#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_ORegAnno_bin	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_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
BRAT1	221927	hgsc.bcm.edu	37	7	2578946	2578946	+	Missense_Mutation	SNP	A	A	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:2578946A>C	ENST00000340611.4	-	13	1893	c.1637T>G	c.(1636-1638)gTg>gGg	p.V546G	BRAT1_ENST00000473879.1_Intron	NM_152743.3	NP_689956.2	Q6PJG6	BRAT1_HUMAN	BRCA1-associated ATM activator 1	546					response to ionizing radiation (GO:0010212)	membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	23						CAGCTGAGGCACCTCTGAAGC	0.652																																																	0			7											29.0	29.0	29.0					7																	2578946		2203	4300	6503	2545472	SO:0001583	missense	221927			BC015632	CCDS5334.1	7p22.3	2011-03-22	2011-02-28	2011-03-22	ENSG00000106009	ENSG00000106009			21701	protein-coding gene	gene with protein product	"""BRCA1-associated protein required for ATM activation protein 1"""	614506	"""chromosome 7 open reading frame 27"""	C7orf27, BAAT1		16452482	Standard	NM_152743		Approved	MGC22916	uc003smi.3	Q6PJG6	OTTHUMG00000119091	ENST00000340611.4:c.1637T>G	7.37:g.2578946A>C	ENSP00000339637:p.Val546Gly		2545472	A4D200|C9JY24|Q8IW85|Q8IZ43|Q8WVR8|Q96IV9|Q9H7J8|Q9UFA3	Missense_Mutation	SNP	ENST00000340611.4	37	CCDS5334.1	.	.	.	.	.	.	.	.	.	.	A	14.59	2.579362	0.46006	.	.	ENSG00000106009	ENST00000340611	T	0.70164	-0.46	5.74	3.38	0.38709	Armadillo-like helical (1);Armadillo-type fold (1);	0.666018	0.15652	N	0.251380	T	0.69780	0.3149	L	0.34521	1.04	0.80722	D	1	D	0.69078	0.997	D	0.63488	0.915	T	0.67581	-0.5634	10	0.87932	D	0	-14.6006	9.8164	0.40856	0.861:0.0:0.139:0.0	.	546	Q6PJG6	BRAT1_HUMAN	G	546	ENSP00000339637:V546G	ENSP00000339637:V546G	V	-	2	0	BRAT1	2545472	0.261000	0.24063	0.188000	0.23233	0.035000	0.12851	2.406000	0.44557	0.460000	0.27045	0.459000	0.35465	GTG		0.652	BRAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239305.2	NM_152743	
CARD11	84433	hgsc.bcm.edu	37	7	2984051	2984051	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:2984051T>C	ENST00000396946.4	-	5	882	c.479A>G	c.(478-480)gAg>gGg	p.E160G	AC004906.3_ENST00000423194.1_RNA	NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	160					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)			NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		CTTCTCATCCTCCAGCTGCCG	0.577			Mis		DLBCL																																			Dom	yes		7	7p22	84433	"""caspase recruitment domain family, member 11"""		L	0			7											110.0	89.0	96.0					7																	2984051		2203	4300	6503	2950577	SO:0001583	missense	84433			AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"""card-maguk protein 1"", ""bcl10-interacting maguk protein 3"""	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.479A>G	7.37:g.2984051T>C	ENSP00000380150:p.Glu160Gly		2950577	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	T	21.1	4.104150	0.76983	.	.	ENSG00000198286	ENST00000396946	T	0.35605	1.3	4.38	4.38	0.52667	.	0.055849	0.64402	D	0.000001	T	0.54240	0.1846	M	0.67397	2.05	0.58432	D	0.999997	D	0.89917	1.0	D	0.70935	0.971	T	0.57917	-0.7728	10	0.87932	D	0	-32.0181	10.1448	0.42758	0.0:0.0:0.1677:0.8323	.	160	Q9BXL7	CAR11_HUMAN	G	160	ENSP00000380150:E160G	ENSP00000380150:E160G	E	-	2	0	CARD11	2950577	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.484000	0.81180	1.750000	0.51863	0.533000	0.62120	GAG		0.577	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415	
