	0			7											96.0	93.0	94.0					7																	20768054		2203	4300	6503	20734579	SO:0001583	missense	340273			U66692	CCDS5371.1, CCDS55090.1, CCDS55091.1, CCDS55092.1	7p14	2012-03-14			ENSG00000004846	ENSG00000004846		"""ATP binding cassette transporters / subfamily B"""	46	protein-coding gene	gene with protein product	"""P-glycoprotein ABCB5"", ""ATP-binding cassette protein"""	611785				8894702, 12960149	Standard	NM_001163942		Approved	EST422562, ABCB5beta, ABCB5alpha	uc010kuh.3	Q2M3G0	OTTHUMG00000094789	ENST00000404938.2:c.2843G>A	7.37:g.20768054G>A	ENSP00000384881:p.Arg948Gln	Somatic		Capture	Illumina HiSeq	Phase_I	20734579	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Missense_Mutation	SNP	ENST00000404938.2	37	CCDS55090.1	.	.	.	.	.	.	.	.	.	.	G	18.54	3.645459	0.67358	.	.	ENSG00000004846	ENST00000404938;ENST00000258738	D;D	0.88741	-2.42;-2.42	3.91	3.91	0.45181	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	3.108400	0.02771	U	0.119757	D	0.90363	0.6984	L	0.36672	1.1	0.34459	D	0.701585	D;P;P	0.58268	0.982;0.892;0.928	P;B;P	0.53988	0.739;0.325;0.527	T	0.82786	-0.0285	10	0.29301	T	0.29	.	14.2264	0.65863	0.0:0.0:1.0:0.0	.	948;126;503	A7BKA4;A0ASV4;Q2M3G0	.;.;ABCB5_HUMAN	Q	948;503	ENSP00000384881:R948Q;ENSP00000258738:R503Q	ENSP00000258738:R503Q	R	+	2	0	ABCB5	20734579	0.545000	0.26449	1.000000	0.80357	0.998000	0.95712	1.544000	0.36158	2.472000	0.83506	0.655000	0.94253	CGA		ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559	
DNAH11	8701	hgsc.bcm.edu	37	7	21781775	21781775	+	Silent	SNP	C	C	T	rs201592689		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr7:21781775C>T	ENST00000409508.3	+	49	8176	c.8145C>T	c.(8143-8145)aaC>aaT	p.N2715N	DNAH11_ENST00000328843.6_Silent_p.N2722N	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	2722	AAA 3. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						ATTTATCAAACGTCTTCCAGG	0.353									Kartagener syndrome																																								0			7											92.0	85.0	87.0					7																	21781775		1840	4098	5938	21748300	SO:0001819	synonymous_variant	8701	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"""Axonemal dyneins"""	2942	protein-coding gene	gene with protein product	"""dynein, ciliary, heavy chain 11"", ""dynein, heavy chain beta-like"""	603339	"""dynein, axonemal, heavy polypeptide 11"""			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.8145C>T	7.37:g.21781775C>T		Somatic		Capture	Illumina HiSeq	Phase_I	21748300	Q9UJ82	Missense_Mutation	SNP	ENST00000409508.3	37																																																																																					DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777	
TRGC1	6966	hgsc.bcm.edu	37	7	38299700	38299700	+	RNA	SNP	C	C	T			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr7:38299700C>T	ENST00000443402.2	-	0	509					NM_001003799.1|NM_001003806.1	NP_001003799.1|NP_001003806.1	P0CF51	TRGC1_HUMAN	T cell receptor gamma constant 1							integral component of membrane (GO:0016021)											TATGATTTCTCTCCATTGCAG	0.473																																																	0			7											43.0	45.0	45.0					7																	38299700		1813	4058	5871	38266225			445347			M14996		7p14	2012-02-07			ENSG00000211689	ENSG00000211689		"""T cell receptors / TRG locus"""	12275	other	T cell receptor gene	"""T-cell receptor, gamma, constant region C1"""	186970		TCRGC1		2879283	Standard	NG_001336		Approved	C1		P0CF51	OTTHUMG00000155219		7.37:g.38299700C>T		Somatic		Capture	Illumina HiSeq	Phase_I	38266225		Missense_Mutation	SNP	ENST00000443402.2	37																																																																																					TRGC1-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	TR_C_gene	TR_C_gene	OTTHUMT00000338825.3	NG_001336	
PLXNA4	91584	hgsc.bcm.edu	37	7	131864591	131864591	+	Silent	SNP	T	T	C	rs3734989	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr7:131864591T>C	ENST00000359827.3	-	20	4691	c.3729A>G	c.(3727-3729)gcA>gcG	p.A1243A	PLXNA4_ENST00000321063.4_Silent_p.A1243A			Q9HCM2	PLXA4_HUMAN	plexin A4	1243					anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						CGCCAGCCACTGCGATGCTGA	0.632													C|||	3918	0.782348	0.9803	0.7305	5008	,	,		17133	0.6329		0.6133	False		,,,				2504	0.8793																0			7						C		4025,351		1855,315,18	15.0	20.0	18.0		3729	-9.8	0.1	7	dbSNP_107	18	5269,3299		1650,1969,665	no	coding-synonymous	PLXNA4	NM_020911.1		3505,2284,683	CC,CT,TT		38.5037,8.021,28.1984		1243/1895	131864591	9294,3650	2188	4284	6472	131515131	SO:0001819	synonymous_variant	91584			AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"""Plexins"""	9102	protein-coding gene	gene with protein product		604280	"""plexin A4, A"", ""plexin A4, B"""	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.3729A>G	7.37:g.131864591T>C		Somatic		Capture	Illumina HiSeq	Phase_I	131515131	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Silent	SNP	ENST00000359827.3	37	CCDS43646.1																																																																																				PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775	
SSPO	23145	hgsc.bcm.edu	37	7	149497386	149497386	+	RNA	SNP	G	G	A	rs572771455	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr7:149497386G>A	ENST00000378016.2	+	0	7144							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CCAGAGCGTCGCCCCAGGACC	0.672													G|||	2	0.000399361	0.0	0.0	5008	,	,		15894	0.0		0.0	False		,,,				2504	0.002																0			7											16.0	22.0	20.0					7																	149497386		2157	4243	6400	149128319			23145			AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149497386G>A		Somatic		Capture	Illumina HiSeq	Phase_I	149128319	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																					SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
CRNKL1	51340	hgsc.bcm.edu	37	20	20032998	20032998	+	Missense_Mutation	SNP	T	T	C	rs2255255	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr20:20032998T>C	ENST00000377340.2	-	2	503	c.472A>G	c.(472-474)Act>Gct	p.T158A	C20orf26_ENST00000377306.1_5'Flank|CRNKL1_ENST00000377327.4_Missense_Mutation_p.T146A|C20orf26_ENST00000389656.3_5'Flank|C20orf26_ENST00000377309.2_5'Flank|C20orf26_ENST00000245957.5_5'Flank|CRNKL1_ENST00000536226.1_5'UTR	NM_001278628.1|NM_016652.4	NP_001265557.1|NP_057736.4	Q9BZJ0	CRNL1_HUMAN	crooked neck pre-mRNA splicing factor 1	158			T -> A (in dbSNP:rs2255255).		mRNA splicing, via spliceosome (GO:0000398)|spliceosomal complex assembly (GO:0000245)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(2)|cervix(2)|endometrium(7)|large_intestine(11)|lung(12)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(6)	45						TCTGCAGCAGTCGACCTCTGG	0.607													C|||	2599	0.51897	0.4425	0.549	5008	,	,		18253	0.7024		0.4871	False		,,,				2504	0.4448																0			20						C	ALA/THR	1944,2462	615.9+/-392.7	429,1086,688	41.0	42.0	41.0		472	-0.5	0.0	20	dbSNP_100	41	4087,4513	587.3+/-392.2	963,2161,1176	yes	missense	CRNKL1	NM_016652.4	58	1392,3247,1864	CC,CT,TT		47.5233,44.1217,46.3709	benign	158/849	20032998	6031,6975	2203	4300	6503	19980998	SO:0001583	missense	51340			AF255443	CCDS33446.1, CCDS63238.1, CCDS63239.1	20p11.2	2013-10-03	2013-10-03		ENSG00000101343	ENSG00000101343			15762	protein-coding gene	gene with protein product	"""SYF3 pre-mRNA-splicing factor"""	610952	"""crooked neck (Drosophila Crn homolog)-like 1"", ""Crn, crooked neck-like 1 (Drosophila)"", ""crooked neck pre-mRNA splicing factor-like 1 (Drosophila)"""				Standard	NM_016652		Approved	CRN, CLF, SYF3, Clf1	uc002wrs.3	Q9BZJ0	OTTHUMG00000032000	ENST00000377340.2:c.472A>G	20.37:g.20032998T>C	ENSP00000366557:p.Thr158Ala	Somatic		Capture	Illumina HiSeq	Phase_I	19980998	A8K9T4|Q5JY64|Q8WYI5|Q9BZI9|Q9BZJ1|Q9BZJ2|Q9GZW7|Q9H8F8|Q9NQH5|Q9NYD8	Missense_Mutation	SNP	ENST00000377340.2	37	CCDS33446.1	1181	0.5407509157509157	216	0.43902439024390244	188	0.5193370165745856	402	0.7027972027972028	375	0.4947229551451187	C	3.383	-0.125925	0.06795	0.441217	0.475233	ENSG00000101343	ENST00000377327;ENST00000377340	T;T	0.28895	1.59;1.59	5.38	-0.469	0.12142	.	3.252220	0.01008	N	0.003785	T	0.00012	0.0000	N	0.08118	0	0.51482	P	7.500000000004725E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43458	-0.9390	9	0.02654	T	1	11.7577	2.5872	0.04833	0.3895:0.3588:0.1141:0.1376	rs2255255;rs61548236;rs2255255	146;158	Q5JY65;Q9BZJ0	.;CRNL1_HUMAN	A	146;158	ENSP00000366544:T146A;ENSP00000366557:T158A	ENSP00000366544:T146A	T	-	1	0	CRNKL1	19980998	0.000000	0.05858	0.000000	0.03702	0.055000	0.15305	-0.451000	0.06795	-0.461000	0.06993	-0.119000	0.15052	ACT		CRNKL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000127787.1		
NOL4L	140688	hgsc.bcm.edu	37	20	31041518	31041518	+	Missense_Mutation	SNP	A	A	G			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr20:31041518A>G	ENST00000359676.5	-	4	576	c.434T>C	c.(433-435)gTc>gCc	p.V145A	RP5-1184F4.5_ENST00000442179.1_RNA|C20orf112_ENST00000475781.1_5'UTR	NM_001256798.1|NM_080616.4	NP_001243727.1|NP_542183.2	Q96MY1	NOL4L_HUMAN		145						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(3)|kidney(2)|large_intestine(5)|lung(5)	15						GCAGCCGCTGACCTCGGTCTT	0.602																																																	0			20											56.0	45.0	49.0					20																	31041518		2181	4265	6446	30505179	SO:0001583	missense	140688																														ENST00000359676.5:c.434T>C	20.37:g.31041518A>G	ENSP00000352704:p.Val145Ala	Somatic		Capture	Illumina HiSeq	Phase_I	30505179	Q5JYB7|Q6P0Y4|Q9BR34|Q9NQF6	Missense_Mutation	SNP	ENST00000359676.5	37	CCDS13202.1	.	.	.	.	.	.	.	.	.	.	A	13.46	2.242680	0.39598	.	.	ENSG00000197183	ENST00000359676;ENST00000397984	.	.	.	5.04	3.95	0.45737	.	0.369444	0.26190	N	0.025815	T	0.42223	0.1193	L	0.34521	1.04	0.80722	D	1	B	0.28998	0.23	B	0.20955	0.032	T	0.27020	-1.0086	9	0.38643	T	0.18	-19.865	9.5375	0.39231	0.8516:0.0:0.1484:0.0	.	145	Q96MY1	CT112_HUMAN	A	145	.	ENSP00000352704:V145A	V	-	2	0	C20orf112	30505179	1.000000	0.71417	1.000000	0.80357	0.759000	0.43091	6.713000	0.74686	0.944000	0.37579	0.379000	0.24179	GTC		C20orf112-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078628.2		
ZNF341	84905	hgsc.bcm.edu	37	20	32379263	32379263	+	Silent	SNP	T	T	C	rs2626551	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr20:32379263T>C	ENST00000375200.1	+	15	2870	c.2505T>C	c.(2503-2505)gcT>gcC	p.A835A	ZNF341_ENST00000342427.2_Silent_p.A828A|RP4-553F4.6_ENST00000443171.1_RNA|RP4-553F4.6_ENST00000439444.1_RNA|RP4-553F4.6_ENST00000423074.1_RNA	NM_001282933.1	NP_001269862.1	Q9BYN7	ZN341_HUMAN	zinc finger protein 341	835					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	31						AGCTGCAGGCTGGGGCCGAGG	0.667													C|||	4074	0.813498	0.9743	0.7493	5008	,	,		15185	0.9355		0.6282	False		,,,				2504	0.7065																0			20						C		3999,403		1818,363,20	27.0	24.0	25.0		2484	-9.5	0.2	20	dbSNP_100	25	5544,3050		1820,1904,573	no	coding-synonymous	ZNF341	NM_032819.3		3638,2267,593	CC,CT,TT		35.4899,9.1549,26.5697		828/848	32379263	9543,3453	2201	4297	6498	31842924	SO:0001819	synonymous_variant	84905			AK027550	CCDS13227.1, CCDS74719.1	20q11.22	2013-01-08			ENSG00000131061	ENSG00000131061		"""Zinc fingers, C2H2-type"""	15992	protein-coding gene	gene with protein product							Standard	NM_001282933		Approved	dJ553F4.3	uc002wzx.3	Q9BYN7	OTTHUMG00000032275	ENST00000375200.1:c.2505T>C	20.37:g.32379263T>C		Somatic		Capture	Illumina HiSeq	Phase_I	31842924	A2RUF4|B2RXE5|B7ZM09|Q5JXM8|Q96ST5	Silent	SNP	ENST00000375200.1	37																																																																																					ZNF341-201	KNOWN	basic	protein_coding	protein_coding			
LBP	3929	hgsc.bcm.edu	37	20	36982828	36982828	+	Silent	SNP	G	G	A			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr20:36982828G>A	ENST00000217407.2	+	4	674	c.513G>A	c.(511-513)tcG>tcA	p.S171S		NM_004139.3	NP_004130.2	P18428	LBP_HUMAN	lipopolysaccharide binding protein	171					acute-phase response (GO:0006953)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of molecule of bacterial origin (GO:0032490)|innate immune response (GO:0045087)|leukocyte chemotaxis involved in inflammatory response (GO:0002232)|lipopolysaccharide transport (GO:0015920)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation involved in immune response (GO:0002281)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of tumor necrosis factor production (GO:0032720)|opsonization (GO:0008228)|positive regulation of chemokine production (GO:0032722)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of macrophage activation (GO:0043032)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of respiratory burst involved in inflammatory response (GO:0060265)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|response to lipopolysaccharide (GO:0032496)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)|lipoteichoic acid binding (GO:0070891)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(1)|urinary_tract(1)	28		Myeloproliferative disorder(115;0.00878)				TGGACATGTCGGGAGACTTGG	0.617																																																	0			20											42.0	37.0	39.0					20																	36982828		2203	4300	6503	36416242	SO:0001819	synonymous_variant	3929				CCDS13304.1	20q11.23	2011-08-16	2001-11-28		ENSG00000129988	ENSG00000129988		"""BPI fold containing"""	6517	protein-coding gene	gene with protein product	"""BPI fold containing family D, member 2"""	151990	"""lipopolysaccharide-binding protein"""			8432532	Standard	NM_004139		Approved	BPIFD2	uc002xic.2	P18428	OTTHUMG00000032447	ENST00000217407.2:c.513G>A	20.37:g.36982828G>A		Somatic		Capture	Illumina HiSeq	Phase_I	36416242	B2R938|O43438|Q92672|Q9H403|Q9UD66	Silent	SNP	ENST00000217407.2	37	CCDS13304.1																																																																																				LBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079174.2	NM_004139	
GNAS	2778	hgsc.bcm.edu	37	20	57484420	57484420	+	Missense_Mutation	SNP	C	C	A	rs11554273		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr20:57484420C>A	ENST00000371085.3	+	8	1025	c.601C>A	c.(601-603)Cgt>Agt	p.R201S	GNAS_ENST00000371100.4_Missense_Mutation_p.R844S|GNAS_ENST00000371095.3_Missense_Mutation_p.R187S|GNAS_ENST00000306090.10_Missense_Mutation_p.R187S|GNAS_ENST00000371075.3_3'UTR|GNAS_ENST00000354359.7_Missense_Mutation_p.R202S|GNAS_ENST00000313949.7_3'UTR|GNAS_ENST00000464624.2_3'UTR|GNAS_ENST00000265620.7_Missense_Mutation_p.R186S|GNAS_ENST00000371102.4_Missense_Mutation_p.R830S	NM_000516.4	NP_000507.1	P63092	GNAS2_HUMAN	GNAS complex locus	201			R -> C (in MAS and somatotrophinoma; dbSNP:rs11554273). {ECO:0000269|PubMed:1944469, ECO:0000269|PubMed:2549426}.|R -> G (in MAS). {ECO:0000269|PubMed:10571700}.|R -> H (in MAS, somatotrophinoma and AIMAH1). {ECO:0000269|PubMed:12727968, ECO:0000269|PubMed:1594625, ECO:0000269|PubMed:1944469, ECO:0000269|PubMed:2549426}.|R -> L (in non-MAS endocrine tumors). {ECO:0000269|PubMed:7751320}.|R -> S (in AIMAH1, pituitary tumor and polyostotic fibrous dysplasia). {ECO:0000269|PubMed:12727968, ECO:0000269|PubMed:8766942, ECO:0000269|PubMed:9267696}.		activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|bone development (GO:0060348)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|cognition (GO:0050890)|developmental growth (GO:0048589)|energy reserve metabolic process (GO:0006112)|hair follicle placode formation (GO:0060789)|intracellular transport (GO:0046907)|platelet aggregation (GO:0070527)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of insulin secretion (GO:0050796)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intrinsic component of membrane (GO:0031224)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	adenylate cyclase activity (GO:0004016)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)	p.R201C(228)|p.R844C(9)|p.R201S(5)		adrenal_gland(12)|autonomic_ganglia(1)|biliary_tract(5)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(37)|liver(9)|lung(9)|ovary(16)|pancreas(56)|parathyroid(5)|pituitary(228)|prostate(2)|small_intestine(1)|stomach(1)|testis(2)|thyroid(35)|upper_aerodigestive_tract(3)|urinary_tract(1)	441	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			GCTTCGCTGCCGTGTCCTGAC	0.428			Mis		pituitary adenoma		"""McCune-Albright syndrome; pseudohypoparathyroidism, type IA"""			TSP Lung(22;0.16)																											Colon(117;935 1597 6045 8307 46442)			Dom	yes		20	20q13.2	2778	"""guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"""	yes	E	242	Substitution - Missense(242)	pituitary(141)|pancreas(35)|large_intestine(14)|ovary(12)|thyroid(10)|adrenal_gland(7)|biliary_tract(6)|parathyroid(5)|liver(3)|kidney(3)|testis(2)|upper_aerodigestive_tract(2)|autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)	20											80.0	78.0	79.0					20																	57484420		2203	4300	6503	56917815	SO:0001583	missense	2778			M21142	CCDS13471.1, CCDS13472.1, CCDS42892.1, CCDS46622.1, CCDS46623.1, CCDS46624.1	20q13.2-q13.3	2010-03-01	2001-12-19	2001-12-20	ENSG00000087460	ENSG00000087460			4392	protein-coding gene	gene with protein product	"""secretogranin VI"""	139320	"""guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"""	GNAS1			Standard	NM_000516		Approved	NESP55, NESP, GNASXL, GPSA, SCG6	uc002xzw.3	O95467	OTTHUMG00000033069	ENST00000371085.3:c.601C>A	20.37:g.57484420C>A	ENSP00000360126:p.Arg201Ser	Somatic		Capture	Illumina HiSeq	Phase_I	56917815	A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	Missense_Mutation	SNP	ENST00000371085.3	37	CCDS13472.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.420255	0.83559	.	.	ENSG00000087460	ENST00000371100;ENST00000371102;ENST00000371095;ENST00000371085;ENST00000354359;ENST00000265620;ENST00000306090	D;D;D;D;D;D;D	0.99458	-5.93;-5.93;-5.93;-5.93;-5.93;-2.93;-5.93	5.53	4.53	0.55603	G protein alpha subunit, helical insertion (2);	0.000000	0.85682	D	0.000000	D	0.99701	0.9886	H	0.98256	4.185	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.97110	0.997;0.995;0.984;1.0	D	0.97309	0.9936	10	0.87932	D	0	.	13.0593	0.58997	0.2437:0.7563:0.0:0.0	.	201;202;186;844	P63092;A6NI00;P63092-3;Q5JWF2	GNAS2_HUMAN;.;.;GNAS1_HUMAN	S	844;830;187;201;202;186;187	ENSP00000360141:R844S;ENSP00000360143:R830S;ENSP00000360136:R187S;ENSP00000360126:R201S;ENSP00000346328:R202S;ENSP00000265620:R186S;ENSP00000304472:R187S	ENSP00000265620:R186S	R	+	1	0	GNAS	56917815	1.000000	0.71417	0.998000	0.56505	0.941000	0.58515	4.055000	0.57441	2.596000	0.87737	0.563000	0.77884	CGT		GNAS-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080431.2	NM_000516	
CHRNA4	1137	hgsc.bcm.edu	37	20	61982174	61982174	+	Missense_Mutation	SNP	G	G	A	rs144716263		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr20:61982174G>A	ENST00000370263.4	-	5	810	c.589C>T	c.(589-591)Cgc>Tgc	p.R197C	CHRNA4_ENST00000463705.1_5'UTR	NM_000744.6|NM_001256573.1	NP_000735.1|NP_001243502.1	P43681	ACHA4_HUMAN	cholinergic receptor, nicotinic, alpha 4 (neuronal)	197					action potential (GO:0001508)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cognition (GO:0050890)|DNA repair (GO:0006281)|exploration behavior (GO:0035640)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|neurological system process (GO:0050877)|regulation of dopamine secretion (GO:0014059)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of membrane potential (GO:0042391)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(19)|prostate(3)|skin(3)|soft_tissue(1)	33	all_cancers(38;1.71e-10)				Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Nicotine(DB00184)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)|Varenicline(DB01273)	TGGTCCACGCGGCTGTGCATG	0.582													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17801	0.0		0.0	False		,,,				2504	0.0																0			20						G	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	130.0	107.0	115.0		589	4.9	1.0	20	dbSNP_134	115	1,8597	1.2+/-3.3	0,1,4298	no	missense	CHRNA4	NM_000744.5	180	0,2,6500	AA,AG,GG		0.0116,0.0227,0.0154	probably-damaging	197/628	61982174	2,13002	2203	4299	6502	61452618	SO:0001583	missense	1137				CCDS13517.1	20q13.33	2013-09-20	2012-02-07		ENSG00000101204	ENSG00000101204		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1958	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 4 (neuronal)"""	118504	"""cholinergic receptor, nicotinic, alpha polypeptide 4"""	EBN, EBN1		1505988	Standard	NM_000744		Approved	BFNC	uc002yes.3	P43681	OTTHUMG00000033080	ENST00000370263.4:c.589C>T	20.37:g.61982174G>A	ENSP00000359285:p.Arg197Cys	Somatic		Capture	Illumina HiSeq	Phase_I	61452618	Q4JGR7|Q4VAQ5|Q4VAQ6	Missense_Mutation	SNP	ENST00000370263.4	37	CCDS13517.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	20.8	4.052353	0.75960	2.27E-4	1.16E-4	ENSG00000101204	ENST00000370258;ENST00000370263;ENST00000539366	T	0.79749	-1.3	4.87	4.87	0.63330	Neurotransmitter-gated ion-channel ligand-binding (3);	0.098667	0.64402	D	0.000002	D	0.86096	0.5851	L	0.46157	1.445	0.51767	D	0.999933	D;D	0.76494	0.999;0.992	P;D	0.64776	0.892;0.929	D	0.87607	0.2501	10	0.66056	D	0.02	.	18.0032	0.89203	0.0:0.0:1.0:0.0	.	126;197	Q4VAQ5;P43681	.;ACHA4_HUMAN	C	103;197;126	ENSP00000359285:R197C	ENSP00000359280:R103C	R	-	1	0	CHRNA4	61452618	0.982000	0.34865	0.996000	0.52242	0.903000	0.53119	2.160000	0.42348	2.227000	0.72691	0.561000	0.74099	CGC		CHRNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080508.3		
MLC1	23209	hgsc.bcm.edu	37	22	50502491	50502491	+	Missense_Mutation	SNP	T	T	C	rs11568188	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr22:50502491T>C	ENST00000311597.5	-	11	1637	c.1031A>G	c.(1030-1032)aAc>aGc	p.N344S	MLC1_ENST00000395876.2_Missense_Mutation_p.N344S|MLC1_ENST00000483836.1_5'UTR|MLC1_ENST00000535444.1_Missense_Mutation_p.N265S|MLC1_ENST00000431262.2_Missense_Mutation_p.N314S|MLC1_ENST00000450140.2_Missense_Mutation_p.N292S|MLC1_ENST00000538737.1_Missense_Mutation_p.N310S	NM_015166.3	NP_055981.1	Q15049	MLC1_HUMAN	megalencephalic leukoencephalopathy with subcortical cysts 1	344			N -> S (in dbSNP:rs11568188).		caveolin-mediated endocytosis (GO:0072584)|cellular response to cholesterol (GO:0071397)|ion transport (GO:0006811)|positive regulation of intracellular transport (GO:0032388)|protein oligomerization (GO:0051259)|regulation of response to osmotic stress (GO:0047484)|transport (GO:0006810)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	protein complex binding (GO:0032403)|protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|pancreas(1)|prostate(3)	18		all_cancers(38;7.69e-11)|all_epithelial(38;9.52e-10)|all_lung(38;3.67e-05)|Breast(42;0.000776)|Lung NSC(38;0.000946)|Ovarian(80;0.0365)|Lung SC(80;0.113)		READ - Rectum adenocarcinoma(2;0.000669)|Colorectal(2;0.00242)|LUAD - Lung adenocarcinoma(64;0.0695)|BRCA - Breast invasive adenocarcinoma(115;0.216)		CTGCGGGCCGTTCTGGGTGTC	0.706													t|||	657	0.13119	0.059	0.1758	5008	,	,		11900	0.0923		0.1312	False		,,,				2504	0.2372																0			22							SER/ASN,SER/ASN	292,4112		14,264,1924	37.0	35.0	36.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1031,1031	1.7	0.0	22	dbSNP_120	36	1094,7506		84,926,3290	yes	missense,missense	MLC1	NM_015166.3,NM_139202.2	46,46	98,1190,5214	CC,CT,TT		12.7209,6.6303,10.6583	benign,benign	344/378,344/378	50502491	1386,11618	2202	4300	6502	48844618	SO:0001583	missense	23209			D25217	CCDS14083.1	22q13.33	2007-03-20			ENSG00000100427	ENSG00000100427			17082	protein-coding gene	gene with protein product		605908				7584026, 7584028	Standard	XR_430476		Approved	MLC, KIAA0027, LVM, VL	uc003bjg.1	Q15049	OTTHUMG00000150236	ENST00000311597.5:c.1031A>G	22.37:g.50502491T>C	ENSP00000310375:p.Asn344Ser	Somatic		Capture	Illumina HiSeq	Phase_I	48844618	B3KW61|B7Z659|Q5JZ83|Q8TAG4|Q96RP5|Q9UGY8	Missense_Mutation	SNP	ENST00000311597.5	37	CCDS14083.1	245	0.11217948717948718	41	0.08333333333333333	58	0.16022099447513813	53	0.09265734265734266	93	0.12269129287598944	t	0.798	-0.756380	0.03019	0.066303	0.127209	ENSG00000100427	ENST00000395876;ENST00000311597;ENST00000538737;ENST00000431262;ENST00000535444;ENST00000450140	D;D;D;D;D;D	0.85484	-1.99;-1.99;-1.99;-1.99;-1.99;-1.99	3.83	1.67	0.24075	.	1.397770	0.04286	N	0.344697	T	0.00384	0.0012	N	0.02011	-0.69	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.0;0.0	T	0.30707	-0.9969	9	0.07644	T	0.81	-1.0819	2.0661	0.03603	0.1148:0.2091:0.4716:0.2045	rs11568188	310;314;344	F5H1B9;B7Z659;Q15049	.;.;MLC1_HUMAN	S	344;344;310;314;265;292	ENSP00000379216:N344S;ENSP00000310375:N344S;ENSP00000445805:N310S;ENSP00000415877:N314S;ENSP00000438910:N265S;ENSP00000412448:N292S	ENSP00000310375:N344S	N	-	2	0	MLC1	48844618	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.621000	0.24418	0.357000	0.24183	-1.438000	0.01074	AAC		MLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316979.2	NM_015166	
HNRNPC	3183	hgsc.bcm.edu	37	14	21681138	21681138	+	Silent	SNP	T	T	C			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr14:21681138T>C	ENST00000320084.7	-	5	782	c.543A>G	c.(541-543)ggA>ggG	p.G181G	HNRNPC_ENST00000420743.2_Silent_p.G181G|HNRNPC_ENST00000557201.1_Silent_p.G181G|HNRNPC_ENST00000556628.1_Silent_p.G101G|HNRNPC_ENST00000449098.1_Silent_p.G168G|HNRNPC_ENST00000553753.1_Silent_p.G168G|HNRNPC_ENST00000555883.1_Intron|HNRNPC_ENST00000430246.2_Silent_p.G168G|HNRNPC_ENST00000556142.1_Silent_p.G181G|HNRNPC_ENST00000556897.1_Silent_p.G168G|HNRNPC_ENST00000556513.1_Silent_p.G181G|HNRNPC_ENST00000554969.1_Silent_p.G168G|HNRNPC_ENST00000553300.1_Silent_p.G168G|HNRNPC_ENST00000555914.1_Silent_p.G168G|HNRNPC_ENST00000336053.6_Silent_p.G168G|HNRNPC_ENST00000555309.1_Silent_p.G181G|HNRNPC_ENST00000554455.1_Silent_p.G181G	NM_001077442.1	NP_001070910.1	P07910	HNRPC_HUMAN	heterogeneous nuclear ribonucleoprotein C (C1/C2)	181	Asp/Glu-rich (acidic).				3'-UTR-mediated mRNA stabilization (GO:0070935)|ATP-dependent chromatin remodeling (GO:0043044)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|spliceosomal complex (GO:0005681)	identical protein binding (GO:0042802)|mRNA 3'-UTR binding (GO:0003730)|nucleosomal DNA binding (GO:0031492)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)			breast(1)|liver(1)|lung(6)|skin(1)	9	all_cancers(95;0.00176)		Epithelial(56;1.08e-06)|all cancers(55;8.95e-06)	GBM - Glioblastoma multiforme(265;0.00783)		ACTTGGAAGATCCCCGCTGTC	0.423																																					NSCLC(108;607 2244 12726 38757)												0			14											105.0	112.0	110.0					14																	21681138		2190	4289	6479	20750978	SO:0001819	synonymous_variant	3183				CCDS41915.1, CCDS45079.1	14q11.2	2013-06-12		2007-08-16	ENSG00000092199	ENSG00000092199		"""RNA binding motif (RRM) containing"""	5035	protein-coding gene	gene with protein product		164020		HNRPC		3457372	Standard	NM_031314		Approved	hnRNPC	uc001waa.3	P07910	OTTHUMG00000170757	ENST00000320084.7:c.543A>G	14.37:g.21681138T>C		Somatic		Capture	Illumina HiSeq	Phase_I	20750978	D3DS19|D3DS22|P22628|Q53EX2|Q59FD3|Q5FWE8|Q86SF8|Q86U45|Q96HK7|Q96HM4|Q96IY5|Q9BTS3	Silent	SNP	ENST00000320084.7	37	CCDS41915.1	.	.	.	.	.	.	.	.	.	.	T	8.489	0.861496	0.17178	.	.	ENSG00000092199	ENST00000452166	.	.	.	4.53	0.232	0.15381	.	.	.	.	.	T	0.43299	0.1241	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.23332	-1.0191	4	.	.	.	.	3.0517	0.06172	0.1324:0.0856:0.3985:0.3835	.	.	.	.	G	141	.	.	D	-	2	0	HNRNPC	20750978	0.870000	0.30015	0.998000	0.56505	0.985000	0.73830	-0.202000	0.09451	0.185000	0.20105	-0.490000	0.04691	GAT		HNRNPC-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410235.1		
ADCY4	196883	hgsc.bcm.edu	37	14	24793331	24793331	+	Silent	SNP	T	T	C			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr14:24793331T>C	ENST00000310677.4	-	17	2096	c.1983A>G	c.(1981-1983)ggA>ggG	p.G661G	ADCY4_ENST00000554068.2_Silent_p.G661G|ADCY4_ENST00000396747.3_Silent_p.G354G|ADCY4_ENST00000418030.2_Silent_p.G661G	NM_001198568.1|NM_001198592.1|NM_139247.3	NP_001185497.1|NP_001185521.1|NP_640340.2	Q8NFM4	ADCY4_HUMAN	adenylate cyclase 4	661					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(265;0.0192)		CTATTCTCAGTCCTGGTCGTG	0.612																																																	0			14											71.0	65.0	67.0					14																	24793331		2203	4300	6503	23863171	SO:0001819	synonymous_variant	196883			AF497516	CCDS9627.1	14q11.2	2013-02-04			ENSG00000129467	ENSG00000129467	4.6.1.1	"""Adenylate cyclases"""	235	protein-coding gene	gene with protein product		600292				7766992	Standard	NM_001198592		Approved	AC4	uc001woy.3	Q8NFM4	OTTHUMG00000029347	ENST00000310677.4:c.1983A>G	14.37:g.24793331T>C		Somatic		Capture	Illumina HiSeq	Phase_I	23863171	B3KV74|D3DS75|Q17R40|Q6ZTM6|Q96ML7	Silent	SNP	ENST00000310677.4	37	CCDS9627.1																																																																																				ADCY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073200.4		
ACTN1	87	hgsc.bcm.edu	37	14	69387768	69387768	+	Missense_Mutation	SNP	A	A	C			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr14:69387768A>C	ENST00000193403.6	-	3	678	c.295T>G	c.(295-297)Ttc>Gtc	p.F99V	ACTN1_ENST00000438964.2_Missense_Mutation_p.F99V|ACTN1_ENST00000394419.4_Missense_Mutation_p.F99V|ACTN1_ENST00000538545.2_Missense_Mutation_p.F99V|ACTN1_ENST00000376839.3_Missense_Mutation_p.F34V|ACTN1_ENST00000554508.1_5'Flank	NM_001102.3	NP_001093.1	P12814	ACTN1_HUMAN	actinin, alpha 1	99	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|negative regulation of cellular component movement (GO:0051271)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of apoptotic process (GO:0042981)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|double-stranded RNA binding (GO:0003725)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|vinculin binding (GO:0017166)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(9)|prostate(2)|urinary_tract(1)	27				BRCA - Breast invasive adenocarcinoma(234;0.00605)|all cancers(60;0.00846)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		CTGGCTATGAAATCCAGGGCC	0.547																																																	0			14											238.0	187.0	205.0					14																	69387768		2203	4300	6503	68457521	SO:0001583	missense	87			M95178	CCDS9792.1, CCDS45129.1, CCDS45130.1	14q24.1	2014-08-08			ENSG00000072110	ENSG00000072110		"""EF-hand domain containing"""	163	protein-coding gene	gene with protein product		102575				2349951	Standard	NM_001102		Approved		uc001xkm.3	P12814	OTTHUMG00000171386	ENST00000193403.6:c.295T>G	14.37:g.69387768A>C	ENSP00000193403:p.Phe99Val	Somatic		Capture	Illumina HiSeq	Phase_I	68457521	B3V8S3|B4DHH3|B7TY16|Q1HE25|Q9BTN1	Missense_Mutation	SNP	ENST00000193403.6	37	CCDS9792.1	.	.	.	.	.	.	.	.	.	.	A	27.5	4.834536	0.91036	.	.	ENSG00000072110	ENST00000193403;ENST00000394419;ENST00000438964;ENST00000376839;ENST00000538545;ENST00000555616;ENST00000556433;ENST00000553370;ENST00000553779;ENST00000556571	D;D;D;D;D;D;D;D;D;D	0.95949	-3.86;-3.86;-3.86;-3.86;-3.86;-3.86;-3.86;-3.86;-3.86;-3.86	4.9	4.9	0.64082	Calponin homology domain (5);	0.053778	0.85682	D	0.000000	D	0.97284	0.9112	M	0.80183	2.485	0.80722	D	1	D;P;P;P	0.61080	0.989;0.816;0.941;0.731	D;P;P;P	0.66084	0.941;0.808;0.855;0.72	D	0.97887	1.0295	10	0.87932	D	0	.	13.6324	0.62202	1.0:0.0:0.0:0.0	.	99;99;99;99	B7TY16;P12814-2;Q1HE25;P12814	.;.;.;ACTN1_HUMAN	V	99;99;99;34;99;34;78;34;34;76	ENSP00000193403:F99V;ENSP00000377941:F99V;ENSP00000414272:F99V;ENSP00000366035:F34V;ENSP00000439828:F99V;ENSP00000450903:F34V;ENSP00000450764:F78V;ENSP00000450925:F34V;ENSP00000450618:F34V;ENSP00000452423:F76V	ENSP00000193403:F99V	F	-	1	0	ACTN1	68457521	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.867000	0.92314	2.073000	0.62155	0.459000	0.35465	TTC		ACTN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413233.3	NM_001102	
PAPLN	89932	hgsc.bcm.edu	37	14	73730428	73730428	+	Silent	SNP	C	C	T	rs145397376	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr14:73730428C>T	ENST00000554301.1	+	19	2962	c.2799C>T	c.(2797-2799)gaC>gaT	p.D933D	PAPLN_ENST00000427855.1_Silent_p.D933D|PAPLN_ENST00000340738.5_Silent_p.D906D|PAPLN_ENST00000554314.1_Intron|PAPLN_ENST00000381166.3_Silent_p.D933D|PAPLN_ENST00000555445.1_Silent_p.D917D			O95428	PPN_HUMAN	papilin, proteoglycan-like sulfated glycoprotein	933	Ig-like C2-type 1.					basement membrane (GO:0005604)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)	p.D906E(1)		NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(3)	42				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)		CCTGCTCAGACGACACTGCCC	0.627													C|||	38	0.00758786	0.0	0.0014	5008	,	,		15881	0.0159		0.002	False		,,,				2504	0.0194																1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	14						C		4,4402	8.1+/-20.4	0,4,2199	68.0	63.0	64.0		2718	-9.8	0.0	14	dbSNP_134	64	20,8580	14.6+/-50.1	0,20,4280	no	coding-synonymous	PAPLN	NM_173462.3		0,24,6479	TT,TC,CC		0.2326,0.0908,0.1845		906/1252	73730428	24,12982	2203	4300	6503	72800181	SO:0001819	synonymous_variant	89932			BC042057	CCDS32114.1	14q24.2	2013-01-11				ENSG00000100767		"""Immunoglobulin superfamily / I-set domain containing"""	19262	protein-coding gene	gene with protein product						11076767, 19734141	Standard	NM_173462		Approved	MGC50452	uc001xnw.4	O95428		ENST00000554301.1:c.2799C>T	14.37:g.73730428C>T		Somatic		Capture	Illumina HiSeq	Phase_I	72800181	B4DES8|B4DGE6|Q659F2|Q6UXJ4|Q6ZNM1|Q6ZUJ0|Q7Z681|Q8IVU0	Silent	SNP	ENST00000554301.1	37																																																																																					PAPLN-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000413182.1	NM_173462	
CEP128	145508	hgsc.bcm.edu	37	14	81025624	81025624	+	Splice_Site	SNP	G	G	A	rs140154637	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr14:81025624G>A	ENST00000555265.1	-	21	3254	c.2879C>T	c.(2878-2880)aCg>aTg	p.T960M	CEP128_ENST00000281129.3_Splice_Site_p.T960M			Q6ZU80	CE128_HUMAN	centrosomal protein 128kDa	960						centriole (GO:0005814)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)				NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	51						CCAACTTACCGTTTCTAATGC	0.328													G|||	2	0.000399361	0.0	0.0014	5008	,	,		14809	0.001		0.0	False		,,,				2504	0.0																0			14						G	MET/THR	0,4406		0,0,2203	84.0	83.0	83.0		2879	1.8	1.0	14	dbSNP_134	83	1,8599	1.2+/-3.3	0,1,4299	yes	missense-near-splice	CEP128	NM_152446.3	81	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	960/1095	81025624	1,13005	2203	4300	6503	80095377	SO:0001630	splice_region_variant	145508			AK056756	CCDS32130.1	14q31.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000100629	ENSG00000100629			20359	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 61"", ""chromosome 14 open reading frame 145"""	C14orf61, C14orf145		21399614	Standard	NM_152446		Approved		uc001xux.2	Q6ZU80		ENST00000555265.1:c.2880+1C>T	14.37:g.81025624G>A		Somatic		Capture	Illumina HiSeq	Phase_I	80095377	B9EK52|Q86X97|Q96ML4	Missense_Mutation	SNP	ENST00000555265.1	37	CCDS32130.1	.	.	.	.	.	.	.	.	.	.	G	12.42	1.932072	0.34096	0.0	1.16E-4	ENSG00000100629	ENST00000281129;ENST00000555265;ENST00000393619	T;T	0.30448	1.53;1.53	5.87	1.8	0.24995	.	0.440685	0.21369	N	0.075669	T	0.10423	0.0255	N	0.03608	-0.345	0.80722	D	1	B	0.30281	0.275	B	0.15870	0.014	T	0.12372	-1.0550	10	0.42905	T	0.14	.	5.5878	0.17283	0.2493:0.1462:0.6046:0.0	.	960	Q6ZU80	CE128_HUMAN	M	960	ENSP00000281129:T960M;ENSP00000451162:T960M	ENSP00000281129:T960M	T	-	2	0	CEP128	80095377	0.992000	0.36948	1.000000	0.80357	0.968000	0.65278	-0.042000	0.12063	0.473000	0.27368	0.655000	0.94253	ACG		CEP128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413415.1	NM_152446	Missense_Mutation
FLRT2	23768	hgsc.bcm.edu	37	14	86088994	86088994	+	Missense_Mutation	SNP	C	C	T			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr14:86088994C>T	ENST00000330753.4	+	2	1903	c.1136C>T	c.(1135-1137)cCg>cTg	p.P379L	FLRT2_ENST00000554746.1_Missense_Mutation_p.P379L	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	379					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)|regulation of neuron migration (GO:2001222)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	73				BRCA - Breast invasive adenocarcinoma(234;0.0319)		ACAGCTTCTCCGACCACTCAG	0.562																																																	0			14											83.0	88.0	87.0					14																	86088994		2203	4300	6503	85158747	SO:0001583	missense	23768			AF169676	CCDS9877.1	14q24-q32	2013-02-11				ENSG00000185070		"""Fibronectin type III domain containing"""	3761	protein-coding gene	gene with protein product		604807				10644439, 16872596	Standard	XM_005267490		Approved		uc001xvr.3	O43155		ENST00000330753.4:c.1136C>T	14.37:g.86088994C>T	ENSP00000332879:p.Pro379Leu	Somatic		Capture	Illumina HiSeq	Phase_I	85158747	A0AV84|B7ZLP3	Missense_Mutation	SNP	ENST00000330753.4	37	CCDS9877.1	.	.	.	.	.	.	.	.	.	.	C	0.137	-1.106306	0.01828	.	.	ENSG00000185070	ENST00000330753;ENST00000554746;ENST00000535800	T;T	0.58210	0.35;0.35	6.17	4.36	0.52297	.	0.108090	0.64402	D	0.000005	T	0.37865	0.1019	N	0.22421	0.69	0.46131	D	0.998888	D	0.61080	0.989	B	0.43413	0.419	T	0.07424	-1.0773	10	0.20519	T	0.43	-8.4603	11.8668	0.52499	0.1234:0.8137:0.0:0.063	.	379	O43155	FLRT2_HUMAN	L	379;379;32	ENSP00000332879:P379L;ENSP00000451050:P379L	ENSP00000332879:P379L	P	+	2	0	FLRT2	85158747	0.717000	0.27966	0.003000	0.11579	0.041000	0.13682	4.792000	0.62467	0.933000	0.37291	-0.150000	0.13652	CCG		FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1		