WIPF3	644150	hgsc.bcm.edu	37	7	29923977	29923977	+	Silent	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:29923977T>C	ENST00000409290.1	+	4	867	c.867T>C	c.(865-867)ccT>ccC	p.P289P	WIPF3_ENST00000409123.1_Silent_p.P289P|WIPF3_ENST00000242140.5_Silent_p.P289P	NM_001080529.2	NP_001073998.2	A6NGB9	WIPF3_HUMAN	WAS/WASL interacting protein family, member 3	289	Poly-Pro.				cell differentiation (GO:0030154)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)				breast(2)|large_intestine(3)|lung(6)|ovary(1)	12						CGCAGGAGCCTCCCGCCCCGC	0.687																																																	0			7											3.0	3.0	3.0					7																	29923977		1482	3505	4987	29890502	SO:0001819	synonymous_variant	644150			AK094250	CCDS56472.1	7p15.1	2006-10-12			ENSG00000122574	ENSG00000122574			22004	protein-coding gene	gene with protein product		612432					Standard	NM_001080529		Approved	CR16, FLJ36931	uc022aaz.1	A6NGB9	OTTHUMG00000152761	ENST00000409290.1:c.867T>C	7.37:g.29923977T>C			29890502	B8ZZV2	Silent	SNP	ENST00000409290.1	37	CCDS56472.1																																																																																				0.687	WIPF3-002	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327705.1		
POU6F2	11281	hgsc.bcm.edu	37	7	39379423	39379423	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:39379423T>C	ENST00000403058.1	+	6	848	c.694T>C	c.(694-696)Tct>Cct	p.S232P	POU6F2_ENST00000517348.1_3'UTR|POU6F2_ENST00000559001.1_Missense_Mutation_p.S224P|POU6F2_ENST00000518318.2_Missense_Mutation_p.S232P	NM_001166018.1|NM_007252.3	NP_001159490.1|NP_009183.3	P78424	PO6F2_HUMAN	POU class 6 homeobox 2	232	Gln-rich.|Pro-rich.				central nervous system development (GO:0007417)|ganglion mother cell fate determination (GO:0007402)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	42						accacccgcctctcagcagcc	0.682																																																	0			7											47.0	52.0	51.0					7																	39379423		2185	4262	6447	39345948	SO:0001583	missense	11281			U91934	CCDS34620.2, CCDS55103.1	7p14.1	2011-06-20	2007-07-13		ENSG00000106536	ENSG00000106536		"""Homeoboxes / POU class"""	21694	protein-coding gene	gene with protein product	"""Retina-derived POU-domain factor-1"""	609062	"""POU domain, class 6, transcription factor 2"""			8601806	Standard	NM_007252		Approved	RPF-1	uc003thb.2	P78424	OTTHUMG00000150803	ENST00000403058.1:c.694T>C	7.37:g.39379423T>C	ENSP00000384004:p.Ser232Pro		39345948	A4D1W2|C4AMB9|P78425|Q75ME8|Q86UM6|Q9UDS7	Missense_Mutation	SNP	ENST00000403058.1	37	CCDS34620.2	.	.	.	.	.	.	.	.	.	.	T	11.26	1.585129	0.28268	.	.	ENSG00000106536	ENST00000403058;ENST00000518318	T;D	0.85556	0.96;-2.0	3.56	2.38	0.29361	.	2.806260	0.03871	N	0.275598	T	0.74876	0.3774	N	0.19112	0.55	0.09310	N	1	B;B	0.11235	0.004;0.0	B;B	0.09377	0.004;0.0	T	0.61138	-0.7123	10	0.33940	T	0.23	.	5.2419	0.15477	0.0:0.2103:0.0:0.7897	.	232;232	P78424-2;P78424	.;PO6F2_HUMAN	P	232	ENSP00000384004:S232P;ENSP00000430514:S232P	ENSP00000384004:S232P	S	+	1	0	POU6F2	39345948	0.994000	0.37717	0.969000	0.41365	0.981000	0.71138	1.390000	0.34464	1.474000	0.48178	0.455000	0.32223	TCT		0.682	POU6F2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320146.3	NM_007252	