AZU1	566	hgsc.bcm.edu	37	19	830820	830820	+	Missense_Mutation	SNP	G	G	A	rs28626600	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr19:830820G>A	ENST00000233997.2	+	4	494	c.473G>A	c.(472-474)cGc>cAc	p.R158H		NM_001700.3	NP_001691.1	P20160	CAP7_HUMAN	azurocidin 1	158	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cellular extravasation (GO:0045123)|defense response to Gram-negative bacterium (GO:0050829)|glial cell migration (GO:0008347)|induction of positive chemotaxis (GO:0050930)|inflammatory response (GO:0006954)|macrophage chemotaxis (GO:0048246)|microglial cell activation (GO:0001774)|monocyte activation (GO:0042117)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell adhesion (GO:0045785)|positive regulation of fractalkine biosynthetic process (GO:0050754)|positive regulation of interleukin-1 beta biosynthetic process (GO:0050725)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of phagocytosis (GO:0050766)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of vascular permeability (GO:0043114)	azurophil granule (GO:0042582)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)|toxic substance binding (GO:0015643)			NS(1)|endometrium(1)|kidney(1)|lung(4)|pancreas(1)|upper_aerodigestive_tract(2)	10		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGGAGCCAGCGCAGTGGGGGG	0.657													G|||	285	0.0569089	0.0045	0.0576	5008	,	,		15019	0.0079		0.1223	False		,,,				2504	0.1104																0			19						G	HIS/ARG	73,4331	58.7+/-95.3	1,71,2130	29.0	28.0	29.0		473	-0.8	0.0	19	dbSNP_125	29	869,7731	189.1+/-236.0	48,773,3479	yes	missense	AZU1	NM_001700.3	29	49,844,5609	AA,AG,GG		10.1047,1.6576,7.2439	probably-damaging	158/252	830820	942,12062	2202	4300	6502	781820	SO:0001583	missense	566			X58794	CCDS12044.1	19p13.3	2012-03-30	2008-08-01		ENSG00000172232	ENSG00000172232			913	protein-coding gene	gene with protein product	"""cationic antimicrobial protein 37"", ""heparin-binding protein"", ""neutrophil azurocidin"""	162815				1919011	Standard	NM_001700		Approved	AZU, CAP37, AZAMP, HBP, NAZC, HUMAZUR	uc002lpz.1	P20160		ENST00000233997.2:c.473G>A	19.37:g.830820G>A	ENSP00000233997:p.Arg158His	Somatic		Capture	Illumina HiSeq	Phase_I	781820	P80014|Q52LG4|Q9UCM1|Q9UCT5	Missense_Mutation	SNP	ENST00000233997.2	37	CCDS12044.1	124	0.056776556776556776	2	0.0040650406504065045	26	0.0718232044198895	3	0.005244755244755245	93	0.12269129287598944	G	10.53	1.374773	0.24857	0.016576	0.101047	ENSG00000172232	ENST00000334630;ENST00000233997	D	0.88896	-2.44	1.51	-0.763	0.11030	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.04048	0.0113	N	0.16307	0.4	0.09310	N	1	D	0.65815	0.995	B	0.43950	0.437	T	0.40850	-0.9541	9	0.42905	T	0.14	.	3.9576	0.09396	0.4496:0.0:0.5504:0.0	rs28626600	158	P20160	CAP7_HUMAN	H	172;158	ENSP00000233997:R158H	ENSP00000233997:R158H	R	+	2	0	AZU1	781820	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.143000	0.16115	-0.178000	0.10672	-0.258000	0.10820	CGC		AZU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457472.2	NM_001700	
S1PR4	8698	hgsc.bcm.edu	37	19	3179472	3179472	+	Missense_Mutation	SNP	C	C	T			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr19:3179472C>T	ENST00000246115.3	+	1	737	c.682C>T	c.(682-684)Cgc>Tgc	p.R228C	S1PR4_ENST00000591346.1_3'UTR	NM_003775.3	NP_003766.1	O95977	S1PR4_HUMAN	sphingosine-1-phosphate receptor 4	228					activation of phospholipase C activity (GO:0007202)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)|sphingosine-1-phosphate receptor activity (GO:0038036)			breast(1)|kidney(2)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	13						GGCCATCTTCCGCCTGGTGCA	0.672																																					GBM(82;318 1638 33279 49708)												0			19											63.0	68.0	67.0					19																	3179472		2203	4296	6499	3130472	SO:0001583	missense	8698			AJ000479	CCDS12105.1	19p13.3	2012-08-08	2008-04-30	2008-04-30		ENSG00000125910		"""GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"""	3170	protein-coding gene	gene with protein product		603751	"""endothelial differentiation, G-protein-coupled receptor 6"", ""endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 6"""	EDG6		9790765	Standard	NM_003775		Approved		uc002lxg.3	O95977		ENST00000246115.3:c.682C>T	19.37:g.3179472C>T	ENSP00000246115:p.Arg228Cys	Somatic		Capture	Illumina HiSeq	Phase_I	3130472	D6W612	Missense_Mutation	SNP	ENST00000246115.3	37	CCDS12105.1	.	.	.	.	.	.	.	.	.	.	C	10.08	1.252765	0.22965	.	.	ENSG00000125910	ENST00000246115	T	0.39406	1.08	4.23	1.94	0.25998	GPCR, rhodopsin-like superfamily (1);	0.307616	0.30219	N	0.010131	T	0.27765	0.0683	L	0.38838	1.175	0.42614	D	0.993321	B	0.15473	0.013	B	0.08055	0.003	T	0.05886	-1.0858	10	0.38643	T	0.18	.	5.4596	0.16610	0.3988:0.5025:0.0:0.0987	.	228	O95977	S1PR4_HUMAN	C	228	ENSP00000246115:R228C	ENSP00000246115:R228C	R	+	1	0	S1PR4	3130472	0.780000	0.28664	0.186000	0.23195	0.674000	0.39518	0.796000	0.26986	0.181000	0.19994	0.462000	0.41574	CGC		S1PR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452517.1	NM_003775	
MUC16	94025	hgsc.bcm.edu	37	19	9047485	9047485	+	Silent	SNP	A	A	G			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr19:9047485A>G	ENST00000397910.4	-	5	34349	c.34146T>C	c.(34144-34146)agT>agC	p.S11382S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	11384	Thr-rich.				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						CTGCCCCAGGACTGGTGGCTA	0.483																																																	0			19											233.0	226.0	228.0					19																	9047485		1973	4157	6130	8908485	SO:0001819	synonymous_variant	94025			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.34146T>C	19.37:g.9047485A>G		Somatic		Capture	Illumina HiSeq	Phase_I	8908485	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																				MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
SYDE1	85360	hgsc.bcm.edu	37	19	15220577	15220577	+	Missense_Mutation	SNP	C	C	T			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr19:15220577C>T	ENST00000342784.2	+	3	524	c.493C>T	c.(493-495)Cgc>Tgc	p.R165C	SYDE1_ENST00000600440.1_Missense_Mutation_p.R98C|SYDE1_ENST00000600252.1_5'UTR	NM_033025.4	NP_149014.3	Q6ZW31	SYDE1_HUMAN	synapse defective 1, Rho GTPase, homolog 1 (C. elegans)	165					activation of Rho GTPase activity (GO:0032862)|positive regulation of synaptic transmission (GO:0050806)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptonemal complex assembly (GO:0007130)	cerebellar mossy fiber (GO:0044300)|cytosol (GO:0005829)|synaptic membrane (GO:0097060)	Rho GTPase activator activity (GO:0005100)			endometrium(4)|kidney(1)|large_intestine(7)|lung(2)|ovary(1)|pancreas(1)|skin(1)	17						CCCCGCCAGGCGCCTCTCCAT	0.716																																																	0			19											3.0	3.0	3.0					19																	15220577		1911	3773	5684	15081577	SO:0001583	missense	85360			BC029926	CCDS12324.1, CCDS74299.1	19p13.12	2008-02-05				ENSG00000105137			25824	protein-coding gene	gene with protein product						12477932	Standard	XM_005260126		Approved	7h3, FLJ13511	uc002nah.1	Q6ZW31		ENST00000342784.2:c.493C>T	19.37:g.15220577C>T	ENSP00000341489:p.Arg165Cys	Somatic		Capture	Illumina HiSeq	Phase_I	15081577	Q7L2I8|Q8N6J2|Q9H8K4	Missense_Mutation	SNP	ENST00000342784.2	37	CCDS12324.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.940098	0.73557	.	.	ENSG00000105137	ENST00000342784	T	0.15718	2.4	3.98	3.98	0.46160	.	0.191857	0.35739	N	0.003015	T	0.29976	0.0750	L	0.47716	1.5	0.39881	D	0.973645	D;D	0.89917	1.0;1.0	D;D	0.67725	0.953;0.943	T	0.04678	-1.0934	10	0.72032	D	0.01	.	9.4437	0.38684	0.2123:0.7877:0.0:0.0	.	98;165	Q6ZW31-2;Q6ZW31	.;SYDE1_HUMAN	C	165	ENSP00000341489:R165C	ENSP00000341489:R165C	R	+	1	0	SYDE1	15081577	0.954000	0.32549	0.996000	0.52242	0.928000	0.56348	1.795000	0.38784	1.960000	0.56953	0.573000	0.79308	CGC		SYDE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465666.1	NM_033025	
CPAMD8	27151	hgsc.bcm.edu	37	19	17014404	17014404	+	Silent	SNP	C	C	T			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr19:17014404C>T	ENST00000443236.1	-	34	4609	c.4578G>A	c.(4576-4578)gtG>gtA	p.V1526V		NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	1479						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						CCTTGGCACTCACAAACAGCC	0.612																																																	0			19											93.0	111.0	105.0					19																	17014404		2033	4177	6210	16875404	SO:0001819	synonymous_variant	27151			AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.4578G>A	19.37:g.17014404C>T		Somatic		Capture	Illumina HiSeq	Phase_I	16875404	Q8NC09|Q9ULD7	Silent	SNP	ENST00000443236.1	37	CCDS42519.1																																																																																				CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
APLP1	333	hgsc.bcm.edu	37	19	36362573	36362573	+	Silent	SNP	G	G	A	rs201024631	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr19:36362573G>A	ENST00000221891.4	+	5	789	c.597G>A	c.(595-597)tcG>tcA	p.S199S	APLP1_ENST00000537454.2_Silent_p.S160S|APLP1_ENST00000586861.1_Silent_p.S193S|NPHS1_ENST00000591817.1_5'Flank	NM_001024807.1|NM_005166.3	NP_001019978.1|NP_005157.1	P51693	APLP1_HUMAN	amyloid beta (A4) precursor-like protein 1	199					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular response to norepinephrine stimulus (GO:0071874)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|mRNA polyadenylation (GO:0006378)|negative regulation of cAMP biosynthetic process (GO:0030818)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|regulation of translation (GO:0006417)	basement membrane (GO:0005604)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|alpha-2B adrenergic receptor binding (GO:0031695)|alpha-2C adrenergic receptor binding (GO:0031696)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|transition metal ion binding (GO:0046914)			breast(4)|endometrium(2)|kidney(2)|large_intestine(12)|liver(1)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)	33	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CCTGTGGCTCGGATCGGTTCC	0.642													G|||	4	0.000798722	0.0008	0.0043	5008	,	,		15417	0.0		0.0	False		,,,				2504	0.0																0			19											114.0	104.0	107.0					19																	36362573		2203	4300	6503	41054413	SO:0001819	synonymous_variant	333			U48437	CCDS32997.1	19q	2008-07-15							597	protein-coding gene	gene with protein product	"""amyloid-like protein 1"", ""amyloid precursor-like protein 1"""	104775				8432545	Standard	NM_001024807		Approved	APLP	uc002ocf.3	P51693		ENST00000221891.4:c.597G>A	19.37:g.36362573G>A		Somatic		Capture	Illumina HiSeq	Phase_I	41054413	O00113|Q96A92	Silent	SNP	ENST00000221891.4	37	CCDS32997.1																																																																																				APLP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452564.1	NM_001024807	
DMWD	1762	hgsc.bcm.edu	37	19	46289503	46289503	+	Silent	SNP	C	C	T	rs8109951	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr19:46289503C>T	ENST00000270223.6	-	3	1296	c.1251G>A	c.(1249-1251)ccG>ccA	p.P417P	AC011530.4_ENST00000593999.1_5'Flank|DMWD_ENST00000377735.3_Silent_p.P417P|DMWD_ENST00000601370.1_5'Flank	NM_004943.1	NP_004934.1	Q09019	DMWD_HUMAN	dystrophia myotonica, WD repeat containing	417										central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	16		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00604)|GBM - Glioblastoma multiforme(486;0.0807)|Epithelial(262;0.236)		GTGGAGAGAGCGGGGCGCCCC	0.692													C|||	1455	0.290535	0.3079	0.2291	5008	,	,		12564	0.2887		0.329	False		,,,				2504	0.273																0			19						C		1250,3120		209,832,1144	15.0	18.0	17.0		1251	-8.4	0.0	19	dbSNP_116	17	3086,5450		602,1882,1784	no	coding-synonymous	DMWD	NM_004943.1		811,2714,2928	TT,TC,CC		36.1528,28.6041,33.5968		417/675	46289503	4336,8570	2185	4268	6453	50981343	SO:0001819	synonymous_variant	1762			L19267	CCDS33054.1	19q13.32	2013-01-09	2007-02-20		ENSG00000185800	ENSG00000185800		"""WD repeat domain containing"""	2936	protein-coding gene	gene with protein product		609857	"""dystrophia myotonica-containing WD repeat motif"""			1302022	Standard	NM_004943		Approved	DMR-N9, gene59, D19S593E	uc021uwc.1	Q09019	OTTHUMG00000169044	ENST00000270223.6:c.1251G>A	19.37:g.46289503C>T		Somatic		Capture	Illumina HiSeq	Phase_I	50981343		Silent	SNP	ENST00000270223.6	37	CCDS33054.1																																																																																				DMWD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402063.1	NM_004943	
LIG1	3978	hgsc.bcm.edu	37	19	48657140	48657140	+	Missense_Mutation	SNP	T	T	C			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr19:48657140T>C	ENST00000263274.7	-	6	874	c.455A>G	c.(454-456)aAg>aGg	p.K152R	LIG1_ENST00000536218.1_Intron|LIG1_ENST00000427526.2_Missense_Mutation_p.K122R|LIG1_ENST00000599165.1_Intron	NM_000234.1	NP_000225.1	P18858	DNLI1_HUMAN	ligase I, DNA, ATP-dependent	152			K -> E (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		anatomical structure morphogenesis (GO:0009653)|base-excision repair (GO:0006284)|cell division (GO:0051301)|DNA biosynthetic process (GO:0071897)|DNA ligation involved in DNA repair (GO:0051103)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|response to hydrogen peroxide (GO:0042542)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromosome (GO:0005694)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(22)|prostate(2)|skin(1)	44		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)	ttcctcctccttcttcctctt	0.577								Nucleotide excision repair (NER)																																									0			19											196.0	113.0	141.0					19																	48657140		2203	4300	6503	53348952	SO:0001583	missense	26018				CCDS12711.1, CCDS74409.1, CCDS74410.1	19q13.2-q13.3	2014-09-17				ENSG00000105486	6.5.1.1		6598	protein-coding gene	gene with protein product		126391					Standard	XM_005258934		Approved		uc002pia.1	P18858		ENST00000263274.7:c.455A>G	19.37:g.48657140T>C	ENSP00000263274:p.Lys152Arg	Somatic		Capture	Illumina HiSeq	Phase_I	53348952	B2RAI8|Q2TB12|Q32P23	Missense_Mutation	SNP	ENST00000263274.7	37	CCDS12711.1	.	.	.	.	.	.	.	.	.	.	T	6.386	0.439422	0.12104	.	.	ENSG00000105486	ENST00000263274;ENST00000544761;ENST00000427526	T;T	0.58506	0.44;0.33	3.99	2.94	0.34122	.	0.866238	0.10215	N	0.701604	T	0.48714	0.1515	L	0.54323	1.7	0.80722	D	1	B;B	0.09022	0.001;0.002	B;B	0.08055	0.003;0.001	T	0.28839	-1.0031	10	0.18710	T	0.47	-18.4584	7.3918	0.26913	0.0:0.0:0.2229:0.7771	.	122;152	B4DTU4;P18858	.;DNLI1_HUMAN	R	152;184;122	ENSP00000263274:K152R;ENSP00000442841:K122R	ENSP00000263274:K152R	K	-	2	0	LIG1	53348952	0.292000	0.24362	0.892000	0.35008	0.244000	0.25665	1.067000	0.30616	0.837000	0.34925	0.496000	0.49642	AAG		LIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465575.1	NM_000234	
SIGLEC10	89790	hgsc.bcm.edu	37	19	51919302	51919302	+	Missense_Mutation	SNP	T	T	C	rs201376644	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr19:51919302T>C	ENST00000339313.5	-	5	990	c.874A>G	c.(874-876)Aac>Gac	p.N292D	CTD-2616J11.2_ENST00000526996.1_RNA|CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000441969.3_Missense_Mutation_p.N234D|SIGLEC10_ENST00000436984.2_Missense_Mutation_p.N244D|CTD-2616J11.3_ENST00000532473.1_RNA|SIGLEC10_ENST00000356298.5_Missense_Mutation_p.N292D|SIGLEC10_ENST00000442846.3_Intron|SIGLEC10_ENST00000432469.2_Missense_Mutation_p.N209D|SIGLEC10_ENST00000439889.2_Missense_Mutation_p.N234D|SIGLEC10_ENST00000353836.5_Missense_Mutation_p.N292D|SIGLEC10_ENST00000525998.1_Intron			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	292	Ig-like C2-type 2.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		AGGACTCTGTTCTGCAGGACC	0.652																																																	0			19											19.0	24.0	22.0					19																	51919302		2201	4299	6500	56611114	SO:0001583	missense	89790			AF310233	CCDS12832.1, CCDS54301.1, CCDS54302.1, CCDS54303.1, CCDS54304.1, CCDS54305.1	19q13.3	2013-01-29			ENSG00000142512	ENSG00000142512		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15620	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 10 Ig-like lectin 7"", ""siglec-like gene 2"""	606091				11284738	Standard	NM_033130		Approved	SIGLEC-10, SLG2, PRO940, MGC126774	uc002pwo.3	Q96LC7	OTTHUMG00000165521	ENST00000339313.5:c.874A>G	19.37:g.51919302T>C	ENSP00000345243:p.Asn292Asp	Somatic		Capture	Illumina HiSeq	Phase_I	56611114	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Missense_Mutation	SNP	ENST00000339313.5	37	CCDS12832.1	.	.	.	.	.	.	.	.	.	.	.	7.755	0.704152	0.15172	.	.	ENSG00000142512	ENST00000353836;ENST00000432469;ENST00000356298;ENST00000441969;ENST00000439889;ENST00000436984;ENST00000339313;ENST00000529627	T;T;T;T;T;T;T;T	0.40476	1.61;1.61;1.61;1.61;1.61;1.61;1.61;1.03	4.37	1.07	0.20283	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.427133	0.19965	N	0.102128	T	0.13841	0.0335	N	0.02854	-0.475	0.09310	N	1	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.04013	0.001;0.001;0.001;0.001;0.001;0.001	T	0.33701	-0.9858	10	0.02654	T	1	.	7.7519	0.28903	0.0:0.684:0.0:0.316	.	244;292;292;234;234;292	C9JM10;B7ZL04;Q96LC7-2;Q96LC7-6;Q96LC7-3;Q96LC7	.;.;.;.;.;SIG10_HUMAN	D	292;209;292;234;234;244;292;106	ENSP00000342389:N292D;ENSP00000396742:N209D;ENSP00000348646:N292D;ENSP00000408387:N234D;ENSP00000389132:N234D;ENSP00000414324:N244D;ENSP00000345243:N292D;ENSP00000435281:N106D	ENSP00000345243:N292D	N	-	1	0	SIGLEC10	56611114	0.000000	0.05858	0.002000	0.10522	0.047000	0.14425	0.182000	0.16900	-0.072000	0.12864	-1.945000	0.00491	AAC		SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
ZNF415	55786	hgsc.bcm.edu	37	19	53612683	53612683	+	Silent	SNP	T	T	C			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr19:53612683T>C	ENST00000500065.4	-	4	948	c.615A>G	c.(613-615)caA>caG	p.Q205Q	ZNF415_ENST00000421033.1_Silent_p.Q217Q|ZNF415_ENST00000440291.1_Silent_p.Q192Q|ZNF415_ENST00000601493.1_5'UTR|ZNF415_ENST00000243643.4_Silent_p.Q205Q|ZNF415_ENST00000448501.1_Silent_p.Q253Q|ZNF415_ENST00000597503.1_3'UTR|ZNF415_ENST00000455735.2_Silent_p.Q253Q|ZNF415_ENST00000594011.1_3'UTR|ZNF415_ENST00000597748.1_3'UTR|ZNF415_ENST00000595193.1_3'UTR	NM_001136038.2	NP_001129510.2	Q09FC8	ZN415_HUMAN	zinc finger protein 415	253					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				GBM - Glioblastoma multiforme(134;0.0191)		ATTTCTGTTCTTGTGTGAGTA	0.378																																																	0			19											138.0	112.0	121.0					19																	53612683		2203	4300	6503	58304495	SO:0001819	synonymous_variant	55786			AK002053	CCDS12860.1, CCDS54313.1	19q13.42	2014-03-18			ENSG00000170954	ENSG00000170954		"""Zinc fingers, C2H2-type"", ""-"""	20636	protein-coding gene	gene with protein product						14702039	Standard	NM_001136038		Approved		uc002qaw.3	Q09FC8	OTTHUMG00000182865	ENST00000500065.4:c.615A>G	19.37:g.53612683T>C		Somatic		Capture	Illumina HiSeq	Phase_I	58304495	F5H287|Q09FC7|Q09FC9|Q09FD0|Q6NSZ2|Q6P3S0|Q9NUR2	Silent	SNP	ENST00000500065.4	37	CCDS54313.1																																																																																				ZNF415-025	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464043.1	NM_018355	
KIR3DL1	3811	hgsc.bcm.edu	37	19	55344246	55344246	+	IGR	SNP	G	G	A	rs374252476	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr19:55344246G>A	ENST00000391728.4	+	0	1871				KIR3DL1_ENST00000402254.2_Intron|KIR2DS4_ENST00000339924.8_RNA	NM_013289.2	NP_037421.2	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1						immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		TCATCATGGCGTGTGTTGGTG	0.622													.|||	74	0.0147764	0.0038	0.013	5008	,	,		14966	0.0149		0.0169	False		,,,				2504	0.0286																0			19											180.0	165.0	170.0					19																	55344246		2172	4177	6349	60036058	SO:0001628	intergenic_variant	3809			L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933		19.37:g.55344246G>A		Somatic		Capture	Illumina HiSeq	Phase_I	60036058	O43473|Q14946|Q16541	Silent	SNP	ENST00000391728.4	37	CCDS42621.1																																																																																				KIR3DL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141238.1	NM_013289	
GP6	51206	hgsc.bcm.edu	37	19	55526345	55526345	+	Missense_Mutation	SNP	T	T	G	rs1671152	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr19:55526345T>G	ENST00000417454.1	-	8	991	c.964A>C	c.(964-966)Aac>Cac	p.N322H	CTC-550B14.7_ENST00000586845.1_RNA|GP6_ENST00000310373.3_Missense_Mutation_p.K323T|CTC-550B14.7_ENST00000593060.1_RNA|GP6_ENST00000333884.2_Missense_Mutation_p.N304H	NM_016363.4	NP_057447	Q9HCN6	GPVI_HUMAN	glycoprotein VI (platelet)	322			N -> H (in dbSNP:rs1671152). {ECO:0000269|PubMed:11027634, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		blood coagulation (GO:0007596)|enzyme linked receptor protein signaling pathway (GO:0007167)|leukocyte migration (GO:0050900)|platelet activation (GO:0030168)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)	collagen binding (GO:0005518)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19			BRCA - Breast invasive adenocarcinoma(297;0.156)	GBM - Glioblastoma multiforme(193;0.0515)		TGACCCCCGTTTGATTTCCGG	0.662													G|||	4122	0.823083	0.6672	0.9164	5008	,	,		14866	0.9673		0.8588	False		,,,				2504	0.7822																0			19						G	HIS/ASN,THR/LYS	2707,1215		943,821,197	23.0	26.0	25.0	http://www.ncbi.nlm.nih.gov/pubmed?term	964,968	2.7	0.0	19	dbSNP_89	25	7026,1254		2988,1050,102	yes	missense,missense	GP6	NM_016363.4,NM_001083899.1	68,78	3931,1871,299	GG,GT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	15.1449,30.9791,20.2344	benign,benign	322/340,323/621	55526345	9733,2469	1961	4140	6101	60218157	SO:0001583	missense	51206			AB035073	CCDS42626.1, CCDS46184.1, CCDS58678.1	19q13.4	2013-01-29			ENSG00000088053	ENSG00000088053		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14388	protein-coding gene	gene with protein product		605546				11027634	Standard	NM_001083899		Approved	GPVI	uc002qil.3	Q9HCN6	OTTHUMG00000159709	ENST00000417454.1:c.964A>C	19.37:g.55526345T>G	ENSP00000394922:p.Asn322His	Somatic		Capture	Illumina HiSeq	Phase_I	60218157	Q9HCN7|Q9UIF2	Missense_Mutation	SNP	ENST00000417454.1	37	CCDS46184.1	1874|1874	0.858058608058608|0.858058608058608	338|338	0.6869918699186992|0.6869918699186992	328|328	0.9060773480662984|0.9060773480662984	562|562	0.9825174825174825|0.9825174825174825	646|646	0.8522427440633246|0.8522427440633246	G|G	0.026|0.026	-1.370532|-1.370532	0.01225|0.01225	0.690209|0.690209	0.848551|0.848551	ENSG00000088053|ENSG00000088053	ENST00000310373|ENST00000417454;ENST00000333884	T|T;T	0.00557|0.00492	6.62|7.05;7.01	2.65|2.65	2.65|2.65	0.31530|0.31530	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	B|B;B	0.02656|0.02656	0.0|0.0;0.0	B|B;B	0.01281|0.01281	0.0|0.0;0.0	T|T	0.46816|0.46816	-0.9164|-0.9164	7|7	0.02654|0.31617	T|T	1|0.26	.|.	6.9339|6.9339	0.24457|0.24457	0.0:0.0:0.7258:0.2742|0.0:0.0:0.7258:0.2742	rs1671152;rs16986173;rs59836180;rs1671152|rs1671152;rs16986173;rs59836180;rs1671152	323|304;322	Q9HCN6-3|Q9HCN6-2;Q9HCN6	.|.;GPVI_HUMAN	T|H	323|322;304	ENSP00000308782:K323T|ENSP00000394922:N322H;ENSP00000334552:N304H	ENSP00000308782:K323T|ENSP00000334552:N304H	K|N	-|-	2|1	0|0	GP6|GP6	60218157|60218157	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.001000|0.001000	0.01503|0.01503	0.067000|0.067000	0.14510|0.14510	0.680000|0.680000	0.31366|0.31366	-0.217000|-0.217000	0.12591|0.12591	AAA|AAC		GP6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357006.1		
TCEA1	6917	hgsc.bcm.edu	37	8	54923039	54923039	+	Missense_Mutation	SNP	T	T	C			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr8:54923039T>C	ENST00000521604.2	-	2	480	c.77A>G	c.(76-78)gAt>gGt	p.D26G	TCEA1_ENST00000396401.3_Intron|TCEA1_ENST00000518784.1_Missense_Mutation_p.D26G|TCEA1_ENST00000522635.1_Missense_Mutation_p.D26G|TCEA1_ENST00000520534.1_Missense_Mutation_p.D26G|TCEA1_ENST00000521086.2_5'UTR	NM_006756.2	NP_006747.1	P23193	TCEA1_HUMAN	transcription elongation factor A (SII), 1	26	TFIIS N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00649}.				DNA repair (GO:0006281)|erythrocyte differentiation (GO:0030218)|gene expression (GO:0010467)|nucleotide-excision repair (GO:0006289)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|regulation of DNA-templated transcription, elongation (GO:0032784)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(1)|lung(1)|skin(1)	4		Lung NSC(129;0.109)|all_epithelial(80;0.11)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;9.1e-07)|Epithelial(17;9.44e-05)|all cancers(17;0.000699)			CTTTAGCAAATCCAATGCTCC	0.343			T	PLAG1	salivary adenoma																																			Dom	yes		8	8q11.2	6917	"""transcription elongation factor A (SII), 1"""		E	0			8											32.0	30.0	31.0					8																	54923039		1795	4063	5858	55085592	SO:0001583	missense	6917			X62585	CCDS47857.1, CCDS47858.1	8q11.2	2011-01-25			ENSG00000187735	ENSG00000187735		"""General transcription factors"""	11612	protein-coding gene	gene with protein product		601425		TCEA, GTF2S		8812434, 8112616	Standard	NM_006756		Approved	SII, TF2S, TFIIS	uc003xru.3	P23193	OTTHUMG00000164262	ENST00000521604.2:c.77A>G	8.37:g.54923039T>C	ENSP00000428426:p.Asp26Gly	Somatic		Capture	Illumina HiSeq	Phase_I	55085592	A6NF25|A8K339|Q15563|Q6FG87	Missense_Mutation	SNP	ENST00000521604.2	37	CCDS47858.1	.	.	.	.	.	.	.	.	.	.	T	15.16	2.750844	0.49257	.	.	ENSG00000187735	ENST00000521604;ENST00000522635;ENST00000520534;ENST00000518784;ENST00000519704	.	.	.	5.42	5.42	0.78866	Transcription factor IIS, N-terminal (4);Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type (1);	0.000000	0.85682	U	0.000000	T	0.82107	0.4965	M	0.87381	2.88	0.54753	D	0.999989	P;P	0.43392	0.805;0.789	P;P	0.59424	0.857;0.833	D	0.84511	0.0622	9	0.62326	D	0.03	-22.1168	12.9809	0.58564	0.0:0.0:0.0:1.0	.	26;26	B7Z4S1;P23193	.;TCEA1_HUMAN	G	26	.	ENSP00000428868:D26G	D	-	2	0	TCEA1	55085592	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.413000	0.66399	2.063000	0.61619	0.459000	0.35465	GAT		TCEA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377975.2	NM_006756	
VPS13B	157680	hgsc.bcm.edu	37	8	100454774	100454774	+	Missense_Mutation	SNP	C	C	A			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr8:100454774C>A	ENST00000358544.2	+	23	3467	c.3356C>A	c.(3355-3357)cCt>cAt	p.P1119H	VPS13B_ENST00000357162.2_Missense_Mutation_p.P1119H|VPS13B_ENST00000395996.1_Missense_Mutation_p.P1119H	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	1119					protein transport (GO:0015031)			p.P1119L(1)		NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			CTCTGTTTGCCTCAAATAAAG	0.438																																					Colon(161;2205 2542 7338 31318)												1	Substitution - Missense(1)	skin(1)	8											122.0	114.0	116.0					8																	100454774		2203	4300	6503	100523950	SO:0001583	missense	157680			AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"""Cohen syndrome 1"""	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.3356C>A	8.37:g.100454774C>A	ENSP00000351346:p.Pro1119His	Somatic		Capture	Illumina HiSeq	Phase_I	100523950	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	37	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.766807	0.90020	.	.	ENSG00000132549	ENST00000357162;ENST00000358544;ENST00000395996	T;T;T	0.46063	0.88;0.88;0.88	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.58395	0.2119	L	0.36672	1.1	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.986;0.998;0.999	T	0.59573	-0.7429	10	0.87932	D	0	.	19.8633	0.96793	0.0:1.0:0.0:0.0	.	1118;1119;1119;1119	Q7Z7G8-6;Q7Z7G8-2;Q7Z7G8;Q7Z7G8-3	.;.;VP13B_HUMAN;.	H	1119	ENSP00000349685:P1119H;ENSP00000351346:P1119H;ENSP00000379318:P1119H	ENSP00000349685:P1119H	P	+	2	0	VPS13B	100523950	1.000000	0.71417	0.991000	0.47740	0.966000	0.64601	7.216000	0.77974	2.697000	0.92050	0.591000	0.81541	CCT		VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042	
RAD21	5885	hgsc.bcm.edu	37	8	117864237	117864237	+	Nonsense_Mutation	SNP	G	G	A			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr8:117864237G>A	ENST00000297338.2	-	11	1707	c.1420C>T	c.(1420-1422)Cag>Tag	p.Q474*	RAD21_ENST00000523986.1_5'UTR|RAD21_ENST00000517749.1_5'Flank|RAD21_ENST00000518055.1_Nonsense_Mutation_p.Q19*	NM_006265.2	NP_006256.1	O60216	RAD21_HUMAN	RAD21 homolog (S. pombe)	474	Pro-rich.				apoptotic process (GO:0006915)|chromosome segregation (GO:0007059)|DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|protein localization to chromatin (GO:0071168)|reciprocal meiotic recombination (GO:0007131)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear meiotic cohesin complex (GO:0034991)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.Q474*(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(1)|stomach(1)	32	all_cancers(13;1.21e-21)|Lung NSC(37;0.000134)|Ovarian(258;0.0172)					TTAACTCCCTGAGGTGGTGGT	0.473																																																	1	Substitution - Nonsense(1)	lung(1)	8											133.0	119.0	124.0					8																	117864237		2203	4300	6503	117933418	SO:0001587	stop_gained	5885			BC050381	CCDS6321.1	8q24.11	2014-09-17	2001-11-28		ENSG00000164754	ENSG00000164754			9811	protein-coding gene	gene with protein product	"""sister chromatid cohesion 1"""	606462	"""RAD21 (S. pombe) homolog"""			8812457	Standard	NM_006265		Approved	KIAA0078, hHR21, SCC1	uc003yod.3	O60216	OTTHUMG00000164959	ENST00000297338.2:c.1420C>T	8.37:g.117864237G>A	ENSP00000297338:p.Gln474*	Somatic		Capture	Illumina HiSeq	Phase_I	117933418	A8K0E0|Q15001|Q99568	Nonsense_Mutation	SNP	ENST00000297338.2	37	CCDS6321.1	.	.	.	.	.	.	.	.	.	.	G	42	9.727148	0.99249	.	.	ENSG00000164754	ENST00000297338;ENST00000518055	.	.	.	5.71	5.71	0.89125	.	0.108239	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07175	T	0.84	-21.6355	19.8625	0.96789	0.0:0.0:1.0:0.0	.	.	.	.	X	474;19	.	ENSP00000297338:Q474X	Q	-	1	0	RAD21	117933418	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	9.429000	0.97481	2.689000	0.91719	0.655000	0.94253	CAG		RAD21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381184.1	NM_006265	
NOV	4856	hgsc.bcm.edu	37	8	120428844	120428844	+	Silent	SNP	T	T	C			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr8:120428844T>C	ENST00000259526.3	+	1	299	c.72T>C	c.(70-72)caT>caC	p.H24H		NM_002514.3	NP_002505.1	Q9UIW2	PLXA1_HUMAN	nephroblastoma overexpressed	0					axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|skin(3)	21	all_cancers(13;3.84e-26)|Lung NSC(37;1.19e-08)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.000507)			TGCTTCTCCATCTCCTGGGAC	0.562											OREG0018940	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					0			8											113.0	97.0	102.0					8																	120428844		2203	4300	6503	120498025	SO:0001819	synonymous_variant	6134			X96584	CCDS6328.1	8q24.12	2012-02-27	2012-02-27		ENSG00000136999	ENSG00000136999			7885	protein-coding gene	gene with protein product		164958	"""nephroblastoma overexpressed gene"""			1334251	Standard	NM_002514		Approved	IGFBP9, CCN3	uc003yoq.2	P48745	OTTHUMG00000164984	ENST00000259526.3:c.72T>C	8.37:g.120428844T>C		Somatic	1503	Capture	Illumina HiSeq	Phase_I	120498025		Silent	SNP	ENST00000259526.3	37	CCDS6328.1																																																																																				NOV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381301.1	NM_002514	
ZC3H3	23144	hgsc.bcm.edu	37	8	144550819	144550819	+	Silent	SNP	A	A	G			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr8:144550819A>G	ENST00000262577.5	-	6	1945	c.1914T>C	c.(1912-1914)gaT>gaC	p.D638D		NM_015117.2	NP_055932.2	Q8IXZ2	ZC3H3_HUMAN	zinc finger CCCH-type containing 3	638					mRNA polyadenylation (GO:0006378)|poly(A)+ mRNA export from nucleus (GO:0016973)|regulation of mRNA export from nucleus (GO:0010793)	nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	23	all_cancers(97;8.64e-11)|all_epithelial(106;6.43e-09)|Lung NSC(106;0.000202)|all_lung(105;0.000548)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.107)			TGCCTGCAGGATCCAGCCGGC	0.687																																																	0			8											27.0	31.0	30.0					8																	144550819		2116	4172	6288	144621962	SO:0001819	synonymous_variant	23144			D63484	CCDS6402.1	8q24.3	2012-07-05	2005-06-02	2005-06-02	ENSG00000014164	ENSG00000014164		"""Zinc fingers, CCCH-type domain containing"""	28972	protein-coding gene	gene with protein product			"""zinc finger CCCH-type domain containing 3"""	ZC3HDC3		8590280	Standard	NM_015117		Approved	KIAA0150	uc003yyd.2	Q8IXZ2	OTTHUMG00000165127	ENST00000262577.5:c.1914T>C	8.37:g.144550819A>G		Somatic		Capture	Illumina HiSeq	Phase_I	144621962	Q14163|Q8N4E2|Q9BUS4	Silent	SNP	ENST00000262577.5	37	CCDS6402.1																																																																																				ZC3H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382011.2	NM_015117	
TONSL	4796	hgsc.bcm.edu	37	8	145661320	145661320	+	Silent	SNP	G	G	A	rs2721140	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr8:145661320G>A	ENST00000409379.3	-	17	2525	c.2496C>T	c.(2494-2496)gcC>gcT	p.A832A	AC084125.4_ENST00000544423.1_RNA|AC084125.4_ENST00000442850.1_RNA	NM_013432.4	NP_038460.4	Q96HA7	TONSL_HUMAN	tonsoku-like, DNA repair protein	832					cytoplasmic sequestering of transcription factor (GO:0042994)|double-strand break repair via homologous recombination (GO:0000724)|regulation of RNA biosynthetic process (GO:2001141)|replication fork processing (GO:0031297)	cytoplasm (GO:0005737)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	histone binding (GO:0042393)|transcription corepressor activity (GO:0003714)			biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|lung(14)|ovary(3)|prostate(1)|skin(1)	26						GCCAGTCCCCGGCCAGGCACT	0.741													g|||	2347	0.46865	0.4115	0.438	5008	,	,		13786	0.4246		0.4662	False		,,,				2504	0.6155																0			8								1747,2459		402,943,758	8.0	11.0	10.0		2496	-8.9	0.0	8	dbSNP_100	10	3725,4593		923,1879,1357	no	coding-synonymous	TONSL	NM_013432.4		1325,2822,2115	AA,AG,GG		44.7824,41.5359,43.6921		832/1379	145661320	5472,7052	2103	4159	6262	145632128	SO:0001819	synonymous_variant	0				CCDS34968.2	8q24.3	2013-01-10	2010-12-02	2010-11-30	ENSG00000160949	ENSG00000160949		"""Ankyrin repeat domain containing"""	7801	protein-coding gene	gene with protein product		604546	"""nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 2"""	NFKBIL2		7738005, 11246458	Standard	NM_013432		Approved	IKBR	uc011llg.2	Q96HA7	OTTHUMG00000153122	ENST00000409379.3:c.2496C>T	8.37:g.145661320G>A		Somatic		Capture	Illumina HiSeq	Phase_I	145632128	B5MDP0|C9JKB1|C9JNV8|Q13006|Q9UGJ2	Silent	SNP	ENST00000409379.3	37	CCDS34968.2																																																																																				TONSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329668.2	NM_013432	
MFSD3	113655	hgsc.bcm.edu	37	8	145737816	145737816	+	IGR	SNP	C	C	T	rs4251691	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr8:145737816C>T	ENST00000301327.4	+	0	1548				RECQL4_ENST00000428558.2_Missense_Mutation_p.R1005Q|RECQL4_ENST00000532237.1_5'UTR|CTD-2517M22.17_ENST00000580385.1_RNA	NM_138431.1	NP_612440.1	Q96ES6	MFSD3_HUMAN	major facilitator superfamily domain containing 3						transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(1)|kidney(1)|lung(4)	8	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			GCAGAGAGCCCGCCGCACAGA	0.667													C|||	1925	0.384385	0.0635	0.4899	5008	,	,		17898	0.4762		0.4543	False		,,,				2504	0.5767																0			8						C	GLN/ARG	543,3685		54,435,1625	22.0	31.0	28.0		3015	0.3	0.1	8	dbSNP_111	28	3802,4678		875,2052,1313	no	missense	RECQL4	NM_004260.3	43	929,2487,2938	TT,TC,CC		44.8349,12.843,34.1911	benign	1005/1209	145737816	4345,8363	2114	4240	6354	145708624	SO:0001628	intergenic_variant	9401				CCDS6431.1	8q24.3	2005-11-17			ENSG00000167700	ENSG00000167700			25157	protein-coding gene	gene with protein product							Standard	NM_138431		Approved		uc003zdi.1	Q96ES6	OTTHUMG00000165177		8.37:g.145737816C>T		Somatic		Capture	Illumina HiSeq	Phase_I	145708624		Silent	SNP	ENST00000301327.4	37	CCDS6431.1																																																																																				MFSD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382478.2	NM_138431	
PRAMEF10	343071	hgsc.bcm.edu	37	1	12955474	12955474	+	Missense_Mutation	SNP	G	G	T			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr1:12955474G>T	ENST00000235347.4	-	2	284	c.205C>A	c.(205-207)Ctg>Atg	p.L69M		NM_001039361.3	NP_001034450.2	O60809	PRA10_HUMAN	PRAME family member 10	69					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					NS(2)|breast(1)|large_intestine(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	12	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GTCTTCATCAGGGATCCCAGA	0.577																																																	0			1											78.0	73.0	75.0					1																	12955474		2124	3827	5951	12878061	SO:0001583	missense	343071			AL049682	CCDS41255.1	1p36.21	2013-01-17			ENSG00000187545	ENSG00000187545		"""-"""	27997	protein-coding gene	gene with protein product							Standard	NM_001039361		Approved		uc001auo.3	O60809	OTTHUMG00000001981	ENST00000235347.4:c.205C>A	1.37:g.12955474G>T	ENSP00000235347:p.Leu69Met	Somatic		Capture	Illumina HiSeq	Phase_I	12878061	Q2M1V2	Missense_Mutation	SNP	ENST00000235347.4	37	CCDS41255.1	.	.	.	.	.	.	.	.	.	.	.	11.77	1.737912	0.30774	.	.	ENSG00000187545	ENST00000235347	T	0.15487	2.42	1.99	1.99	0.26369	.	0.302894	0.27088	N	0.020983	T	0.38665	0.1049	M	0.82517	2.595	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.03695	-1.1012	10	0.56958	D	0.05	.	7.5431	0.27751	0.0:0.0:1.0:0.0	.	69	O60809	PRA10_HUMAN	M	69	ENSP00000235347:L69M	ENSP00000235347:L69M	L	-	1	2	PRAMEF10	12878061	0.518000	0.26234	0.018000	0.16275	0.034000	0.12701	0.646000	0.24797	1.431000	0.47355	0.400000	0.26472	CTG		PRAMEF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005512.2	XM_496342	
PRAMEF10	343071	hgsc.bcm.edu	37	1	12955488	12955488	+	Missense_Mutation	SNP	A	A	T			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr1:12955488A>T	ENST00000235347.4	-	2	270	c.191T>A	c.(190-192)cTc>cAc	p.L64H		NM_001039361.3	NP_001034450.2	O60809	PRA10_HUMAN	PRAME family member 10	64					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					NS(2)|breast(1)|large_intestine(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	12	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TCCCAGAGGGAGGCTGAGGAA	0.582																																																	0			1											83.0	76.0	79.0					1																	12955488		2125	3831	5956	12878075	SO:0001583	missense	343071			AL049682	CCDS41255.1	1p36.21	2013-01-17			ENSG00000187545	ENSG00000187545		"""-"""	27997	protein-coding gene	gene with protein product							Standard	NM_001039361		Approved		uc001auo.3	O60809	OTTHUMG00000001981	ENST00000235347.4:c.191T>A	1.37:g.12955488A>T	ENSP00000235347:p.Leu64His	Somatic		Capture	Illumina HiSeq	Phase_I	12878075	Q2M1V2	Missense_Mutation	SNP	ENST00000235347.4	37	CCDS41255.1	.	.	.	.	.	.	.	.	.	.	.	12.20	1.865739	0.32977	.	.	ENSG00000187545	ENST00000235347	T	0.14516	2.5	1.99	1.99	0.26369	.	0.000000	0.64402	D	0.000003	T	0.41696	0.1170	H	0.94264	3.515	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.19418	-1.0306	10	0.87932	D	0	.	6.0147	0.19596	1.0:0.0:0.0:0.0	.	64	O60809	PRA10_HUMAN	H	64	ENSP00000235347:L64H	ENSP00000235347:L64H	L	-	2	0	PRAMEF10	12878075	0.831000	0.29352	0.054000	0.19295	0.012000	0.07955	1.654000	0.37334	1.174000	0.42811	0.329000	0.21502	CTC		PRAMEF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005512.2	XM_496342	