HECW1	23072	hgsc.bcm.edu	37	7	43531697	43531697	+	Silent	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:43531697A>G	ENST00000395891.2	+	18	3863	c.3258A>G	c.(3256-3258)agA>agG	p.R1086R	HECW1_ENST00000453890.1_Silent_p.R1052R	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	1086					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						CTAGAAACAGAGGAGCCTCTT	0.398																																																	0			7											58.0	58.0	58.0					7																	43531697		1835	4086	5921	43498222	SO:0001819	synonymous_variant	23072			AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.3258A>G	7.37:g.43531697A>G			43498222	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Silent	SNP	ENST00000395891.2	37	CCDS5469.2																																																																																				0.398	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052	
HECW1	23072	hgsc.bcm.edu	37	7	43591929	43591929	+	Silent	SNP	C	C	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:43591929C>A	ENST00000395891.2	+	28	5109	c.4504C>A	c.(4504-4506)Cgg>Agg	p.R1502R	HECW1_ENST00000453890.1_Silent_p.R1468R	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	1502	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						CACTGAGTACCGGGGAGGTGA	0.483																																																	0			7											89.0	93.0	92.0					7																	43591929		2028	4174	6202	43558454	SO:0001819	synonymous_variant	23072			AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.4504C>A	7.37:g.43591929C>A			43558454	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Silent	SNP	ENST00000395891.2	37	CCDS5469.2																																																																																				0.483	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052	
NACAD	23148	hgsc.bcm.edu	37	7	45124256	45124256	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:45124256T>C	ENST00000490531.2	-	2	1542	c.1523A>G	c.(1522-1524)gAg>gGg	p.E508G		NM_001146334.1	NP_001139806.1	O15069	NACAD_HUMAN	NAC alpha domain containing	508					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(2)|skin(2)	5						TGTTTCTTCCTCCCCAGCCTG	0.607																																																	0			7											62.0	60.0	61.0					7																	45124256		692	1591	2283	45090781	SO:0001583	missense	23148			AB002361	CCDS47582.1	7p13	2010-07-14			ENSG00000136274	ENSG00000136274			22196	protein-coding gene	gene with protein product							Standard	NM_001146334		Approved	KIAA0363	uc003tmt.3	O15069	OTTHUMG00000159170	ENST00000490531.2:c.1523A>G	7.37:g.45124256T>C	ENSP00000420477:p.Glu508Gly		45090781		Missense_Mutation	SNP	ENST00000490531.2	37	CCDS47582.1	.	.	.	.	.	.	.	.	.	.	T	7.480	0.648382	0.14516	.	.	ENSG00000136274	ENST00000490531	T	0.12672	2.66	3.66	-3.11	0.05299	.	.	.	.	.	T	0.05502	0.0145	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.40459	-0.9562	9	0.22706	T	0.39	2.6366	1.6028	0.02678	0.1669:0.4066:0.1695:0.257	.	508	O15069	NACAD_HUMAN	G	508	ENSP00000420477:E508G	ENSP00000420477:E508G	E	-	2	0	NACAD	45090781	0.000000	0.05858	0.000000	0.03702	0.068000	0.16541	-1.059000	0.03479	-0.816000	0.04340	0.379000	0.24179	GAG		0.607	NACAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353652.2	NM_001146334	
POM121L12	285877	hgsc.bcm.edu	37	7	53103987	53103987	+	Missense_Mutation	SNP	G	G	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:53103987G>A	ENST00000408890.4	+	1	639	c.623G>A	c.(622-624)cGg>cAg	p.R208Q		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	208										endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						GGTGGCAGGCGGAACCTGCAG	0.667																																																	0			7											45.0	55.0	52.0					7																	53103987		1990	4134	6124	53071481	SO:0001583	missense	285877				CCDS43584.1	7p12.1	2012-03-13	2012-03-13		ENSG00000221900	ENSG00000221900			25369	protein-coding gene	gene with protein product			"""POM121 membrane glycoprotein-like 12"""				Standard	NM_182595		Approved	DKFZp564N2472	uc003tpz.3	Q8N7R1	OTTHUMG00000155995	ENST00000408890.4:c.623G>A	7.37:g.53103987G>A	ENSP00000386133:p.Arg208Gln		53071481	Q8NDI9	Missense_Mutation	SNP	ENST00000408890.4	37	CCDS43584.1	.	