WNT4	54361	hgsc.bcm.edu	37	1	22456337	22456337	+	Missense_Mutation	SNP	C	C	T			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr1:22456337C>T	ENST00000290167.6	-	2	128	c.85G>A	c.(85-87)Gcc>Acc	p.A29T	WNT4_ENST00000542383.1_5'UTR	NM_030761.4	NP_110388.2	P56705	WNT4_HUMAN	wingless-type MMTV integration site family, member 4	29					adrenal gland development (GO:0030325)|androgen biosynthetic process (GO:0006702)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cellular response to starvation (GO:0009267)|cellular response to transforming growth factor beta stimulus (GO:0071560)|embryonic epithelial tube formation (GO:0001838)|epithelial to mesenchymal transition (GO:0001837)|establishment of protein localization to plasma membrane (GO:0090002)|female gonad development (GO:0008585)|female sex determination (GO:0030237)|immature T cell proliferation in thymus (GO:0033080)|kidney development (GO:0001822)|liver development (GO:0001889)|male gonad development (GO:0008584)|mammary gland epithelium development (GO:0061180)|mesenchymal to epithelial transition (GO:0060231)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric nephron morphogenesis (GO:0072273)|metanephric tubule formation (GO:0072174)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell differentiation (GO:0045596)|negative regulation of cell migration (GO:0030336)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of gene expression (GO:0010629)|negative regulation of male gonad development (GO:2000019)|negative regulation of steroid biosynthetic process (GO:0010894)|negative regulation of testicular blood vessel morphogenesis (GO:0061369)|negative regulation of testosterone biosynthetic process (GO:2000225)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of wound healing (GO:0061045)|neuron differentiation (GO:0030182)|non-canonical Wnt signaling pathway via MAPK cascade (GO:0038030)|oocyte development (GO:0048599)|paramesonephric duct development (GO:0061205)|positive regulation of aldosterone biosynthetic process (GO:0032349)|positive regulation of bone mineralization (GO:0030501)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of cortisol biosynthetic process (GO:2000066)|positive regulation of dermatome development (GO:0061184)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of meiosis (GO:0045836)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription, DNA-templated (GO:0045893)|protein palmitoylation (GO:0018345)|regulation of cell-cell adhesion (GO:0022407)|renal vesicle formation (GO:0072033)|renal vesicle induction (GO:0072034)|smooth muscle cell differentiation (GO:0051145)|somatotropin secreting cell differentiation (GO:0060126)|tertiary branching involved in mammary gland duct morphogenesis (GO:0060748)|thyroid-stimulating hormone-secreting cell differentiation (GO:0060129)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(2)	8		Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;6.55e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;9.02e-26)|Colorectal(126;1.71e-07)|COAD - Colon adenocarcinoma(152;1.17e-05)|GBM - Glioblastoma multiforme(114;2.01e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000568)|KIRC - Kidney renal clear cell carcinoma(1967;0.00277)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)		GACAGCTTGGCCAGGTACCTG	0.627																																																	0			1											130.0	125.0	127.0					1																	22456337		2203	4300	6503	22328924	SO:0001583	missense	54361			AL031281	CCDS223.1	1p36.23-p35.1	2013-02-28			ENSG00000162552	ENSG00000162552		"""Wingless-type MMTV integration sites"", ""Endogenous ligands"""	12783	protein-coding gene	gene with protein product		603490				8168088	Standard	NM_030761		Approved	WNT-4	uc001bfs.4	P56705	OTTHUMG00000002894	ENST00000290167.6:c.85G>A	1.37:g.22456337C>T	ENSP00000290167:p.Ala29Thr	Somatic		Capture	Illumina HiSeq	Phase_I	22328924	B4DJF9|Q5TZQ0|Q96T81|Q9BXF5|Q9H1J8|Q9UJM2	Missense_Mutation	SNP	ENST00000290167.6	37	CCDS223.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	29.7|29.7	5.030694|5.030694	0.93575|0.93575	.|.	.|.	ENSG00000162552|ENSG00000162552	ENST00000290167;ENST00000374655|ENST00000415567	T|.	0.77098|.	-1.07|.	5.09|5.09	5.09|5.09	0.68999|0.68999	.|.	0.348088|.	0.24599|.	U|.	0.037160|.	T|T	0.45296|0.45296	0.1335|0.1335	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	D|.	0.71674|.	0.998|.	D|.	0.64237|.	0.923|.	T|T	0.42207|0.42207	-0.9465|-0.9465	10|5	0.87932|.	D|.	0|.	.|.	17.0573|17.0573	0.86537|0.86537	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	29|.	P56705|.	WNT4_HUMAN|.	T|D	29|3	ENSP00000290167:A29T|.	ENSP00000290167:A29T|.	A|G	-|-	1|2	0|0	WNT4|WNT4	22328924|22328924	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.896000|0.896000	0.52359|0.52359	7.810000|7.810000	0.86072|0.86072	2.360000|2.360000	0.80028|0.80028	0.462000|0.462000	0.41574|0.41574	GCC|GGC		WNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008088.2		
ZC3H12A	80149	hgsc.bcm.edu	37	1	37949058	37949058	+	Missense_Mutation	SNP	T	T	C			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr1:37949058T>C	ENST00000373087.6	+	6	1762	c.1646T>C	c.(1645-1647)cTg>cCg	p.L549P		NM_025079.2	NP_079355.2			zinc finger CCCH-type containing 12A											NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GCAGGCAGCCTGGCCAAGGAG	0.662																																																	0			1											49.0	59.0	55.0					1																	37949058		2203	4300	6503	37721645	SO:0001583	missense	80149				CCDS417.1	1p34.3	2012-07-05			ENSG00000163874	ENSG00000163874		"""Zinc fingers, CCCH-type domain containing"""	26259	protein-coding gene	gene with protein product	"""MCP induced protein 1"""	610562				18178554, 22055188	Standard	NM_025079		Approved	FLJ23231, MCPIP1	uc001cbb.4	Q5D1E8	OTTHUMG00000004221	ENST00000373087.6:c.1646T>C	1.37:g.37949058T>C	ENSP00000362179:p.Leu549Pro	Somatic		Capture	Illumina HiSeq	Phase_I	37721645		Missense_Mutation	SNP	ENST00000373087.6	37	CCDS417.1	.	.	.	.	.	.	.	.	.	.	T	12.49	1.953790	0.34471	.	.	ENSG00000163874	ENST00000373087;ENST00000373082	T	0.51574	0.7	5.15	5.15	0.70609	.	0.601634	0.14339	N	0.325840	T	0.43122	0.1233	L	0.51422	1.61	0.35754	D	0.819624	B;B	0.33637	0.42;0.003	B;B	0.29077	0.098;0.003	T	0.52548	-0.8561	10	0.35671	T	0.21	-20.9358	14.9753	0.71267	0.0:0.0:0.0:1.0	.	344;549	B3KSD3;Q5D1E8	.;ZC12A_HUMAN	P	549	ENSP00000362179:L549P	ENSP00000362174:L549P	L	+	2	0	ZC3H12A	37721645	0.285000	0.24296	0.999000	0.59377	0.976000	0.68499	1.842000	0.39250	1.938000	0.56188	0.459000	0.35465	CTG		ZC3H12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012154.2	NM_025079	
ERICH3	127254	hgsc.bcm.edu	37	1	75039139	75039139	+	Missense_Mutation	SNP	G	G	A			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr1:75039139G>A	ENST00000326665.5	-	14	2473	c.2255C>T	c.(2254-2256)gCa>gTa	p.A752V	C1orf173_ENST00000433746.2_5'UTR	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		752	Glu-rich.									NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						TGAGTTGATTGCTGCTGTTTC	0.408																																																	0			1											85.0	87.0	87.0					1																	75039139		2203	4300	6503	74811727	SO:0001583	missense	127254																														ENST00000326665.5:c.2255C>T	1.37:g.75039139G>A	ENSP00000322609:p.Ala752Val	Somatic		Capture	Illumina HiSeq	Phase_I	74811727	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Missense_Mutation	SNP	ENST00000326665.5	37	CCDS30755.1	.	.	.	.	.	.	.	.	.	.	G	12.55	1.970181	0.34754	.	.	ENSG00000178965	ENST00000326665	T	0.13538	2.58	5.26	-0.176	0.13311	.	.	.	.	.	T	0.01730	0.0055	N	0.08118	0	0.09310	N	1	B	0.18310	0.027	B	0.15052	0.012	T	0.48068	-0.9067	9	0.19590	T	0.45	-0.3026	9.4689	0.38831	0.4148:0.0:0.5852:0.0	.	752	Q5RHP9	CA173_HUMAN	V	752	ENSP00000322609:A752V	ENSP00000322609:A752V	A	-	2	0	C1orf173	74811727	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.165000	0.16564	0.021000	0.15133	0.655000	0.94253	GCA		C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1		
PRRC2C	23215	hgsc.bcm.edu	37	1	171526588	171526588	+	Silent	SNP	T	T	C			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr1:171526588T>C	ENST00000338920.4	+	19	5568	c.5331T>C	c.(5329-5331)gtT>gtC	p.V1777V	PRRC2C_ENST00000426496.2_Silent_p.V1777V|PRRC2C_ENST00000367742.3_Silent_p.V1779V|PRRC2C_ENST00000392078.3_Silent_p.V1779V	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	1777	Ala-rich.				hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										taactccagttccagcctcaa	0.557																																																	0			1											104.0	89.0	94.0					1																	171526588		1693	3015	4708	169793212	SO:0001819	synonymous_variant	0			AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"""BAT2 domain containing 1"", ""HLA-B associated transcript 2-like 2"""	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.5331T>C	1.37:g.171526588T>C		Somatic		Capture	Illumina HiSeq	Phase_I	169793212	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Silent	SNP	ENST00000338920.4	37	CCDS1296.2	.	.	.	.	.	.	.	.	.	.	T	12.22	1.874036	0.33069	.	.	ENSG00000117523	ENST00000495585	.	.	.	3.43	-5.74	0.02391	.	.	.	.	.	T	0.05456	0.0144	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.29701	-1.0003	4	.	.	.	.	1.2787	0.02036	0.1468:0.2976:0.3001:0.2556	.	.	.	.	S	325	.	.	F	+	2	0	PRRC2C	169793212	0.000000	0.05858	0.000000	0.03702	0.917000	0.54804	-1.006000	0.03671	-1.295000	0.02357	0.449000	0.29647	TTC		PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172	
IER5	51278	hgsc.bcm.edu	37	1	181058345	181058345	+	Missense_Mutation	SNP	G	G	A	rs200142413	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr1:181058345G>A	ENST00000367577.4	+	1	708	c.307G>A	c.(307-309)Gag>Aag	p.E103K	RP11-309G3.3_ENST00000606938.1_lincRNA	NM_016545.4	NP_057629.2	Q5VY09	IER5_HUMAN	immediate early response 5	103										lung(1)|ovary(1)|pancreas(1)|urinary_tract(1)	4						GCCGCAGCCGGAGCGCTCCTC	0.776													G|||	29	0.00579073	0.0008	0.0029	5008	,	,		7139	0.0		0.0139	False		,,,				2504	0.0123																0			1						G	LYS/GLU	16,4268		0,16,2126	10.0	12.0	11.0		307	2.0	0.0	1		11	149,8269		1,147,4061	no	missense	IER5	NM_016545.4	56	1,163,6187	AA,AG,GG		1.77,0.3735,1.299	benign	103/328	181058345	165,12537	2142	4209	6351	179324968	SO:0001583	missense	51278			BC000128	CCDS1343.1	1q25.3	2008-02-05			ENSG00000162783	ENSG00000162783			5393	protein-coding gene	gene with protein product		607177				10049588, 11102586	Standard	NM_016545		Approved		uc001got.4	Q5VY09	OTTHUMG00000035178	ENST00000367577.4:c.307G>A	1.37:g.181058345G>A	ENSP00000356549:p.Glu103Lys	Somatic		Capture	Illumina HiSeq	Phase_I	179324968	B2RBV3|Q8WY68|Q9NY49|Q9NZP9	Missense_Mutation	SNP	ENST00000367577.4	37	CCDS1343.1	15	0.006868131868131868	3	0.006097560975609756	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	G	8.592	0.884749	0.17540	0.003735	0.0177	ENSG00000162783	ENST00000367577;ENST00000545568	T	0.09255	3.0	3.0	2.02	0.26589	.	0.468679	0.17106	U	0.186814	T	0.04272	0.0118	L	0.46157	1.445	0.26327	N	0.97759	B	0.34181	0.44	B	0.32090	0.14	T	0.17653	-1.0362	10	0.48119	T	0.1	.	7.6479	0.28331	0.0:0.2819:0.7181:0.0	.	103	Q5VY09	IER5_HUMAN	K	103	ENSP00000356549:E103K	ENSP00000356549:E103K	E	+	1	0	IER5	179324968	0.005000	0.15991	0.008000	0.14137	0.033000	0.12548	0.899000	0.28417	0.535000	0.28714	0.448000	0.29417	GAG		IER5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085142.1	NM_016545	
FAM129A	116496	hgsc.bcm.edu	37	1	184868326	184868326	+	Missense_Mutation	SNP	A	A	T			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr1:184868326A>T	ENST00000367511.3	-	2	365	c.172T>A	c.(172-174)Ttt>Att	p.F58I		NM_052966.2	NP_443198.1	Q9BZQ8	NIBAN_HUMAN	family with sequence similarity 129, member A	58					negative regulation of protein phosphorylation (GO:0001933)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(6)|liver(1)|lung(22)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	45						GTCTTCAAAAACTGTGACGTT	0.393																																																	0			1											183.0	165.0	171.0					1																	184868326		2203	4300	6503	183134949	SO:0001583	missense	116496			AF288391	CCDS1364.1	1q25	2008-10-08	2006-11-23	2006-11-23	ENSG00000135842	ENSG00000135842			16784	protein-coding gene	gene with protein product	"""cell growth inhibiting protein 39"""		"""chromosome 1 open reading frame 24"""	C1orf24		15085203, 16444351	Standard	NM_052966		Approved	NIBAN, GIG39	uc001gra.4	Q9BZQ8	OTTHUMG00000035388	ENST00000367511.3:c.172T>A	1.37:g.184868326A>T	ENSP00000356481:p.Phe58Ile	Somatic		Capture	Illumina HiSeq	Phase_I	183134949	Q2TTR2|Q5TEM8|Q8TEI5|Q9H593|Q9H9Y8|Q9HCB9	Missense_Mutation	SNP	ENST00000367511.3	37	CCDS1364.1	.	.	.	.	.	.	.	.	.	.	A	9.888	1.203482	0.22121	.	.	ENSG00000135842	ENST00000367511	T	0.13538	2.58	5.6	0.671	0.17929	.	0.296824	0.38605	N	0.001636	T	0.11281	0.0275	L	0.60455	1.87	0.22354	N	0.999176	B	0.10296	0.003	B	0.13407	0.009	T	0.23226	-1.0194	10	0.38643	T	0.18	-1.6788	3.5413	0.07812	0.5679:0.0:0.1534:0.2788	.	58	Q9BZQ8	NIBAN_HUMAN	I	58	ENSP00000356481:F58I	ENSP00000356481:F58I	F	-	1	0	FAM129A	183134949	0.048000	0.20356	0.028000	0.17463	0.368000	0.29767	0.265000	0.18515	-0.129000	0.11620	-0.309000	0.09137	TTT		FAM129A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085786.1		
OBSCN	84033	hgsc.bcm.edu	37	1	228399766	228399766	+	Silent	SNP	T	T	C	rs55971985	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr1:228399766T>C	ENST00000422127.1	+	2	326	c.282T>C	c.(280-282)gcT>gcC	p.A94A	C1orf145_ENST00000295012.5_Intron|OBSCN_ENST00000570156.2_Silent_p.A94A|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Silent_p.A94A|OBSCN_ENST00000366707.4_5'UTR	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	94	Ig-like 1.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CCTTCGCTGCTGTGGGCCTGC	0.711													C|||	3637	0.726238	0.7057	0.6441	5008	,	,		9624	0.8244		0.6372	False		,,,				2504	0.8027																0			1						C	,	2546,1150		933,680,235	6.0	7.0	7.0		282,282	-9.3	0.0	1	dbSNP_129	7	4756,2942		1563,1630,656	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	2496,2310,891	CC,CT,TT		38.2177,31.1147,35.9136	,	94/7969,94/6621	228399766	7302,4092	1848	3849	5697	226466389	SO:0001819	synonymous_variant	84033			AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.282T>C	1.37:g.228399766T>C		Somatic		Capture	Illumina HiSeq	Phase_I	226466389	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																				OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
OBSCN	84033	hgsc.bcm.edu	37	1	228479800	228479800	+	Missense_Mutation	SNP	A	A	G			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr1:228479800A>G	ENST00000422127.1	+	39	10585	c.10541A>G	c.(10540-10542)gAc>gGc	p.D3514G	OBSCN_ENST00000570156.2_Missense_Mutation_p.D3943G|OBSCN_ENST00000359599.6_Missense_Mutation_p.D2361G|OBSCN_ENST00000366709.4_Missense_Mutation_p.D633G|OBSCN_ENST00000366707.4_Missense_Mutation_p.D633G|OBSCN_ENST00000284548.11_Missense_Mutation_p.D3514G	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3514	Ig-like 35.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GCCATGGCGGACGCCGGGGAG	0.622																																																	0			1											106.0	115.0	112.0					1																	228479800		2119	4210	6329	226546423	SO:0001583	missense	84033			AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.10541A>G	1.37:g.228479800A>G	ENSP00000409493:p.Asp3514Gly	Somatic		Capture	Illumina HiSeq	Phase_I	226546423	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	A	19.14	3.769011	0.69992	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709;ENST00000359599	D;D;D;D;D	0.81739	-1.53;-1.53;-1.53;-1.53;-1.53	5.1	5.1	0.69264	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.94351	0.8184	H	0.99507	4.6	0.58432	D	0.999996	D;D	0.89917	0.997;1.0	D;D	0.97110	0.999;1.0	D	0.96665	0.9492	10	0.72032	D	0.01	.	15.0425	0.71803	1.0:0.0:0.0:0.0	.	3514;3514	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	G	3514;3514;633;633;2361	ENSP00000284548:D3514G;ENSP00000409493:D3514G;ENSP00000355668:D633G;ENSP00000355670:D633G;ENSP00000352613:D2361G	ENSP00000284548:D3514G	D	+	2	0	OBSCN	226546423	0.999000	0.42202	0.784000	0.31847	0.031000	0.12232	4.087000	0.57671	2.138000	0.66242	0.418000	0.28097	GAC		OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
ACTA1	58	hgsc.bcm.edu	37	1	229567840	229567840	+	Missense_Mutation	SNP	A	A	G			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr1:229567840A>G	ENST00000366684.3	-	5	811	c.709T>C	c.(709-711)Tcc>Ccc	p.S237P	ACTA1_ENST00000366683.2_Missense_Mutation_p.S149P	NM_001100.3	NP_001091.1	P68133	ACTS_HUMAN	actin, alpha 1, skeletal muscle	237					cell growth (GO:0016049)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to extracellular stimulus (GO:0009991)|response to lithium ion (GO:0010226)|response to mechanical stimulus (GO:0009612)|response to steroid hormone (GO:0048545)|skeletal muscle fiber adaptation (GO:0043503)|skeletal muscle fiber development (GO:0048741)|skeletal muscle thin filament assembly (GO:0030240)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|striated muscle thin filament (GO:0005865)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|myosin binding (GO:0017022)|structural constituent of cytoskeleton (GO:0005200)			endometrium(4)|large_intestine(4)|lung(18)|prostate(1)|urinary_tract(1)	28	Breast(184;0.0858)|Ovarian(103;0.103)	Prostate(94;0.167)				TTTTCCAGGGAGGAGGAGGAG	0.642																																																	0			1											37.0	32.0	34.0					1																	229567840		2203	4298	6501	227634463	SO:0001583	missense	58			J00068	CCDS1578.1	1q42.13	2014-09-17			ENSG00000143632	ENSG00000143632			129	protein-coding gene	gene with protein product	"""nemaline myopathy type 3"""	102610		ACTA		10072583, 6865942	Standard	NM_001100		Approved	NEM3	uc001htm.3	P68133	OTTHUMG00000038006	ENST00000366684.3:c.709T>C	1.37:g.229567840A>G	ENSP00000355645:p.Ser237Pro	Somatic		Capture	Illumina HiSeq	Phase_I	227634463	P02568|P99020|Q5T8M9	Missense_Mutation	SNP	ENST00000366684.3	37	CCDS1578.1	.	.	.	.	.	.	.	.	.	.	A	11.79	1.744528	0.30865	.	.	ENSG00000143632	ENST00000366684;ENST00000308794;ENST00000366683;ENST00000366682	D;D	0.94457	-3.43;-3.43	4.28	4.28	0.50868	.	0.150780	0.44902	D	0.000401	D	0.95059	0.8400	M	0.87827	2.91	0.58432	D	0.999997	B	0.21225	0.053	B	0.31191	0.125	D	0.94537	0.7741	10	0.87932	D	0	.	13.5673	0.61826	1.0:0.0:0.0:0.0	.	237	P68133	ACTS_HUMAN	P	237;147;149;202	ENSP00000355645:S237P;ENSP00000355644:S149P	ENSP00000312351:S147P	S	-	1	0	ACTA1	227634463	1.000000	0.71417	1.000000	0.80357	0.157000	0.22087	8.970000	0.93415	1.786000	0.52430	0.460000	0.39030	TCC		ACTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092781.1	NM_001100	
GALNT2	2590	hgsc.bcm.edu	37	1	230372463	230372463	+	Missense_Mutation	SNP	G	G	A	rs369808855		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr1:230372463G>A	ENST00000366672.4	+	6	671	c.599G>A	c.(598-600)cGa>cAa	p.R200Q	GALNT2_ENST00000543760.1_Missense_Mutation_p.R162Q|GALNT2_ENST00000541865.1_Missense_Mutation_p.R110Q	NM_004481.3	NP_004472.1	Q10471	GALT2_HUMAN	polypeptide N-acetylgalactosaminyltransferase 2	200	Catalytic subdomain A.				cellular protein metabolic process (GO:0044267)|immunoglobulin biosynthetic process (GO:0002378)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|protein O-linked glycosylation via serine (GO:0018242)|protein O-linked glycosylation via threonine (GO:0018243)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|manganese ion binding (GO:0030145)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(5)|skin(2)	32	Breast(184;0.193)|Ovarian(103;0.249)	all_cancers(173;0.156)|Prostate(94;0.179)				AGAAATGATCGACGAGAAGGT	0.398																																																	0			1											98.0	99.0	99.0					1																	230372463		2203	4300	6503	228439086	SO:0001583	missense	2590			BC041120	CCDS1582.1	1q41-q42	2014-03-13	2014-03-13		ENSG00000143641	ENSG00000143641	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4124	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 2"""	602274	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 (GalNAc-T2)"""			9592121, 7592619	Standard	NM_004481		Approved	GalNAc-T2	uc010pwa.1	Q10471	OTTHUMG00000037771	ENST00000366672.4:c.599G>A	1.37:g.230372463G>A	ENSP00000355632:p.Arg200Gln	Somatic		Capture	Illumina HiSeq	Phase_I	228439086	A8K1Y3|B7Z8V8|C5HU00|Q9NPY4	Missense_Mutation	SNP	ENST00000366672.4	37	CCDS1582.1	.	.	.	.	.	.	.	.	.	.	G	13.60	2.286606	0.40494	.	.	ENSG00000143641	ENST00000543760;ENST00000366672;ENST00000543291;ENST00000541865	T;T;T	0.61158	0.13;0.13;0.13	5.3	5.3	0.74995	Glycosyl transferase, family 2 (1);	0.000000	0.85682	D	0.000000	T	0.39009	0.1062	N	0.11698	0.16	0.80722	D	1	B;B	0.31274	0.317;0.11	B;B	0.16722	0.016;0.006	T	0.28427	-1.0044	10	0.34782	T	0.22	.	17.7155	0.88335	0.0:0.0:1.0:0.0	.	200;162	Q10471;G3V1S6	GALT2_HUMAN;.	Q	162;200;81;110	ENSP00000445017:R162Q;ENSP00000355632:R200Q;ENSP00000444346:R110Q	ENSP00000355632:R200Q	R	+	2	0	GALNT2	228439086	1.000000	0.71417	0.998000	0.56505	0.971000	0.66376	8.280000	0.89903	2.466000	0.83321	0.561000	0.74099	CGA		GALNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092158.1	NM_004481	
B4GALNT4	338707	hgsc.bcm.edu	37	11	372700	372700	+	Silent	SNP	G	G	C	rs35475866	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr11:372700G>C	ENST00000329962.6	+	3	294	c.294G>C	c.(292-294)ggG>ggC	p.G98G		NM_178537.4	NP_848632.2	Q76KP1	B4GN4_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 4	98					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			endometrium(2)|kidney(4)|large_intestine(1)|liver(2)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	24		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TTCCTGGGGGGGCTGGGAGGC	0.647													.|||	1656	0.330671	0.3253	0.2997	5008	,	,		10061	0.3839		0.2952	False		,,,				2504	0.3415																0			11						G		1430,2946		245,940,1003	18.0	21.0	20.0		294	-1.3	0.0	11	dbSNP_126	20	2375,6187		331,1713,2237	no	coding-synonymous	B4GALNT4	NM_178537.4		576,2653,3240	CC,CG,GG		27.7388,32.6782,29.4095		98/1040	372700	3805,9133	2188	4281	6469	362700	SO:0001819	synonymous_variant	338707			AB089939	CCDS7694.1	11p15.5	2013-02-19			ENSG00000182272	ENSG00000182272	2.4.1.-	"""Beta 4-glycosyltransferases"""	26315	protein-coding gene	gene with protein product						15044014	Standard	NM_178537		Approved	FLJ25045, NGalNAc-T1	uc001lpb.3	Q76KP1	OTTHUMG00000119075	ENST00000329962.6:c.294G>C	11.37:g.372700G>C		Somatic		Capture	Illumina HiSeq	Phase_I	362700	Q96LV2	Silent	SNP	ENST00000329962.6	37	CCDS7694.1																																																																																				B4GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239289.2	NM_178537	
MUC2	4583	hgsc.bcm.edu	37	11	1092954	1092954	+	Splice_Site	SNP	G	G	A	rs56352686		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr11:1092954G>A	ENST00000359061.5	+	30	4776	c.4776G>A	c.(4774-4776)acG>acA	p.T1592T	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000441003.2_Silent_p.T1591T|MUC2_ENST00000333592.6_5'Flank			Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ccaccactacggtgaccccaa	0.627																																																	0			11											52.0	85.0	74.0					11																	1092954		1812	3296	5108	1082954	SO:0001630	splice_region_variant	4583			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	ENST00000359061.5:c.4776+1G>A	11.37:g.1092954G>A		Somatic		Capture	Illumina HiSeq	Phase_I	1082954	Q14878	Silent	SNP	ENST00000359061.5	37																																																																																					MUC2-202	KNOWN	basic	protein_coding	protein_coding		NM_002457	Silent
LSP1	4046	hgsc.bcm.edu	37	11	1874404	1874404	+	Silent	SNP	C	C	T	rs2089910	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr11:1874404C>T	ENST00000311604.3	+	1	205	c.30C>T	c.(28-30)gcC>gcT	p.A10A		NM_002339.2	NP_002330.1	P33241	LSP1_HUMAN	lymphocyte-specific protein 1	10					cellular component movement (GO:0006928)|cellular defense response (GO:0006968)|chemotaxis (GO:0006935)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|signal transducer activity (GO:0004871)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	16		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|Lung(200;0.0729)|LUSC - Lung squamous cell carcinoma(625;0.0856)		ACCCGGGTGCCGAGGAGCGGG	0.657													C|||	1462	0.291933	0.2799	0.2795	5008	,	,		13920	0.4623		0.2654	False		,,,				2504	0.1687																0			11						C		1155,3241	375.1+/-321.5	150,855,1193	65.0	65.0	65.0		30	-5.1	0.0	11	dbSNP_96	65	1971,6619	325.8+/-317.1	236,1499,2560	no	coding-synonymous	LSP1	NM_002339.2		386,2354,3753	TT,TC,CC		22.9453,26.2739,24.0721		10/340	1874404	3126,9860	2198	4295	6493	1830980	SO:0001819	synonymous_variant	390387			M33552	CCDS31334.1, CCDS31335.1, CCDS58110.1	11p15.5	2008-02-05			ENSG00000130592	ENSG00000130592			6707	protein-coding gene	gene with protein product		153432				2174784	Standard	NM_001242932		Approved	WP34	uc001luj.3	P33241	OTTHUMG00000012252	ENST00000311604.3:c.30C>T	11.37:g.1874404C>T		Somatic		Capture	Illumina HiSeq	Phase_I	1830980	B3KPP1|B3KRR6|E9PBV6|E9PFP3|Q16096|Q53H48|Q6FHM3|Q9BUY8	Silent	SNP	ENST00000311604.3	37	CCDS31334.1																																																																																				LSP1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000034045.3	NM_002339	
TCIRG1	10312	hgsc.bcm.edu	37	11	67816592	67816592	+	Missense_Mutation	SNP	A	A	G	rs576389893	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr11:67816592A>G	ENST00000265686.3	+	15	1826	c.1718A>G	c.(1717-1719)gAg>gGg	p.E573G	RP11-802E16.3_ENST00000526897.1_RNA|RP11-802E16.3_ENST00000529934.1_RNA|TCIRG1_ENST00000532635.1_Missense_Mutation_p.E357G	NM_006019.3	NP_006010.2	Q13488	VPP3_HUMAN	T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 subunit A3	573					ATP hydrolysis coupled proton transport (GO:0015991)|cellular defense response (GO:0006968)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|positive regulation of cell proliferation (GO:0008284)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	hydrogen ion transmembrane transporter activity (GO:0015078)|transporter activity (GO:0005215)			breast(1)|endometrium(4)|large_intestine(3)|lung(4)|ovary(3)|prostate(1)	16						ACGCTGCCGGAGCTCACCTTC	0.662													A|||	5	0.000998403	0.0	0.0	5008	,	,		15878	0.0		0.001	False		,,,				2504	0.0041																0			11											103.0	94.0	97.0					11																	67816592		2200	4294	6494	67573168	SO:0001583	missense	10312			AF025374	CCDS8177.1, CCDS53670.1	11q13.2	2014-09-17	2006-01-20		ENSG00000110719	ENSG00000110719		"""ATPases / V-type"""	11647	protein-coding gene	gene with protein product	"""T-cell immune response cDNA 7"""	604592	"""T-cell, immune regulator 1"", ""T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein a isoform 3"", ""T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein A3"""			8579597, 9806637	Standard	NM_006019		Approved	TIRC7, OC-116, OC116, ATP6N1C, Atp6i, a3, ATP6V0A3	uc001one.3	Q13488	OTTHUMG00000167358	ENST00000265686.3:c.1718A>G	11.37:g.67816592A>G	ENSP00000265686:p.Glu573Gly	Somatic		Capture	Illumina HiSeq	Phase_I	67573168	O75877|Q8WVC5	Missense_Mutation	SNP	ENST00000265686.3	37	CCDS8177.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.693773	0.88735	.	.	ENSG00000110719	ENST00000265686;ENST00000532635	D;D	0.85773	-2.03;-2.03	4.53	4.53	0.55603	.	0.054616	0.64402	D	0.000001	D	0.87261	0.6133	L	0.37850	1.14	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.85299	0.1072	10	0.29301	T	0.29	-23.7346	12.8543	0.57876	1.0:0.0:0.0:0.0	.	573	Q13488	VPP3_HUMAN	G	573;357	ENSP00000265686:E573G;ENSP00000434407:E357G	ENSP00000265686:E573G	E	+	2	0	TCIRG1	67573168	1.000000	0.71417	0.999000	0.59377	0.958000	0.62258	9.041000	0.93788	1.904000	0.55121	0.454000	0.30748	GAG		TCIRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394305.1	NM_006019	
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249452	71249452	+	Silent	SNP	C	C	G			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr11:71249452C>G	ENST00000398534.3	+	1	382	c.351C>G	c.(349-351)tcC>tcG	p.S117S		NM_021046.2	NP_066384.2	O75690	KRA58_HUMAN	keratin associated protein 5-8	117	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|lung(2)|skin(1)|stomach(1)	6						GTTCCCAGTCCAGCTGTTGTA	0.607																																																	0			11											166.0	178.0	174.0					11																	71249452		2200	4294	6494	70927100	SO:0001819	synonymous_variant	440021			AB126077	CCDS41683.1	11q13.4	2008-02-05			ENSG00000241233	ENSG00000241233		"""Keratin associated proteins"""	23603	protein-coding gene	gene with protein product						15144888	Standard	NM_021046		Approved	KRTAP5.8, UHSKerB, KRTAP5-2	uc001oqr.1	O75690	OTTHUMG00000057571	ENST00000398534.3:c.351C>G	11.37:g.71249452C>G		Somatic		Capture	Illumina HiSeq	Phase_I	70927100	Q6L8G7|Q6UTX6	Silent	SNP	ENST00000398534.3	37	CCDS41683.1																																																																																				KRTAP5-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127954.1	NM_021046	
ATM	472	hgsc.bcm.edu	37	11	108199938	108199938	+	Missense_Mutation	SNP	T	T	C			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr11:108199938T>C	ENST00000452508.2	+	50	7469	c.7280T>C	c.(7279-7281)cTt>cCt	p.L2427P	ATM_ENST00000278616.4_Missense_Mutation_p.L2427P|C11orf65_ENST00000525729.1_Intron			Q13315	ATM_HUMAN	ATM serine/threonine kinase	2427	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.		Missing (in AT; associated with T- prolymphocytic leukemia). {ECO:0000269|PubMed:7792600, ECO:0000269|PubMed:8845835, ECO:0000269|PubMed:9463314}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.L2427R(1)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	GTAGGTCTCCTTAGGGAACAT	0.358			"""D, Mis, N, F, S"""		T-PLL	"""leukemia, lymphoma, medulloblastoma, glioma"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																													yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"""L, O"""	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	11											61.0	61.0	61.0					11																	108199938		2201	4298	6499	107705148	SO:0001583	missense	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"""TEL1, telomere maintenance 1, homolog (S. cerevisiae)"""	607585	"""ataxia telangiectasia mutated (includes complementation groups A, C and D)"", ""ataxia telangiectasia mutated"""	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.7280T>C	11.37:g.108199938T>C	ENSP00000388058:p.Leu2427Pro	Somatic		Capture	Illumina HiSeq	Phase_I	107705148	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.314935	0.81358	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	T;T	0.74209	-0.82;-0.82	5.54	5.54	0.83059	PIK-related kinase (1);PIK-related kinase, FAT (1);Armadillo-type fold (1);	0.266767	0.40302	N	0.001125	D	0.83936	0.5362	M	0.61703	1.905	0.80722	D	1	D	0.67145	0.996	D	0.71870	0.975	D	0.85217	0.1024	10	0.59425	D	0.04	.	15.6843	0.77396	0.0:0.0:0.0:1.0	.	2427	Q13315	ATM_HUMAN	P	2427	ENSP00000278616:L2427P;ENSP00000388058:L2427P	ENSP00000278616:L2427P	L	+	2	0	ATM	107705148	1.000000	0.71417	0.954000	0.39281	0.975000	0.68041	8.033000	0.88852	2.107000	0.64212	0.528000	0.53228	CTT		ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	
PHIP	55023	hgsc.bcm.edu	37	6	79650577	79650577	+	Missense_Mutation	SNP	T	T	C			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr6:79650577T>C	ENST00000275034.4	-	40	5466	c.5299A>G	c.(5299-5301)Aga>Gga	p.R1767G	PHIP_ENST00000479165.1_5'UTR	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	1767			R -> I (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		TTTCTAGTTCTCATGTGGGGT	0.408																																																	0			6											554.0	545.0	548.0					6																	79650577		2203	4300	6503	79707296	SO:0001583	missense	55023			AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	15673	protein-coding gene	gene with protein product	"""DDB1 and CUL4 associated factor 14"""	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.5299A>G	6.37:g.79650577T>C	ENSP00000275034:p.Arg1767Gly	Somatic		Capture	Illumina HiSeq	Phase_I	79707296	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000275034.4	37	CCDS4987.1	.	.	.	.	.	.	.	.	.	.	T	15.65	2.896101	0.52121	.	.	ENSG00000146247	ENST00000275034	T	0.47177	0.85	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.20170	0.0485	L	0.29908	0.895	0.58432	D	0.999993	P;P	0.44734	0.842;0.842	B;B	0.34536	0.185;0.185	T	0.03945	-1.0990	9	.	.	.	-19.0401	15.5447	0.76090	0.0:0.0:0.0:1.0	.	1767;1767	A7J992;Q8WWQ0	.;PHIP_HUMAN	G	1767	ENSP00000275034:R1767G	.	R	-	1	2	PHIP	79707296	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.084000	0.71335	2.267000	0.75376	0.528000	0.53228	AGA		PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2		
SYNE1	23345	hgsc.bcm.edu	37	6	152477212	152477212	+	Silent	SNP	C	C	T			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr6:152477212C>T	ENST00000367255.5	-	132	24412	c.23811G>A	c.(23809-23811)gaG>gaA	p.E7937E	SYNE1_ENST00000423061.1_Silent_p.E7866E|SYNE1_ENST00000265368.4_Silent_p.E7937E|SYNE1_ENST00000356820.4_Silent_p.E2461E|SYNE1_ENST00000354674.4_Silent_p.E92E|SYNE1_ENST00000341594.5_Silent_p.E7549E|SYNE1_ENST00000448038.1_Silent_p.E7866E|SYNE1_ENST00000347037.5_5'UTR|SYNE1_ENST00000539504.1_Silent_p.E92E	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	7937					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)		TACTGTGCTTCTCTATGTCTC	0.473										HNSCC(10;0.0054)																																							0			6											122.0	111.0	115.0					6																	152477212		2203	4300	6503	152518905	SO:0001819	synonymous_variant	23345			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.23811G>A	6.37:g.152477212C>T		Somatic		Capture	Illumina HiSeq	Phase_I	152518905	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	37	CCDS5236.2																																																																																				SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
THBS2	7058	hgsc.bcm.edu	37	6	169620355	169620355	+	Missense_Mutation	SNP	A	A	G			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr6:169620355A>G	ENST00000366787.3	-	22	3698	c.3449T>C	c.(3448-3450)cTg>cCg	p.L1150P	XXyac-YX65C7_A.2_ENST00000444188.1_RNA|THBS2_ENST00000488355.1_5'UTR	NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	1150	TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		AAATAGACCCAGCCGCCCGCC	0.458																																					Esophageal Squamous(91;219 1934 18562 44706)												0			6											131.0	136.0	134.0					6																	169620355		2203	4300	6503	169362280	SO:0001583	missense	7058				CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.3449T>C	6.37:g.169620355A>G	ENSP00000355751:p.Leu1150Pro	Somatic		Capture	Illumina HiSeq	Phase_I	169362280	A6H8N1|A7E232|Q5RI52	Missense_Mutation	SNP	ENST00000366787.3	37	CCDS34574.1	.	.	.	.	.	.	.	.	.	.	A	19.94	3.920319	0.73098	.	.	ENSG00000186340	ENST00000366787;ENST00000392099	D	0.97279	-4.32	4.64	4.64	0.57946	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Thrombospondin, C-terminal (2);	0.000000	0.32161	U	0.006491	D	0.98210	0.9408	M	0.86178	2.8	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99513	1.0956	10	0.87932	D	0	-24.657	14.078	0.64903	1.0:0.0:0.0:0.0	.	1150	P35442	TSP2_HUMAN	P	1150;408	ENSP00000355751:L1150P	ENSP00000355751:L1150P	L	-	2	0	THBS2	169362280	1.000000	0.71417	0.622000	0.29159	0.822000	0.46500	8.668000	0.91158	1.719000	0.51432	0.391000	0.25812	CTG		THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247	
SGSM2	9905	hgsc.bcm.edu	37	17	2266812	2266812	+	Silent	SNP	T	T	C	rs2003968	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr17:2266812T>C	ENST00000426855.2	+	7	901	c.726T>C	c.(724-726)tgT>tgC	p.C242C	SGSM2_ENST00000574563.1_Silent_p.C242C|SGSM2_ENST00000268989.3_Silent_p.C242C	NM_001098509.1	NP_001091979.1	O43147	SGSM2_HUMAN	small G protein signaling modulator 2	242					late endosome to Golgi transport (GO:0034499)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)		Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(2;5.15e-05)|READ - Rectum adenocarcinoma(2;0.000115)		TGGCTGCCTGTGCCCGCGAGT	0.642													C|||	2836	0.566294	0.5431	0.3444	5008	,	,		16364	0.7639		0.4314	False		,,,				2504	0.6902																0			17						C	,	2372,2034		640,1092,471	25.0	28.0	27.0		726,726	-11.5	0.1	17	dbSNP_92	27	3921,4677		893,2135,1271	yes	coding-synonymous,coding-synonymous	SGSM2	NM_001098509.1,NM_014853.2	,	1533,3227,1742	CC,CT,TT		45.6036,46.1643,48.3928	,	242/1007,242/1052	2266812	6293,6711	2203	4299	6502	2213562	SO:0001819	synonymous_variant	9905			BC039204	CCDS32526.1, CCDS45570.1	17p13.3	2013-07-10	2007-08-14	2007-08-14		ENSG00000141258		"""Small G protein signaling modulators"""	29026	protein-coding gene	gene with protein product		611418	"""RUN and TBC1 domain containing 1"""	RUTBC1		9455477, 17509819, 21808068	Standard	NM_014853		Approved	KIAA0397	uc002fum.4	O43147		ENST00000426855.2:c.726T>C	17.37:g.2266812T>C		Somatic		Capture	Illumina HiSeq	Phase_I	2213562	A5LGW2|B4DH69|Q49AC2|Q6ZUY2|Q8IXU4	Silent	SNP	ENST00000426855.2	37	CCDS45570.1																																																																																				SGSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438186.1	NM_014853	
KCNJ12	3768	hgsc.bcm.edu	37	17	21319868	21319868	+	Missense_Mutation	SNP	G	G	T	rs73979902	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr17:21319868G>T	ENST00000583088.1	+	3	2109	c.1214G>T	c.(1213-1215)aGc>aTc	p.S405I	KCNJ12_ENST00000331718.5_Missense_Mutation_p.S405I	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	405				S -> I (in Ref. 2; AAC50615). {ECO:0000305}.	muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	GACGGCCTCAGCCCCCAGGCC	0.662										Prostate(3;0.18)																																							0			17																																								21260461	SO:0001583	missense	3768			L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6258	protein-coding gene	gene with protein product		602323	"""potassium inwardly-rectifying channel, subfamily J, inhibitor 1"""	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.1214G>T	17.37:g.21319868G>T	ENSP00000463778:p.Ser405Ile	Somatic		Capture	Illumina HiSeq	Phase_I	21260461	O43401|Q15756|Q8NG63	Missense_Mutation	SNP	ENST00000583088.1	37	CCDS11219.1	.	.	.	.	.	.	.	.	.	.	G	16.91	3.252898	0.59212	.	.	ENSG00000184185	ENST00000331718	D	0.88354	-2.37	5.83	5.83	0.93111	.	1.356490	0.04362	N	0.357607	D	0.89410	0.6707	L	0.51422	1.61	0.09310	P	0.99999754014	B	0.23442	0.085	B	0.19946	0.027	T	0.74352	-0.3693	9	0.51188	T	0.08	.	18.3013	0.90164	0.0:0.0:1.0:0.0	.	405	Q14500	IRK12_HUMAN	I	405	ENSP00000328150:S405I	ENSP00000328150:S405I	S	+	2	0	KCNJ12	21260461	1.000000	0.71417	0.718000	0.30602	0.849000	0.48306	5.226000	0.65299	2.758000	0.94735	0.655000	0.94253	AGC		KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012	
NF1	4763	hgsc.bcm.edu	37	17	29546136	29546136	+	Splice_Site	SNP	G	G	A			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr17:29546136G>A	ENST00000358273.4	+	14	2024	c.1641G>A	c.(1639-1641)gaG>gaA	p.E547E	NF1_ENST00000431387.4_Splice_Site_p.E547E|NF1_ENST00000356175.3_Splice_Site_p.E547E	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	547					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(6)|p.N510_E547del(1)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		AAGCAATGGAGGTAAGGGGAA	0.453			"""D, Mis, N, F, S, O"""		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																													yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	15	Whole gene deletion(8)|Unknown(6)|Deletion - In frame(1)	soft_tissue(8)|autonomic_ganglia(3)|central_nervous_system(2)|stomach(1)|lung(1)	17											63.0	57.0	59.0					17																	29546136		2203	4300	6503	26570262	SO:0001630	splice_region_variant	4763	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"""neurofibromatosis"", ""von Recklinghausen disease"", ""Watson disease"""	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.1641+1G>A	17.37:g.29546136G>A		Somatic		Capture	Illumina HiSeq	Phase_I	26570262	O00662|Q14284|Q14930|Q14931|Q9UMK3	Silent	SNP	ENST00000358273.4	37	CCDS42292.1																																																																																				NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267	Silent
NF1	4763	hgsc.bcm.edu	37	17	29684030	29684030	+	Silent	SNP	A	A	G			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr17:29684030A>G	ENST00000358273.4	+	53	8174	c.7791A>G	c.(7789-7791)tcA>tcG	p.S2597S	NF1_ENST00000417592.2_3'UTR|NF1_ENST00000444181.2_Silent_p.S390S|NF1_ENST00000356175.3_Silent_p.S2576S	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	2597					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(3)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		GTAAAGTTTCAGTGTCTGAAT	0.413			"""D, Mis, N, F, S, O"""		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																													yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	11	Whole gene deletion(8)|Unknown(3)	soft_tissue(7)|autonomic_ganglia(2)|lung(1)|central_nervous_system(1)	17											201.0	189.0	193.0					17																	29684030		2203	4300	6503	26708156	SO:0001819	synonymous_variant	4763	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"""neurofibromatosis"", ""von Recklinghausen disease"", ""Watson disease"""	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.7791A>G	17.37:g.29684030A>G		Somatic		Capture	Illumina HiSeq	Phase_I	26708156	O00662|Q14284|Q14930|Q14931|Q9UMK3	Silent	SNP	ENST00000358273.4	37	CCDS42292.1																																																																																				NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267	
PPM1E	22843	hgsc.bcm.edu	37	17	56833491	56833491	+	Missense_Mutation	SNP	T	T	C	rs58091258	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr17:56833491T>C	ENST00000308249.2	+	1	262	c.133T>C	c.(133-135)Tcc>Ccc	p.S45P		NM_014906.4	NP_055721.3	Q96MI6	PPM1M_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1E	0	PP2C-like.				protein dephosphorylation (GO:0006470)	nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)|manganese ion binding (GO:0030145)			biliary_tract(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)	33	Medulloblastoma(34;0.127)|all_neural(34;0.237)		BRCA - Breast invasive adenocarcinoma(1;5.76e-11)			cgaacccgagtccgagcccga	0.706													T|||	35	0.00698882	0.0129	0.0029	5008	,	,		8544	0.0069		0.001	False		,,,				2504	0.0082																0			17																																								54188490	SO:0001583	missense	22843			AB028995	CCDS11613.1	17q24.2	2012-04-17	2010-03-05		ENSG00000175175	ENSG00000175175		"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	19322	protein-coding gene	gene with protein product	"""partner of PIX 1"", ""nuclear calmodulin-dependent protein kinase phosphatase"""		"""protein phosphatase 1E (PP2C domain containing)"""			11864573, 10470851	Standard	NR_048561		Approved	POPX1, KIAA1072, PP2CH, CaMKP-N	uc002iwx.4	Q8WY54		ENST00000308249.2:c.133T>C	17.37:g.56833491T>C	ENSP00000312411:p.Ser45Pro	Somatic		Capture	Illumina HiSeq	Phase_I	54188490	Q8N8J9|Q96DB8	Missense_Mutation	SNP	ENST00000308249.2	37	CCDS11613.1	.	.	.	.	.	.	.	.	.	.	T	0.181	-1.062190	0.01950	.	.	ENSG00000175175	ENST00000308249	T	0.22945	1.93	4.15	-1.34	0.09143	.	.	.	.	.	T	0.10551	0.0258	N	0.14661	0.345	0.52099	P	5.100000000002325E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.45920	-0.9228	8	0.02654	T	1	1.5526	8.0241	0.30427	0.0:0.5961:0.0:0.4039	rs58091258;rs62648074	45	Q8WY54-2	.	P	45	ENSP00000312411:S45P	ENSP00000312411:S45P	S	+	1	0	PPM1E	54188490	0.903000	0.30736	0.954000	0.39281	0.160000	0.22226	0.122000	0.15687	-0.124000	0.11724	-1.425000	0.01104	TCC		PPM1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445458.1	NM_014906	
DNAI2	64446	hgsc.bcm.edu	37	17	72295954	72295954	+	Silent	SNP	G	G	A	rs140295057		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr17:72295954G>A	ENST00000311014.6	+	7	889	c.822G>A	c.(820-822)tcG>tcA	p.S274S	DNAI2_ENST00000446837.2_Silent_p.S274S|DNAI2_ENST00000579490.1_Silent_p.S331S|DNAI2_ENST00000307504.5_Silent_p.S131S|DNAI2_ENST00000582036.1_Silent_p.S274S			Q9GZS0	DNAI2_HUMAN	dynein, axonemal, intermediate chain 2	274					cilium assembly (GO:0042384)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|liver(2)|lung(19)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						GGCTGCAGTCGAAGACGGGCA	0.622									Kartagener syndrome				G|||	1	0.000199681	0.0	0.0014	5008	,	,		16985	0.0		0.0	False		,,,				2504	0.0																0			17						G	,	1,4405		0,1,2202	68.0	50.0	56.0		822,822	-10.3	0.2	17	dbSNP_134	56	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	DNAI2	NM_001172810.1,NM_023036.4	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	274/594,274/606	72295954	1,13005	2203	4300	6503	69807549	SO:0001819	synonymous_variant	64446	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AF250288	CCDS11697.1, CCDS58589.1	17q25	2013-02-19	2006-09-04			ENSG00000171595		"""Axonemal dyneins"", ""WD repeat domain containing"""	18744	protein-coding gene	gene with protein product	"""dynein intermediate chain 2"""	605483	"""dynein, axonemal, intermediate polypeptide 2"""			11153919, 21953912	Standard	NM_023036		Approved	CILD9, DIC2	uc002jkf.3	Q9GZS0		ENST00000311014.6:c.822G>A	17.37:g.72295954G>A		Somatic		Capture	Illumina HiSeq	Phase_I	69807549	C9J0S6|Q8IUW4|Q9H179|Q9NT53	Silent	SNP	ENST00000311014.6	37	CCDS11697.1																																																																																				DNAI2-001	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442537.1	NM_023036	
CASKIN2	57513	hgsc.bcm.edu	37	17	73498463	73498463	+	Missense_Mutation	SNP	C	C	T			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr17:73498463C>T	ENST00000321617.3	-	18	3278	c.2692G>A	c.(2692-2694)Ggg>Agg	p.G898R	CASKIN2_ENST00000433559.2_Missense_Mutation_p.G816R	NM_020753.3	NP_065804.2	Q8WXE0	CSKI2_HUMAN	CASK interacting protein 2	898	Pro-rich.					cytoplasm (GO:0005737)				endometrium(1)|kidney(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	18	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;4.57e-07)|Epithelial(20;2.92e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			CCTGTGGCCCCTTCCTTGGGC	0.731																																																	0			17											4.0	5.0	4.0					17																	73498463		1921	3842	5763	71010058	SO:0001583	missense	57513			AB032965	CCDS11723.1, CCDS45775.1	17q25.1	2014-09-04			ENSG00000177303	ENSG00000177303		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	18200	protein-coding gene	gene with protein product		612185				12040031	Standard	NM_020753		Approved	KIAA1139, FLJ21609, ANKS5B	uc002joc.4	Q8WXE0	OTTHUMG00000179683	ENST00000321617.3:c.2692G>A	17.37:g.73498463C>T	ENSP00000325355:p.Gly898Arg	Somatic		Capture	Illumina HiSeq	Phase_I	71010058	B4DTT3|B7Z9H1|Q7LG69|Q9ULT1	Missense_Mutation	SNP	ENST00000321617.3	37	CCDS11723.1	.	.	.	.	.	.	.	.	.	.	C	14.48	2.548804	0.45383	.	.	ENSG00000177303	ENST00000321617;ENST00000433559	T;T	0.72942	-0.7;-0.49	4.87	3.9	0.45041	.	0.000000	0.38897	N	0.001540	T	0.49389	0.1554	N	0.14661	0.345	0.22412	N	0.99912	B	0.14805	0.011	B	0.08055	0.003	T	0.44221	-0.9342	10	0.87932	D	0	.	5.5231	0.16943	0.0:0.6636:0.0:0.3364	.	898	Q8WXE0	CSKI2_HUMAN	R	898;816	ENSP00000325355:G898R;ENSP00000406963:G816R	ENSP00000325355:G898R	G	-	1	0	CASKIN2	71010058	.	.	0.936000	0.37596	0.810000	0.45777	.	.	1.290000	0.44636	0.491000	0.48974	GGG		CASKIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447609.1	NM_020753	
PRCD	768206	hgsc.bcm.edu	37	17	74536240	74536240	+	Missense_Mutation	SNP	T	T	C			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr17:74536240T>C	ENST00000586148.1	+	1	69	c.17T>C	c.(16-18)tTc>tCc	p.F6S	CYGB_ENST00000293230.5_5'Flank|CYGB_ENST00000589342.1_5'Flank|CYGB_ENST00000589145.1_Intron|PRCD_ENST00000592014.1_Missense_Mutation_p.F6S|PRCD_ENST00000592432.1_Intron			Q00LT1	PRCD_HUMAN	progressive rod-cone degeneration	6					response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)											ACCACCCTTTTCCTGCTCAGC	0.662																																																	0			17											18.0	21.0	20.0					17																	74536240		2022	4173	6195	72047835	SO:0001583	missense	768206			DQ390338	CCDS42382.1	17q25.1	2008-10-24			ENSG00000214140	ENSG00000214140			32528	protein-coding gene	gene with protein product		610598				16938425	Standard	NM_001077620		Approved	RP36	uc002jrw.1	Q00LT1	OTTHUMG00000132200	ENST00000586148.1:c.17T>C	17.37:g.74536240T>C	ENSP00000465932:p.Phe6Ser	Somatic		Capture	Illumina HiSeq	Phase_I	72047835	B9EJD4	Missense_Mutation	SNP	ENST00000586148.1	37	CCDS42382.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.686217	0.88639	.	.	ENSG00000214140	ENST00000397630	.	.	.	4.85	4.85	0.62838	.	.	.	.	.	T	0.47911	0.1471	.	.	.	0.25118	N	0.990664	B	0.34015	0.435	B	0.41332	0.354	T	0.49753	-0.8906	7	0.87932	D	0	.	10.7494	0.46200	0.0:0.0:0.0:1.0	.	6	Q00LT1	PRCD_HUMAN	S	6	.	ENSP00000380754:F6S	F	+	2	0	PRCD	72047835	0.993000	0.37304	1.000000	0.80357	0.983000	0.72400	4.228000	0.58619	2.042000	0.60477	0.528000	0.53228	TTC		PRCD-008	KNOWN	alternative_3_UTR|NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450598.1		
CEP131	22994	hgsc.bcm.edu	37	17	79176093	79176093	+	Silent	SNP	C	C	T			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr17:79176093C>T	ENST00000269392.4	-	7	982	c.735G>A	c.(733-735)ggG>ggA	p.G245G	AZI1_ENST00000570482.2_5'UTR|AZI1_ENST00000374782.3_Silent_p.G245G|AZI1_ENST00000450824.2_Silent_p.G245G|RP11-455O6.2_ENST00000571085.1_RNA|AZI1_ENST00000575907.1_Silent_p.G245G	NM_014984.2	NP_055799.2	Q9UPN4	CP131_HUMAN		245					cell differentiation (GO:0030154)|G2/M transition of mitotic cell cycle (GO:0000086)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular protein transport (GO:0090316)|regulation of centrosome duplication (GO:0010824)|spermatogenesis (GO:0007283)	BBSome (GO:0034464)|cell projection (GO:0042995)|centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(1)|lung(12)|ovary(2)|prostate(3)|urinary_tract(5)	36	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			CCGTGCTGCCCCCAGTATTGT	0.642																																																	0			17											85.0	72.0	77.0					17																	79176093		2203	4300	6503	76790688	SO:0001819	synonymous_variant	22994																														ENST00000269392.4:c.735G>A	17.37:g.79176093C>T		Somatic		Capture	Illumina HiSeq	Phase_I	76790688	A6NHI8|B2RN11|Q96F50	Silent	SNP	ENST00000269392.4	37																																																																																					AZI1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000256070.1		
TIAM1	7074	hgsc.bcm.edu	37	21	32624330	32624330	+	Missense_Mutation	SNP	C	C	T			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr21:32624330C>T	ENST00000286827.3	-	6	1610	c.1139G>A	c.(1138-1140)cGt>cAt	p.R380H	TIAM1_ENST00000541036.1_Missense_Mutation_p.R380H|TIAM1_ENST00000469412.1_5'UTR	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	380					apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						CACCCCCTGACGAGCCGCATC	0.662																																																	0			21											55.0	62.0	60.0					21																	32624330		2203	4299	6502	31546201	SO:0001583	missense	7074				CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.1139G>A	21.37:g.32624330C>T	ENSP00000286827:p.Arg380His	Somatic		Capture	Illumina HiSeq	Phase_I	31546201	B7ZLR6|F5GZ53|Q17RT7	Missense_Mutation	SNP	ENST00000286827.3	37	CCDS13609.1	.	.	.	.	.	.	.	.	.	.	C	33	5.222847	0.95139	.	.	ENSG00000156299	ENST00000286827;ENST00000399841;ENST00000541036	T;T	0.50277	0.75;0.78	4.86	4.86	0.63082	.	0.304511	0.34879	N	0.003609	T	0.59500	0.2198	L	0.55481	1.735	0.58432	D	0.999991	D;D;D	0.71674	0.998;0.997;0.997	P;P;P	0.55615	0.78;0.607;0.607	T	0.63915	-0.6529	10	0.72032	D	0.01	.	18.1782	0.89768	0.0:1.0:0.0:0.0	.	380;380;380	F5GZ53;B7ZLR6;Q13009	.;.;TIAM1_HUMAN	H	380;221;380	ENSP00000286827:R380H;ENSP00000441570:R380H	ENSP00000286827:R380H	R	-	2	0	TIAM1	31546201	0.998000	0.40836	0.981000	0.43875	0.990000	0.78478	4.187000	0.58344	2.497000	0.84241	0.655000	0.94253	CGT		TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253	
PRR35	146325	hgsc.bcm.edu	37	16	615048	615048	+	Missense_Mutation	SNP	G	G	A	rs113068385	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr16:615048G>A	ENST00000409413.3	+	3	1736	c.1457G>A	c.(1456-1458)cGg>cAg	p.R486Q	NHLRC4_ENST00000424439.2_5'Flank|PIGQ_ENST00000409527.2_5'Flank|NHLRC4_ENST00000540585.1_5'Flank	NM_145270.2	NP_660313.1	P0CG20	PRR35_HUMAN		486										central_nervous_system(1)|endometrium(1)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	10						GCGTGGGGGCGGCCCGAGCTG	0.726													G|||	51	0.0101837	0.0008	0.0029	5008	,	,		11854	0.0		0.0447	False		,,,				2504	0.0031																0			16						G	GLN/ARG	21,3429		0,21,1704	5.0	7.0	7.0		1457	-7.7	0.0	16	dbSNP_132	7	278,7486		4,270,3608	no	missense	C16orf11	NM_145270.2	43	4,291,5312	AA,AG,GG		3.5806,0.6087,2.6663	benign	486/572	615048	299,10915	1725	3882	5607	555049	SO:0001583	missense	146325																														ENST00000409413.3:c.1457G>A	16.37:g.615048G>A	ENSP00000386499:p.Arg486Gln	Somatic		Capture	Illumina HiSeq	Phase_I	555049	B8ZZ27|Q8N233|Q96AX3|Q96S23	Missense_Mutation	SNP	ENST00000409413.3	37	CCDS45365.1	35	0.016025641025641024	0	0.0	3	0.008287292817679558	0	0.0	32	0.04221635883905013	G	8.830	0.939587	0.18281	0.006087	0.035806	ENSG00000161992	ENST00000409413	.	.	.	3.84	-7.67	0.01272	.	3.460850	0.01504	N	0.017638	T	0.01558	0.0050	N	0.01048	-1.04	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.15492	-1.0435	9	0.21540	T	0.41	.	1.6347	0.02740	0.3014:0.373:0.1849:0.1407	.	486	P0CG20	CP011_HUMAN	Q	486	.	ENSP00000386499:R486Q	R	+	2	0	C16orf11	555049	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.058000	0.14301	-1.772000	0.01292	-1.622000	0.00790	CGG		C16orf11-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000333913.1		
WFIKKN1	117166	hgsc.bcm.edu	37	16	681284	681284	+	Silent	SNP	C	C	T	rs8062289	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr16:681284C>T	ENST00000319070.2	+	1	353	c.31C>T	c.(31-33)Ctg>Ttg	p.L11L		NM_053284.2	NP_444514.1	Q96NZ8	WFKN1_HUMAN	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 1	11					muscle fiber development (GO:0048747)|negative regulation of DNA binding (GO:0043392)|negative regulation of protein binding (GO:0032091)|palate development (GO:0060021)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)	metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(1)|prostate(1)|upper_aerodigestive_tract(1)	4		Hepatocellular(780;0.00335)				CCTGCCGCTCCTGCTCCTCCT	0.741													c|||	1093	0.218251	0.3986	0.0965	5008	,	,		11117	0.0357		0.1859	False		,,,				2504	0.2822																0			16								1488,2824		287,914,955	10.0	11.0	11.0		31	0.8	0.0	16	dbSNP_116	11	1579,6943		165,1249,2847	no	coding-synonymous	WFIKKN1	NM_053284.2		452,2163,3802	TT,TC,CC		18.5285,34.5083,23.8975		11/549	681284	3067,9767	2156	4261	6417	621285	SO:0001819	synonymous_variant	117166			AK075356	CCDS10414.1	16p13	2013-01-21			ENSG00000127578	ENSG00000127578		"""Immunoglobulin superfamily / I-set domain containing"", ""WAP four-disulfide core domain containing"""	30912	protein-coding gene	gene with protein product	"""WAP four-disulfide core domain 20A"""	608021	"""chromosome 16 open reading frame 12"""	C16orf12		11274388, 11928817	Standard	NM_053284		Approved	RJD2, WFIKKN, WFDC20A	uc002cht.1	Q96NZ8	OTTHUMG00000090359	ENST00000319070.2:c.31C>T	16.37:g.681284C>T		Somatic		Capture	Illumina HiSeq	Phase_I	621285	Q7LDW0|Q8NBQ1|Q96S20	Silent	SNP	ENST00000319070.2	37	CCDS10414.1																																																																																				WFIKKN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206731.2	NM_053284	
FBXL16	146330	hgsc.bcm.edu	37	16	747029	747029	+	Missense_Mutation	SNP	C	C	T			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr16:747029C>T	ENST00000397621.1	-	2	708	c.377G>A	c.(376-378)cGc>cAc	p.R126H	FBXL16_ENST00000562585.1_5'Flank|FBXL16_ENST00000324361.5_Missense_Mutation_p.R126H|FBXL16_ENST00000562563.1_5'Flank	NM_153350.3	NP_699181.2	Q8N461	FXL16_HUMAN	F-box and leucine-rich repeat protein 16	126	F-box.									endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|ovary(1)	10		Hepatocellular(780;0.0218)				GTACAGCACGCGCCGCCAGGC	0.632																																																	0			16											36.0	34.0	35.0					16																	747029		2199	4299	6498	687030	SO:0001583	missense	146330			BC036680	CCDS10421.1	16p13.3	2011-06-09	2004-06-15	2004-06-16	ENSG00000127585	ENSG00000127585		"""F-boxes / Leucine-rich repeats"""	14150	protein-coding gene	gene with protein product		609082	"""chromosome 16 open reading frame 22"""	C16orf22		11157797	Standard	NM_153350		Approved	MGC33974, Fbl16	uc021taa.1	Q8N461	OTTHUMG00000090420	ENST00000397621.1:c.377G>A	16.37:g.747029C>T	ENSP00000380746:p.Arg126His	Somatic		Capture	Illumina HiSeq	Phase_I	687030	B3KR59|D3DU60|Q2MHR2|Q96S14|Q9UJI0	Missense_Mutation	SNP	ENST00000397621.1	37	CCDS10421.1	.	.	.	.	.	.	.	.	.	.	c	13.76	2.332124	0.41297	.	.	ENSG00000127585	ENST00000397621;ENST00000324361	T;T	0.25579	1.79;1.79	4.01	4.01	0.46588	F-box domain, Skp2-like (1);	0.064020	0.64402	D	0.000011	T	0.24198	0.0586	L	0.47716	1.5	0.38375	D	0.944963	D	0.64830	0.994	B	0.41036	0.346	T	0.21008	-1.0258	10	0.44086	T	0.13	.	15.1067	0.72326	0.0:1.0:0.0:0.0	.	126	Q8N461	FXL16_HUMAN	H	126	ENSP00000380746:R126H;ENSP00000318674:R126H	ENSP00000318674:R126H	R	-	2	0	FBXL16	687030	1.000000	0.71417	0.997000	0.53966	0.879000	0.50718	5.607000	0.67648	1.798000	0.52647	0.313000	0.20887	CGC		FBXL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206851.2	NM_153350	
SLC6A2	6530	hgsc.bcm.edu	37	16	55719134	55719134	+	Missense_Mutation	SNP	A	A	G			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr16:55719134A>G	ENST00000379906.2	+	4	979	c.724A>G	c.(724-726)Atg>Gtg	p.M242V	SLC6A2_ENST00000567238.1_Missense_Mutation_p.M137V|SLC6A2_ENST00000568943.1_Missense_Mutation_p.M242V|SLC6A2_ENST00000219833.8_Missense_Mutation_p.M242V|SLC6A2_ENST00000561820.1_Missense_Mutation_p.M242V|SLC6A2_ENST00000414754.3_Missense_Mutation_p.M242V|SLC6A2_ENST00000566163.1_Missense_Mutation_p.M242V	NM_001043.3	NP_001034.1	P23975	SC6A2_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 2	242					monoamine transport (GO:0015844)|norepinephrine transport (GO:0015874)|response to drug (GO:0042493)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	monoamine transmembrane transporter activity (GO:0008504)|norepinephrine:sodium symporter activity (GO:0005334)			breast(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(20)|ovary(3)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(1)	41				BRCA - Breast invasive adenocarcinoma(181;0.01)|Kidney(780;0.0267)	Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Bupropion(DB01156)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Diethylpropion(DB00937)|Dopamine(DB00988)|Doxepin(DB01142)|Droxidopa(DB06262)|Duloxetine(DB00476)|Ephedra(DB01363)|Ephedrine(DB01364)|Ergotamine(DB00696)|Escitalopram(DB01175)|Ginkgo biloba(DB01381)|Guanadrel(DB00226)|Guanethidine(DB01170)|Imipramine(DB00458)|Iobenguane(DB06704)|Ketamine(DB01221)|Levomilnacipran(DB08918)|Levonordefrin(DB06707)|Loxapine(DB00408)|Maprotiline(DB00934)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Milnacipran(DB04896)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Orphenadrine(DB01173)|Paroxetine(DB00715)|Pethidine(DB00454)|Phendimetrazine(DB01579)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Reboxetine(DB00234)|Sibutramine(DB01105)|Tapentadol(DB06204)|Tramadol(DB00193)|Trimipramine(DB00726)|Venlafaxine(DB00285)	GCTCTGTCTGATGGTCGTCGT	0.532																																																	0			16											135.0	123.0	127.0					16																	55719134		2198	4300	6498	54276635	SO:0001583	missense	6530				CCDS10754.1, CCDS54011.1, CCDS58463.1	16q12.2	2013-07-19	2013-07-19		ENSG00000103546	ENSG00000103546		"""Solute carriers"""	11048	protein-coding gene	gene with protein product	"""norepinephrine transporter"""	163970	"""solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2"""	NET1, NAT1, SLC6A5		2008212	Standard	NM_001043		Approved	NET	uc021tio.1	P23975	OTTHUMG00000133208	ENST00000379906.2:c.724A>G	16.37:g.55719134A>G	ENSP00000369237:p.Met242Val	Somatic		Capture	Illumina HiSeq	Phase_I	54276635	B2R707|B4DX48|Q96KH8	Missense_Mutation	SNP	ENST00000379906.2	37	CCDS10754.1	.	.	.	.	.	.	.	.	.	.	A	4.858	0.159443	0.09236	.	.	ENSG00000103546	ENST00000414754;ENST00000537705;ENST00000379906;ENST00000219833	T;T;T	0.72615	-0.67;-0.67;-0.67	5.65	-2.88	0.05682	.	0.445192	0.29133	N	0.013043	T	0.26412	0.0645	N	0.00504	-1.425	0.19575	N	0.999967	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.002;0.0;0.002;0.001	T	0.30794	-0.9966	10	0.33141	T	0.24	.	1.5769	0.02626	0.3508:0.0973:0.1358:0.416	.	242;1;137;242	Q96KH8;F5H0T4;B4DX48;P23975	.;.;.;SC6A2_HUMAN	V	242;1;242;242	ENSP00000394956:M242V;ENSP00000369237:M242V;ENSP00000219833:M242V	ENSP00000219833:M242V	M	+	1	0	SLC6A2	54276635	0.810000	0.29049	0.082000	0.20525	0.494000	0.33585	1.169000	0.31871	-0.457000	0.07033	-1.407000	0.01130	ATG		SLC6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256922.2		
SLC38A7	55238	hgsc.bcm.edu	37	16	58706132	58706132	+	Missense_Mutation	SNP	A	A	G			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr16:58706132A>G	ENST00000570101.1	-	8	1782	c.899T>C	c.(898-900)cTg>cCg	p.L300P	SLC38A7_ENST00000564010.1_Missense_Mutation_p.L211P|SLC38A7_ENST00000219320.4_Missense_Mutation_p.L300P|SLC38A7_ENST00000564100.1_Intron|SLC38A7_ENST00000566953.1_5'UTR			Q9NVC3	S38A7_HUMAN	solute carrier family 38, member 7	300					sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	L-alanine transmembrane transporter activity (GO:0015180)|L-amino acid transmembrane transporter activity (GO:0015179)|L-asparagine transmembrane transporter activity (GO:0015182)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|L-glutamine transmembrane transporter activity (GO:0015186)|L-histidine transmembrane transporter activity (GO:0005290)|L-leucine transmembrane transporter activity (GO:0015190)|L-methionine transmembrane transporter activity (GO:0015191)|L-serine transmembrane transporter activity (GO:0015194)			endometrium(1)|large_intestine(2)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	13						TCCAAAGGTCAGGAAGCCACA	0.617																																																	0			16											38.0	33.0	35.0					16																	58706132		2189	4294	6483	57263633	SO:0001583	missense	55238			BC001961	CCDS10800.1	16q21	2013-05-22			ENSG00000103042	ENSG00000103042		"""Solute carriers"""	25582	protein-coding gene	gene with protein product		614236					Standard	XM_006721229		Approved	FLJ10815	uc002eod.1	Q9NVC3	OTTHUMG00000133491	ENST00000570101.1:c.899T>C	16.37:g.58706132A>G	ENSP00000454646:p.Leu300Pro	Somatic		Capture	Illumina HiSeq	Phase_I	57263633	Q53GJ9|Q9H9I5	Missense_Mutation	SNP	ENST00000570101.1	37	CCDS10800.1	.	.	.	.	.	.	.	.	.	.	A	16.73	3.202928	0.58234	.	.	ENSG00000103042	ENST00000219320	T	0.03272	3.99	5.36	5.36	0.76844	.	0.067302	0.64402	N	0.000009	T	0.19005	0.0456	M	0.80616	2.505	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.00397	-1.1765	9	.	.	.	.	14.5336	0.67944	1.0:0.0:0.0:0.0	.	300	Q9NVC3	S38A7_HUMAN	P	300	ENSP00000219320:L300P	.	L	-	2	0	SLC38A7	57263633	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.853000	0.92222	2.020000	0.59435	0.482000	0.46254	CTG		SLC38A7-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422206.2	NM_018231	
HYDIN	54768	hgsc.bcm.edu	37	16	70863708	70863708	+	Missense_Mutation	SNP	C	C	T			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr16:70863708C>T	ENST00000393567.2	-	81	14075	c.13925G>A	c.(13924-13926)cGc>cAc	p.R4642H		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	4642					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				GTGCTTGGAGCGCACCTGGCA	0.577																																																	0			16											2.0	2.0	2.0					16																	70863708		1419	3306	4725	69421209	SO:0001583	missense	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.13925G>A	16.37:g.70863708C>T	ENSP00000377197:p.Arg4642His	Somatic		Capture	Illumina HiSeq	Phase_I	69421209	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.648491	0.87958	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.01933	4.55	5.0	5.0	0.66597	.	0.000000	0.33813	U	0.004539	T	0.15825	0.0381	M	0.87456	2.885	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.01337	-1.1381	10	0.44086	T	0.13	.	17.9456	0.89036	0.0:1.0:0.0:0.0	.	4641	F8WD23	.	H	4642;4641	ENSP00000377197:R4642H	ENSP00000313052:R4641H	R	-	2	0	HYDIN	69421209	1.000000	0.71417	1.000000	0.80357	0.686000	0.39977	7.416000	0.80143	2.334000	0.79466	0.505000	0.49811	CGC		HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
HP	3240	hgsc.bcm.edu	37	16	72093037	72093037	+	Missense_Mutation	SNP	A	A	T			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr16:72093037A>T	ENST00000355906.5	+	6	450	c.392A>T	c.(391-393)aAg>aTg	p.K131M	HP_ENST00000398131.2_Missense_Mutation_p.K72M|HP_ENST00000562526.1_Missense_Mutation_p.K72M|HP_ENST00000357763.4_Missense_Mutation_p.K167M|HP_ENST00000569639.1_Missense_Mutation_p.K72M|HP_ENST00000570083.1_Missense_Mutation_p.K72M|HP_ENST00000565574.1_Intron|HPR_ENST00000356967.5_Intron	NM_005143.3	NP_005134.1	P00738	HPT_HUMAN	haptoglobin	131	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				acute-phase response (GO:0006953)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|immune system process (GO:0002376)|negative regulation of hydrogen peroxide catabolic process (GO:2000296)|negative regulation of oxidoreductase activity (GO:0051354)|positive regulation of cell death (GO:0010942)|response to hydrogen peroxide (GO:0042542)	blood microparticle (GO:0072562)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|haptoglobin-hemoglobin complex (GO:0031838)	antioxidant activity (GO:0016209)|hemoglobin binding (GO:0030492)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|urinary_tract(1)	7		Renal(780;9.67e-05)|Ovarian(137;0.00327)|Hepatocellular(780;0.114)		BRCA - Breast invasive adenocarcinoma(221;0.00015)|Kidney(780;0.000529)		AACAATGAGAAGCAGTGGATA	0.483																																																	0			16											122.0	132.0	129.0					16																	72093037		1786	4080	5866	70650538	SO:0001583	missense	10395				CCDS45524.1, CCDS45525.1	16q22.2	2012-10-02			ENSG00000257017	ENSG00000257017			5141	protein-coding gene	gene with protein product		140100				11109501, 9352226	Standard	NM_005143		Approved		uc002fbr.4	P00738		ENST00000355906.5:c.392A>T	16.37:g.72093037A>T	ENSP00000348170:p.Lys131Met	Somatic		Capture	Illumina HiSeq	Phase_I	70650538	B0AZL5|P00737|Q0VAC4|Q0VAC5|Q2PP15|Q3B7J0|Q6LBY9|Q9UC67	Missense_Mutation	SNP	ENST00000355906.5	37	CCDS45524.1	.	.	.	.	.	.	.	.	.	.	A	11.83	1.754477	0.31046	.	.	ENSG00000257017	ENST00000355906;ENST00000398131	T;T	0.50548	0.74;0.74	4.24	4.24	0.50183	Complement control module (2);Sushi/SCR/CCP (2);	0.188909	0.35903	N	0.002917	T	0.68495	0.3007	M	0.84585	2.705	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.73263	-0.4038	10	0.87932	D	0	.	9.8991	0.41338	1.0:0.0:0.0:0.0	.	131	P00738	HPT_HUMAN	M	131;72	ENSP00000348170:K131M;ENSP00000381199:K72M	ENSP00000348170:K131M	K	+	2	0	HP	70650538	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	2.473000	0.45145	1.902000	0.55061	0.482000	0.46254	AAG		HP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421680.1	NM_005143	
CMIP	80790	hgsc.bcm.edu	37	16	81478932	81478932	+	Missense_Mutation	SNP	C	C	T			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr16:81478932C>T	ENST00000537098.3	+	1	158	c.86C>T	c.(85-87)gCc>gTc	p.A29V		NM_198390.2	NP_938204.2	Q8IY22	CMIP_HUMAN	c-Maf inducing protein	29						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(5)|kidney(1)|lung(7)	13						GACGTGTCGGCCCCCGAAGGC	0.701																																																	0			16											14.0	16.0	15.0					16																	81478932		1900	4094	5994	80036433	SO:0001583	missense	80790			AB051481	CCDS54044.1, CCDS54045.1	16q23	2011-08-04			ENSG00000153815	ENSG00000153815			24319	protein-coding gene	gene with protein product		610112				11214970, 12939343	Standard	NM_030629		Approved		uc002fgp.3	Q8IY22		ENST00000537098.3:c.86C>T	16.37:g.81478932C>T	ENSP00000446100:p.Ala29Val	Somatic		Capture	Illumina HiSeq	Phase_I	80036433	Q9C0G9	Missense_Mutation	SNP	ENST00000537098.3	37	CCDS54044.1	.	.	.	.	.	.	.	.	.	.	C	15.31	2.794218	0.50102	.	.	ENSG00000153815	ENST00000537098	T	0.49432	0.78	3.02	2.01	0.26516	Pleckstrin homology domain (1);	.	.	.	.	T	0.27697	0.0681	N	0.08118	0	0.80722	D	1	B	0.15473	0.013	B	0.12156	0.007	T	0.05599	-1.0875	9	0.56958	D	0.05	.	11.5377	0.50648	0.0:0.8171:0.1829:0.0	.	29	Q8IY22	CMIP_HUMAN	V	29	ENSP00000446100:A29V	ENSP00000446100:A29V	A	+	2	0	CMIP	80036433	0.993000	0.37304	0.995000	0.50966	0.962000	0.63368	1.565000	0.36386	0.202000	0.20498	0.306000	0.20318	GCC		CMIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432399.2	NM_030629	
LAMA1	284217	hgsc.bcm.edu	37	18	6958514	6958514	+	Silent	SNP	C	C	T			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr18:6958514C>T	ENST00000389658.3	-	55	8019	c.7926G>A	c.(7924-7926)tcG>tcA	p.S2642S	RP11-781P6.1_ENST00000584722.1_RNA	NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2642	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				AGCCATGGAACGATCTTCTCA	0.463																																																	0			18											164.0	122.0	137.0					18																	6958514		2203	4300	6503	6948514	SO:0001819	synonymous_variant	284217			X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.7926G>A	18.37:g.6958514C>T		Somatic		Capture	Illumina HiSeq	Phase_I	6948514		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																				LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
LAMA1	284217	hgsc.bcm.edu	37	18	6985393	6985393	+	Missense_Mutation	SNP	C	C	G			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr18:6985393C>G	ENST00000389658.3	-	39	5596	c.5503G>C	c.(5503-5505)Gag>Cag	p.E1835Q		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1835	Domain II and I.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				TGGTGATCCTCTAAGTGCTAC	0.378																																																	0			18											125.0	118.0	120.0					18																	6985393		2203	4300	6503	6975393	SO:0001583	missense	284217			X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.5503G>C	18.37:g.6985393C>G	ENSP00000374309:p.Glu1835Gln	Somatic		Capture	Illumina HiSeq	Phase_I	6975393		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	C	14.97	2.694868	0.48202	.	.	ENSG00000101680	ENST00000389658	T	0.18174	2.23	5.58	5.58	0.84498	.	0.126892	0.51477	D	0.000097	T	0.27098	0.0664	L	0.57536	1.79	0.45097	D	0.998119	D	0.59357	0.985	P	0.49887	0.625	T	0.01242	-1.1408	10	0.21014	T	0.42	.	17.741	0.88407	0.0:1.0:0.0:0.0	.	1835	P25391	LAMA1_HUMAN	Q	1835	ENSP00000374309:E1835Q	ENSP00000374309:E1835Q	E	-	1	0	LAMA1	6975393	1.000000	0.71417	0.484000	0.27391	0.195000	0.23768	6.149000	0.71795	2.631000	0.89168	0.655000	0.94253	GAG		LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
SMAD4	4089	hgsc.bcm.edu	37	18	48591925	48591925	+	Missense_Mutation	SNP	G	G	A	rs377767349		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr18:48591925G>A	ENST00000342988.3	+	9	1626	c.1088G>A	c.(1087-1089)tGt>tAt	p.C363Y	SMAD4_ENST00000588745.1_Missense_Mutation_p.C267Y|SMAD4_ENST00000398417.2_Missense_Mutation_p.C363Y	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	363	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(2)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		GATCGCTTTTGTTTGGGTCAA	0.418																																																	38	Whole gene deletion(36)|Unknown(2)	pancreas(26)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)	18	GRCh37	CD064635	SMAD4	D							155.0	129.0	138.0					18																	48591925		2203	4300	6503	46845923	SO:0001583	missense	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"""SMADs"""	6770	protein-coding gene	gene with protein product		600993	"""MAD, mothers against decapentaplegic homolog 4 (Drosophila)"", ""SMAD, mothers against DPP homolog 4 (Drosophila)"""	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.1088G>A	18.37:g.48591925G>A	ENSP00000341551:p.Cys363Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	46845923	A8K405	Missense_Mutation	SNP	ENST00000342988.3	37	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.921255	0.92249	.	.	ENSG00000141646	ENST00000342988;ENST00000544926;ENST00000398417	D;D	0.99226	-5.59;-5.59	5.86	5.86	0.93980	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.000000	0.85682	D	0.000000	D	0.99635	0.9866	H	0.95294	3.65	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97962	1.0338	10	0.87932	D	0	.	18.9646	0.92691	0.0:0.0:1.0:0.0	.	363	Q13485	SMAD4_HUMAN	Y	363	ENSP00000341551:C363Y;ENSP00000381452:C363Y	ENSP00000341551:C363Y	C	+	2	0	SMAD4	46845923	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.676000	0.98643	2.771000	0.95319	0.563000	0.77884	TGT		SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359	
RAF1	5894	hgsc.bcm.edu	37	3	12641307	12641307	+	Splice_Site	SNP	T	T	C			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr3:12641307T>C	ENST00000251849.4	-	10	1430	c.991A>G	c.(991-993)Agg>Ggg	p.R331G	RAF1_ENST00000534997.1_Splice_Site_p.R116G|RAF1_ENST00000542177.1_Splice_Site_p.R250G|RAF1_ENST00000442415.2_Splice_Site_p.R351G	NM_002880.3	NP_002871.1	P04049	RAF1_HUMAN	Raf-1 proto-oncogene, serine/threonine kinase	331	Interaction with PEBP1/RKIP.				activation of adenylate cyclase activity (GO:0007190)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|death-inducing signaling complex assembly (GO:0071550)|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)|insulin receptor signaling pathway (GO:0008286)|intermediate filament cytoskeleton organization (GO:0045104)|ion transmembrane transport (GO:0034220)|MAPK cascade (GO:0000165)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of protein complex assembly (GO:0031333)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of cell differentiation (GO:0045595)|regulation of cell motility (GO:2000145)|regulation of Rho protein signal transduction (GO:0035023)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)		ESRP1/RAF1(4)|RAF1/DAZL(2)|SRGAP3/RAF1(6)	biliary_tract(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)	32					Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)	CCACGAGGCCTCTGAAACAAG	0.408			T	SRGAP3	pilocytic astrocytoma				Noonan syndrome																															Dom	yes		3	3p25	5894	v-raf-1 murine leukemia viral oncogene homolog 1		M	0			3											78.0	79.0	78.0					3																	12641307		2203	4300	6503	12616307	SO:0001630	splice_region_variant	5894	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	X03484	CCDS2612.1	3p25	2014-09-17	2014-06-26		ENSG00000132155	ENSG00000132155			9829	protein-coding gene	gene with protein product	"""C-Raf proto-oncogene, serine/threonine kinase"""	164760	"""v-raf-1 murine leukemia viral oncogene homolog 1"""			1611909	Standard	NM_002880		Approved	Raf-1, c-Raf, CRAF	uc003bxf.4	P04049	OTTHUMG00000129789	ENST00000251849.4:c.991-1A>G	3.37:g.12641307T>C		Somatic		Capture	Illumina HiSeq	Phase_I	12616307	B0LPH8|B2R5N3|Q15278|Q9UC20	Missense_Mutation	SNP	ENST00000251849.4	37	CCDS2612.1	.	.	.	.	.	.	.	.	.	.	T	16.07	3.018417	0.54576	.	.	ENSG00000132155	ENST00000251849;ENST00000442415;ENST00000432427;ENST00000534997;ENST00000542177	T;T;T;T;T	0.75821	-0.93;-0.97;-0.91;-0.92;-0.92	5.17	3.99	0.46301	Protein kinase-like domain (1);	0.079450	0.85682	D	0.000000	T	0.74222	0.3688	M	0.69823	2.125	0.53688	D	0.999976	B;B;P	0.37233	0.019;0.133;0.588	B;B;B	0.40602	0.015;0.065;0.334	T	0.74697	-0.3578	10	0.62326	D	0.03	.	11.1273	0.48325	0.0:0.0:0.1548:0.8452	.	250;116;331	B4E0X2;B4E1N6;P04049	.;.;RAF1_HUMAN	G	331;351;210;116;250	ENSP00000251849:R331G;ENSP00000401888:R351G;ENSP00000398591:R210G;ENSP00000441186:R116G;ENSP00000443567:R250G	ENSP00000251849:R331G	R	-	1	2	RAF1	12616307	1.000000	0.71417	1.000000	0.80357	0.806000	0.45545	4.887000	0.63156	0.890000	0.36211	-0.460000	0.05396	AGG		RAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252015.2	NM_002880	Missense_Mutation
RBM6	10180	hgsc.bcm.edu	37	3	50098948	50098948	+	Silent	SNP	T	T	C			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr3:50098948T>C	ENST00000266022.4	+	14	2666	c.2407T>C	c.(2407-2409)Ttg>Ctg	p.L803L	RBM6_ENST00000441115.1_3'UTR|RBM6_ENST00000539992.1_Silent_p.L145L|RBM6_ENST00000442092.1_Silent_p.L281L|RBM6_ENST00000422955.1_Silent_p.L281L|RBM6_ENST00000443081.1_Silent_p.L671L	NM_005777.2	NP_005768.1	P78332	RBM6_HUMAN	RNA binding motif protein 6	803					RNA processing (GO:0006396)	nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(3)|prostate(1)|skin(4)|urinary_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)		TTATGACCCCTTGGCAGGAAC	0.373																																																	0			3											163.0	154.0	157.0					3																	50098948		2203	4300	6503	50073952	SO:0001819	synonymous_variant	10180			AF069517	CCDS2809.1, CCDS54586.1	3p21.3	2013-01-28			ENSG00000004534	ENSG00000004534		"""RNA binding motif (RRM) containing"", ""G patch domain containing"""	9903	protein-coding gene	gene with protein product		606886				10352938	Standard	NM_001167582		Approved	DEF-3, 3G2, NY-LU-12, g16, DEF3	uc003cyc.3	P78332	OTTHUMG00000156736	ENST00000266022.4:c.2407T>C	3.37:g.50098948T>C		Somatic		Capture	Illumina HiSeq	Phase_I	50073952	O60549|O75524|Q86SS3	Silent	SNP	ENST00000266022.4	37	CCDS2809.1																																																																																				RBM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345528.4	NM_005777	