.	.	.	.	.	.	.	.	.	G	7.868	0.727502	0.15439	.	.	ENSG00000221900	ENST00000408890	T	0.11063	2.81	1.84	-2.29	0.06805	.	.	.	.	.	T	0.04634	0.0126	N	0.14661	0.345	0.09310	N	1	B	0.14012	0.009	B	0.09377	0.004	T	0.42749	-0.9433	9	0.22706	T	0.39	.	2.9968	0.06001	0.4771:0.2402:0.2827:0.0	.	208	Q8N7R1	P1L12_HUMAN	Q	208	ENSP00000386133:R208Q	ENSP00000386133:R208Q	R	+	2	0	POM121L12	53071481	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.364000	0.01080	-0.707000	0.05022	-0.258000	0.10820	CGG		0.667	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595	
EGFR	1956	hgsc.bcm.edu	37	7	55210077	55210077	+	Missense_Mutation	SNP	G	G	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:55210077G>A	ENST00000275493.2	+	2	364	c.187G>A	c.(187-189)Ggg>Agg	p.G63R	EGFR_ENST00000420316.2_Missense_Mutation_p.G63R|EGFR_ENST00000442591.1_Missense_Mutation_p.G63R|EGFR_ENST00000455089.1_Missense_Mutation_p.G63R|EGFR_ENST00000344576.2_Missense_Mutation_p.G63R|EGFR_ENST00000454757.2_Missense_Mutation_p.G10R|EGFR_ENST00000342916.3_Missense_Mutation_p.G63R	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	63			Missing (variant EGFR vIII; found in a lung cancer sample; somatic mutation; induces lung cancer when exogenously expressed). {ECO:0000269|PubMed:16672372}.		activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)	p.G63R(1)		NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	GGTGGTCCTTGGGAATTTGGA	0.398		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																													yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"""epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"""		"""E, O"""	1	Substitution - Missense(1)	central_nervous_system(1)	7											174.0	167.0	169.0					7																	55210077		2203	4300	6503	55177571	SO:0001583	missense	1956	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"""erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"""	131550	"""epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"""	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.187G>A	7.37:g.55210077G>A	ENSP00000275493:p.Gly63Arg		55177571	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	SNP	ENST00000275493.2	37	CCDS5514.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.325432	0.81580	.	.	ENSG00000146648	ENST00000455089;ENST00000342916;ENST00000344576;ENST00000420316;ENST00000275493;ENST00000442591;ENST00000450046;ENST00000454757	D;D;D;D;D;D;D;D	0.89939	-2.59;-2.59;-2.59;-2.59;-2.59;-2.59;-2.59;-2.59	6.05	6.05	0.98169	EGF receptor, L domain (1);	0.096922	0.64402	D	0.000001	D	0.96002	0.8698	H	0.95187	3.635	0.37218	D	0.905126	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.993;0.999;0.973;0.993;0.999	D	0.97967	1.0341	10	0.87932	D	0	.	13.4187	0.60985	0.0752:0.0:0.9248:0.0	.	63;63;63;63;63	Q504U8;P00533;P00533-3;P00533-4;P00533-2	.;EGFR_HUMAN;.;.;.	R	63;63;63;63;63;63;10;10	ENSP00000415559:G63R;ENSP00000342376:G63R;ENSP00000345973:G63R;ENSP00000413843:G63R;ENSP00000275493:G63R;ENSP00000410031:G63R;ENSP00000413354:G10R;ENSP00000395243:G10R	ENSP00000275493:G63R	G	+	1	0	EGFR	55177571	1.000000	0.71417	0.998000	0.56505	0.695000	0.40330	7.677000	0.84024	2.878000	0.98634	0.650000	0.86243	GGG		0.398	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