SEMA3G	56920	hgsc.bcm.edu	37	3	52475665	52475665	+	Nonsense_Mutation	SNP	G	G	A			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr3:52475665G>A	ENST00000231721.2	-	6	591	c.592C>T	c.(592-594)Cga>Tga	p.R198*		NM_020163.1	NP_064548.1	Q9NS98	SEM3G_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3G	198	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)			kidney(1)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)	18				BRCA - Breast invasive adenocarcinoma(193;1.69e-05)|Kidney(197;0.00173)|KIRC - Kidney renal clear cell carcinoma(197;0.00196)|OV - Ovarian serous cystadenocarcinoma(275;0.0333)		ATGGCCTCTCGCCCCAGGAAG	0.657																																																	0			3											55.0	55.0	55.0					3																	52475665		2203	4300	6503	52450705	SO:0001587	stop_gained	56920				CCDS2856.1	3p21.1	2013-01-11			ENSG00000010319	ENSG00000010319		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	30400	protein-coding gene	gene with protein product						11214971	Standard	XM_005265327		Approved	FLJ00014, sem2	uc003dea.1	Q9NS98	OTTHUMG00000158570	ENST00000231721.2:c.592C>T	3.37:g.52475665G>A	ENSP00000231721:p.Arg198*	Somatic		Capture	Illumina HiSeq	Phase_I	52450705	Q7L9D9|Q9H7Q3	Nonsense_Mutation	SNP	ENST00000231721.2	37	CCDS2856.1	.	.	.	.	.	.	.	.	.	.	G	15.02	2.708207	0.48412	.	.	ENSG00000010319	ENST00000231721	.	.	.	4.84	4.84	0.62591	.	0.054016	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.6002	0.50997	0.0:0.0:0.6927:0.3073	.	.	.	.	X	198	.	ENSP00000231721:R198X	R	-	1	2	SEMA3G	52450705	0.788000	0.28762	0.963000	0.40424	0.526000	0.34562	2.727000	0.47311	2.249000	0.74217	0.462000	0.41574	CGA		SEMA3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351354.1	NM_020163	
DZIP1L	199221	hgsc.bcm.edu	37	3	137787047	137787047	+	Missense_Mutation	SNP	C	C	T	rs199606339|rs374045	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr3:137787047C>T	ENST00000327532.2	-	13	2140	c.1778G>A	c.(1777-1779)cGc>cAc	p.R593H	DZIP1L_ENST00000488595.1_5'Flank	NM_173543.2	NP_775814.2	Q8IYY4	DZI1L_HUMAN	DAZ interacting zinc finger protein 1-like	593			R -> H (in dbSNP:rs374045). {ECO:0000269|PubMed:15489334}.		cilium assembly (GO:0042384)	ciliary basal body (GO:0036064)	metal ion binding (GO:0046872)			breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(2)|prostate(1)|skin(1)	35						CAGTCCGGGGCGTGGAGCGGG	0.697													C|||	3149	0.628794	0.3094	0.7767	5008	,	,		14534	0.626		0.8608	False		,,,				2504	0.7198																0			3						C	HIS/ARG	1930,2476	539.0+/-375.1	417,1096,690	43.0	47.0	46.0		1778	2.2	0.0	3	dbSNP_80	46	7483,1117	760.0+/-407.6	3260,963,77	no	missense	DZIP1L	NM_173543.2	29	3677,2059,767	TT,TC,CC		12.9884,43.8039,27.6257	benign	593/768	137787047	9413,3593	2203	4300	6503	139269737	SO:0001583	missense	199221			AK057406	CCDS3096.1, CCDS54645.1	3q22.3	2013-05-22	2013-05-22		ENSG00000158163	ENSG00000158163			26551	protein-coding gene	gene with protein product			"""DAZ interacting protein 1-like"""			12477932	Standard	NM_173543		Approved	FLJ32844, DZIP2	uc003erq.3	Q8IYY4	OTTHUMG00000159819	ENST00000327532.2:c.1778G>A	3.37:g.137787047C>T	ENSP00000332148:p.Arg593His	Somatic		Capture	Illumina HiSeq	Phase_I	139269737	C9JUG5|Q96M38	Missense_Mutation	SNP	ENST00000327532.2	37	CCDS3096.1	1465	0.6707875457875457	179	0.3638211382113821	271	0.7486187845303868	365	0.6381118881118881	650	0.8575197889182058	C	11.55	1.673457	0.29693	0.438039	0.870116	ENSG00000158163	ENST00000327532	T	0.38722	1.12	4.91	2.16	0.27623	.	0.815396	0.11163	N	0.592824	T	0.00012	0.0000	L	0.45581	1.43	0.80722	P	0.0	B	0.19073	0.033	B	0.12156	0.007	T	0.22138	-1.0225	9	0.28530	T	0.3	-0.6235	6.6861	0.23146	0.0:0.7076:0.0:0.2924	rs374045;rs17853174;rs58860132	593	Q8IYY4	DZI1L_HUMAN	H	593	ENSP00000332148:R593H	ENSP00000332148:R593H	R	-	2	0	DZIP1L	139269737	0.001000	0.12720	0.002000	0.10522	0.043000	0.13939	0.080000	0.14802	0.268000	0.21939	0.650000	0.86243	CGC		DZIP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357548.1	NM_173543	
ATR	545	hgsc.bcm.edu	37	3	142176502	142176502	+	Silent	SNP	T	T	C			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr3:142176502T>C	ENST00000350721.4	-	45	7720	c.7599A>G	c.(7597-7599)cgA>cgG	p.R2533R	ATR_ENST00000383101.3_Silent_p.R2469R	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	2533	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						CACATGCTCTTCGAAAAAGAC	0.403								Other conserved DNA damage response genes																																									0			3											105.0	98.0	101.0					3																	142176502		2203	4300	6503	143659192	SO:0001819	synonymous_variant	390502			U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"""MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"""	601215	"""ataxia telangiectasia and Rad3 related"""			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.7599A>G	3.37:g.142176502T>C		Somatic		Capture	Illumina HiSeq	Phase_I	143659192	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Silent	SNP	ENST00000350721.4	37	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	T	10.87	1.473823	0.26423	.	.	ENSG00000175054	ENST00000513291	.	.	.	5.2	4.04	0.47022	.	.	.	.	.	T	0.60971	0.2310	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59139	-0.7510	4	.	.	.	-9.8182	10.6321	0.45543	0.0:0.0757:0.0:0.9243	.	.	.	.	E	380	.	.	K	-	1	0	ATR	143659192	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.301000	0.33447	2.102000	0.63906	0.397000	0.26171	AAG		ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184	
GPR149	344758	hgsc.bcm.edu	37	3	154056059	154056059	+	Splice_Site	SNP	C	C	T	rs199967865		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr3:154056059C>T	ENST00000389740.2	-	4	1724	c.1625G>A	c.(1624-1626)cGt>cAt	p.R542H		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	542					antral ovarian follicle growth (GO:0001547)|estrous cycle phase (GO:0060206)|negative regulation of ovulation (GO:0060280)|preantral ovarian follicle growth (GO:0001546)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.R542H(1)		autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			ATAACCGGAACGCTGGGGACA	0.413													C|||	1	0.000199681	0.0	0.0	5008	,	,		19095	0.0		0.001	False		,,,				2504	0.0																1	Substitution - Missense(1)	ovary(1)	3											76.0	77.0	77.0					3																	154056059		1876	4103	5979	155538753	SO:0001630	splice_region_variant	344758			AY255534	CCDS43162.1	3q25.2	2012-08-21			ENSG00000174948	ENSG00000174948		"""GPCR / Class A : Orphans"""	23627	protein-coding gene	gene with protein product						12679517	Standard	NM_001038705		Approved	PGR10, IEDA	uc003faa.3	Q86SP6	OTTHUMG00000159131	ENST00000389740.2:c.1624-1G>A	3.37:g.154056059C>T		Somatic		Capture	Illumina HiSeq	Phase_I	155538753		Missense_Mutation	SNP	ENST00000389740.2	37	CCDS43162.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	24.3	4.519500	0.85495	.	.	ENSG00000174948	ENST00000389740	.	.	.	5.77	4.89	0.63831	.	0.063289	0.64402	D	0.000006	T	0.74230	0.3689	L	0.59436	1.845	0.80722	D	1	D	0.89917	1.0	D	0.65987	0.94	T	0.76462	-0.2950	9	0.87932	D	0	-13.5998	15.0929	0.72211	0.0:0.9311:0.0:0.0689	.	542	Q86SP6	GP149_HUMAN	H	542	.	ENSP00000374390:R542H	R	-	2	0	GPR149	155538753	1.000000	0.71417	0.981000	0.43875	0.825000	0.46686	5.746000	0.68681	2.726000	0.93360	0.655000	0.94253	CGT		GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580	Missense_Mutation
SI	6476	hgsc.bcm.edu	37	3	164716351	164716351	+	Missense_Mutation	SNP	T	T	C			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr3:164716351T>C	ENST00000264382.3	-	38	4579	c.4517A>G	c.(4516-4518)gAc>gGc	p.D1506G		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	1506	Sucrase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)			NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	GTCCATGTTGTCCCATCGTGC	0.398										HNSCC(35;0.089)																																							0			3											209.0	185.0	193.0					3																	164716351		2203	4300	6503	166199045	SO:0001583	missense	6490			X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"""Oligosaccharide alpha-1,6-glucosidase"""	609845	"""sucrase-isomaltase"""			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.4517A>G	3.37:g.164716351T>C	ENSP00000264382:p.Asp1506Gly	Somatic		Capture	Illumina HiSeq	Phase_I	166199045	A2RUC3|Q1JQ80|Q1RMC2	Missense_Mutation	SNP	ENST00000264382.3	37	CCDS3196.1	.	.	.	.	.	.	.	.	.	.	T	17.78	3.474720	0.63737	.	.	ENSG00000090402	ENST00000264382	D	0.93763	-3.28	4.76	3.63	0.41609	Glycoside hydrolase, superfamily (1);	0.442401	0.25302	N	0.031646	D	0.94591	0.8257	L	0.56124	1.755	0.39636	D	0.970257	P	0.46859	0.885	D	0.64237	0.923	D	0.94513	0.7720	10	0.59425	D	0.04	.	10.6283	0.45521	0.0:0.0806:0.0:0.9194	.	1506	P14410	SUIS_HUMAN	G	1506	ENSP00000264382:D1506G	ENSP00000264382:D1506G	D	-	2	0	SI	166199045	1.000000	0.71417	0.995000	0.50966	0.634000	0.38068	3.092000	0.50207	2.127000	0.65507	0.528000	0.53228	GAC		SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041	
GNB4	59345	hgsc.bcm.edu	37	3	179132783	179132783	+	Missense_Mutation	SNP	G	G	A	rs267599699		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr3:179132783G>A	ENST00000232564.3	-	6	606	c.320C>T	c.(319-321)cCc>cTc	p.P107L	GNB4_ENST00000465153.1_5'Flank|GNB4_ENST00000468623.1_Missense_Mutation_p.P107L	NM_021629.3	NP_067642.1	Q9HAV0	GBB4_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 4	107					cell death (GO:0008219)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	protein complex binding (GO:0032403)|signal transducer activity (GO:0004871)	p.P107L(2)		endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	16	all_cancers(143;2.01e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.237)			ATTACCAGAGGGAGCATAAGC	0.458																																					Melanoma(105;1405 1491 7265 20440 33721)												2	Substitution - Missense(2)	skin(2)	3											121.0	119.0	120.0					3																	179132783		2203	4300	6503	180615477	SO:0001583	missense	59345			AF300648	CCDS3230.1	3q27.1	2013-01-10			ENSG00000114450	ENSG00000114450		"""WD repeat domain containing"""	20731	protein-coding gene	gene with protein product		610863				10644457, 11842130	Standard	NM_021629		Approved		uc003fjv.4	Q9HAV0	OTTHUMG00000157440	ENST00000232564.3:c.320C>T	3.37:g.179132783G>A	ENSP00000232564:p.Pro107Leu	Somatic		Capture	Illumina HiSeq	Phase_I	180615477	B3KMH5|D3DNR8	Missense_Mutation	SNP	ENST00000232564.3	37	CCDS3230.1	.	.	.	.	.	.	.	.	.	.	G	19.58	3.853706	0.71719	.	.	ENSG00000114450	ENST00000232564;ENST00000468623	T;T	0.71222	-0.55;-0.55	5.38	5.38	0.77491	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);G-protein, beta subunit (1);	0.000000	0.85682	D	0.000000	D	0.88901	0.6563	H	0.95611	3.695	0.80722	D	1	D;D	0.71674	0.998;0.992	D;D	0.65573	0.932;0.936	D	0.91898	0.5529	10	0.87932	D	0	-14.7066	19.4892	0.95044	0.0:0.0:1.0:0.0	.	107;107	Q9HAV0;A8K3F6	GBB4_HUMAN;.	L	107	ENSP00000232564:P107L;ENSP00000419693:P107L	ENSP00000232564:P107L	P	-	2	0	GNB4	180615477	1.000000	0.71417	0.979000	0.43373	0.133000	0.20885	9.717000	0.98755	2.663000	0.90544	0.655000	0.94253	CCC		GNB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258218.1	NM_021629	
MUC4	4585	hgsc.bcm.edu	37	3	195508661	195508661	+	Missense_Mutation	SNP	A	A	G	rs543282847	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr3:195508661A>G	ENST00000463781.3	-	2	10249	c.9790T>C	c.(9790-9792)Tct>Cct	p.S3264P	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.S3264P|MUC4_ENST00000349607.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACAGGAAGAGAGGTGGTGTCA	0.567													.|||	13	0.00259585	0.0068	0.0014	5008	,	,		10587	0.002		0.001	False		,,,				2504	0.0																0			3											4.0	4.0	4.0					3																	195508661		561	1353	1914	196993440	SO:0001583	missense	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.9790T>C	3.37:g.195508661A>G	ENSP00000417498:p.Ser3264Pro	Somatic		Capture	Illumina HiSeq	Phase_I	196993440	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	a	2.624	-0.287852	0.05605	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.35605	1.37;1.3	1.03	-1.6	0.08426	.	.	.	.	.	T	0.16257	0.0391	N	0.08118	0	0.19575	N	0.999961	B	0.19935	0.04	B	0.24848	0.056	T	0.26573	-1.0099	8	.	.	.	.	6.2977	0.21095	0.7909:0.0:0.2091:0.0	.	3136	E7ESK3	.	P	3264	ENSP00000417498:S3264P;ENSP00000420243:S3264P	.	S	-	1	0	MUC4	196993440	0.000000	0.05858	0.002000	0.10522	0.017000	0.09413	-1.206000	0.03011	-2.006000	0.00958	-1.895000	0.00532	TCT		MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
KRAS	3845	hgsc.bcm.edu	37	12	25398285	25398285	+	Missense_Mutation	SNP	C	C	T	rs121913530		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr12:25398285C>T	ENST00000256078.4	-	2	97	c.34G>A	c.(34-36)Ggt>Agt	p.G12S	KRAS_ENST00000311936.3_Missense_Mutation_p.G12S|KRAS_ENST00000557334.1_Missense_Mutation_p.G12S|KRAS_ENST00000556131.1_Missense_Mutation_p.G12S	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12C(3001)|p.G12S(1288)|p.G12R(789)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12W(3)|p.A11_G12insGA(2)|p.G12Y(2)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			CCTACGCCACCAGCTCCAACT	0.348	G12C(CALU1_LUNG)|G12C(HCC44_LUNG)|G12C(IALM_LUNG)|G12C(KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(KYSE410_OESOPHAGUS)|G12C(LU65_LUNG)|G12C(LU99_LUNG)|G12C(MIAPACA2_PANCREAS)|G12C(NCIH1373_LUNG)|G12C(NCIH1792_LUNG)|G12C(NCIH2030_LUNG)|G12C(NCIH2122_LUNG)|G12C(NCIH23_LUNG)|G12C(NCIH358_LUNG)|G12C(OV56_OVARY)|G12C(SW1463_LARGE_INTESTINE)|G12C(SW1573_LUNG)|G12C(SW837_LARGE_INTESTINE)|G12C(UMUC3_URINARY_TRACT)|G12R(CAL62_THYROID)|G12R(HS274T_BREAST)|G12R(HUPT3_PANCREAS)|G12R(KP2_PANCREAS)|G12R(PSN1_PANCREAS)|G12R(TCCPAN2_PANCREAS)|G12S(A549_LUNG)|G12S(KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12S(LS123_LARGE_INTESTINE)	119	Mis		"""pancreatic, colorectal, lung, thyroid, AML, others"""				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)			Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"""L, E, M, O"""	5144	Substitution - Missense(5142)|Insertion - In frame(2)	large_intestine(2360)|lung(1649)|pancreas(656)|biliary_tract(125)|ovary(56)|endometrium(54)|haematopoietic_and_lymphoid_tissue(49)|thyroid(42)|stomach(21)|cervix(19)|upper_aerodigestive_tract(17)|urinary_tract(17)|soft_tissue(15)|small_intestine(13)|prostate(11)|breast(9)|skin(8)|testis(7)|liver(6)|oesophagus(3)|peritoneum(1)|autonomic_ganglia(1)|kidney(1)|central_nervous_system(1)|NS(1)|penis(1)|adrenal_gland(1)	12	GRCh37	CM076251	KRAS	M	rs121913530						93.0	83.0	86.0					12																	25398285		2203	4300	6503	25289552	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"""v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog"", ""v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"""	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.34G>A	12.37:g.25398285C>T	ENSP00000256078:p.Gly12Ser	Somatic		Capture	Illumina HiSeq	Phase_I	25289552	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	35	5.441396	0.96187	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.76316	-1.01;-1.01;-1.01;-1.01	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.78559	0.4302	L	0.28344	0.845	0.80722	D	1	P;P	0.39665	0.557;0.682	P;P	0.50570	0.525;0.644	T	0.80254	-0.1459	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	S	12	ENSP00000308495:G12S;ENSP00000452512:G12S;ENSP00000256078:G12S;ENSP00000451856:G12S	ENSP00000256078:G12S	G	-	1	0	KRAS	25289552	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360	
PRICKLE1	144165	hgsc.bcm.edu	37	12	42853901	42853901	+	Missense_Mutation	SNP	G	G	T			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr12:42853901G>T	ENST00000455697.1	-	8	2491	c.2206C>A	c.(2206-2208)Cat>Aat	p.H736N	RP11-328C8.4_ENST00000547824.1_RNA|PRICKLE1_ENST00000548696.1_Missense_Mutation_p.H736N|PRICKLE1_ENST00000445766.2_Missense_Mutation_p.H736N|PRICKLE1_ENST00000345127.3_Missense_Mutation_p.H736N|PRICKLE1_ENST00000552240.1_Missense_Mutation_p.H736N	NM_001144882.1|NM_001144883.1	NP_001138354.1|NP_001138355.1	Q96MT3	PRIC1_HUMAN	prickle homolog 1 (Drosophila)	736					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell myoblast differentiation (GO:2000691)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(13)|ovary(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	47	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)		GAAGTGGCATGGGCGTACTGT	0.498																																																	0			12											123.0	122.0	122.0					12																	42853901		2203	4300	6503	41140168	SO:0001583	missense	144165			AK056499	CCDS8742.1	12p11-q12	2010-08-13	2006-09-12			ENSG00000139174			17019	protein-coding gene	gene with protein product		608500	"""prickle-like 1 (Drosophila)"""			12525887, 18976727	Standard	NM_153026		Approved	FLJ31937, EPM1B	uc010skv.2	Q96MT3		ENST00000455697.1:c.2206C>A	12.37:g.42853901G>T	ENSP00000401060:p.His736Asn	Somatic		Capture	Illumina HiSeq	Phase_I	41140168	Q14C83|Q71QF8|Q96N00	Missense_Mutation	SNP	ENST00000455697.1	37	CCDS8742.1	.	.	.	.	.	.	.	.	.	.	G	11.05	1.523436	0.27299	.	.	ENSG00000139174	ENST00000455697;ENST00000445766;ENST00000548696;ENST00000345127;ENST00000552240	D;D;D;D;D	0.84516	-1.86;-1.86;-1.86;-1.86;-1.86	5.34	5.34	0.76211	.	0.076438	0.53938	D	0.000042	T	0.75087	0.3802	N	0.16478	0.41	0.27331	N	0.956786	B	0.06786	0.001	B	0.04013	0.001	T	0.65352	-0.6189	10	0.41790	T	0.15	-1.7478	14.2827	0.66224	0.0:0.0:0.8513:0.1486	.	736	Q96MT3	PRIC1_HUMAN	N	736	ENSP00000401060:H736N;ENSP00000398947:H736N;ENSP00000448359:H736N;ENSP00000345064:H736N;ENSP00000449819:H736N	ENSP00000345064:H736N	H	-	1	0	PRICKLE1	41140168	0.999000	0.42202	0.336000	0.25522	0.877000	0.50540	2.836000	0.48183	2.667000	0.90743	0.655000	0.94253	CAT		PRICKLE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404069.1		
RAB21	23011	hgsc.bcm.edu	37	12	72149035	72149035	+	Silent	SNP	C	C	T			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr12:72149035C>T	ENST00000261263.3	+	1	382	c.126C>T	c.(124-126)aaC>aaT	p.N42N		NM_014999.2	NP_055814.1	Q9UL25	RAB21_HUMAN	RAB21, member RAS oncogene family	42					GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			large_intestine(1)|lung(4)|prostate(1)	6						ACTGCGAGAACAAGTTTAACG	0.682																																																	0			12											47.0	33.0	38.0					12																	72149035		2201	4295	6496	70435302	SO:0001819	synonymous_variant	23011			AF091035	CCDS9003.1	12q21.1	2014-09-04			ENSG00000080371	ENSG00000080371		"""RAB, member RAS oncogene"""	18263	protein-coding gene	gene with protein product		612398				10887961, 11697911, 16754960	Standard	NM_014999		Approved	KIAA0118	uc001swt.3	Q9UL25	OTTHUMG00000169572	ENST00000261263.3:c.126C>T	12.37:g.72149035C>T		Somatic		Capture	Illumina HiSeq	Phase_I	70435302	Q14466|Q569H3	Silent	SNP	ENST00000261263.3	37	CCDS9003.1																																																																																				RAB21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404855.1		
APAF1	317	hgsc.bcm.edu	37	12	99043328	99043328	+	Missense_Mutation	SNP	A	A	G			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr12:99043328A>G	ENST00000551964.1	+	4	1128	c.392A>G	c.(391-393)aAg>aGg	p.K131R	APAF1_ENST00000552268.1_Missense_Mutation_p.K131R|APAF1_ENST00000547045.1_Missense_Mutation_p.K131R|APAF1_ENST00000550527.1_Missense_Mutation_p.K120R|APAF1_ENST00000357310.1_Missense_Mutation_p.K131R|APAF1_ENST00000333991.1_Missense_Mutation_p.K131R|APAF1_ENST00000339433.3_Missense_Mutation_p.K131R|APAF1_ENST00000549007.1_Missense_Mutation_p.K131R|APAF1_ENST00000359972.2_Missense_Mutation_p.K120R	NM_181861.1	NP_863651.1	O14727	APAF_HUMAN	apoptotic peptidase activating factor 1	131	NB-ARC.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic process (GO:0006915)|forebrain development (GO:0030900)|intrinsic apoptotic signaling pathway (GO:0097193)|nervous system development (GO:0007399)|neural tube closure (GO:0001843)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|regulation of apoptotic DNA fragmentation (GO:1902510)|regulation of apoptotic process (GO:0042981)|response to G1 DNA damage checkpoint signaling (GO:0072432)	apoptosome (GO:0043293)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|nucleotide binding (GO:0000166)	p.K131M(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(1)	42					Adenosine triphosphate(DB00171)	ACAAGGAAGAAGCTGGTGAAT	0.438																																																	1	Substitution - Missense(1)	lung(1)	12											128.0	120.0	122.0					12																	99043328		2203	4300	6503	97567459	SO:0001583	missense	317			AF013263	CCDS9069.1, CCDS9070.1, CCDS9071.1, CCDS55862.1, CCDS55863.1	12q23	2013-01-10	2006-10-23			ENSG00000120868		"""WD repeat domain containing"""	576	protein-coding gene	gene with protein product		602233	"""apoptotic protease activating factor"", ""apoptotic peptidase activating factor"""			9267021, 10702682	Standard	NM_181861		Approved	CED4, APAF-1	uc001tfz.3	O14727	OTTHUMG00000170214	ENST00000551964.1:c.392A>G	12.37:g.99043328A>G	ENSP00000448165:p.Lys131Arg	Somatic		Capture	Illumina HiSeq	Phase_I	97567459	B2RMX8|O43297|Q7Z438|Q9BXZ6|Q9UBZ5|Q9UGN8|Q9UGN9|Q9UGP0|Q9UJ58|Q9UJ59|Q9UJ60|Q9UJ61|Q9UJ62|Q9UJ63|Q9UJ64|Q9UJ65|Q9UJ66|Q9UJ67|Q9UNC9	Missense_Mutation	SNP	ENST00000551964.1	37	CCDS9069.1	.	.	.	.	.	.	.	.	.	.	A	11.42	1.634508	0.29068	.	.	ENSG00000120868	ENST00000551964;ENST00000359972;ENST00000357310;ENST00000339433;ENST00000333991;ENST00000552268;ENST00000550527;ENST00000547045;ENST00000549007	T;T;T;T;T;T;T;T;T	0.77358	-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09;-1.09	5.55	5.55	0.83447	NB-ARC (1);	0.183845	0.64402	D	0.000019	T	0.72120	0.3421	L	0.36672	1.1	0.42714	D	0.993655	B;B;B;B;B	0.24317	0.017;0.09;0.007;0.096;0.101	B;B;B;B;B	0.32022	0.022;0.139;0.012;0.061;0.018	T	0.67821	-0.5571	10	0.27785	T	0.31	-13.726	15.676	0.77321	1.0:0.0:0.0:0.0	.	131;131;120;131;120	O14727-6;O14727-4;O14727-3;O14727;O14727-2	.;.;.;APAF_HUMAN;.	R	131;120;131;131;131;131;120;131;131	ENSP00000448165:K131R;ENSP00000353059:K120R;ENSP00000349862:K131R;ENSP00000341830:K131R;ENSP00000334558:K131R;ENSP00000448826:K131R;ENSP00000448449:K120R;ENSP00000449791:K131R;ENSP00000448161:K131R	ENSP00000334558:K131R	K	+	2	0	APAF1	97567459	1.000000	0.71417	1.000000	0.80357	0.211000	0.24417	5.715000	0.68430	2.109000	0.64355	0.533000	0.62120	AAG		APAF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408006.1	NM_181861.1	
HNF1A	6927	hgsc.bcm.edu	37	12	121426689	121426689	+	Missense_Mutation	SNP	A	A	G			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr12:121426689A>G	ENST00000257555.6	+	2	606	c.380A>G	c.(379-381)aAc>aGc	p.N127S	HNF1A_ENST00000543427.1_Missense_Mutation_p.N10S|HNF1A_ENST00000402929.1_Missense_Mutation_p.N127S|HNF1A_ENST00000541395.1_Missense_Mutation_p.N127S|HNF1A_ENST00000400024.2_Missense_Mutation_p.N127S|HNF1A_ENST00000544413.1_Missense_Mutation_p.N127S|HNF1A_ENST00000538626.1_Intron			P20823	HNF1A_HUMAN	HNF1 homeobox A	127			N -> Y (in a hepatocellular carcinoma sample; somatic mutation). {ECO:0000269|PubMed:12355088}.		glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CAGCAGCACAACATCCCACAG	0.622									Hepatic Adenoma, Familial Clustering of																																								0			12	GRCh37	CD020597	HNF1A	D							163.0	124.0	138.0					12																	121426689		2203	4300	6503	119911072	SO:0001583	missense	6927	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	M57732	CCDS9209.1	12q24.31	2014-09-17	2007-08-24	2007-08-24	ENSG00000135100	ENSG00000135100		"""Homeoboxes / HNF class"""	11621	protein-coding gene	gene with protein product		142410	"""transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor"""	MODY3, TCF1		1535333, 7795649	Standard	NM_000545		Approved	HNF1, LFB1	uc001tzg.3	P20823	OTTHUMG00000151015	ENST00000257555.6:c.380A>G	12.37:g.121426689A>G	ENSP00000257555:p.Asn127Ser	Somatic		Capture	Illumina HiSeq	Phase_I	119911072	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Missense_Mutation	SNP	ENST00000257555.6	37	CCDS9209.1	.	.	.	.	.	.	.	.	.	.	A	27.2	4.807340	0.90623	.	.	ENSG00000135100	ENST00000257555;ENST00000535125;ENST00000543536;ENST00000544680;ENST00000537424;ENST00000543027;ENST00000543427;ENST00000545458;ENST00000541395;ENST00000340577;ENST00000344370;ENST00000544413	D;D;D;D	0.99277	-5.67;-5.67;-5.67;-5.67	5.08	5.08	0.68730	Hepatocyte nuclear factor 1, N-terminal (1);Lambda repressor-like, DNA-binding (2);	0.000000	0.85682	D	0.000000	D	0.99168	0.9712	M	0.63843	1.955	0.80722	D	1	D;P;D;P	0.89917	1.0;0.948;1.0;0.948	D;D;D;P	0.91635	0.999;0.917;0.999;0.797	D	0.99529	1.0960	10	0.62326	D	0.03	-37.6886	14.0164	0.64527	1.0:0.0:0.0:0.0	.	127;127;127;127	F5H0K0;P20823;E7EUQ4;E7EMR0	.;HNF1A_HUMAN;.;.	S	127;127;127;127;127;127;10;127;127;127;127;127	ENSP00000257555:N127S;ENSP00000439721:N10S;ENSP00000443112:N127S;ENSP00000438804:N127S	ENSP00000257555:N127S	N	+	2	0	HNF1A	119911072	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.889000	0.92470	1.902000	0.55061	0.433000	0.28618	AAC		HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545	
DISP2	85455	hgsc.bcm.edu	37	15	40661726	40661726	+	Missense_Mutation	SNP	A	A	G			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr15:40661726A>G	ENST00000267889.3	+	8	3500	c.3413A>G	c.(3412-3414)gAc>gGc	p.D1138G	LINC00594_ENST00000561261.1_lincRNA|RP11-64K12.4_ENST00000558421.1_RNA	NM_033510.1	NP_277045.1	A7MBM2	DISP2_HUMAN	dispatched homolog 2 (Drosophila)	1138					smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)	30		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.39e-06)|Colorectal(105;0.0114)|READ - Rectum adenocarcinoma(2;0.0649)|BRCA - Breast invasive adenocarcinoma(123;0.0798)|Lung(196;0.15)|LUAD - Lung adenocarcinoma(183;0.247)		GGTACTGGGGACCCTGGTGGG	0.622																																																	0			15											35.0	37.0	36.0					15																	40661726		2202	4300	6502	38449018	SO:0001583	missense	85455			AB051529	CCDS10056.1	15q14	2004-01-15			ENSG00000140323	ENSG00000140323			19712	protein-coding gene	gene with protein product		607503				11214970, 10619433	Standard	NM_033510		Approved	DISPB, KIAA1742, HsT16908	uc001zlk.1	A7MBM2	OTTHUMG00000129983	ENST00000267889.3:c.3413A>G	15.37:g.40661726A>G	ENSP00000267889:p.Asp1138Gly	Somatic		Capture	Illumina HiSeq	Phase_I	38449018	Q6AHW3|Q9C0C1	Missense_Mutation	SNP	ENST00000267889.3	37	CCDS10056.1	.	.	.	.	.	.	.	.	.	.	A	19.96	3.922967	0.73213	.	.	ENSG00000140323	ENST00000267889	T	0.12147	2.71	5.33	5.33	0.75918	.	0.807228	0.11440	N	0.563954	T	0.07728	0.0194	N	0.04508	-0.205	0.24000	N	0.996211	B	0.22211	0.066	B	0.24006	0.05	T	0.33420	-0.9869	10	0.24483	T	0.36	-10.5959	12.0949	0.53748	0.7379:0.2621:0.0:0.0	.	1138	A7MBM2	DISP2_HUMAN	G	1138	ENSP00000267889:D1138G	ENSP00000267889:D1138G	D	+	2	0	DISP2	38449018	0.999000	0.42202	0.896000	0.35187	0.812000	0.45895	4.145000	0.58065	2.237000	0.73441	0.459000	0.35465	GAC		DISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252249.1	NM_033510	
IQGAP1	8826	hgsc.bcm.edu	37	15	91017007	91017007	+	Missense_Mutation	SNP	T	T	C			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr15:91017007T>C	ENST00000268182.5	+	20	2534	c.2410T>C	c.(2410-2412)Tcc>Ccc	p.S804P	IQGAP1_ENST00000560738.1_Missense_Mutation_p.S232P	NM_003870.3	NP_003861.1	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	804	IQ 2. {ECO:0000255|PROSITE- ProRule:PRU00116}.				cellular response to calcium ion (GO:0071277)|cellular response to epidermal growth factor stimulus (GO:0071364)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerular visceral epithelial cell development (GO:0072015)|negative regulation of catalytic activity (GO:0043086)|negative regulation of dephosphorylation (GO:0035305)|neuron projection extension (GO:1990138)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|regulation of cytokine production (GO:0001817)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	actin filament (GO:0005884)|axon (GO:0030424)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|midbody (GO:0030496)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activator activity (GO:0043539)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			TTACCTGCGCTCCCACAAAGA	0.433																																																	0			15											95.0	84.0	88.0					15																	91017007		2198	4298	6496	88818011	SO:0001583	missense	8826			D29640	CCDS10362.1	15q26.1	2008-07-18			ENSG00000140575	ENSG00000140575			6110	protein-coding gene	gene with protein product	"""RasGAP-like with IQ motifs"""	603379				8051149, 8670801	Standard	XM_005254984		Approved	p195, KIAA0051, SAR1, HUMORFA01	uc002bpl.1	P46940	OTTHUMG00000149832	ENST00000268182.5:c.2410T>C	15.37:g.91017007T>C	ENSP00000268182:p.Ser804Pro	Somatic		Capture	Illumina HiSeq	Phase_I	88818011	A7MBM3	Missense_Mutation	SNP	ENST00000268182.5	37	CCDS10362.1	.	.	.	.	.	.	.	.	.	.	T	13.14	2.148181	0.37923	.	.	ENSG00000140575	ENST00000268182	D	0.95238	-3.65	5.91	0.468	0.16732	.	0.298649	0.32357	N	0.006218	D	0.89354	0.6691	L	0.27053	0.805	0.28569	N	0.910734	B	0.26744	0.158	B	0.27262	0.078	T	0.78342	-0.2241	10	0.31617	T	0.26	-5.5698	16.4491	0.83973	0.0:0.0:0.7237:0.2762	.	804	P46940	IQGA1_HUMAN	P	804	ENSP00000268182:S804P	ENSP00000268182:S804P	S	+	1	0	IQGAP1	88818011	1.000000	0.71417	0.981000	0.43875	0.634000	0.38068	3.279000	0.51670	0.096000	0.17463	0.533000	0.62120	TCC		IQGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313493.1	NM_003870	
DCAF8L2	347442	hgsc.bcm.edu	37	X	27765530	27765530	+	Missense_Mutation	SNP	A	A	G			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chrX:27765530A>G	ENST00000451261.2	+	5	917	c.518A>G	c.(517-519)gAg>gGg	p.E173G		NM_001136533.1	NP_001130005.1	P0C7V8	DC8L2_HUMAN	DDB1 and CUL4 associated factor 8-like 2	173	Glu-rich.									central_nervous_system(1)|endometrium(9)|kidney(3)|lung(7)|pancreas(1)|skin(3)	24						GCGCTGGAGGAGTGGGTTTCC	0.602																																																	0			X											47.0	41.0	43.0					X																	27765530		692	1591	2283	27675451	SO:0001583	missense	0				CCDS59162.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17		ENSG00000189186		"""WD repeat domain containing"""	31811	protein-coding gene	gene with protein product			"""WD repeat domain 42C"""	WDR42C			Standard	NM_001136533		Approved		uc011mjy.2	P0C7V8		ENST00000451261.2:c.518A>G	X.37:g.27765530A>G	ENSP00000462745:p.Glu173Gly	Somatic		Capture	Illumina HiSeq	Phase_I	27675451	B2RXH9|J3KT06	Missense_Mutation	SNP	ENST00000451261.2	37	CCDS59162.1																																																																																				DCAF8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056143.4	XM_293354	
TAB3	257397	hgsc.bcm.edu	37	X	30872751	30872751	+	Missense_Mutation	SNP	C	C	T			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chrX:30872751C>T	ENST00000378933.1	-	3	1208	c.1031G>A	c.(1030-1032)gGa>gAa	p.G344E	TAB3_ENST00000378932.2_Missense_Mutation_p.G344E|TAB3_ENST00000378928.1_5'Flank|TAB3_ENST00000378930.3_Missense_Mutation_p.G344E|TAB3_ENST00000288422.2_Missense_Mutation_p.G344E|TAB3-AS2_ENST00000445240.1_RNA	NM_152787.3	NP_690000.2	Q8N5C8	TAB3_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 3	344	Pro-rich.				activation of MAPK activity (GO:0000187)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|skin(1)	27						TGAATGGCTTCCCTGTTTCTG	0.453																																					Pancreas(164;1598 1985 29022 43301 49529)												0			X											130.0	119.0	123.0					X																	30872751		2202	4300	6502	30782672	SO:0001583	missense	257397			AY331591	CCDS14226.1	Xp21.2	2010-02-05	2010-02-05	2010-02-05	ENSG00000157625	ENSG00000157625			30681	protein-coding gene	gene with protein product	"""TAK1 binding protein 3"""	300480	"""mitogen-activated protein kinase kinase kinase 7 interacting protein 3"""	MAP3K7IP3		14633987, 14670075	Standard	XM_005274482		Approved		uc004dcj.3	Q8N5C8	OTTHUMG00000021329	ENST00000378933.1:c.1031G>A	X.37:g.30872751C>T	ENSP00000368215:p.Gly344Glu	Somatic		Capture	Illumina HiSeq	Phase_I	30782672	A6NDD9|Q6VQR0	Missense_Mutation	SNP	ENST00000378933.1	37	CCDS14226.1	.	.	.	.	.	.	.	.	.	.	C	16.34	3.096596	0.56075	.	.	ENSG00000157625	ENST00000378933;ENST00000378930;ENST00000288422;ENST00000378932	T;T;T;T	0.78364	-1.07;-1.07;-1.07;-1.17	5.06	5.06	0.68205	.	0.205851	0.48286	D	0.000192	T	0.75125	0.3807	N	0.24115	0.695	0.37805	D	0.927831	D;D	0.57257	0.979;0.964	P;P	0.51193	0.662;0.461	T	0.80388	-0.1403	10	0.52906	T	0.07	-3.8377	17.8235	0.88657	0.0:1.0:0.0:0.0	.	344;344	Q8N5C8-2;Q8N5C8	.;TAB3_HUMAN	E	344	ENSP00000368215:G344E;ENSP00000368212:G344E;ENSP00000288422:G344E;ENSP00000368214:G344E	ENSP00000288422:G344E	G	-	2	0	TAB3	30782672	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.804000	0.62554	2.229000	0.72834	0.538000	0.68166	GGA		TAB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056173.1	NM_152787	
DMD	1756	hgsc.bcm.edu	37	X	32486674	32486674	+	Missense_Mutation	SNP	G	G	T			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chrX:32486674G>T	ENST00000357033.4	-	23	3309	c.3103C>A	c.(3103-3105)Cag>Aag	p.Q1035K	DMD_ENST00000378677.2_Missense_Mutation_p.Q1031K	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	1035					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)				TCAACCAGCTGGGAGGAGAGC	0.393																																																	0			X											64.0	57.0	60.0					X																	32486674		2202	4300	6502	32396595	SO:0001583	missense	1756			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.3103C>A	X.37:g.32486674G>T	ENSP00000354923:p.Gln1035Lys	Somatic		Capture	Illumina HiSeq	Phase_I	32396595	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	37	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	G	0.053	-1.243723	0.01481	.	.	ENSG00000198947	ENST00000534884;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280	T;T	0.49432	0.78;0.78	5.12	4.22	0.49857	.	0.000000	0.32503	U	0.006013	T	0.35451	0.0932	L	0.34521	1.04	0.80722	D	1	B;B;B	0.31383	0.002;0.321;0.002	B;B;B	0.35859	0.009;0.212;0.015	T	0.11084	-1.0602	10	0.02654	T	1	.	13.9995	0.64424	0.0:0.0:0.8474:0.1526	.	1027;1035;1031	P11532-4;P11532;E9PDN5	.;DMD_HUMAN;.	K	1027;1031;1035;1035;912	ENSP00000367948:Q1031K;ENSP00000354923:Q1035K	ENSP00000354923:Q1035K	Q	-	1	0	DMD	32396595	1.000000	0.71417	0.189000	0.23252	0.024000	0.10985	5.718000	0.68455	0.974000	0.38366	0.538000	0.68166	CAG		DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
GPKOW	27238	hgsc.bcm.edu	37	X	48978806	48978806	+	Missense_Mutation	SNP	A	A	T			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chrX:48978806A>T	ENST00000156109.5	-	3	476	c.398T>A	c.(397-399)aTc>aAc	p.I133N		NM_015698.4	NP_056513.2	Q92917	GPKOW_HUMAN	G patch domain and KOW motifs	133						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(11)|ovary(2)	21						TCCTTTCTGGATCATGGGGAT	0.587																																																	0			X											49.0	42.0	44.0					X																	48978806		2203	4300	6503	48865750	SO:0001583	missense	27238			U66359	CCDS35251.1	Xp11.23	2013-01-28			ENSG00000068394	ENSG00000068394		"""G patch domain containing"""	30677	protein-coding gene	gene with protein product	"""G patch domain containing 5"""					21880142, 22365833	Standard	NM_015698		Approved	T54, GPATC5, GPATCH5, Spp2	uc004dmr.3	Q92917	OTTHUMG00000021511	ENST00000156109.5:c.398T>A	X.37:g.48978806A>T	ENSP00000156109:p.Ile133Asn	Somatic		Capture	Illumina HiSeq	Phase_I	48865750	Q59EK5|Q9BQA8	Missense_Mutation	SNP	ENST00000156109.5	37	CCDS35251.1	.	.	.	.	.	.	.	.	.	.	A	18.81	3.702460	0.68501	.	.	ENSG00000068394	ENST00000156109	.	.	.	4.17	4.17	0.49024	.	0.059284	0.64402	D	0.000004	T	0.60130	0.2245	L	0.51422	1.61	0.35377	D	0.789536	D	0.67145	0.996	P	0.61940	0.896	T	0.68530	-0.5384	9	0.45353	T	0.12	-2.347	9.2152	0.37342	1.0:0.0:0.0:0.0	.	133	Q92917	GPKOW_HUMAN	N	133	.	ENSP00000156109:I133N	I	-	2	0	GPKOW	48865750	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.091000	0.50199	1.630000	0.50440	0.413000	0.27773	ATC		GPKOW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056535.2	NM_015698	
WNK3	65267	hgsc.bcm.edu	37	X	54328283	54328283	+	Missense_Mutation	SNP	G	G	T			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chrX:54328283G>T	ENST00000375159.2	-	5	1098	c.1099C>A	c.(1099-1101)Cca>Aca	p.P367T	WNK3_ENST00000354646.2_Missense_Mutation_p.P367T|WNK3_ENST00000375169.3_Missense_Mutation_p.P367T			Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3	367	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of ion transmembrane transporter activity (GO:0032414)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of rubidium ion transmembrane transporter activity (GO:2000688)|positive regulation of rubidium ion transport (GO:2000682)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(24)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80						AAGCTGGCTGGTTTTATGCCC	0.338																																																	0			X											146.0	115.0	125.0					X																	54328283		2203	4300	6503	54345008	SO:0001583	missense	65267			AJ409088	CCDS14357.1, CCDS35302.1	Xp11.22	2008-05-14	2005-01-19	2005-01-22	ENSG00000196632	ENSG00000196632			14543	protein-coding gene	gene with protein product		300358	"""protein kinase, lysine deficient 3"""	PRKWNK3			Standard	NM_020922		Approved		uc004dtc.2	Q9BYP7	OTTHUMG00000021626	ENST00000375159.2:c.1099C>A	X.37:g.54328283G>T	ENSP00000364301:p.Pro367Thr	Somatic		Capture	Illumina HiSeq	Phase_I	54345008	B1AKG2|Q5JRC1|Q6JP76|Q8TCX6|Q9HCK6	Missense_Mutation	SNP	ENST00000375159.2	37	CCDS14357.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.323725	0.81580	.	.	ENSG00000196632	ENST00000375169;ENST00000354646;ENST00000375159	T;T;T	0.27256	1.68;1.68;1.68	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	0.000027	T	0.51432	0.1674	M	0.71036	2.16	0.53688	D	0.999971	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.56318	-0.7999	10	0.87932	D	0	-10.6732	16.2996	0.82804	0.0:0.0:1.0:0.0	.	367;367	Q9BYP7-3;Q9BYP7	.;WNK3_HUMAN	T	367	ENSP00000364312:P367T;ENSP00000346667:P367T;ENSP00000364301:P367T	ENSP00000346667:P367T	P	-	1	0	WNK3	54345008	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.760000	0.98935	2.100000	0.63781	0.529000	0.55759	CCA		WNK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056799.2	NM_020922	
THOC2	57187	hgsc.bcm.edu	37	X	122820467	122820467	+	Silent	SNP	T	T	C			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chrX:122820467T>C	ENST00000245838.8	-	8	730	c.699A>G	c.(697-699)gaA>gaG	p.E233E	THOC2_ENST00000491737.1_Silent_p.E118E|THOC2_ENST00000355725.4_Silent_p.E233E	NM_001081550.1	NP_001075019.1	Q8NI27	THOC2_HUMAN	THO complex 2	233					mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			breast(2)|endometrium(13)|kidney(4)|large_intestine(11)|lung(26)|ovary(3)|skin(1)|upper_aerodigestive_tract(3)	63						TCATGTAAGATTCTAACAAAG	0.348																																																	0			X											128.0	115.0	119.0					X																	122820467		1856	4089	5945	122648148	SO:0001819	synonymous_variant	57187			AF441770	CCDS43988.1	Xq25-q26.3	2013-02-11	2004-08-09		ENSG00000125676	ENSG00000125676		"""THO complex subunits"""	19073	protein-coding gene	gene with protein product		300395	"""chromosome X open reading frame 3"""	CXorf3		11979277	Standard	NM_001081550		Approved	THO2, dJ506G2.1	uc004etu.3	Q8NI27	OTTHUMG00000022334	ENST00000245838.8:c.699A>G	X.37:g.122820467T>C		Somatic		Capture	Illumina HiSeq	Phase_I	122648148	A6NM50|Q5JZ12|Q6IN92|Q9H8I6	Silent	SNP	ENST00000245838.8	37	CCDS43988.1																																																																																				THOC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058153.3		