COL1A2	1278	hgsc.bcm.edu	37	7	94052425	94052425	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:94052425A>G	ENST00000297268.6	+	40	3031	c.2560A>G	c.(2560-2562)Act>Gct	p.T854A		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	854			Missing (in OI2). {ECO:0000269|PubMed:1339453}.		blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)		COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	AGAGGCTGGTACTGCTGTAAG	0.483										HNSCC(75;0.22)																																							0			7											114.0	105.0	108.0					7																	94052425		2203	4300	6503	93890361	SO:0001583	missense	1278			Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"""Collagens"""	2198	protein-coding gene	gene with protein product	"""alpha 2(I)-collagen"", ""alpha-2 collagen type I"", ""type I procollagen"", ""collagen I, alpha-2 polypeptide"", ""collagen of skin, tendon and bone, alpha-2 chain"""	120160	"""osteogenesis imperfecta type IV"""	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.2560A>G	7.37:g.94052425A>G	ENSP00000297268:p.Thr854Ala		93890361	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Missense_Mutation	SNP	ENST00000297268.6	37	CCDS34682.1	.	.	.	.	.	.	.	.	.	.	A	14.12	2.440086	0.43326	.	.	ENSG00000164692	ENST00000297268;ENST00000545487	D	0.93133	-3.17	5.32	2.92	0.33932	.	0.268284	0.38605	N	0.001638	T	0.81800	0.4899	N	0.10972	0.075	0.26343	N	0.977322	B	0.02656	0.0	B	0.01281	0.0	T	0.67856	-0.5562	10	0.25751	T	0.34	.	4.1071	0.10041	0.5647:0.1801:0.2552:0.0	.	854	P08123	CO1A2_HUMAN	A	854;855	ENSP00000297268:T854A	ENSP00000297268:T854A	T	+	1	0	COL1A2	93890361	0.977000	0.34250	1.000000	0.80357	0.933000	0.57130	0.542000	0.23222	0.974000	0.38366	0.460000	0.39030	ACT		0.483	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089	
EPHB4	2050	hgsc.bcm.edu	37	7	100417812	100417812	+	Silent	SNP	G	G	A	rs139571805		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:100417812G>A	ENST00000358173.3	-	5	1383	c.915C>T	c.(913-915)cgC>cgT	p.R305R	EPHB4_ENST00000477446.1_5'UTR|EPHB4_ENST00000360620.3_Silent_p.R305R|RN7SL750P_ENST00000582814.1_RNA	NM_004444.4	NP_004435.3	P54760	EPHB4_HUMAN	EPH receptor B4	305	Cys-rich.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|ephrin receptor signaling pathway (GO:0048013)|heart morphogenesis (GO:0003007)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(3)	47	Lung NSC(181;0.041)|all_lung(186;0.0581)					AGTACCCGACGCGGCACTGGC	0.642																																					GBM(200;2113 3072 25865 52728)												0			7						G		1,4405	2.1+/-5.4	0,1,2202	92.0	103.0	100.0		915	-0.3	0.1	7	dbSNP_134	100	0,8600		0,0,4300	no	coding-synonymous	EPHB4	NM_004444.4		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		305/988	100417812	1,13005	2203	4300	6503	100255748	SO:0001819	synonymous_variant	2050			AY056047	CCDS5706.1	7q22	2013-02-11	2004-10-28		ENSG00000196411	ENSG00000196411		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3395	protein-coding gene	gene with protein product		600011	"""EphB4"""	HTK		8188704	Standard	NM_004444		Approved	Tyro11	uc003uwn.1	P54760	OTTHUMG00000157040	ENST00000358173.3:c.915C>T	7.37:g.100417812G>A			100255748	B5A970|B5A971|B5A972|Q7Z635|Q9BTA5|Q9BXP0	Silent	SNP	ENST00000358173.3	37	CCDS5706.1																																																																																				0.642	EPHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347222.1	NM_004444	