TFDP3	51270	hgsc.bcm.edu	37	X	132351846	132351846	+	Missense_Mutation	SNP	C	C	T			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chrX:132351846C>T	ENST00000310125.4	-	1	530	c.442G>A	c.(442-444)Gcc>Acc	p.A148T		NM_016521.2	NP_057605.3	Q5H9I0	TFDP3_HUMAN	transcription factor Dp family, member 3	148					cellular response to DNA damage stimulus (GO:0006974)|G1/S transition of mitotic cell cycle (GO:0000082)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(4)|large_intestine(1)|lung(8)|ovary(1)|prostate(2)	19	Acute lymphoblastic leukemia(192;0.000127)					TTTGGTGAGGCGTGGTTGCTG	0.537													C|||	1	0.000264901	0.0008	0.0	3775	,	,		15677	0.0		0.0	False		,,,				2504	0.0																0			X											96.0	87.0	90.0					X																	132351846		2202	4299	6501	132179512	SO:0001583	missense	51270			AF219119	CCDS14636.2	Xq26.2	2009-03-25			ENSG00000183434	ENSG00000183434			24603	protein-coding gene	gene with protein product	"""E2F-like protein"", ""cancer/testis antigen 30"""	300772				12097419	Standard	NM_016521		Approved	HCA661, E2F-like, CT30	uc004exb.1	Q5H9I0	OTTHUMG00000022433	ENST00000310125.4:c.442G>A	X.37:g.132351846C>T	ENSP00000385461:p.Ala148Thr	Somatic		Capture	Illumina HiSeq	Phase_I	132179512	Q6DK49|Q9NZ54	Missense_Mutation	SNP	ENST00000310125.4	37	CCDS14636.2	.	.	.	.	.	.	.	.	.	.	c	1.648	-0.514681	0.04200	.	.	ENSG00000183434	ENST00000310125	T	0.22336	1.96	0.208	-0.415	0.12355	Transcription factor E2F/dimerisation partner (TDP) (1);Winged helix-turn-helix transcription repressor DNA-binding (1);	.	.	.	.	T	0.07503	0.0189	N	0.04746	-0.17	0.22240	N	0.99927	B	0.06786	0.001	B	0.15484	0.013	T	0.37731	-0.9693	9	0.17369	T	0.5	.	2.1527	0.03804	0.0:0.3376:0.3429:0.3194	.	148	Q5H9I0	TFDP3_HUMAN	T	148	ENSP00000385461:A148T	ENSP00000385461:A148T	A	-	1	0	TFDP3	132179512	1.000000	0.71417	0.003000	0.11579	0.003000	0.03518	1.941000	0.40233	-0.952000	0.03649	-0.960000	0.02634	GCC		TFDP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058337.1	NM_016521	
FLNA	2316	hgsc.bcm.edu	37	X	153585989	153585989	+	Silent	SNP	A	A	G			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chrX:153585989A>G	ENST00000369850.3	-	29	4994	c.4758T>C	c.(4756-4758)gaT>gaC	p.D1586D	FLNA_ENST00000344736.4_Silent_p.D1586D|FLNA_ENST00000360319.4_Silent_p.D1586D|FLNA_ENST00000369856.3_5'UTR|FLNA_ENST00000422373.1_Silent_p.D1586D	NM_001110556.1	NP_001104026.1	P21333	FLNA_HUMAN	filamin A, alpha	1586	Interaction with furin. {ECO:0000250}.				actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|cilium assembly (GO:0042384)|cytoplasmic sequestering of protein (GO:0051220)|early endosome to late endosome transport (GO:0045022)|epithelial to mesenchymal transition (GO:0001837)|establishment of protein localization (GO:0045184)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription factor import into nucleus (GO:0042993)|protein localization to cell surface (GO:0034394)|protein stabilization (GO:0050821)|receptor clustering (GO:0043113)|spindle assembly involved in mitosis (GO:0090307)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|apical dendrite (GO:0097440)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|Myb complex (GO:0031523)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|Fc-gamma receptor I complex binding (GO:0034988)|glycoprotein binding (GO:0001948)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)|Rho GTPase binding (GO:0017048)|signal transducer activity (GO:0004871)|small GTPase binding (GO:0031267)|transcription factor binding (GO:0008134)			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TGCCTTCGGGATCCTGTGTGG	0.627																																																	0			X											115.0	111.0	112.0					X																	153585989		2153	4228	6381	153239183	SO:0001819	synonymous_variant	2316			X70082	CCDS44021.1, CCDS48194.1	Xq28	2009-07-23	2009-07-23		ENSG00000196924	ENSG00000196924			3754	protein-coding gene	gene with protein product	"""actin binding protein 280"""	300017	"""filamin A, alpha (actin binding protein 280)"""	FLN1, FLN, OPD2, OPD1		8406501, 12612583	Standard	NM_001456		Approved	ABP-280	uc004fkk.2	P21333	OTTHUMG00000022712	ENST00000369850.3:c.4758T>C	X.37:g.153585989A>G		Somatic		Capture	Illumina HiSeq	Phase_I	153239183	E9KL45|Q5HY53|Q5HY55|Q8NF52	Silent	SNP	ENST00000369850.3	37	CCDS48194.1																																																																																				FLNA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058942.3		
FLNA	2316	hgsc.bcm.edu	37	X	153590348	153590348	+	Splice_Site	SNP	T	T	C			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chrX:153590348T>C	ENST00000369850.3	-	19	3061	c.2825A>G	c.(2824-2826)cAg>cGg	p.Q942R	FLNA_ENST00000344736.4_Splice_Site_p.Q942R|FLNA_ENST00000360319.4_Splice_Site_p.Q942R|FLNA_ENST00000422373.1_Splice_Site_p.Q942R	NM_001110556.1	NP_001104026.1	P21333	FLNA_HUMAN	filamin A, alpha	942					actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|cilium assembly (GO:0042384)|cytoplasmic sequestering of protein (GO:0051220)|early endosome to late endosome transport (GO:0045022)|epithelial to mesenchymal transition (GO:0001837)|establishment of protein localization (GO:0045184)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription factor import into nucleus (GO:0042993)|protein localization to cell surface (GO:0034394)|protein stabilization (GO:0050821)|receptor clustering (GO:0043113)|spindle assembly involved in mitosis (GO:0090307)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|apical dendrite (GO:0097440)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|Myb complex (GO:0031523)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|Fc-gamma receptor I complex binding (GO:0034988)|glycoprotein binding (GO:0001948)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)|Rho GTPase binding (GO:0017048)|signal transducer activity (GO:0004871)|small GTPase binding (GO:0031267)|transcription factor binding (GO:0008134)			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TGTGGCTACCTGCTGGACAGG	0.572																																																	0			X											70.0	79.0	76.0					X																	153590348		2162	4222	6384	153243542	SO:0001630	splice_region_variant	2316			X70082	CCDS44021.1, CCDS48194.1	Xq28	2009-07-23	2009-07-23		ENSG00000196924	ENSG00000196924			3754	protein-coding gene	gene with protein product	"""actin binding protein 280"""	300017	"""filamin A, alpha (actin binding protein 280)"""	FLN1, FLN, OPD2, OPD1		8406501, 12612583	Standard	NM_001456		Approved	ABP-280	uc004fkk.2	P21333	OTTHUMG00000022712	ENST00000369850.3:c.2826+1A>G	X.37:g.153590348T>C		Somatic		Capture	Illumina HiSeq	Phase_I	153243542	E9KL45|Q5HY53|Q5HY55|Q8NF52	Missense_Mutation	SNP	ENST00000369850.3	37	CCDS48194.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.025168	0.75390	.	.	ENSG00000196924	ENST00000360319;ENST00000369852;ENST00000422373;ENST00000369850;ENST00000344736	D;D;D;D	0.84516	-1.86;-1.86;-1.86;-1.86	4.71	4.71	0.59529	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.073575	0.56097	D	0.000039	D	0.89343	0.6688	L	0.52126	1.63	0.80722	D	1	P;D	0.76494	0.833;0.999	P;D	0.70227	0.84;0.968	D	0.90157	0.4225	10	0.66056	D	0.02	.	13.624	0.62153	0.0:0.0:0.0:1.0	.	942;942	P21333-2;P21333	.;FLNA_HUMAN	R	942;915;942;942;942	ENSP00000353467:Q942R;ENSP00000416926:Q942R;ENSP00000358866:Q942R;ENSP00000358863:Q942R	ENSP00000358863:Q942R	Q	-	2	0	FLNA	153243542	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	7.934000	0.87649	1.659000	0.50751	0.425000	0.28330	CAG		FLNA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058942.3		Missense_Mutation
CRIPAK	285464	hgsc.bcm.edu	37	4	1388759	1388759	+	Missense_Mutation	SNP	C	C	T	rs112233131	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr4:1388759C>T	ENST00000324803.4	+	1	3420	c.460C>T	c.(460-462)Cgg>Tgg	p.R154W		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	154					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.R154W(2)		NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CGTGCCCATGCGGAGTGCCCG	0.701																																																	2	Substitution - Missense(2)	NS(1)|skin(1)	4											84.0	72.0	76.0					4																	1388759		2202	4282	6484	1378759	SO:0001583	missense	285464			AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.460C>T	4.37:g.1388759C>T	ENSP00000323978:p.Arg154Trp	Somatic		Capture	Illumina HiSeq	Phase_I	1378759	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	0.074|0.074	-1.196289|-1.196289	0.01594|0.01594	.|.	.|.	ENSG00000179979|ENSG00000179979	ENST00000382944|ENST00000324803	.|T	.|0.19806	.|2.12	0.948|0.948	-1.9|-1.9	0.07665|0.07665	.|.	.|.	.|.	.|.	.|.	T|T	0.07908|0.07908	0.0198|0.0198	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B	.|0.22851	.|0.076	.|B	.|0.04013	.|0.001	T|T	0.18116|0.18116	-1.0347|-1.0347	6|9	0.02654|0.49607	T|T	1|0.09	.|.	0.8279|0.8279	0.01124|0.01124	0.1649:0.1747:0.3249:0.3355|0.1649:0.1747:0.3249:0.3355	.|.	.|154	.|Q8N1N5	.|CRPAK_HUMAN	V|W	137|154	.|ENSP00000323978:R154W	ENSP00000372402:A137V|ENSP00000323978:R154W	A|R	+|+	2|1	0|2	CRIPAK|CRIPAK	1378759|1378759	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.017000|0.017000	0.09413|0.09413	-2.063000|-2.063000	0.01388|0.01388	-3.215000|-3.215000	0.00213|0.00213	-1.709000|-1.709000	0.00716|0.00716	GCG|CGG		CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388817	1388817	+	Missense_Mutation	SNP	C	C	G	rs200606324	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr4:1388817C>G	ENST00000324803.4	+	1	3478	c.518C>G	c.(517-519)cCa>cGa	p.P173R		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	173					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CACACGTGCCCATGTGGAGTG	0.677													N|||	940	0.1877	0.3328	0.1398	5008	,	,		18475	0.0992		0.0378	False		,,,				2504	0.271																0			4											192.0	130.0	151.0					4																	1388817		2194	4201	6395	1378817	SO:0001583	missense	285464			AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.518C>G	4.37:g.1388817C>G	ENSP00000323978:p.Pro173Arg	Somatic		Capture	Illumina HiSeq	Phase_I	1378817	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	c	1.909	-0.451230	0.04572	.	.	ENSG00000179979	ENST00000324803	T	0.19250	2.16	1.25	0.276	0.15663	Post-SET domain (1);	.	.	.	.	T	0.08358	0.0208	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40079	-0.9582	9	0.17369	T	0.5	.	4.4738	0.11726	0.0:0.5796:0.2425:0.1779	.	173	Q8N1N5	CRPAK_HUMAN	R	173	ENSP00000323978:P173R	ENSP00000323978:P173R	P	+	2	0	CRIPAK	1378817	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.368000	0.07543	-0.338000	0.08413	-1.976000	0.00459	CCA		CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
CRIPAK	285464	hgsc.bcm.edu	37	4	1389156	1389156	+	Missense_Mutation	SNP	T	T	C	rs71614972	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr4:1389156T>C	ENST00000324803.4	+	1	3817	c.857T>C	c.(856-858)aTg>aCg	p.M286T		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	286					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CATGTGCCGATGTGGAGTGCC	0.677													T|||	3799	0.758586	0.9349	0.7954	5008	,	,		13659	0.7014		0.6392	False		,,,				2504	0.6759																0			4											131.0	131.0	131.0					4																	1389156		2202	4299	6501	1379156	SO:0001583	missense	285464			AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.857T>C	4.37:g.1389156T>C	ENSP00000323978:p.Met286Thr	Somatic		Capture	Illumina HiSeq	Phase_I	1379156	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	T	0.854	-0.737538	0.03111	.	.	ENSG00000179979	ENST00000324803;ENST00000382944	T	0.17691	2.26	0.815	-1.63	0.08345	Post-SET domain (1);	.	.	.	.	T	0.06826	0.0174	N	0.08118	0	0.80722	P	0.0	B	0.12630	0.006	B	0.06405	0.002	T	0.38067	-0.9678	8	0.25106	T	0.35	.	5.1474	0.14993	0.0:0.3546:0.0:0.6454	.	286	Q8N1N5	CRPAK_HUMAN	T	286;228	ENSP00000323978:M286T	ENSP00000323978:M286T	M	+	2	0	CRIPAK	1379156	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.361000	0.01083	-0.674000	0.05253	-0.530000	0.04314	ATG		CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
CRIPAK	285464	hgsc.bcm.edu	37	4	1389384	1389384	+	Missense_Mutation	SNP	C	C	T	rs148729919		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr4:1389384C>T	ENST00000324803.4	+	1	4045	c.1085C>T	c.(1084-1086)cCg>cTg	p.P362L		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	362					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			GTGGAGTGCCCGCCTGCTCAC	0.672																																																	0			4											173.0	178.0	176.0					4																	1389384		2203	4299	6502	1379384	SO:0001583	missense	285464			AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.1085C>T	4.37:g.1389384C>T	ENSP00000323978:p.Pro362Leu	Somatic		Capture	Illumina HiSeq	Phase_I	1379384	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	-	5.247	0.231053	0.09969	.	.	ENSG00000179979	ENST00000324803;ENST00000382944	T	0.33438	1.41	0.757	-0.648	0.11464	.	.	.	.	.	T	0.11281	0.0275	N	0.08118	0	0.09310	N	0.999993	B	0.18968	0.032	B	0.06405	0.002	T	0.28427	-1.0044	9	0.20519	T	0.43	.	1.6297	0.02730	0.3327:0.398:0.0:0.2693	.	362	Q8N1N5	CRPAK_HUMAN	L	362;304	ENSP00000323978:P362L	ENSP00000323978:P362L	P	+	2	0	CRIPAK	1379384	0.021000	0.18746	0.005000	0.12908	0.052000	0.14988	0.367000	0.20382	-0.286000	0.09076	0.205000	0.17691	CCG		CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
FGFR3	2261	hgsc.bcm.edu	37	4	1807830	1807830	+	Missense_Mutation	SNP	T	T	C			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr4:1807830T>C	ENST00000260795.2	+	13	1991	c.1889T>C	c.(1888-1890)gTg>gCg	p.V630A	FGFR3_ENST00000352904.1_Missense_Mutation_p.V518A|FGFR3_ENST00000481110.2_Missense_Mutation_p.V631A|FGFR3_ENST00000412135.2_Missense_Mutation_p.V518A|FGFR3_ENST00000340107.4_Missense_Mutation_p.V632A|FGFR3_ENST00000440486.2_Missense_Mutation_p.V630A			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	630	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				alveolar secondary septum development (GO:0061144)|axonogenesis involved in innervation (GO:0060385)|bone maturation (GO:0070977)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cell-cell signaling (GO:0007267)|central nervous system myelination (GO:0022010)|chondrocyte differentiation (GO:0002062)|chondrocyte proliferation (GO:0035988)|cochlea development (GO:0090102)|digestive tract morphogenesis (GO:0048546)|endochondral bone growth (GO:0003416)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell fate commitment (GO:0072148)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor apoptotic signaling pathway (GO:1902178)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade (GO:0007259)|lens fiber cell development (GO:0070307)|lens morphogenesis in camera-type eye (GO:0002089)|MAPK cascade (GO:0000165)|morphogenesis of an epithelium (GO:0002009)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of developmental growth (GO:0048640)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|protein tyrosine kinase activity (GO:0004713)			NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607)	3091		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)|Pazopanib(DB06589)|Ponatinib(DB08901)	GAGGACAACGTGATGAAGATC	0.657		1	"""Mis, T"""	"""IGH@, ETV6"""	"""bladder, MM, T-cell lymphoma"""		"""Hypochondroplasia, Thanatophoric dysplasia"""		Saethre-Chotzen syndrome;Muenke syndrome																															Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"""L, E"""	0			4											47.0	46.0	46.0					4																	1807830		2202	4300	6502	1777628	SO:0001583	missense	2261	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	M64347	CCDS3353.1, CCDS3354.1, CCDS54706.1	4p16.3	2013-01-11	2008-08-01		ENSG00000068078	ENSG00000068078		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3690	protein-coding gene	gene with protein product		134934	"""achondroplasia, thanatophoric dwarfism"""	ACH		1847508	Standard	NM_000142		Approved	CEK2, JTK4, CD333	uc003gdu.2	P22607	OTTHUMG00000121148	ENST00000260795.2:c.1889T>C	4.37:g.1807830T>C	ENSP00000260795:p.Val630Ala	Somatic		Capture	Illumina HiSeq	Phase_I	1777628	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Missense_Mutation	SNP	ENST00000260795.2	37	CCDS3353.1	.	.	.	.	.	.	.	.	.	.	t	18.57	3.651523	0.67472	.	.	ENSG00000068078	ENST00000481110;ENST00000340107;ENST00000440486;ENST00000412135;ENST00000260795;ENST00000352904	D;D;D;D;D;D	0.91792	-2.91;-2.91;-2.91;-2.91;-2.91;-2.91	4.31	4.31	0.51392	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.063240	0.64402	D	0.000007	D	0.93311	0.7868	L	0.37466	1.105	0.80722	D	1	D;P;D;D	0.89917	0.995;0.72;0.996;1.0	D;B;D;D	0.77004	0.971;0.379;0.98;0.989	D	0.94015	0.7287	10	0.72032	D	0.01	.	13.7991	0.63188	0.0:0.0:0.0:1.0	.	632;518;630;631	P22607-2;P22607-3;P22607;F8W9L4	.;.;FGFR3_HUMAN;.	A	631;632;630;518;630;518	ENSP00000420533:V631A;ENSP00000339824:V632A;ENSP00000414914:V630A;ENSP00000412903:V518A;ENSP00000260795:V630A;ENSP00000231803:V518A	ENSP00000260795:V630A	V	+	2	0	FGFR3	1777628	1.000000	0.71417	1.000000	0.80357	0.760000	0.43138	7.693000	0.84214	1.723000	0.51488	0.363000	0.22086	GTG		FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142	
PRKG2	5593	hgsc.bcm.edu	37	4	82065433	82065433	+	Silent	SNP	T	T	C			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr4:82065433T>C	ENST00000395578.1	-	10	1322	c.1206A>G	c.(1204-1206)gaA>gaG	p.E402E	PRKG2_ENST00000418486.2_Silent_p.E402E|PRKG2_ENST00000264399.1_Silent_p.E402E|PRKG2_ENST00000545647.1_5'UTR|PRKG2_ENST00000509169.1_5'UTR			Q13237	KGP2_HUMAN	protein kinase, cGMP-dependent, type II	402					blood coagulation (GO:0007596)|circadian regulation of gene expression (GO:0032922)|nitric oxide metabolic process (GO:0046209)|protein phosphorylation (GO:0006468)|regulation of nitric-oxide synthase activity (GO:0050999)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)|protein kinase activity (GO:0004672)			NS(1)|breast(4)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	37						CCACATATCCTTCAAGGTATT	0.408																																																	0			4											173.0	160.0	164.0					4																	82065433		2203	4300	6503	82284457	SO:0001819	synonymous_variant	5593			X94612	CCDS3589.1, CCDS75150.1	4q13.1-q21.1	2009-07-10			ENSG00000138669	ENSG00000138669	2.7.11.1		9416	protein-coding gene	gene with protein product		601591				7498513	Standard	XM_005263126		Approved	cGKII, PRKGR2	uc003hmh.2	Q13237	OTTHUMG00000130296	ENST00000395578.1:c.1206A>G	4.37:g.82065433T>C		Somatic		Capture	Illumina HiSeq	Phase_I	82284457	B4DMX3|E7EPE6|O00125|O60916	Silent	SNP	ENST00000395578.1	37	CCDS3589.1																																																																																				PRKG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252639.1	NM_006259	
DSPP	1834	hgsc.bcm.edu	37	4	88537435	88537435	+	Silent	SNP	C	C	T			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr4:88537435C>T	ENST00000282478.7	+	4	3654	c.3621C>T	c.(3619-3621)agC>agT	p.S1207S	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.S1207S			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1207	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gtagtgatagcagtgacagca	0.557																																																	0			4																																								88756459	SO:0001819	synonymous_variant	1834			AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3621C>T	4.37:g.88537435C>T		Somatic		Capture	Illumina HiSeq	Phase_I	88756459	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																				DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
TENM3	55714	hgsc.bcm.edu	37	4	183696105	183696105	+	Silent	SNP	C	C	T	rs369200143		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr4:183696105C>T	ENST00000511685.1	+	24	5226	c.5103C>T	c.(5101-5103)gaC>gaT	p.D1701D	TENM3_ENST00000406950.2_Silent_p.D1701D|RP11-18D7.2_ENST00000513255.1_RNA			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1701					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										TTGGTTATGACGGCTCCCTCA	0.468																																																	0			4						C		0,3738		0,0,1869	35.0	35.0	35.0		5103	-9.5	0.2	4		35	1,8205		0,1,4102	no	coding-synonymous	ODZ3	NM_001080477.1		0,1,5971	TT,TC,CC		0.0122,0.0,0.0084		1701/2700	183696105	1,11943	1869	4103	5972	183933099	SO:0001819	synonymous_variant	55714			AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"""odz, odd Oz/ten-m homolog 3 (Drosophila)"""	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.5103C>T	4.37:g.183696105C>T		Somatic		Capture	Illumina HiSeq	Phase_I	183933099	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Silent	SNP	ENST00000511685.1	37	CCDS47165.1																																																																																				TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1		
KCNF1	3754	hgsc.bcm.edu	37	2	11053815	11053815	+	Silent	SNP	C	C	T	rs144040411	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr2:11053815C>T	ENST00000295082.1	+	1	1753	c.1263C>T	c.(1261-1263)acC>acT	p.T421T		NM_002236.4	NP_002227.2	Q9H3M0	KCNF1_HUMAN	potassium voltage-gated channel, subfamily F, member 1	421					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)			NS(1)|endometrium(2)|large_intestine(2)|lung(10)|ovary(2)|skin(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.128)		TCCTGGAGACCGCGGCCAAGC	0.617																																																	0			2											92.0	76.0	82.0					2																	11053815		2203	4300	6503	10971266	SO:0001819	synonymous_variant	3754			AF033382	CCDS1676.1	2p25	2011-07-05			ENSG00000162975	ENSG00000162975		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6246	protein-coding gene	gene with protein product		603787		KCNF		9434767, 16382104	Standard	NM_002236		Approved	Kv5.1, kH1, IK8	uc002rax.3	Q9H3M0	OTTHUMG00000119054	ENST00000295082.1:c.1263C>T	2.37:g.11053815C>T		Somatic		Capture	Illumina HiSeq	Phase_I	10971266	O43527|Q585L3	Silent	SNP	ENST00000295082.1	37	CCDS1676.1																																																																																				KCNF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239265.1	NM_002236	
E2F6	1876	hgsc.bcm.edu	37	2	11587813	11587813	+	Missense_Mutation	SNP	T	T	C			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr2:11587813T>C	ENST00000381525.3	-	6	1008	c.739A>G	c.(739-741)Agg>Ggg	p.R247G	E2F6_ENST00000307236.4_Missense_Mutation_p.R215G|E2F6_ENST00000362009.4_3'UTR|E2F6_ENST00000542100.1_Missense_Mutation_p.R172G|E2F6_ENST00000546212.1_Missense_Mutation_p.R172G	NM_198256.2	NP_937987.2	O75461	E2F6_HUMAN	E2F transcription factor 6	247	Transcription repression.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)	MLL1 complex (GO:0071339)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			cervix(1)|kidney(1)|lung(3)|prostate(1)|skin(2)	8	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.114)|OV - Ovarian serous cystadenocarcinoma(76;0.168)		CCTTCAGACCTTTTGTTACTG	0.458																																																	0			2											102.0	93.0	96.0					2																	11587813		1880	4105	5985	11505264	SO:0001583	missense	1876			AF041381	CCDS1680.2, CCDS62858.1, CCDS62859.1	2p25.1	2008-02-05			ENSG00000169016	ENSG00000169016			3120	protein-coding gene	gene with protein product		602944				9501179	Standard	NM_198256		Approved	E2F-6	uc002rbh.4	O75461	OTTHUMG00000090565	ENST00000381525.3:c.739A>G	2.37:g.11587813T>C	ENSP00000370936:p.Arg247Gly	Somatic		Capture	Illumina HiSeq	Phase_I	11505264	A8K2Z8|G5E936|O60544|Q53QY9|Q6Q9Z6|Q7Z2H6	Missense_Mutation	SNP	ENST00000381525.3	37	CCDS1680.2	.	.	.	.	.	.	.	.	.	.	T	9.749	1.167010	0.21621	.	.	ENSG00000169016	ENST00000381525;ENST00000307236;ENST00000542100;ENST00000546212	T;T;T;T	0.11495	2.77;2.77;2.77;2.77	4.88	-7.31	0.01441	.	3.278190	0.00654	N	0.000577	T	0.04048	0.0113	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34925	-0.9809	10	0.48119	T	0.1	17.3777	3.0861	0.06278	0.1853:0.1219:0.0931:0.5996	.	247;215	O75461;G5E936	E2F6_HUMAN;.	G	247;215;172;172	ENSP00000370936:R247G;ENSP00000302159:R215G;ENSP00000446315:R172G;ENSP00000438864:R172G	ENSP00000302159:R215G	R	-	1	2	E2F6	11505264	0.000000	0.05858	0.000000	0.03702	0.105000	0.19272	-0.524000	0.06222	-1.305000	0.02327	0.533000	0.62120	AGG		E2F6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207101.2	NM_001952	
ITSN2	50618	hgsc.bcm.edu	37	2	24438977	24438977	+	Missense_Mutation	SNP	C	C	T			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr2:24438977C>T	ENST00000355123.4	-	32	4374	c.3931G>A	c.(3931-3933)Gga>Aga	p.G1311R	AC009228.1_ENST00000413254.1_RNA|AC009228.1_ENST00000413989.1_RNA|AC009228.1_ENST00000430105.1_RNA|ITSN2_ENST00000361999.3_Missense_Mutation_p.G1284R	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	1311	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				endocytosis (GO:0006897)|positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|SH3/SH2 adaptor activity (GO:0005070)	p.G1310*(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(8)|large_intestine(11)|liver(3)|lung(28)|ovary(2)|stomach(1)	61	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGAGCTGCTCCATTAAGCTGG	0.522																																																	1	Substitution - Nonsense(1)	kidney(1)	2											79.0	79.0	79.0					2																	24438977		2203	4300	6503	24292481	SO:0001583	missense	50618			AB033082	CCDS1710.2, CCDS1711.2, CCDS46230.1	2p23.3	2013-09-19	2002-10-30		ENSG00000198399	ENSG00000198399		"""Rho guanine nucleotide exchange factors"", ""EF-hand domain containing"""	6184	protein-coding gene	gene with protein product	"""SH3 domain protein 1B"", ""SH3P18-like WASP associated protein"""	604464	"""SH3 domain protein 1B"""	SH3D1B		10922467, 11748279	Standard	NM_006277		Approved	KIAA1256, SWAP, SH3P18, SWA, PRO2015	uc002rfe.2	Q9NZM3	OTTHUMG00000090818	ENST00000355123.4:c.3931G>A	2.37:g.24438977C>T	ENSP00000347244:p.Gly1311Arg	Somatic		Capture	Illumina HiSeq	Phase_I	24292481	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Missense_Mutation	SNP	ENST00000355123.4	37	CCDS1710.2	.	.	.	.	.	.	.	.	.	.	C	22.3	4.273906	0.80580	.	.	ENSG00000198399	ENST00000361999;ENST00000355123;ENST00000380868	T;T;T	0.62788	0.0;0.0;0.0	5.38	5.38	0.77491	Dbl homology (DH) domain (5);	0.242049	0.20718	U	0.086974	T	0.78717	0.4327	L	0.61218	1.895	0.58432	D	0.999996	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.79685	-0.1700	10	0.87932	D	0	.	19.5838	0.95484	0.0:1.0:0.0:0.0	.	1284;1311	Q9NZM3-2;Q9NZM3	.;ITSN2_HUMAN	R	1284;1311;1284	ENSP00000354561:G1284R;ENSP00000347244:G1311R;ENSP00000370250:G1284R	ENSP00000347244:G1311R	G	-	1	0	ITSN2	24292481	1.000000	0.71417	0.967000	0.41034	0.985000	0.73830	7.395000	0.79876	2.711000	0.92665	0.650000	0.86243	GGA		ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277	
PLEKHH2	130271	hgsc.bcm.edu	37	2	43927014	43927014	+	Missense_Mutation	SNP	T	T	C			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr2:43927014T>C	ENST00000282406.4	+	8	1027	c.917T>C	c.(916-918)cTc>cCc	p.L306P		NM_172069.3	NP_742066.2	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	306					negative regulation of actin filament depolymerization (GO:0030835)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	actin binding (GO:0003779)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(24)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	56		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				ACATCCACCCTCTCCAGTCAC	0.517																																																	0			2											68.0	62.0	64.0					2																	43927014		2203	4300	6503	43780518	SO:0001583	missense	130271			AB095948	CCDS1812.1	2p22	2013-01-10			ENSG00000152527	ENSG00000152527		"""Pleckstrin homology (PH) domain containing"""	30506	protein-coding gene	gene with protein product		612723					Standard	NM_172069		Approved	KIAA2028, PLEKHH1L	uc010yny.2	Q8IVE3	OTTHUMG00000128657	ENST00000282406.4:c.917T>C	2.37:g.43927014T>C	ENSP00000282406:p.Leu306Pro	Somatic		Capture	Illumina HiSeq	Phase_I	43780518	Q5JPJ6|Q6P4Q1|Q8N3Q3	Missense_Mutation	SNP	ENST00000282406.4	37	CCDS1812.1	.	.	.	.	.	.	.	.	.	.	T	5.892	0.348670	0.11126	.	.	ENSG00000152527	ENST00000282406	T	0.74526	-0.85	5.54	5.54	0.83059	.	0.401318	0.25708	N	0.028821	T	0.66177	0.2763	L	0.50333	1.59	0.29250	N	0.872071	B;B	0.17667	0.004;0.023	B;B	0.18871	0.007;0.023	T	0.57562	-0.7790	10	0.21014	T	0.42	-5.8876	10.0883	0.42432	0.0:0.0748:0.0:0.9252	.	306;306	Q8IVE3;Q8IVE3-3	PKHH2_HUMAN;.	P	306	ENSP00000282406:L306P	ENSP00000282406:L306P	L	+	2	0	PLEKHH2	43780518	0.905000	0.30787	0.098000	0.21074	0.107000	0.19398	4.852000	0.62904	2.104000	0.64026	0.460000	0.39030	CTC		PLEKHH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250537.1	NM_172069	
SLC1A4	6509	hgsc.bcm.edu	37	2	65243581	65243581	+	Missense_Mutation	SNP	C	C	T			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr2:65243581C>T	ENST00000234256.3	+	5	1051	c.808C>T	c.(808-810)Cct>Tct	p.P270S	SLC1A4_ENST00000531327.1_Intron|SLC1A4_ENST00000493121.1_3'UTR	NM_003038.4	NP_003029.2	P43007	SATT_HUMAN	solute carrier family 1 (glutamate/neutral amino acid transporter), member 4	270					amino acid transport (GO:0006865)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|cognition (GO:0050890)|glutamine transport (GO:0006868)|hydroxyproline transport (GO:0034589)|ion transport (GO:0006811)|L-alanine transport (GO:0015808)|L-cystine transport (GO:0015811)|L-serine transport (GO:0015825)|proline transmembrane transport (GO:0035524)|proline transport (GO:0015824)|synaptic transmission, glutamatergic (GO:0035249)|threonine transport (GO:0015826)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|centrosome (GO:0005813)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intermediate filament (GO:0005882)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)|L-alanine transmembrane transporter activity (GO:0015180)|L-cystine transmembrane transporter activity (GO:0015184)|L-glutamine transmembrane transporter activity (GO:0015186)|L-hydroxyproline transmembrane transporter activity (GO:0034590)|L-proline transmembrane transporter activity (GO:0015193)|L-serine transmembrane transporter activity (GO:0015194)|L-threonine transmembrane transporter activity (GO:0015195)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|urinary_tract(1)	13					L-Alanine(DB00160)	TAGGTACGTACCTGTGGGCAT	0.507																																																	0			2											156.0	134.0	141.0					2																	65243581		2203	4300	6503	65097085	SO:0001583	missense	6509				CCDS1879.1, CCDS54362.1	2p15-p13	2013-05-22			ENSG00000115902	ENSG00000115902		"""Solute carriers"""	10942	protein-coding gene	gene with protein product	"""alanine/serine/cysteine/threonine transporter"""	600229				7896285, 8910405	Standard	NM_003038		Approved	SATT, ASCT1	uc010yqa.2	P43007	OTTHUMG00000129537	ENST00000234256.3:c.808C>T	2.37:g.65243581C>T	ENSP00000234256:p.Pro270Ser	Somatic		Capture	Illumina HiSeq	Phase_I	65097085	B7Z3C0|D6W5F0	Missense_Mutation	SNP	ENST00000234256.3	37	CCDS1879.1	.	.	.	.	.	.	.	.	.	.	C	33	5.283135	0.95489	.	.	ENSG00000115902	ENST00000448784;ENST00000234256	D	0.90844	-2.74	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	D	0.97639	0.9226	H	0.98612	4.28	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.98231	1.0483	10	0.87932	D	0	-37.3515	20.5632	0.99335	0.0:1.0:0.0:0.0	.	270;270	P43007;B2R7N6	SATT_HUMAN;.	S	190;270	ENSP00000234256:P270S	ENSP00000234256:P270S	P	+	1	0	SLC1A4	65097085	0.999000	0.42202	0.680000	0.29994	0.942000	0.58702	7.773000	0.85462	2.937000	0.99478	0.650000	0.86243	CCT		SLC1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251726.2	NM_003038	
ANKRD53	79998	hgsc.bcm.edu	37	2	71209119	71209119	+	Missense_Mutation	SNP	T	T	C			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr2:71209119T>C	ENST00000360589.3	+	4	705	c.671T>C	c.(670-672)cTg>cCg	p.L224P	ANKRD53_ENST00000272421.6_Missense_Mutation_p.L224P|ANKRD53_ENST00000457410.1_Missense_Mutation_p.L190P|AC007040.11_ENST00000606025.1_Intron|ANKRD53_ENST00000441349.1_Intron	NM_001115116.1	NP_001108588.1	Q8N9V6	ANR53_HUMAN	ankyrin repeat domain 53	224										endometrium(2)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	11						GACGGCTTGCTGGACTGTGTG	0.577																																																	0			2											77.0	67.0	71.0					2																	71209119		2203	4300	6503	71062627	SO:0001583	missense	79998			BC035234	CCDS1913.1, CCDS46321.1	2p13.3	2013-01-10			ENSG00000144031	ENSG00000144031		"""Ankyrin repeat domain containing"""	25691	protein-coding gene	gene with protein product							Standard	NM_024933		Approved	FLJ12056, FLJ36160	uc002shl.4	Q8N9V6	OTTHUMG00000129712	ENST00000360589.3:c.671T>C	2.37:g.71209119T>C	ENSP00000353796:p.Leu224Pro	Somatic		Capture	Illumina HiSeq	Phase_I	71062627	Q8IYP8	Missense_Mutation	SNP	ENST00000360589.3	37	CCDS46321.1	.	.	.	.	.	.	.	.	.	.	T	17.45	3.392890	0.62066	.	.	ENSG00000144031	ENST00000272421;ENST00000457410;ENST00000360589	T;T;T	0.68903	-0.36;-0.36;-0.36	5.47	5.47	0.80525	Ankyrin repeat-containing domain (4);	0.000000	0.44902	D	0.000402	T	0.68824	0.3043	N	0.25286	0.73	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.71797	-0.4484	10	0.66056	D	0.02	-22.1427	9.1627	0.37032	0.1623:0.0:0.0:0.8377	.	224;224	Q8N9V6;Q8N9V6-2	ANR53_HUMAN;.	P	224;190;224	ENSP00000272421:L224P;ENSP00000407004:L190P;ENSP00000353796:L224P	ENSP00000272421:L224P	L	+	2	0	ANKRD53	71062627	1.000000	0.71417	0.985000	0.45067	0.514000	0.34195	2.701000	0.47094	2.216000	0.71823	0.459000	0.35465	CTG		ANKRD53-004	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330275.2	NM_024933	
CTNNA2	1496	hgsc.bcm.edu	37	2	80101318	80101318	+	Silent	SNP	C	C	T			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr2:80101318C>T	ENST00000402739.4	+	5	707	c.702C>T	c.(700-702)gcC>gcT	p.A234A	CTNNA2_ENST00000466387.1_Silent_p.A234A|CTNNA2_ENST00000361291.4_Silent_p.A268A|CTNNA2_ENST00000496558.1_Silent_p.A234A|CTNNA2_ENST00000541047.1_Silent_p.A234A|CTNNA2_ENST00000540488.1_Silent_p.A234A	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	234					axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						CAGATGTCGCCGCTACGAGAG	0.577																																																	0			2											50.0	54.0	53.0					2																	80101318		2075	4219	6294	79954826	SO:0001819	synonymous_variant	1496				CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"""cadherin-associated protein, related"", ""cancer/testis antigen 114"""	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	ENST00000402739.4:c.702C>T	2.37:g.80101318C>T		Somatic		Capture	Illumina HiSeq	Phase_I	79954826	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Silent	SNP	ENST00000402739.4	37																																																																																					CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	NM_004389	
GLI2	2736	hgsc.bcm.edu	37	2	121729540	121729540	+	Silent	SNP	C	C	T	rs138680216		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr2:121729540C>T	ENST00000452319.1	+	8	1143	c.1083C>T	c.(1081-1083)gcC>gcT	p.A361A	GLI2_ENST00000435313.2_3'UTR|GLI2_ENST00000361492.4_Silent_p.A361A|GLI2_ENST00000314490.11_Silent_p.A33A					GLI family zinc finger 2											NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				GTGAGTCGGCCGTCAGCAGCA	0.597																																																	0			2						T		2,4404	4.2+/-10.8	0,2,2201	65.0	58.0	60.0		1083	-9.6	0.2	2	dbSNP_134	60	0,8600		0,0,4300	no	coding-synonymous	GLI2	NM_005270.4		0,2,6501	TT,TC,CC		0.0,0.0454,0.0154		361/1587	121729540	2,13004	2203	4300	6503	121446010	SO:0001819	synonymous_variant	2736				CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"""Zinc fingers, C2H2-type"""	4318	protein-coding gene	gene with protein product	"""tax-responsive element-2 holding protein"", ""tax helper protein 1"", ""tax helper protein 2"""	165230	"""GLI-Kruppel family member GLI2"", ""glioma-associated oncogene family zinc finger 2"""			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	ENST00000452319.1:c.1083C>T	2.37:g.121729540C>T		Somatic		Capture	Illumina HiSeq	Phase_I	121446010		Silent	SNP	ENST00000452319.1	37	CCDS33283.1																																																																																				GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270	
SMPD4	55627	hgsc.bcm.edu	37	2	130911373	130911373	+	Missense_Mutation	SNP	A	A	G			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr2:130911373A>G	ENST00000409031.1	-	17	3060	c.1912T>C	c.(1912-1914)Tac>Cac	p.Y638H	SMPD4_ENST00000473720.1_5'Flank|SMPD4_ENST00000443958.2_Missense_Mutation_p.Y302H|SMPD4_ENST00000351288.6_Missense_Mutation_p.Y609H|SMPD4_ENST00000431183.2_Missense_Mutation_p.Y536H|SMPD4_ENST00000339679.7_Missense_Mutation_p.Y496H|SMPD4_ENST00000453750.1_Missense_Mutation_p.Y387H|SMPD4_ENST00000426662.2_Missense_Mutation_p.Y274H|SMPD4_ENST00000452225.2_Missense_Mutation_p.Y379H	NM_017951.4	NP_060421.2	Q9NXE4	NSMA3_HUMAN	sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3)	599					cellular response to tumor necrosis factor (GO:0071356)|ceramide biosynthetic process (GO:0046513)|glycerophospholipid catabolic process (GO:0046475)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767)|sphingomyelin phosphodiesterase D activity (GO:0050290)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(17)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29	Colorectal(110;0.1)				Phosphatidylserine(DB00144)	TTGGCTGTGTAGGAGCCATTG	0.587																																																	0			2											82.0	81.0	81.0					2																	130911373		2203	4300	6503	130627843	SO:0001583	missense	55627			AF052134	CCDS2156.2, CCDS42751.1, CCDS54398.1	2q21.1	2009-11-06			ENSG00000136699	ENSG00000136699			32949	protein-coding gene	gene with protein product		610457				16517606	Standard	NM_001171083		Approved	FLJ20297, FLJ20756, nSMase-3, KIAA1418, NSMASE3, NET13	uc002tqr.2	Q9NXE4	OTTHUMG00000131624	ENST00000409031.1:c.1912T>C	2.37:g.130911373A>G	ENSP00000386531:p.Tyr638His	Somatic		Capture	Illumina HiSeq	Phase_I	130627843	B4DM23|B4DQ31|B4DRB8|B4DWK7|B4E0L6|E7ESA2|E9PCE6|Q6FI76|Q6P1P7|Q6ZT43|Q9H0M2|Q9NW20|Q9NWL2|Q9P2C9	Missense_Mutation	SNP	ENST00000409031.1	37	CCDS42751.1	.	.	.	.	.	.	.	.	.	.	.	13.27	2.188058	0.38609	.	.	ENSG00000136699	ENST00000351288;ENST00000409031;ENST00000431183;ENST00000453750;ENST00000443958;ENST00000339679;ENST00000452225;ENST00000426662;ENST00000457039;ENST00000449159	.	.	.	3.94	3.94	0.45596	.	0.466770	0.24152	N	0.041072	T	0.64000	0.2559	L	0.53249	1.67	0.38383	D	0.94518	P;B;D;D;D;D;D;D;P;D	0.58620	0.941;0.333;0.966;0.966;0.983;0.958;0.973;0.98;0.911;0.979	P;B;P;P;P;P;P;P;P;P	0.60886	0.735;0.08;0.735;0.735;0.731;0.487;0.751;0.861;0.563;0.88	T	0.62101	-0.6925	9	0.19147	T	0.46	.	10.7651	0.46288	1.0:0.0:0.0:0.0	.	274;379;536;496;387;570;599;638;645;170	B4E0L6;B4DQ31;E7ESA2;B4E0T5;B4DM23;Q9NXE4-2;Q9NXE4;B1PBA3;Q9NXE4-4;Q9NXE4-5	.;.;.;.;.;.;NSMA3_HUMAN;.;.;.	H	609;638;536;387;302;496;379;274;235;148	.	ENSP00000339721:Y496H	Y	-	1	0	SMPD4	130627843	1.000000	0.71417	0.710000	0.30468	0.024000	0.10985	6.805000	0.75191	1.404000	0.46819	0.454000	0.30748	TAC		SMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254516.3	NM_017751	
NCKAP5	344148	hgsc.bcm.edu	37	2	133541426	133541426	+	Silent	SNP	C	C	T	rs189440819		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr2:133541426C>T	ENST00000409261.1	-	14	3331	c.2958G>A	c.(2956-2958)ccG>ccA	p.P986P	NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000473859.1_5'Flank|NCKAP5_ENST00000317721.6_Silent_p.P986P	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	986										NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						CTGTCGTGGCCGGATTAGAAG	0.507													c|||	1	0.000199681	0.0	0.0	5008	,	,		17844	0.001		0.0	False		,,,				2504	0.0																0			2						T	,	1,3805		0,1,1902	31.0	34.0	33.0		2958,	-1.4	0.0	2		33	0,8240		0,0,4120	no	coding-synonymous,intron	NCKAP5	NM_207363.2,NM_207481.3	,	0,1,6022	TT,TC,CC		0.0,0.0263,0.0083	,	986/1910,	133541426	1,12045	1903	4120	6023	133257896	SO:0001819	synonymous_variant	0			AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"""Nck associated protein 5"", ""peripheral clock protein"""	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.2958G>A	2.37:g.133541426C>T		Somatic		Capture	Illumina HiSeq	Phase_I	133257896	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Silent	SNP	ENST00000409261.1	37	CCDS46418.1																																																																																				NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481	
FMNL2	114793	hgsc.bcm.edu	37	2	153476069	153476069	+	Silent	SNP	C	C	A			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr2:153476069C>A	ENST00000288670.9	+	15	2041	c.1674C>A	c.(1672-1674)ccC>ccA	p.P558P	FMNL2_ENST00000475377.2_5'Flank	NM_052905.3	NP_443137.2	Q96PY5	FMNL2_HUMAN	formin-like 2	558	Pro-rich.				cortical actin cytoskeleton organization (GO:0030866)|cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)		p.P558P(1)		central_nervous_system(2)|endometrium(3)|large_intestine(5)|liver(2)|lung(3)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	23						CGCCGCCGccccctcctccac	0.592																																																	1	Substitution - coding silent(1)	ovary(1)	2											4.0	4.0	4.0					2																	153476069		1457	3387	4844	153184315	SO:0001819	synonymous_variant	114793			AB067489	CCDS46429.1	2q23.3	2008-02-05	2003-12-02	2003-12-03	ENSG00000157827	ENSG00000157827			18267	protein-coding gene	gene with protein product			"""formin homology 2 domain containing 2"""	FHOD2			Standard	XM_005246263		Approved	KIAA1902	uc002tye.3	Q96PY5	OTTHUMG00000154035	ENST00000288670.9:c.1674C>A	2.37:g.153476069C>A		Somatic		Capture	Illumina HiSeq	Phase_I	153184315	B2RZH5|Q14CC9|Q4ZG52|Q8N3E0	Silent	SNP	ENST00000288670.9	37	CCDS46429.1																																																																																				FMNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333582.2	NM_052905	
TTN	7273	hgsc.bcm.edu	37	2	179497919	179497919	+	Missense_Mutation	SNP	A	A	G			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr2:179497919A>G	ENST00000591111.1	-	183	38382	c.38158T>C	c.(38158-38160)Tcc>Ccc	p.S12720P	TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.S5421P|TTN_ENST00000460472.2_Missense_Mutation_p.S5296P|TTN_ENST00000342175.6_Missense_Mutation_p.S5488P|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.S11793P|TTN_ENST00000589042.1_Missense_Mutation_p.S14361P|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589907.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12720			S -> F (in a metastatic melanoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTTACAGGGGAAGCTGTCAAA	0.413																																																	0			2											52.0	51.0	51.0					2																	179497919		1833	4086	5919	179206164	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.38158T>C	2.37:g.179497919A>G	ENSP00000465570:p.Ser12720Pro	Somatic		Capture	Illumina HiSeq	Phase_I	179206164	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	A	12.77	2.037485	0.35989	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.39406	1.08;1.08;1.08;1.08	6.17	6.17	0.99709	Immunoglobulin subtype (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.72622	0.3483	M	0.91510	3.215	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.80764	0.994;0.994;0.994;0.994	T	0.79230	-0.1889	9	0.87932	D	0	.	16.8222	0.85835	1.0:0.0:0.0:0.0	.	5296;5421;5488;12720	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	P	11793;5296;5488;5421;5296	ENSP00000343764:S11793P;ENSP00000434586:S5296P;ENSP00000340554:S5488P;ENSP00000352154:S5421P	ENSP00000340554:S5488P	S	-	1	0	TTN	179206164	1.000000	0.71417	1.000000	0.80357	0.719000	0.41307	9.281000	0.95811	2.371000	0.80710	0.533000	0.62120	TCC		TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ASIC4	55515	hgsc.bcm.edu	37	2	220402397	220402397	+	Missense_Mutation	SNP	C	C	G			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr2:220402397C>G	ENST00000347842.3	+	8	1783	c.1769C>G	c.(1768-1770)aCc>aGc	p.T590S	ASIC4_ENST00000358078.4_Missense_Mutation_p.T609S	NM_182847.2	NP_878267.2	Q96FT7	ASIC4_HUMAN	acid-sensing (proton-gated) ion channel family member 4	590					ion transmembrane transport (GO:0034220)|sodium ion transmembrane transport (GO:0035725)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)	ion channel activity (GO:0005216)|sodium channel activity (GO:0005272)|sodium ion transmembrane transporter activity (GO:0015081)										CGTCCCAAGACCCCCCTGCGG	0.597																																																	0			2											35.0	35.0	35.0					2																	220402397		2203	4300	6503	220110641	SO:0001583	missense	55515			AJ271643	CCDS2442.1	2q36.1	2012-02-22	2012-02-22	2012-02-22	ENSG00000072182	ENSG00000072182		"""Ion channels / Acid-sensing (proton-gated) ion channels"""	21263	protein-coding gene	gene with protein product		606715	"""amiloride-sensitive cation channel 4, pituitary"", ""amiloride-sensitive cation channel family member 4, pituitary"""	ACCN4		10852210	Standard	NM_182847		Approved	BNAC4	uc002vma.3	Q96FT7	OTTHUMG00000058928	ENST00000347842.3:c.1769C>G	2.37:g.220402397C>G	ENSP00000326627:p.Thr590Ser	Somatic		Capture	Illumina HiSeq	Phase_I	220110641	Q53SB7|Q6GMS1|Q6PIN9|Q9NQA4	Missense_Mutation	SNP	ENST00000347842.3	37	CCDS2442.1	.	.	.	.	.	.	.	.	.	.	C	12.39	1.923549	0.33908	.	.	ENSG00000072182	ENST00000347842;ENST00000358078	T;T	0.61274	0.12;0.12	4.76	4.76	0.60689	.	0.838767	0.10824	N	0.630143	T	0.28532	0.0706	N	0.00841	-1.15	0.38282	D	0.942445	B;B	0.16802	0.006;0.019	B;B	0.20955	0.002;0.032	T	0.17592	-1.0364	10	0.07482	T	0.82	-30.8304	16.5063	0.84273	0.0:1.0:0.0:0.0	.	590;609	Q96FT7;Q96FT7-4	ACCN4_HUMAN;.	S	590;609	ENSP00000326627:T590S;ENSP00000350786:T609S	ENSP00000326627:T590S	T	+	2	0	ACCN4	220110641	0.986000	0.35501	1.000000	0.80357	0.996000	0.88848	2.898000	0.48672	2.641000	0.89580	0.591000	0.81541	ACC		ASIC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000130263.1	NM_018674	
HJURP	55355	hgsc.bcm.edu	37	2	234749731	234749731	+	Silent	SNP	T	T	C			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr2:234749731T>C	ENST00000411486.2	-	8	1760	c.1695A>G	c.(1693-1695)ccA>ccG	p.P565P	HJURP_ENST00000432087.1_Silent_p.P511P|HJURP_ENST00000441687.1_Silent_p.P480P|HJURP_ENST00000434039.1_5'Flank	NM_018410.3	NP_060880.3	Q8NCD3	HJURP_HUMAN	Holliday junction recognition protein	565					cell cycle (GO:0007049)|CENP-A containing nucleosome assembly (GO:0034080)|chromosome segregation (GO:0007059)|nucleosome assembly (GO:0006334)|regulation of DNA binding (GO:0051101)|regulation of protein complex assembly (GO:0043254)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|identical protein binding (GO:0042802)			NS(2)|breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(3)|lung(11)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Breast(86;0.00204)|all_lung(227;0.00433)|Renal(207;0.00685)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0719)|Lung SC(224;0.128)		Epithelial(121;2.01e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000186)|Lung(119;0.00521)|LUSC - Lung squamous cell carcinoma(224;0.00829)		CTTCTTTATCTGGGACTGAAA	0.448																																																	0			2											96.0	100.0	99.0					2																	234749731		2203	4300	6503	234414470	SO:0001819	synonymous_variant	55355				CCDS33406.1, CCDS63166.1, CCDS63167.1	2q37.1	2007-12-06			ENSG00000123485	ENSG00000123485			25444	protein-coding gene	gene with protein product		612667				17823411	Standard	NM_001282962		Approved	DKFZp762E1312, URLC9, hFLEG1, FAKTS	uc002vvg.3	Q8NCD3	OTTHUMG00000059125	ENST00000411486.2:c.1695A>G	2.37:g.234749731T>C		Somatic		Capture	Illumina HiSeq	Phase_I	234414470	A8IRH5|B4DWR0|B4DZV4|Q9BUT2|Q9NSL8	Silent	SNP	ENST00000411486.2	37	CCDS33406.1																																																																																				HJURP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000130996.6	NM_018410	
MLLT3	4300	hgsc.bcm.edu	37	9	20414298	20414298	+	Silent	SNP	A	A	G	rs143254940	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr9:20414298A>G	ENST00000380338.4	-	5	832	c.546T>C	c.(544-546)agT>agC	p.S182S	MLLT3_ENST00000475957.1_5'UTR|MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000429426.2_Silent_p.S179S	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3	182	Poly-Ser.				anterior/posterior pattern specification (GO:0009952)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of transcription, DNA-templated (GO:0006355)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		tgctgctgctactgctgctgc	0.522			T	MLL	ALL								A|||	7	0.00139776	0.0008	0.0014	5008	,	,		12006	0.0		0.005	False		,,,				2504	0.0							Dom	yes		9	9p22	4300	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 (AF9)"""		L	0			9						A		5,4401	6.2+/-15.9	0,5,2198	41.0	49.0	46.0		546	-7.1	0.9	9	dbSNP_134	46	34,8564	15.3+/-51.7	1,32,4266	no	coding-synonymous	MLLT3	NM_004529.2		1,37,6464	GG,GA,AA		0.3954,0.1135,0.2999		182/569	20414298	39,12965	2203	4299	6502	20404298	SO:0001819	synonymous_variant	4300			L13744	CCDS6494.1	9p22	2008-02-05	2001-11-28		ENSG00000171843	ENSG00000171843			7136	protein-coding gene	gene with protein product		159558	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 3"""			8506309, 8414510	Standard	NM_001286691		Approved	AF-9, AF9, YEATS3	uc003zoe.2	P42568	OTTHUMG00000019650	ENST00000380338.4:c.546T>C	9.37:g.20414298A>G		Somatic		Capture	Illumina HiSeq	Phase_I	20404298	B1AMQ2|B2R7B3|B7Z755|D3DRJ8|Q8IVB0	Silent	SNP	ENST00000380338.4	37	CCDS6494.1																																																																																				MLLT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051872.1	NM_004529	
TAF1L	138474	hgsc.bcm.edu	37	9	32630106	32630106	+	Missense_Mutation	SNP	G	G	T	rs202147126		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr9:32630106G>T	ENST00000242310.4	-	1	5561	c.5472C>A	c.(5470-5472)caC>caA	p.H1824Q		NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1824			H -> Q (in a lung adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)	p.H1824Q(2)		breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		TTCATTTTCCGTGCCCATCCT	0.493																																																	2	Substitution - Missense(2)	lung(2)	9											191.0	138.0	156.0					9																	32630106		2203	4300	6503	32620106	SO:0001583	missense	138474			AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"""TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"""			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.5472C>A	9.37:g.32630106G>T	ENSP00000418379:p.His1824Gln	Somatic		Capture	Illumina HiSeq	Phase_I	32620106	Q0VG57	Missense_Mutation	SNP	ENST00000242310.4	37	CCDS35003.1	.	.	.	.	.	.	.	.	.	.	A	9.056	0.993239	0.19043	.	.	ENSG00000122728	ENST00000242310	T	0.07114	3.22	0.479	0.479	0.16796	.	0.268520	0.39341	N	0.001400	T	0.02767	0.0083	N	0.08118	0	0.20563	N	0.999884	B	0.32245	0.361	B	0.17722	0.019	T	0.42832	-0.9428	10	0.31617	T	0.26	.	4.0672	0.09866	0.7251:0.0:0.2749:0.0	.	1824	Q8IZX4	TAF1L_HUMAN	Q	1824	ENSP00000418379:H1824Q	ENSP00000418379:H1824Q	H	-	3	2	TAF1L	32620106	1.000000	0.71417	0.981000	0.43875	0.132000	0.20833	3.993000	0.56987	-0.761000	0.04670	-1.298000	0.01336	CAC		TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2		
CDK20	23552	hgsc.bcm.edu	37	9	90586125	90586125	+	Missense_Mutation	SNP	C	C	G			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr9:90586125C>G	ENST00000325303.8	-	3	620	c.315G>C	c.(313-315)aaG>aaC	p.K105N	CDK20_ENST00000605159.1_Missense_Mutation_p.K105N|CDK20_ENST00000375871.4_Missense_Mutation_p.K105N|CDK20_ENST00000375883.3_Missense_Mutation_p.K105N|CDK20_ENST00000336654.5_Missense_Mutation_p.K118N	NM_001039803.2	NP_001034892.1	Q8IZL9	CDK20_HUMAN	cyclin-dependent kinase 20	105	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|cell division (GO:0051301)|multicellular organismal development (GO:0007275)	cilium (GO:0005929)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			skin(1)	1						GCAGGTAGCTCTTGACCTGTG	0.602																																																	0			9											104.0	75.0	85.0					9																	90586125		2203	4300	6503	89775945	SO:0001583	missense	0			AF035013	CCDS6677.1, CCDS6678.1, CCDS35060.1, CCDS55324.1, CCDS65075.1	9q22.1	2011-11-08	2009-12-16	2009-12-16	ENSG00000156345	ENSG00000156345		"""Cyclin-dependent kinases"""	21420	protein-coding gene	gene with protein product		610076	"""cell cycle related kinase"""	CCRK		19884882	Standard	NM_178432		Approved	p42	uc004apr.3	Q8IZL9	OTTHUMG00000020161	ENST00000325303.8:c.315G>C	9.37:g.90586125C>G	ENSP00000322343:p.Lys105Asn	Somatic		Capture	Illumina HiSeq	Phase_I	89775945	A2A389|A2A390|B4DQX1|O95137|Q5EDC4|Q5VYW1|Q9BUF4	Missense_Mutation	SNP	ENST00000325303.8	37	CCDS35060.1	.	.	.	.	.	.	.	.	.	.	.	18.61	3.660113	0.67586	.	.	ENSG00000156345	ENST00000375883;ENST00000336654;ENST00000375871;ENST00000325303;ENST00000286878	T;T;T;T	0.68479	-0.33;-0.33;-0.33;-0.33	3.93	3.93	0.45458	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	D	0.84777	0.5547	M	0.93763	3.455	0.54753	D	0.999983	D;D;D;D	0.89917	0.998;1.0;1.0;1.0	D;D;D;D	0.87578	0.969;0.998;0.998;0.995	D	0.88231	0.2903	10	0.87932	D	0	-30.134	12.156	0.54077	0.0:1.0:0.0:0.0	.	105;118;105;105	Q8IZL9-2;A2A390;E7EQ88;Q8IZL9	.;.;.;CDK20_HUMAN	N	105;118;105;105;105	ENSP00000365043:K105N;ENSP00000338975:K118N;ENSP00000365031:K105N;ENSP00000322343:K105N	ENSP00000286878:K105N	K	-	3	2	CDK20	89775945	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	0.774000	0.26675	2.138000	0.66242	0.462000	0.41574	AAG		CDK20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214996.1	NM_012119	
PTCH1	5727	hgsc.bcm.edu	37	9	98248057	98248057	+	Missense_Mutation	SNP	T	T	C			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr9:98248057T>C	ENST00000331920.6	-	3	793	c.494A>G	c.(493-495)gAa>gGa	p.E165G	PTCH1_ENST00000418258.1_Missense_Mutation_p.E14G|PTCH1_ENST00000468211.2_Missense_Mutation_p.E99G|PTCH1_ENST00000437951.1_Missense_Mutation_p.E99G|PTCH1_ENST00000430669.2_Missense_Mutation_p.E99G|PTCH1_ENST00000421141.1_Missense_Mutation_p.E14G|PTCH1_ENST00000375274.2_Missense_Mutation_p.E164G|PTCH1_ENST00000548379.1_5'UTR|PTCH1_ENST00000429896.2_Missense_Mutation_p.E14G	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	165					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)			NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				ATTAGCACCTTCTTCTTTAGG	0.483																																																	0			9											227.0	236.0	233.0					9																	98248057		2203	4300	6503	97287878	SO:0001583	missense	5727			AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"""patched (Drosophila) homolog"", ""patched homolog (Drosophila)"", ""patched homolog 1 (Drosophila)"""	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.494A>G	9.37:g.98248057T>C	ENSP00000332353:p.Glu165Gly	Somatic		Capture	Illumina HiSeq	Phase_I	97287878	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Missense_Mutation	SNP	ENST00000331920.6	37	CCDS6714.1	.	.	.	.	.	.	.	.	.	.	T	14.19	2.462250	0.43736	.	.	ENSG00000185920	ENST00000331920;ENST00000437951;ENST00000421141;ENST00000418258;ENST00000430669;ENST00000429896;ENST00000375274;ENST00000553011;ENST00000551845;ENST00000547672;ENST00000546820;ENST00000468211;ENST00000551630	D;D;D;D;D;D;D;D;D;D;D;D;T	0.91351	-1.83;-2.82;-2.81;-2.81;-2.82;-2.81;-2.83;-2.17;-2.17;-2.17;-2.17;-1.83;0.95	5.86	4.66	0.58398	.	0.263096	0.45867	D	0.000337	D	0.84902	0.5575	L	0.31926	0.97	0.45607	D	0.998548	B;B;B	0.15141	0.004;0.011;0.012	B;B;B	0.22386	0.014;0.039;0.006	T	0.79909	-0.1604	10	0.25106	T	0.35	-13.0371	12.7596	0.57356	0.0:0.0:0.1368:0.8632	.	99;164;165	Q13635-3;Q13635-2;Q13635	.;.;PTC1_HUMAN	G	165;99;14;14;99;14;164;14;14;14;14;99;14	ENSP00000332353:E165G;ENSP00000389744:E99G;ENSP00000399981:E14G;ENSP00000396135:E14G;ENSP00000410287:E99G;ENSP00000414823:E14G;ENSP00000364423:E164G;ENSP00000447797:E14G;ENSP00000447008:E14G;ENSP00000447878:E14G;ENSP00000448843:E14G;ENSP00000449745:E99G;ENSP00000450131:E14G	ENSP00000332353:E165G	E	-	2	0	PTCH1	97287878	1.000000	0.71417	1.000000	0.80357	0.157000	0.22087	5.919000	0.70005	2.241000	0.73720	0.482000	0.46254	GAA		PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264	
SLC25A25	114789	hgsc.bcm.edu	37	9	130869700	130869700	+	Missense_Mutation	SNP	A	A	G			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr9:130869700A>G	ENST00000373064.5	+	10	1650	c.1387A>G	c.(1387-1389)Acc>Gcc	p.T463A	SLC25A25_ENST00000373069.5_Missense_Mutation_p.T509A|SLC25A25_ENST00000373068.2_Missense_Mutation_p.T497A|SLC25A25_ENST00000433501.1_Missense_Mutation_p.T360A|SLC25A25_ENST00000373066.5_Missense_Mutation_p.T495A|RP11-395P17.11_ENST00000602939.1_RNA|SLC25A25_ENST00000432073.2_Missense_Mutation_p.T483A	NM_052901.4	NP_443133.2	Q6KCM7	SCMC2_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 25	463					adipose tissue development (GO:0060612)|ATP metabolic process (GO:0046034)|calcium ion transmembrane transport (GO:0070588)|camera-type eye development (GO:0043010)|cellular respiration (GO:0045333)|multicellular organism growth (GO:0035264)|response to activity (GO:0014823)|response to dietary excess (GO:0002021)|response to food (GO:0032094)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(3)	10						CCTGAAGATCACCCTGGGCGT	0.652																																																	0			9											73.0	79.0	77.0					9																	130869700		2203	4300	6503	129909521	SO:0001583	missense	114789			AJ619963	CCDS6890.1, CCDS35151.1, CCDS48031.1, CCDS59146.1	9q34	2013-05-22			ENSG00000148339	ENSG00000148339		"""Solute carriers"", ""EF-hand domain containing"""	20663	protein-coding gene	gene with protein product		608745				15123600	Standard	NM_052901		Approved	KIAA1896, PCSCL, MCSC	uc004btb.4	Q6KCM7	OTTHUMG00000020736	ENST00000373064.5:c.1387A>G	9.37:g.130869700A>G	ENSP00000362155:p.Thr463Ala	Somatic		Capture	Illumina HiSeq	Phase_I	129909521	Q5SYW7|Q5SYW8|Q5SYX3|Q5VWU2|Q5VWU3|Q5VWU4|Q6KCM4|Q6KCM6|Q6UX48|Q705K2|Q96PZ1|Q9BSA6	Missense_Mutation	SNP	ENST00000373064.5	37	CCDS6890.1	.	.	.	.	.	.	.	.	.	.	A	8.262	0.811479	0.16537	.	.	ENSG00000148339	ENST00000373068;ENST00000373069;ENST00000432073;ENST00000373066;ENST00000373064;ENST00000433501	T;T;T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19;-1.19;-1.19	5.41	5.41	0.78517	.	0.163456	0.56097	D	0.000039	T	0.54711	0.1875	N	0.02751	-0.505	0.50813	D	0.999895	B;B;B;B	0.13594	0.002;0.0;0.001;0.008	B;B;B;B	0.14023	0.01;0.001;0.006;0.006	T	0.54043	-0.8352	10	0.13853	T	0.58	-44.8174	14.6343	0.68678	1.0:0.0:0.0:0.0	.	463;495;483;497	Q6KCM7;Q6KCM7-5;Q6KCM7-4;Q6KCM7-2	SCMC2_HUMAN;.;.;.	A	497;509;483;495;463;360	ENSP00000362159:T497A;ENSP00000362160:T509A;ENSP00000410053:T483A;ENSP00000362157:T495A;ENSP00000362155:T463A;ENSP00000401672:T360A	ENSP00000362155:T463A	T	+	1	0	SLC25A25	129909521	0.987000	0.35691	1.000000	0.80357	0.944000	0.59088	2.914000	0.48797	2.042000	0.60477	0.533000	0.62120	ACC		SLC25A25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054407.1	NM_052901	
NUP188	23511	hgsc.bcm.edu	37	9	131755942	131755942	+	Missense_Mutation	SNP	A	A	G			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr9:131755942A>G	ENST00000372577.2	+	27	3007	c.2986A>G	c.(2986-2988)Agg>Ggg	p.R996G		NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	996					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				breast(2)|central_nervous_system(3)|endometrium(6)|kidney(4)|large_intestine(9)|lung(20)|ovary(6)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	60						GCAGGATCGGAGGGACAGTGC	0.512																																																	0			9											104.0	85.0	92.0					9																	131755942		2203	4300	6503	130795763	SO:0001583	missense	23511			D79991	CCDS35156.1	9q34.13	2014-01-28	2004-03-19	2004-03-24	ENSG00000095319	ENSG00000095319			17859	protein-coding gene	gene with protein product		615587	"""KIAA0169"""	KIAA0169		11029043	Standard	NM_015354		Approved		uc004bws.2	Q5SRE5	OTTHUMG00000020768	ENST00000372577.2:c.2986A>G	9.37:g.131755942A>G	ENSP00000361658:p.Arg996Gly	Somatic		Capture	Illumina HiSeq	Phase_I	130795763	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Missense_Mutation	SNP	ENST00000372577.2	37	CCDS35156.1	.	.	.	.	.	.	.	.	.	.	A	18.95	3.730863	0.69074	.	.	ENSG00000095319	ENST00000356693;ENST00000372577	T	0.34667	1.35	5.55	3.63	0.41609	.	0.000000	0.85682	D	0.000000	T	0.56906	0.2017	M	0.67953	2.075	0.58432	D	0.999998	D;D	0.89917	1.0;0.993	D;D	0.79784	0.993;0.977	T	0.60156	-0.7318	10	0.72032	D	0.01	-0.0024	13.7712	0.63026	0.3002:0.6998:0.0:0.0	.	329;996	E9PET9;Q5SRE5	.;NU188_HUMAN	G	885;996	ENSP00000361658:R996G	ENSP00000349125:R885G	R	+	1	2	NUP188	130795763	0.960000	0.32886	0.677000	0.29947	0.965000	0.64279	2.230000	0.42999	0.746000	0.32786	-0.213000	0.12676	AGG		NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2		
GFI1B	8328	hgsc.bcm.edu	37	9	135865173	135865173	+	Silent	SNP	C	C	A			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr9:135865173C>A	ENST00000339463.3	+	10	1512	c.693C>A	c.(691-693)cgC>cgA	p.R231R	GFI1B_ENST00000372122.1_Silent_p.R231R|GFI1B_ENST00000450530.1_Silent_p.R231R|GFI1B_ENST00000372123.1_Silent_p.R185R|GFI1B_ENST00000534944.1_Silent_p.R185R|GFI1B_ENST00000372124.1_Silent_p.R185R			Q5VTD9	GFI1B_HUMAN	growth factor independent 1B transcription repressor	231	Interaction with ARIH2.|Mediates interaction with GATA1.		R -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cell proliferation (GO:0008283)|chromatin modification (GO:0016568)|multicellular organismal development (GO:0007275)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of histone H3-K9 methylation (GO:0051574)|regulation of erythrocyte differentiation (GO:0045646)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II transcription factor binding (GO:0001085)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)	21				OV - Ovarian serous cystadenocarcinoma(145;9.04e-07)|Epithelial(140;1.17e-05)		CCTTCAAGCGCTCGTCCACGC	0.652																																																	0			9											73.0	60.0	64.0					9																	135865173		2203	4300	6503	134854994	SO:0001819	synonymous_variant	8328			AF081946	CCDS6957.1, CCDS48049.1	9q34.13	2014-09-17	2007-10-04		ENSG00000165702	ENSG00000165702		"""Zinc fingers, C2H2-type"""	4238	protein-coding gene	gene with protein product		604383	"""growth factor independent 1B (potential regulator of CDKN1A, translocated in CML)"""			9878267	Standard	NM_001135031		Approved		uc004ccg.3	Q5VTD9	OTTHUMG00000020848	ENST00000339463.3:c.693C>A	9.37:g.135865173C>A		Somatic		Capture	Illumina HiSeq	Phase_I	134854994	O95270|Q5VTD8|Q6FHZ2|Q6T888	Silent	SNP	ENST00000339463.3	37	CCDS6957.1																																																																																				GFI1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393840.1	NM_004188	
CACNA1B	774	hgsc.bcm.edu	37	9	140852115	140852115	+	Missense_Mutation	SNP	C	C	T			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr9:140852115C>T	ENST00000371372.1	+	10	1454	c.1309C>T	c.(1309-1311)Cgg>Tgg	p.R437W	CACNA1B_ENST00000371363.1_Missense_Mutation_p.R437W|CACNA1B_ENST00000277551.2_Missense_Mutation_p.R437W|CACNA1B_ENST00000371357.1_Missense_Mutation_p.R438W|CACNA1B_ENST00000371355.4_Missense_Mutation_p.R438W|CACNA1B_ENST00000277549.5_5'UTR	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	437					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	GGGAGAGGACCGGTTTGCAGA	0.567																																																	0			9											85.0	107.0	100.0					9																	140852115		2147	4251	6398	139971936	SO:0001583	missense	774			AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.1309C>T	9.37:g.140852115C>T	ENSP00000360423:p.Arg437Trp	Somatic		Capture	Illumina HiSeq	Phase_I	139971936	B1AQK5	Missense_Mutation	SNP	ENST00000371372.1	37	CCDS59522.1	.	.	.	.	.	.	.	.	.	.	c	22.7	4.318245	0.81469	.	.	ENSG00000148408	ENST00000371372;ENST00000277551;ENST00000371363;ENST00000371357;ENST00000371355	D;D;D;D;D	0.96427	-4.0;-4.01;-4.0;-3.99;-3.99	4.93	4.93	0.64822	.	1.149610	0.06455	N	0.728365	D	0.96531	0.8868	L	0.47190	1.495	0.80722	D	1	D	0.69078	0.997	P	0.53313	0.723	D	0.91977	0.5591	10	0.66056	D	0.02	.	13.89	0.63733	0.0:0.8473:0.1526:0.0	.	437	B1AQK6	.	W	437;437;437;438;438	ENSP00000360423:R437W;ENSP00000277551:R437W;ENSP00000360414:R437W;ENSP00000360408:R438W;ENSP00000360406:R438W	ENSP00000277551:R437W	R	+	1	2	CACNA1B	139971936	1.000000	0.71417	0.987000	0.45799	0.944000	0.59088	5.238000	0.65366	2.311000	0.77944	0.299000	0.19835	CGG		CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718	
BRCA2	675	hgsc.bcm.edu	37	13	32911252	32911252	+	Silent	SNP	C	C	T			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr13:32911252C>T	ENST00000380152.3	+	11	2993	c.2760C>T	c.(2758-2760)ccC>ccT	p.P920P	BRCA2_ENST00000544455.1_Silent_p.P920P			P51587	BRCA2_HUMAN	breast cancer 2, early onset	920	Interaction with NPM1.				brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		TAAACGAACCCATTTTCAAGA	0.343			"""D, Mis, N, F, S"""		"""breast, ovarian, pancreatic"""	"""breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"""		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)		yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"""L, E"""	0			13	GRCh37	CD031025	BRCA2	D	rs80359346						67.0	70.0	69.0					13																	32911252		2203	4297	6500	31809252	SO:0001819	synonymous_variant	675	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"""Fanconi anemia, complementation groups"""	1101	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 2"""	600185	"""Fanconi anemia, complementation group D1"""	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.2760C>T	13.37:g.32911252C>T		Somatic		Capture	Illumina HiSeq	Phase_I	31809252	O00183|O15008|Q13879|Q5TBJ7	Silent	SNP	ENST00000380152.3	37	CCDS9344.1																																																																																				BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059	
BRCA2	675	hgsc.bcm.edu	37	13	32913536	32913536	+	Missense_Mutation	SNP	A	A	G	rs397507756		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr13:32913536A>G	ENST00000380152.3	+	11	5277	c.5044A>G	c.(5044-5046)Agt>Ggt	p.S1682G	BRCA2_ENST00000544455.1_Missense_Mutation_p.S1682G			P51587	BRCA2_HUMAN	breast cancer 2, early onset	1682	Interaction with POLH.				brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		AACTTCTGTGAGTCAGACTTC	0.328			"""D, Mis, N, F, S"""		"""breast, ovarian, pancreatic"""	"""breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"""		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)		yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"""L, E"""	0			13											33.0	36.0	35.0					13																	32913536		2187	4287	6474	31811536	SO:0001583	missense	675	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"""Fanconi anemia, complementation groups"""	1101	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 2"""	600185	"""Fanconi anemia, complementation group D1"""	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.5044A>G	13.37:g.32913536A>G	ENSP00000369497:p.Ser1682Gly	Somatic		Capture	Illumina HiSeq	Phase_I	31811536	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	A	9.258	1.042569	0.19748	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	D;D	0.87650	-2.28;-2.28	5.76	3.22	0.36961	.	0.501323	0.22848	N	0.054886	T	0.79862	0.4519	L	0.35854	1.095	0.19300	N	0.999979	B	0.22909	0.077	B	0.23419	0.046	T	0.68435	-0.5409	10	0.49607	T	0.09	.	8.0637	0.30648	0.8122:0.0:0.0664:0.1214	.	1682	P51587	BRCA2_HUMAN	G	1682	ENSP00000369497:S1682G;ENSP00000439902:S1682G	ENSP00000369497:S1682G	S	+	1	0	BRCA2	31811536	0.216000	0.23585	0.037000	0.18230	0.241000	0.25554	2.109000	0.41863	0.400000	0.25396	0.533000	0.62120	AGT		BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059	
DACH1	1602	hgsc.bcm.edu	37	13	72204807	72204807	+	Missense_Mutation	SNP	G	G	A			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr13:72204807G>A	ENST00000359684.2	-	3	1012	c.1013C>T	c.(1012-1014)gCa>gTa	p.A338V	DACH1_ENST00000305425.4_Missense_Mutation_p.A338V|DACH1_ENST00000313174.7_Missense_Mutation_p.A338V|DACH1_ENST00000354591.4_Intron			Q9UI36	DACH1_HUMAN	dachshund family transcription factor 1	338	Interaction with SIX6 and HDAC3. {ECO:0000250}.				cell proliferation (GO:0008283)|development of primary female sexual characteristics (GO:0046545)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of transcription by competitive promoter binding (GO:0010944)|respiratory gaseous exchange (GO:0007585)|suckling behavior (GO:0001967)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity involved in preinitiation complex assembly (GO:0001075)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(23)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198)		GBM - Glioblastoma multiforme(99;0.00032)		agcaatagctgcattggtagc	0.383																																																	0			13											120.0	109.0	113.0					13																	72204807		1822	4075	5897	71102808	SO:0001583	missense	1602			AJ005670	CCDS41899.1, CCDS53874.1, CCDS53873.1	13q22	2014-02-03	2014-02-03	2004-04-02	ENSG00000165659	ENSG00000276644			2663	protein-coding gene	gene with protein product		603803	"""dachshund homolog (Drosophila)"", ""dachshund homolog 1 (Drosophila)"""	DACH		9933575, 10395809, 15057823	Standard	NM_004392		Approved		uc021rkj.1	Q9UI36	OTTHUMG00000017063	ENST00000359684.2:c.1013C>T	13.37:g.72204807G>A	ENSP00000352712:p.Ala338Val	Somatic		Capture	Illumina HiSeq	Phase_I	71102808	D0FY35|D0FY36|O75523|O75687|Q5VYY3|Q5VYY4|Q96SG3|Q96SG4|Q9H524|Q9UMH4	Missense_Mutation	SNP	ENST00000359684.2	37		.	.	.	.	.	.	.	.	.	.	G	26.0	4.696723	0.88830	.	.	ENSG00000165659	ENST00000305425;ENST00000313174;ENST00000359684;ENST00000377826	T;T;T	0.37058	1.26;1.38;1.22	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	T	0.57007	0.2024	L	0.47716	1.5	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.80764	0.994;0.994	T	0.54827	-0.8235	10	0.72032	D	0.01	-9.1643	20.3736	0.98901	0.0:0.0:1.0:0.0	.	336;336	Q9UI36-3;Q9UI36-2	.;.	V	338	ENSP00000304994:A338V;ENSP00000318506:A338V;ENSP00000352712:A338V	ENSP00000304994:A338V	A	-	2	0	DACH1	71102808	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.357000	0.97099	2.820000	0.97059	0.650000	0.86243	GCA		DACH1-002	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000045240.1	NM_004392	
CALML5	51806	hgsc.bcm.edu	37	10	5541181	5541181	+	Missense_Mutation	SNP	T	T	C	rs10904516|rs373657626|rs386740368	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr10:5541181T>C	ENST00000380332.3	-	1	352	c.221A>G	c.(220-222)aAg>aGg	p.K74R		NM_017422.4	NP_059118.2	Q9NZT1	CALL5_HUMAN	calmodulin-like 5	74	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.		K -> R (polymorphism confirmed at protein level; dbSNP:rs10904516). {ECO:0000269|PubMed:10777582, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17488105}.		epidermis development (GO:0008544)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.K74R(1)		biliary_tract(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|stomach(1)	8						CCTGGCCTTCTTCGCCGCCGT	0.657													T|||	1769	0.353235	0.5121	0.2334	5008	,	,		16118	0.3046		0.3221	False		,,,				2504	0.3057				GBM(149;1055 3356 43077)												1	Substitution - Missense(1)	stomach(1)	10						T	ARG/LYS	530,3876		209,112,1882	42.0	45.0	44.0		221	-1.8	0.0	10	dbSNP_120	44	464,8136		175,114,4011	no	missense	CALML5	NM_017422.4	26	384,226,5893	CC,CT,TT		5.3953,12.0291,7.6426	possibly-damaging	74/147	5541181	994,12012	2203	4300	6503	5531181	SO:0001583	missense	51806			AF172852	CCDS7068.1	10p15.1	2013-01-10			ENSG00000178372	ENSG00000178372		"""EF-hand domain containing"""	18180	protein-coding gene	gene with protein product	"""calmodulin-like skin protein"""	605183				10777582	Standard	NM_017422		Approved	CLSP	uc001iic.2	Q9NZT1	OTTHUMG00000017598	ENST00000380332.3:c.221A>G	10.37:g.5541181T>C	ENSP00000369689:p.Lys74Arg	Somatic		Capture	Illumina HiSeq	Phase_I	5531181	Q5SQI3|Q8IXU8	Missense_Mutation	SNP	ENST00000380332.3	37	CCDS7068.1	738	0.33791208791208793	245	0.49796747967479676	89	0.24585635359116023	165	0.28846153846153844	239	0.3153034300791557	T	3.065	-0.192375	0.06259	0.120291	0.053953	ENSG00000178372	ENST00000380332	T	0.37915	1.17	0.893	-1.79	0.07932	EF-hand-like domain (1);	0.809011	0.11132	N	0.596195	T	0.00012	0.0000	N	0.11023	0.085	0.80722	P	0.0	P	0.41710	0.76	B	0.32624	0.149	T	0.45205	-0.9277	9	0.66056	D	0.02	-3.9447	4.0258	0.09687	0.3917:0.0:0.0:0.6083	rs10904516;rs17846249;rs17859268;rs34351495	74	Q9NZT1	CALL5_HUMAN	R	74	ENSP00000369689:K74R	ENSP00000369689:K74R	K	-	2	0	CALML5	5531181	0.033000	0.19621	0.000000	0.03702	0.000000	0.00434	0.459000	0.21908	-1.160000	0.02804	-1.407000	0.01130	AAG		CALML5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046556.1	NM_017422	
CALML5	51806	hgsc.bcm.edu	37	10	5541183	5541183	+	Silent	SNP	C	C	T	rs10904517|rs202221308|rs373657626|rs386740368	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr10:5541183C>T	ENST00000380332.3	-	1	350	c.219G>A	c.(217-219)gcG>gcA	p.A73A		NM_017422.4	NP_059118.2	Q9NZT1	CALL5_HUMAN	calmodulin-like 5	73	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				epidermis development (GO:0008544)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			biliary_tract(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|stomach(1)	8						TGGCCTTCTTCGCCGCCGTCA	0.662													C|||	1780	0.355431	0.5182	0.2334	5008	,	,		16136	0.3065		0.3231	False		,,,				2504	0.3057				GBM(149;1055 3356 43077)												0			10						C		407,3999		128,151,1924	42.0	45.0	44.0		219	0.5	0.0	10	dbSNP_120	44	354,8246		109,136,4055	no	coding-synonymous	CALML5	NM_017422.4		237,287,5979	TT,TC,CC		4.1163,9.2374,5.8511		73/147	5541183	761,12245	2203	4300	6503	5531183	SO:0001819	synonymous_variant	51806			AF172852	CCDS7068.1	10p15.1	2013-01-10			ENSG00000178372	ENSG00000178372		"""EF-hand domain containing"""	18180	protein-coding gene	gene with protein product	"""calmodulin-like skin protein"""	605183				10777582	Standard	NM_017422		Approved	CLSP	uc001iic.2	Q9NZT1	OTTHUMG00000017598	ENST00000380332.3:c.219G>A	10.37:g.5541183C>T		Somatic		Capture	Illumina HiSeq	Phase_I	5531183	Q5SQI3|Q8IXU8	Silent	SNP	ENST00000380332.3	37	CCDS7068.1																																																																																				CALML5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046556.1	NM_017422	
SKIDA1	387640	hgsc.bcm.edu	37	10	21805486	21805486	+	Silent	SNP	C	C	T			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr10:21805486C>T	ENST00000449193.2	-	4	3518	c.1266G>A	c.(1264-1266)gaG>gaA	p.E422E	SKIDA1_ENST00000444772.3_Silent_p.E343E|SKIDA1_ENST00000487107.1_5'Flank	NM_207371.3	NP_997254.3	Q1XH10	SKDA1_HUMAN	SKI/DACH domain containing 1	341						nucleus (GO:0005634)		p.E422E(2)									cctcttcctcctcctcctcct	0.632																																																	2	Substitution - coding silent(2)	large_intestine(2)	10											5.0	6.0	6.0					10																	21805486		1988	4108	6096	21845492	SO:0001819	synonymous_variant	387640			AK131456	CCDS44363.1	10p12.31	2012-06-13	2012-06-13	2012-06-13	ENSG00000180592	ENSG00000180592			32697	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 140"""	C10orf140			Standard	NM_207371		Approved	FLJ45187	uc021pnx.1	Q1XH10	OTTHUMG00000017797	ENST00000449193.2:c.1266G>A	10.37:g.21805486C>T		Somatic		Capture	Illumina HiSeq	Phase_I	21845492	B1ANA5|Q6ZMX4|Q8N3C3	Silent	SNP	ENST00000449193.2	37	CCDS44363.1																																																																																				SKIDA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286950.2	NM_207371	
GPRIN2	9721	hgsc.bcm.edu	37	10	46998999	46998999	+	Missense_Mutation	SNP	G	G	A	rs3127818	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr10:46998999G>A	ENST00000374317.1	+	3	392	c.119G>A	c.(118-120)cGc>cAc	p.R40H	GPRIN2_ENST00000374314.4_Missense_Mutation_p.R40H	NM_014696.3	NP_055511.2	O60269	GRIN2_HUMAN	G protein regulated inducer of neurite outgrowth 2	40			R -> H (in dbSNP:rs3127818). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9628581}.							breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	18						CCAGAGCTCCGCAAGACTGCC	0.701																																																	0			10																																								46419005	SO:0001583	missense	9721			BC011672	CCDS73101.1	10q11.22	2006-08-24	2006-08-24	2006-08-24	ENSG00000204175	ENSG00000204175			23730	protein-coding gene	gene with protein product		611240	"""KIAA0514"""	KIAA0514		9628581	Standard	NM_014696		Approved	MGC15171	uc001jec.3	O60269	OTTHUMG00000018107	ENST00000374317.1:c.119G>A	10.37:g.46998999G>A	ENSP00000363436:p.Arg40His	Somatic		Capture	Illumina HiSeq	Phase_I	46419005	Q5SVF0	Missense_Mutation	SNP	ENST00000374317.1	37	CCDS31192.1	1096	0.5018315018315018	248	0.5040650406504065	181	0.5	286	0.5	381	0.5026385224274407	G	10.65	1.410753	0.25465	.	.	ENSG00000204175	ENST00000374317;ENST00000374314	T;T	0.07567	3.18;3.18	5.44	0.466	0.16716	.	0.310657	0.23676	N	0.045669	T	0.00012	0.0000	L	0.38531	1.155	0.26770	N	0.969813	B	0.25007	0.116	B	0.19391	0.025	T	0.51236	-0.8731	10	0.45353	T	0.12	-12.7811	5.8237	0.18542	0.2195:0.0:0.6423:0.1382	rs3127818	40	O60269	GRIN2_HUMAN	H	40	ENSP00000363436:R40H;ENSP00000363433:R40H	ENSP00000363433:R40H	R	+	2	0	GPRIN2	46419005	0.010000	0.17322	0.260000	0.24451	0.226000	0.24999	0.187000	0.16998	-0.022000	0.13986	-0.181000	0.13052	CGC		GPRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047836.1	NM_014696	
GPRIN2	9721	hgsc.bcm.edu	37	10	46999019	46999019	+	Missense_Mutation	SNP	G	G	A	rs3127819	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr10:46999019G>A	ENST00000374317.1	+	3	412	c.139G>A	c.(139-141)Gtg>Atg	p.V47M	GPRIN2_ENST00000374314.4_Missense_Mutation_p.V47M	NM_014696.3	NP_055511.2	O60269	GRIN2_HUMAN	G protein regulated inducer of neurite outgrowth 2	47			V -> M (in dbSNP:rs3127819). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9628581}.							breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	18						CAGCAGCACCGTGTGGCAGGC	0.701																																																	0			10																																								46419025	SO:0001583	missense	9721			BC011672	CCDS73101.1	10q11.22	2006-08-24	2006-08-24	2006-08-24	ENSG00000204175	ENSG00000204175			23730	protein-coding gene	gene with protein product		611240	"""KIAA0514"""	KIAA0514		9628581	Standard	NM_014696		Approved	MGC15171	uc001jec.3	O60269	OTTHUMG00000018107	ENST00000374317.1:c.139G>A	10.37:g.46999019G>A	ENSP00000363436:p.Val47Met	Somatic		Capture	Illumina HiSeq	Phase_I	46419025	Q5SVF0	Missense_Mutation	SNP	ENST00000374317.1	37	CCDS31192.1	1091	0.49954212454212454	246	0.5	181	0.5	286	0.5	378	0.49868073878627966	G	20.4	3.977383	0.74360	.	.	ENSG00000204175	ENST00000374317;ENST00000374314	T;T	0.06687	3.27;3.27	5.43	5.43	0.79202	.	0.175186	0.27600	N	0.018643	T	0.00012	0.0000	M	0.64997	1.995	0.09310	N	0.999999	D	0.89917	1.0	P	0.61003	0.882	T	0.10567	-1.0624	10	0.48119	T	0.1	-7.7307	15.1094	0.72343	0.0:0.0:1.0:0.0	rs3127819;rs11499481	47	O60269	GRIN2_HUMAN	M	47	ENSP00000363436:V47M;ENSP00000363433:V47M	ENSP00000363433:V47M	V	+	1	0	GPRIN2	46419025	0.336000	0.24757	0.128000	0.21923	0.967000	0.64934	2.595000	0.46197	2.723000	0.93209	0.650000	0.86243	GTG		GPRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047836.1	NM_014696	
HNRNPH3	3189	hgsc.bcm.edu	37	10	70101793	70101793	+	Silent	SNP	A	A	G			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr10:70101793A>G	ENST00000265866.7	+	10	1188	c.1023A>G	c.(1021-1023)ggA>ggG	p.G341G	HNRNPH3_ENST00000354695.5_Silent_p.G326G|HNRNPH3_ENST00000441000.2_Silent_p.G233G|HNRNPH3_ENST00000469172.1_3'UTR	NM_012207.2|NM_021644.3	NP_036339.1|NP_067676.2	P31942	HNRH3_HUMAN	heterogeneous nuclear ribonucleoprotein H3 (2H9)	341	Gly-rich.				epithelial cell differentiation (GO:0030855)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(5)|ovary(2)|prostate(2)	11						GTGGAGGTGGATGGCGTGGGA	0.428																																																	0			10											126.0	106.0	113.0					10																	70101793		2203	4300	6503	69771799	SO:0001819	synonymous_variant	3189				CCDS7278.1, CCDS7279.1	10q22	2013-02-12		2008-04-18	ENSG00000096746	ENSG00000096746		"""RNA binding motif (RRM) containing"""	5043	protein-coding gene	gene with protein product		602324		HNRPH3		8999868	Standard	NM_021644		Approved	2H9	uc001jnw.4	P31942	OTTHUMG00000018349	ENST00000265866.7:c.1023A>G	10.37:g.70101793A>G		Somatic		Capture	Illumina HiSeq	Phase_I	69771799	A8K682|B3KRE1|Q9BSX1|Q9NP53|Q9NP96|Q9NPA7|Q9NPI4|Q9UFU4|Q9Y4J5	Silent	SNP	ENST00000265866.7	37	CCDS7278.1																																																																																				HNRNPH3-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090165.1		
C5orf38	153571	hgsc.bcm.edu	37	5	2752437	2752437	+	Missense_Mutation	SNP	C	C	T			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr5:2752437C>T	ENST00000334000.3	+	1	176	c.59C>T	c.(58-60)aCg>aTg	p.T20M	C5orf38_ENST00000457752.2_Missense_Mutation_p.T20M|IRX2_ENST00000382611.6_5'Flank|C5orf38_ENST00000505778.1_Missense_Mutation_p.T20M|IRX2_ENST00000502957.1_Intron|IRX2_ENST00000302057.5_5'Flank|C5orf38_ENST00000397835.4_Missense_Mutation_p.T20M|C5orf38_ENST00000515640.1_Missense_Mutation_p.T20M	NM_178569.2	NP_848664.1	Q86SI9	CEI_HUMAN	chromosome 5 open reading frame 38	20						extracellular region (GO:0005576)				endometrium(2)|large_intestine(1)|lung(1)	4				GBM - Glioblastoma multiforme(108;0.205)		CTCACTTCCACGGTCCCGGAC	0.711																																																	0			5											11.0	14.0	13.0					5																	2752437		2171	4249	6420	2805437	SO:0001583	missense	153571			AY249324	CCDS34131.1	5p15.33	2014-06-02			ENSG00000186493	ENSG00000186493			24226	protein-coding gene	gene with protein product	"""coordinated expression to IRX2"", ""IRX2 neighbor"""	610522				16515847, 16750006	Standard	XM_005248256		Approved	CEI, IRX2NB	uc003jdc.3	Q86SI9	OTTHUMG00000161741	ENST00000334000.3:c.59C>T	5.37:g.2752437C>T	ENSP00000334267:p.Thr20Met	Somatic		Capture	Illumina HiSeq	Phase_I	2805437		Missense_Mutation	SNP	ENST00000334000.3	37	CCDS34131.1	.	.	.	.	.	.	.	.	.	.	C	11.83	1.754433	0.31046	.	.	ENSG00000186493	ENST00000457752;ENST00000397835;ENST00000334000;ENST00000505778;ENST00000515640	.	.	.	2.02	2.02	0.26589	.	.	.	.	.	T	0.34308	0.0893	N	0.08118	0	0.09310	N	1	D	0.89917	1.0	D	0.68765	0.96	T	0.12192	-1.0557	8	0.87932	D	0	.	7.5672	0.27885	0.0:1.0:0.0:0.0	.	20	Q86SI9	CEI_HUMAN	M	20	.	ENSP00000334267:T20M	T	+	2	0	C5orf38	2805437	0.003000	0.15002	0.006000	0.13384	0.016000	0.09150	1.940000	0.40223	1.451000	0.47736	0.462000	0.41574	ACG		C5orf38-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365956.2	NM_178569	
SEMA5A	9037	hgsc.bcm.edu	37	5	9380001	9380001	+	Missense_Mutation	SNP	C	C	T	rs370176472		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr5:9380001C>T	ENST00000382496.5	-	3	723	c.58G>A	c.(58-60)Gcc>Acc	p.A20T	CTD-2201E9.4_ENST00000511310.1_RNA	NM_003966.2	NP_003957.2	Q13591	SEM5A_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	20					axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|diencephalon development (GO:0021536)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|nervous system development (GO:0007399)|patterning of blood vessels (GO:0001569)|positive chemotaxis (GO:0050918)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of angiogenesis (GO:0045766)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein kinase B signaling (GO:0051897)|signal clustering (GO:1990256)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|chondroitin sulfate proteoglycan binding (GO:0035373)|heparan sulfate proteoglycan binding (GO:0043395)|semaphorin receptor binding (GO:0030215)|syndecan binding (GO:0045545)	p.A20T(1)		biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(13)|lung(40)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	81						TCTGGGTGGGCGAGTCTCCAC	0.562																																																	1	Substitution - Missense(1)	central_nervous_system(1)	5						C	THR/ALA	0,4406		0,0,2203	130.0	125.0	127.0		58	3.3	0.0	5		127	1,8599	1.2+/-3.3	0,1,4299	no	missense	SEMA5A	NM_003966.2	58	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	20/1075	9380001	1,13005	2203	4300	6503	9433001	SO:0001583	missense	9037			U52840	CCDS3875.1	5p15.2	2008-05-15			ENSG00000112902	ENSG00000112902		"""Semaphorins"""	10736	protein-coding gene	gene with protein product		609297		SEMAF		8817451, 9464278	Standard	NM_003966		Approved	semF	uc003jek.2	Q13591	OTTHUMG00000090501	ENST00000382496.5:c.58G>A	5.37:g.9380001C>T	ENSP00000371936:p.Ala20Thr	Somatic		Capture	Illumina HiSeq	Phase_I	9433001	D3DTC6|O60408|Q1RLL9	Missense_Mutation	SNP	ENST00000382496.5	37	CCDS3875.1	.	.	.	.	.	.	.	.	.	.	C	9.263	1.043726	0.19748	0.0	1.16E-4	ENSG00000112902	ENST00000382496;ENST00000513968	T;T	0.36157	1.27;2.09	5.42	3.31	0.37934	.	0.585291	0.16361	N	0.217779	T	0.20251	0.0487	N	0.19112	0.55	0.09310	N	1	B	0.31837	0.342	B	0.21151	0.033	T	0.12218	-1.0556	10	0.52906	T	0.07	.	8.4262	0.32731	0.0:0.7917:0.0:0.2083	.	20	Q13591	SEM5A_HUMAN	T	20	ENSP00000371936:A20T;ENSP00000421961:A20T	ENSP00000371936:A20T	A	-	1	0	SEMA5A	9433001	0.000000	0.05858	0.008000	0.14137	0.195000	0.23768	0.600000	0.24104	1.299000	0.44798	-0.259000	0.10710	GCC		SEMA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206989.2		
CDC20B	166979	hgsc.bcm.edu	37	5	54424363	54424363	+	Missense_Mutation	SNP	G	G	C			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr5:54424363G>C	ENST00000381375.2	-	7	925	c.780C>G	c.(778-780)aaC>aaG	p.N260K	CDC20B_ENST00000334206.5_Missense_Mutation_p.N260K|CDC20B_ENST00000322374.6_Missense_Mutation_p.N260K|CDC20B_ENST00000296733.1_Missense_Mutation_p.N260K			Q86Y33	CD20B_HUMAN	cell division cycle 20B	260										kidney(1)|large_intestine(5)|lung(7)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	19		Lung NSC(810;0.000744)|Breast(144;0.159)|Prostate(74;0.194)	LUSC - Lung squamous cell carcinoma(15;0.225)			TCCCATTGTGGTTCTCCCCAT	0.433																																																	0			5											160.0	164.0	162.0					5																	54424363		2203	4300	6503	54460120	SO:0001583	missense	166979			AB086378	CCDS3966.1, CCDS47207.1, CCDS54852.1	5q11.2	2013-01-17	2013-01-17		ENSG00000164287	ENSG00000164287		"""WD repeat domain containing"""	24222	protein-coding gene	gene with protein product			"""CDC20 cell division cycle 20 homolog B (S. cerevisiae)"", ""cell division cycle 20 homolog B (S. cerevisiae)"""				Standard	NM_152623		Approved	FLJ37927	uc003jpo.2	Q86Y33	OTTHUMG00000131185	ENST00000381375.2:c.780C>G	5.37:g.54424363G>C	ENSP00000370781:p.Asn260Lys	Somatic		Capture	Illumina HiSeq	Phase_I	54460120	B7WNV8|B9EGL8|C9J6X8|C9JHE9|C9JKL5|Q86Y31|Q86Y32|Q8IUZ8|Q8N1S1|Q8NG56	Missense_Mutation	SNP	ENST00000381375.2	37	CCDS54852.1	.	.	.	.	.	.	.	.	.	.	G	6.880	0.531850	0.13127	.	.	ENSG00000164287	ENST00000334206;ENST00000296733;ENST00000381375;ENST00000322374	T;T;T;T	0.73152	-0.72;-0.72;-0.72;-0.72	4.49	0.267	0.15622	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.782162	0.11142	N	0.595219	T	0.66327	0.2778	M	0.68593	2.085	0.09310	N	1	P;P;P;P	0.46621	0.881;0.617;0.483;0.873	P;B;B;B	0.46299	0.511;0.242;0.122;0.306	T	0.58411	-0.7641	10	0.62326	D	0.03	-16.4791	0.9747	0.01423	0.2438:0.1242:0.3779:0.254	.	260;260;260;260	Q86Y33-4;Q86Y33-3;Q86Y33;Q86Y33-2	.;.;CD20B_HUMAN;.	K	260	ENSP00000335664:N260K;ENSP00000296733:N260K;ENSP00000370781:N260K;ENSP00000315720:N260K	ENSP00000296733:N260K	N	-	3	2	CDC20B	54460120	0.000000	0.05858	0.001000	0.08648	0.168000	0.22595	0.182000	0.16900	-0.158000	0.11040	0.650000	0.86243	AAC		CDC20B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369715.1	NM_152623	
APC	324	hgsc.bcm.edu	37	5	112175205	112175205	+	Missense_Mutation	SNP	C	C	A			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr5:112175205C>A	ENST00000457016.1	+	16	4294	c.3914C>A	c.(3913-3915)gCa>gAa	p.A1305E	APC_ENST00000257430.4_Missense_Mutation_p.A1305E|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Missense_Mutation_p.A1305E			P25054	APC_HUMAN	adenomatous polyposis coli	1305	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.A1305fs*3(1)|p.K1192fs*3(1)|p.?(1)|p.A1305G(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CTGCAAATAGCAGAAATAAAA	0.423		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)		yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	4	Deletion - Frameshift(2)|Substitution - Missense(1)|Unknown(1)	large_intestine(2)|soft_tissue(1)|skin(1)	5											53.0	55.0	54.0					5																	112175205		2202	4300	6502	112203104	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3914C>A	5.37:g.112175205C>A	ENSP00000413133:p.Ala1305Glu	Somatic		Capture	Illumina HiSeq	Phase_I	112203104	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	5.754	0.323594	0.10900	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.89270	-2.49;-2.49;-2.49	5.73	4.84	0.62591	.	0.439882	0.27567	N	0.018787	T	0.80555	0.4645	N	0.24115	0.695	0.30596	N	0.761008	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.72431	-0.4296	9	.	.	.	-9.5709	12.2704	0.54702	0.1341:0.7366:0.1292:0.0	.	1307;1305	Q4LE70;P25054	.;APC_HUMAN	E	1305	ENSP00000413133:A1305E;ENSP00000257430:A1305E;ENSP00000427089:A1305E	.	A	+	2	0	APC	112203104	0.995000	0.38212	0.993000	0.49108	0.766000	0.43426	2.950000	0.49081	1.506000	0.48736	0.655000	0.94253	GCA		APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
PCDHA3	56145	hgsc.bcm.edu	37	5	140182270	140182270	+	Silent	SNP	A	A	G			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr5:140182270A>G	ENST00000522353.2	+	1	1488	c.1488A>G	c.(1486-1488)gaA>gaG	p.E496E	PCDHA1_ENST00000504120.2_Intron|PCDHA3_ENST00000532566.2_Silent_p.E496E|PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000520672.2_Intron|PCDHA2_ENST00000526136.1_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	496	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGCTGGTGGAACGGCGGGTGG	0.682																																																	0			5											74.0	80.0	78.0					5																	140182270		2203	4299	6502	140162454	SO:0001819	synonymous_variant	56145			AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"""Cadherins / Protocadherins : Clustered"""	8669	other	complex locus constituent	"""KIAA0345-like 11"""	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.1488A>G	5.37:g.140182270A>G		Somatic		Capture	Illumina HiSeq	Phase_I	140162454	O75286	Silent	SNP	ENST00000522353.2	37	CCDS54915.1																																																																																				PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906	
SLC36A2	153201	hgsc.bcm.edu	37	5	150722455	150722455	+	Nonsense_Mutation	SNP	C	C	T	rs143350420		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr5:150722455C>T	ENST00000335244.4	-	4	563	c.434G>A	c.(433-435)tGg>tAg	p.W145*	SLC36A2_ENST00000521967.1_Nonsense_Mutation_p.W145*	NM_181776.2	NP_861441.2	Q495M3	S36A2_HUMAN	solute carrier family 36 (proton/amino acid symporter), member 2	145					amino acid transport (GO:0006865)|ion transport (GO:0006811)|proline transmembrane transport (GO:0035524)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine transmembrane transporter activity (GO:0015187)|hydrogen:amino acid symporter activity (GO:0005280)|L-alanine transmembrane transporter activity (GO:0015180)|L-proline transmembrane transporter activity (GO:0015193)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(14)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Cycloserine(DB00260)	TTACCTTCCCCAGTGAGCGTG	0.532																																																	0			5											159.0	123.0	135.0					5																	150722455		2203	4300	6503	150702648	SO:0001587	stop_gained	153201			AY162214	CCDS4315.1	5q33.1	2013-05-22			ENSG00000186335	ENSG00000186335		"""Solute carriers"""	18762	protein-coding gene	gene with protein product		608331				11959859	Standard	NM_181776		Approved	PAT2, tramdorin, TRAMD1	uc003lty.3	Q495M3	OTTHUMG00000130129	ENST00000335244.4:c.434G>A	5.37:g.150722455C>T	ENSP00000334223:p.Trp145*	Somatic		Capture	Illumina HiSeq	Phase_I	150702648	Q495M4|Q495M6|Q6ZWK5|Q7Z6B5	Nonsense_Mutation	SNP	ENST00000335244.4	37	CCDS4315.1	.	.	.	.	.	.	.	.	.	.	C	36	5.695920	0.96802	.	.	ENSG00000186335	ENST00000335244;ENST00000521967	.	.	.	4.77	4.77	0.60923	.	0.117155	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.7126	17.9674	0.89103	0.0:1.0:0.0:0.0	.	.	.	.	X	145	.	ENSP00000334223:W145X	W	-	2	0	SLC36A2	150702648	1.000000	0.71417	1.000000	0.80357	0.733000	0.41908	3.894000	0.56250	2.636000	0.89361	0.655000	0.94253	TGG		SLC36A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252437.1		
IMPG2	50939	hgsc.bcm.edu	37	3	101022988	101022988	+	Splice_Site	SNP	A	A	G			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr3:101022988A>G	ENST00000193391.7	-	3	689		c.e3+1			NM_016247.3	NP_057331.2	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2						visual perception (GO:0007601)	integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)|receptor complex (GO:0043235)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			NS(1)|breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(14)|lung(32)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64					Hyaluronan(DB08818)	TGTGACACTTACCTTCATGAT	0.393																																																	0			3											148.0	143.0	145.0					3																	101022988		2203	4300	6503	102505678	SO:0001630	splice_region_variant	50939			AF173155	CCDS2940.1	3q12.2-q12.3	2014-01-28			ENSG00000081148	ENSG00000081148			18362	protein-coding gene	gene with protein product		607056				10542133	Standard	NM_016247		Approved	IPM200, RP56	uc003duq.2	Q9BZV3	OTTHUMG00000159091	ENST00000193391.7:c.501+1T>C	3.37:g.101022988A>G		Somatic		Capture	Illumina HiSeq	Phase_I	102505678	A8MWT5|Q9UKD4|Q9UKK5	Splice_Site	SNP	ENST00000193391.7	37	CCDS2940.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.040918	0.75732	.	.	ENSG00000081148	ENST00000193391	.	.	.	5.6	5.6	0.85130	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4459	0.75228	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	IMPG2	102505678	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	6.815000	0.75242	2.137000	0.66172	0.528000	0.53228	.		IMPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353256.3		Intron
C2orf71	388939	hgsc.bcm.edu	37	2	29287926	29287927	+	In_Frame_Ins	INS	-	-	GCT	rs139768554|rs72122505|rs201781577|rs35753661	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr2:29287926_29287927insGCT	ENST00000331664.5	-	2	3674_3675	c.3675_3676insAGC	c.(3673-3678)agcgag>agcAGCgag	p.1225_1226insS	C2orf71_ENST00000602958.1_5'Flank	NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	1225			S -> SS. {ECO:0000269|PubMed:21412943}.		response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)		p.S1225_E1226insS(2)		NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						GGGCTCTCCTCGCTGCTGCTGC	0.624														1871	0.373602	0.5257	0.2637	5008	,	,		17644	0.4931		0.2545	False		,,,				2504	0.2454																2	Insertion - In frame(2)	ovary(1)|breast(1)	2								1580,1994		462,656,669						5.2	1.0		dbSNP_130	16	1923,5511		406,1111,2200	no	coding	C2orf71	NM_001029883.1		868,1767,2869	A1A1,A1R,RR		25.8676,44.2082,31.8223				3503,7505				29141431	SO:0001652	inframe_insertion	388939				CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.3673_3675dupAGC	2.37:g.29287933_29287935dupGCT	ENSP00000332809:p.Ser1225_Ser1225dup	Somatic		Capture	Illumina HiSeq	Phase_I	29141430		In_Frame_Ins	INS	ENST00000331664.5	37	CCDS42669.1																																																																																				C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883	
MUC4	4585	hgsc.bcm.edu	37	3	195515367	195515414	+	In_Frame_Del	DEL	GGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT	GGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT	-	rs369312980|rs547775645|rs201510137|rs200193644|rs531942134|rs13060431|rs200400545|rs71180964|rs199583597|rs55868431|rs55803325|rs550428312|rs199702053|rs13065584	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	GGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT	GGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr3:195515367_195515414delGGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT	ENST00000463781.3	-	2	3496_3543	c.3037_3084delAGCCCTTCCTCAGTATCCACAGGTCACACCACCCCTCTTCCTGTCACC	c.(3037-3084)agcccttcctcagtatccacaggtcacaccacccctcttcctgtcaccdel	p.SPSSVSTGHTTPLPVT1013del	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_In_Frame_Del_p.SPSSVSTGHTTPLPVT1013del|MUC4_ENST00000349607.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	448	Repeat.|Ser-rich.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.S1013_T1028delSPSSVSTGHTTPLPVT(4)|p.S1013G(2)|p.T1022A(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGGAAGTGTCGGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCTGGTGACAGGA	0.573																																																	8	Substitution - Missense(4)|Deletion - In frame(4)	stomach(6)|prostate(2)	3																																								196999809	SO:0001651	inframe_deletion	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3037_3084delAGCCCTTCCTCAGTATCCACAGGTCACACCACCCCTCTTCCTGTCACC	3.37:g.195515367_195515414delGGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT	ENSP00000417498:p.Ser1013_Thr1028del	Somatic		Capture	Illumina HiSeq	Phase_I	196999762	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	In_Frame_Del	DEL	ENST00000463781.3	37	CCDS54700.1																																																																																				MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PRKAR2B	5577	hgsc.bcm.edu	37	7	106781331	106781331	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr7:106781331delT	ENST00000265717.4	+	5	779	c.520delT	c.(520-522)ttgfs	p.L174fs	PRKAR2B_ENST00000393613.2_3'UTR	NM_002736.2	NP_002727.2	P31323	KAP3_HUMAN	protein kinase, cAMP-dependent, regulatory, type II, beta	174					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fatty acid metabolic process (GO:0006631)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|mitotic cell cycle (GO:0000278)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	14						GTTTGAAAAATTGGTCAAAGA	0.318																																																	0			7											168.0	164.0	166.0					7																	106781331		2203	4300	6503	106568567	SO:0001589	frameshift_variant	5577				CCDS5740.1	7q22.3	2010-04-22			ENSG00000005249	ENSG00000005249	2.7.11.1		9392	protein-coding gene	gene with protein product		176912		PRKAR2		1358799	Standard	NM_002736		Approved		uc003vdx.3	P31323	OTTHUMG00000137418	ENST00000265717.4:c.520delT	7.37:g.106781331delT	ENSP00000265717:p.Leu174fs	Somatic		Capture	Illumina HiSeq	Phase_I	106568567	A4D0R9	Frame_Shift_Del	DEL	ENST00000265717.4	37	CCDS5740.1																																																																																				PRKAR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268386.1		
GPRIN2	9721	hgsc.bcm.edu	37	10	46999591	46999592	+	In_Frame_Ins	INS	-	-	ATGAGGGAG	rs112620425	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr10:46999591_46999592insATGAGGGAG	ENST00000374317.1	+	3	984_985	c.711_712insATGAGGGAG	c.(712-714)atg>ATGAGGGAGatg	p.238_238M>MREM	GPRIN2_ENST00000374314.4_In_Frame_Ins_p.238_238M>MREM	NM_014696.3	NP_055511.2	O60269	GRIN2_HUMAN	G protein regulated inducer of neurite outgrowth 2	238								p.G237_M238insMRE(1)		breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	18						TACTCTGTGGCATGAGGGAGGT	0.629														2399	0.479034	0.4697	0.4856	5008	,	,		38874	0.4782		0.4761	False		,,,				2504	0.4908																1	Insertion - In frame(1)	breast(1)	10								2080,27,2157		11,3,2055,0,24,39						0.9	0.0		dbSNP_130	49	3974,98,4180		16,7,3935,0,91,77	no	codingComplex	GPRIN2	NM_014696.3		27,10,5990,0,115,116	A1A1,A1A2,A1R,A2A2,A2R,RR		49.3456,49.4137,49.3688				6054,125,6337				46419598	SO:0001652	inframe_insertion	9721			BC011672	CCDS73101.1	10q11.22	2006-08-24	2006-08-24	2006-08-24	ENSG00000204175	ENSG00000204175			23730	protein-coding gene	gene with protein product		611240	"""KIAA0514"""	KIAA0514		9628581	Standard	NM_014696		Approved	MGC15171	uc001jec.3	O60269	OTTHUMG00000018107	ENST00000374317.1:c.712_720dupATGAGGGAG	10.37:g.46999592_46999600dupATGAGGGAG	Exception_encountered	Somatic		Capture	Illumina HiSeq	Phase_I	46419597	Q5SVF0	In_Frame_Ins	INS	ENST00000374317.1	37	CCDS31192.1																																																																																				GPRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047836.1	NM_014696	
OR6C76	390326	hgsc.bcm.edu	37	12	55820959	55820959	+	Frame_Shift_Del	DEL	A	A	-	rs397719965|rs57387180		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr12:55820959delA	ENST00000328314.3	+	1	922	c.922delA	c.(922-924)aaafs	p.K311fs		NM_001005183.1	NP_001005183.1	A6NM76	O6C76_HUMAN	olfactory receptor, family 6, subfamily C, member 76	311						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						GATTTCCCACAAAAAAAAAAA	0.338																																																	0			12											19.0	20.0	19.0					12																	55820959		2110	4120	6230	54107226	SO:0001589	frameshift_variant	390326				CCDS31823.1	12q13.2	2013-09-23			ENSG00000185821	ENSG00000185821		"""GPCR / Class A : Olfactory receptors"""	31305	protein-coding gene	gene with protein product							Standard	NM_001005183		Approved		uc010spm.2	A6NM76	OTTHUMG00000169956	ENST00000328314.3:c.922delA	12.37:g.55820959delA	ENSP00000328402:p.Lys311fs	Somatic		Capture	Illumina HiSeq	Phase_I	54107226		Frame_Shift_Del	DEL	ENST00000328314.3	37	CCDS31823.1																																																																																				OR6C76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406675.1	NM_001005183	
PABPC3	5042	hgsc.bcm.edu	37	13	25670801	25670802	+	Frame_Shift_Ins	INS	-	-	A			TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr13:25670801_25670802insA	ENST00000281589.3	+	1	502_503	c.465_466insA	c.(466-468)aaafs	p.K156fs		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	156	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA metabolic process (GO:0016071)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|pancreas(1)|skin(3)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)		AAAGAGCTATTAAAAAAATGAA	0.396																																																	0			13																																								24568802	SO:0001589	frameshift_variant	5042			AF132026	CCDS9311.1	13q12-q13	2013-02-12	2001-11-28		ENSG00000151846	ENSG00000151846		"""RNA binding motif (RRM) containing"""	8556	protein-coding gene	gene with protein product	"""testis PABP"""	604680	"""poly(A)-binding protein, cytoplasmic 3"""	PABPL3		8432538, 10543404	Standard	NM_030979		Approved	PABP3, tPABP	uc001upy.3	Q9H361	OTTHUMG00000016601	ENST00000281589.3:c.472dupA	13.37:g.25670808_25670808dupA	ENSP00000281589:p.Lys156fs	Somatic		Capture	Illumina HiSeq	Phase_I	24568801	Q8NHV0|Q9H086	Frame_Shift_Ins	INS	ENST00000281589.3	37	CCDS9311.1																																																																																				PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2	NM_030979	
PHGR1	644844	hgsc.bcm.edu	37	15	40648373	40648405	+	In_Frame_Del	DEL	CCAGGGCCCTGCGGGCCACCCCCTGGCCATGGC	CCAGGGCCCTGCGGGCCACCCCCTGGCCATGGC	-	rs528310955|rs371153968|rs190680696|rs9707826|rs374256648	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	CCAGGGCCCTGCGGGCCACCCCCTGGCCATGGC	CCAGGGCCCTGCGGGCCACCCCCTGGCCATGGC					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr15:40648373_40648405delCCAGGGCCCTGCGGGCCACCCCCTGGCCATGGC	ENST00000448599.2	+	4	174_206	c.118_150delCCAGGGCCCTGCGGGCCACCCCCTGGCCATGGC	c.(118-150)ccagggccctgcgggccaccccctggccatggcdel	p.PGPCGPPPGHG40del	DISP2_ENST00000267889.3_5'Flank	NM_001145643.1	NP_001139115.1	C9JFL3	PHGR1_HUMAN	proline/histidine/glycine-rich 1	40	Gly-rich.																CCACCATGGTCCAGGGCCCTGCGGGCCACCCCCTGGCCATGGCCCAGGGCCCT	0.760																																																	0			15																																								38435697	SO:0001651	inframe_deletion	0				CCDS45225.1	15q15.1	2009-10-08				ENSG00000233041			37226	protein-coding gene	gene with protein product							Standard	NM_001145643		Approved		uc010uco.2	C9JFL3		ENST00000448599.2:c.118_150delCCAGGGCCCTGCGGGCCACCCCCTGGCCATGGC	15.37:g.40648373_40648405delCCAGGGCCCTGCGGGCCACCCCCTGGCCATGGC	ENSP00000410024:p.Pro40_Gly50del	Somatic		Capture	Illumina HiSeq	Phase_I	38435665		In_Frame_Del	DEL	ENST00000448599.2	37	CCDS45225.1																																																																																				PHGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418450.1	NM_001145643	
TP53	7157	hgsc.bcm.edu	37	17	7579470	7579471	+	Frame_Shift_Ins	INS	-	-	G	rs56275308|rs587782423		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr17:7579470_7579471insG	ENST00000269305.4	-	4	405_406	c.216_217insC	c.(214-219)cccgtgfs	p.V73fs	TP53_ENST00000445888.2_Frame_Shift_Ins_p.V73fs|TP53_ENST00000359597.4_Frame_Shift_Ins_p.V73fs|TP53_ENST00000413465.2_Frame_Shift_Ins_p.V73fs|TP53_ENST00000420246.2_Frame_Shift_Ins_p.V73fs|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Frame_Shift_Ins_p.V73fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	73	Interaction with HRMT1L2.|Interaction with WWOX.		V -> E (in a sporadic cancer; somatic mutation).|V -> L (in sporadic cancers; somatic mutation).|V -> M (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.V73fs*76(11)|p.0?(8)|p.V73L(3)|p.G59fs*23(3)|p.R72fs*51(2)|p.V73M(2)|p.V73fs*9(1)|p.R65fs*38(1)|p.E68fs*76(1)|p.V73fs*50(1)|p.D48fs*55(1)|p.P13fs*18(1)|p.S33fs*23(1)|p.D57_A76del20(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GCAGGGGCCACGGGGGGAGCAG	0.604		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)		yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	37	Insertion - Frameshift(11)|Deletion - Frameshift(9)|Whole gene deletion(8)|Substitution - Missense(5)|Complex - frameshift(3)|Deletion - In frame(1)	upper_aerodigestive_tract(6)|lung(6)|breast(4)|bone(4)|central_nervous_system(3)|biliary_tract(3)|urinary_tract(3)|large_intestine(2)|stomach(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)|ovary(1)|prostate(1)|liver(1)	17	GRCh37	CI920954	TP53	I																																				7520196	SO:0001589	frameshift_variant	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.217dupC	17.37:g.7579476_7579476dupG	ENSP00000269305:p.Val73fs	Somatic		Capture	Illumina HiSeq	Phase_I	7520195	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Ins	INS	ENST00000269305.4	37	CCDS11118.1																																																																																				TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
KRTAP4-1	85285	hgsc.bcm.edu	37	17	39340796	39340852	+	In_Frame_Del	DEL	CGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG	CGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG	-	rs483929|rs543483191|rs79048996|rs1985673|rs2320229|rs483893|rs572749|rs543006020|rs71155126|rs554407371|rs2320230	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	CGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG	CGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr17:39340796_39340852delCGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG	ENST00000398472.1	-	1	742_798	c.255_311delCCCACTCTGCTGTCAGACCACCTGCCACCCCAGCTGTGGTATGTCCAGCTGCTGCCG	c.(253-312)cgcccactctgctgtcagaccacctgccaccccagctgtggtatgtccagctgctgccgt>cgt	p.85_104RPLCCQTTCHPSCGMSSCCR>R				Q9BYQ7	KRA41_HUMAN	keratin associated protein 4-1	85	18 X 5 AA repeats of C-C-[GRQC]-[SPT]- [VSTL].		Missing (in allele KAP4.10). {ECO:0000269|PubMed:15955084}.			keratin filament (GO:0045095)		p.H90_C108delHPSCGMSSCCRPLCCQTTC(2)|p.H94_C112delHPSCGMSSCCRPLCCQTTC(2)		kidney(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	5		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			ACAGAGTGGACGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGGCGGCAGCAGC	0.646																																																	4	Deletion - In frame(4)	upper_aerodigestive_tract(2)|prostate(2)	17																																								36594378	SO:0001651	inframe_deletion	85285			AC006070		17q21.2	2013-06-25			ENSG00000198443	ENSG00000198443		"""Keratin associated proteins"""	18907	protein-coding gene	gene with protein product			"""keratin associated protein 4-10"""	KRTAP4-10		11279113	Standard	NM_033060		Approved	KAP4.1, KAP4.10	uc002hwe.4	Q9BYQ7	OTTHUMG00000132081	ENST00000398472.1:c.255_311delCCCACTCTGCTGTCAGACCACCTGCCACCCCAGCTGTGGTATGTCCAGCTGCTGCCG	17.37:g.39340796_39340852delCGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG	ENSP00000381489:p.Arg85_Cys103del	Somatic		Capture	Illumina HiSeq	Phase_I	36594322	A8MWS7|Q3SYF2	Frame_Shift_Del	DEL	ENST00000398472.1	37																																																																																					KRTAP4-1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255108.1	NM_033060	
LSR	51599	hgsc.bcm.edu	37	19	35758275	35758276	+	In_Frame_Ins	INS	-	-	GGA	rs397751431|rs79703261|rs35939322|rs142507475		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr19:35758275_35758276insGGA	ENST00000361790.3	+	9	1711_1712	c.1552_1553insGGA	c.(1552-1554)ggg>gGGAgg	p.519_520insR	USF2_ENST00000595068.1_5'Flank|USF2_ENST00000594064.1_5'Flank|AD000684.2_ENST00000602262.1_RNA|LSR_ENST00000427250.1_In_Frame_Ins_p.363_364insR|LSR_ENST00000354900.3_In_Frame_Ins_p.500_501insR|LSR_ENST00000347609.4_In_Frame_Ins_p.461_462insR|LSR_ENST00000360798.3_In_Frame_Ins_p.451_452insR|USF2_ENST00000379134.3_5'Flank|USF2_ENST00000343550.5_5'Flank|USF2_ENST00000222305.3_5'Flank|LSR_ENST00000602122.1_In_Frame_Ins_p.499_500insR	NM_205834.3	NP_991403.1	Q86X29	LSR_HUMAN	lipolysis stimulated lipoprotein receptor	519					embryo development (GO:0009790)|liver development (GO:0001889)	chylomicron (GO:0042627)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|low-density lipoprotein particle (GO:0034362)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	13	all_lung(56;3.91e-09)|Lung NSC(56;5.64e-09)|Esophageal squamous(110;0.162)		Epithelial(14;1.33e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.29e-18)|all cancers(14;7.11e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			GAGTAATGGTGGGAGAAGCCGG	0.723																																																	0			19							,,	2087,1919		640,807,556					,,	0.2	0.7		dbSNP_130	14	5961,1881		2351,1259,311	no	coding,coding,coding	LSR	NM_205835.2,NM_205834.2,NM_015925.5	,,	2991,2066,867	A1A1,A1R,RR		23.9862,47.9031,32.0729	,,	,,		8048,3800				40450116	SO:0001652	inframe_insertion	51599			AF130366	CCDS12449.1, CCDS12450.1, CCDS12451.1, CCDS59376.1	19q13.12	2013-01-11			ENSG00000105699	ENSG00000105699		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29572	protein-coding gene	gene with protein product	"""lipolysis-stimulated remnant"", ""immunoglobulin-like domain containing receptor 3"""					10224102	Standard	NM_015925		Approved	LISCH7, ILDR3	uc002nyl.3	Q86X29		ENST00000361790.3:c.1553_1555dupGGA	19.37:g.35758276_35758278dupGGA	ENSP00000354575:p.Arg520_Arg521dup	Somatic		Capture	Illumina HiSeq	Phase_I	40450115	A6NDW3|B4DKL4|E9PHD4|O00112|O00426|Q6ZT80|Q8NBM0|Q9BT33|Q9UQL3	In_Frame_Ins	INS	ENST00000361790.3	37	CCDS12450.1																																																																																				LSR-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465513.2	NM_015925	
NEFH	4744	hgsc.bcm.edu	37	22	29885567	29885568	+	In_Frame_Ins	INS	-	-	AAGTCCCCTGAGAAGGCC	rs147489453|rs559153194|rs75808076|rs59279731		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr22:29885567_29885568insAAGTCCCCTGAGAAGGCC	ENST00000310624.6	+	4	1971_1972	c.1938_1939insAAGTCCCCTGAGAAGGCC	c.(1939-1941)aag>AAGTCCCCTGAGAAGGCCaag	p.647_647K>KSPEKAK		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	653	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.			Missing (in Ref. 1; CAA33366 and 5; AC000035). {ECO:0000305}.	axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AGGAGGAAGCAAAGTCCCCTGA	0.569																																																	0			22								2816,1448		937,942,253						-5.3	0.0		dbSNP_134	77	5046,3206		1537,1972,617	no	coding	NEFH	NM_021076.3		2474,2914,870	A1A1,A1R,RR		38.8512,33.9587,37.1844				7862,4654				28215568	SO:0001652	inframe_insertion	4744				CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1939_1956dupAAGTCCCCTGAGAAGGCC	22.37:g.29885567_29885568insAAGTCCCCTGAGAAGGCC	Exception_encountered	Somatic		Capture	Illumina HiSeq	Phase_I	28215567	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Ins	INS	ENST00000310624.6	37	CCDS13858.1																																																																																				NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
CDC42EP1	11135	hgsc.bcm.edu	37	22	37964409	37964429	+	In_Frame_Del	DEL	CAGCGCCTGCTGCAAACCCCT	CAGCGCCTGCTGCAAACCCCT	-	rs13056859|rs13055845|rs77417880|rs62235033|rs62235034|rs187761157|rs66468174|rs200195385	byFrequency	TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	CAGCGCCTGCTGCAAACCCCT	CAGCGCCTGCTGCAAACCCCT					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chr22:37964409_37964429delCAGCGCCTGCTGCAAACCCCT	ENST00000249014.4	+	3	1178_1198	c.758_778delCAGCGCCTGCTGCAAACCCCT	c.(757-780)ccagcgcctgctgcaaacccctca>cca	p.APAANPS254del		NM_152243.2	NP_689449.1	Q00587	BORG5_HUMAN	CDC42 effector protein (Rho GTPase binding) 1	254	8 X 7 AA tandem repeats of [PT]-[AT]-A- [ENT]-[PT]-[PTS]-[AG].				positive regulation of pseudopodium assembly (GO:0031274)|regulation of cell shape (GO:0008360)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)		p.N258_A264delNPSAPAA(3)		endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(4)|prostate(5)	15	Melanoma(58;0.0574)					GCAAACCCCCCAGCGCCTGCTGCAAACCCCTCAGCACCTGC	0.665																																																	3	Deletion - In frame(3)	large_intestine(2)|haematopoietic_and_lymphoid_tissue(1)	22								868,3338		98,672,1333						1.5	0.0		dbSNP_130	10	4310,3696		1298,1714,991	no	coding	CDC42EP1	NM_152243.2		1396,2386,2324	A1A1,A1R,RR		46.1654,20.6372,42.4009				5178,7034				36294375	SO:0001651	inframe_deletion	11135			M88338	CCDS13949.1	22q13.1	2008-06-11			ENSG00000128283	ENSG00000128283			17014	protein-coding gene	gene with protein product	"""55 kDa bone marrow stromal/endothelial cell protein"", ""serum constituent protein"""	606084				1629197, 10430899	Standard	NM_152243		Approved	MSE55, CEP1, Borg5	uc003asz.4	Q00587	OTTHUMG00000150591	ENST00000249014.4:c.758_778delCAGCGCCTGCTGCAAACCCCT	22.37:g.37964409_37964429delCAGCGCCTGCTGCAAACCCCT	ENSP00000249014:p.Ala254_Ser260del	Somatic		Capture	Illumina HiSeq	Phase_I	36294355	A8K825|Q96GN1	In_Frame_Del	DEL	ENST00000249014.4	37	CCDS13949.1																																																																																				CDC42EP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318993.1	NM_152243	
SHROOM4	57477	hgsc.bcm.edu	37	X	50350758	50350759	+	In_Frame_Ins	INS	-	-	TGCTGCTGCTGT	rs201922875|rs553160982		TCGA-DC-6155-01A-11D-1657-10	TCGA-DC-6155-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	b6fae581-493a-4b85-9d31-59fecbe1f8e0	7cdfa5f8-673c-4327-9d02-457330206a98	g.chrX:50350758_50350759insTGCTGCTGCTGT	ENST00000289292.7	-	6	3666_3667	c.3383_3384insACAGCAGCAGCA	c.(3382-3384)cag>caACAGCAGCAGCAg	p.1128_1128Q>QQQQQ	SHROOM4_ENST00000460112.3_In_Frame_Ins_p.1012_1012Q>QQQQQ|SHROOM4_ENST00000376020.2_In_Frame_Ins_p.1128_1128Q>QQQQQ			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1128	Gln-rich.				actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					cctgttgcttctgctgctgctg	0.589																																																	0			X								12,1892,1813		0,4,5,3,450,721,267,412,263						-6.4	0.0			16	21,2147,4298		1,7,3,9,306,942,586,1095,1163	no	codingComplex	SHROOM4	NM_020717.3		1,11,8,12,756,1663,853,1507,1426	A1A1,A1A2,A1R,A1,A2A2,A2R,A2,RR,R		33.5292,49.0987,39.9882				33,4039,6111				50367499	SO:0001652	inframe_insertion	57477			AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.3372_3383dupACAGCAGCAGCA	X.37:g.50350758_50350759insTGCTGCTGCTGT	ENSP00000289292:p.GlnGlnGlnGln1128dup	Somatic		Capture	Illumina HiSeq	Phase_I	50367498	A7E2X9|D6RFW0|Q96LA0	In_Frame_Ins	INS	ENST00000289292.7	37	CCDS35277.1																																																																																				SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717	