MUC17	140453	hgsc.bcm.edu	37	7	100678232	100678232	+	Missense_Mutation	SNP	A	A	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:100678232A>C	ENST00000306151.4	+	3	3599	c.3535A>C	c.(3535-3537)Acc>Ccc	p.T1179P		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1179	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					TGAGGCTAACACCCTTTCAAC	0.527																																																	0			7											348.0	297.0	314.0					7																	100678232		2203	4300	6503	100464952	SO:0001583	missense	140453			AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.3535A>C	7.37:g.100678232A>C	ENSP00000302716:p.Thr1179Pro		100464952	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	A	0.435	-0.901363	0.02453	.	.	ENSG00000169876	ENST00000306151	T	0.02525	4.26	0.838	-1.68	0.08212	.	.	.	.	.	T	0.01661	0.0053	N	0.24115	0.695	0.09310	N	1	B	0.21225	0.053	B	0.11329	0.006	T	0.48456	-0.9034	9	0.23891	T	0.37	.	0.0783	0.00029	0.3202:0.2406:0.1996:0.2396	.	1179	Q685J3	MUC17_HUMAN	P	1179	ENSP00000302716:T1179P	ENSP00000302716:T1179P	T	+	1	0	MUC17	100464952	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-2.575000	0.00910	-1.133000	0.02903	0.113000	0.15668	ACC		0.527	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
PIK3CG	5294	hgsc.bcm.edu	37	7	106513212	106513212	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:106513212T>C	ENST00000359195.3	+	4	2426	c.2116T>C	c.(2116-2118)Tcc>Ccc	p.S706P	PIK3CG_ENST00000440650.2_Missense_Mutation_p.S706P|PIK3CG_ENST00000496166.1_Missense_Mutation_p.S706P	NM_001282427.1|NM_002649.2	NP_001269356.1|NP_002640.2	P48736	PK3CG_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	706	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cytokine production (GO:0001816)|dendritic cell chemotaxis (GO:0002407)|endocytosis (GO:0006897)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte apoptotic process (GO:0097284)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|natural killer cell chemotaxis (GO:0035747)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of triglyceride catabolic process (GO:0010897)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion mediated by integrin (GO:0033628)|respiratory burst involved in defense response (GO:0002679)|secretory granule localization (GO:0032252)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell proliferation (GO:0042098)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|ephrin receptor binding (GO:0046875)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(9)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(16)|liver(4)|lung(59)|ovary(4)|pancreas(4)|prostate(3)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	132						GATAGCCCAGTCCAGACACTA	0.438																																																	0			7											109.0	108.0	108.0					7																	106513212		2203	4300	6503	106300448	SO:0001583	missense	5294				CCDS5739.1	7q22	2012-07-13	2012-07-13		ENSG00000105851	ENSG00000105851	2.7.1.153		8978	protein-coding gene	gene with protein product		601232	"""phosphoinositide-3-kinase, catalytic, gamma polypeptide"""				Standard	XM_005250443		Approved		uc003vdw.3	P48736	OTTHUMG00000157641	ENST00000359195.3:c.2116T>C	7.37:g.106513212T>C	ENSP00000352121:p.Ser706Pro		106300448	A4D0Q6|Q8IV23|Q9BZC8	Missense_Mutation	SNP	ENST00000359195.3	37	CCDS5739.1	.	.	.	.	.	.	.	.	.	.	T	32	5.191435	0.94923	.	.	ENSG00000105851	ENST00000440650;ENST00000496166;ENST00000359195	T;T;T	0.62498	0.02;0.02;0.02	5.92	5.92	0.95590	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.68833	0.3044	L	0.39633	1.23	0.80722	D	1	D	0.58970	0.984	P	0.61132	0.884	T	0.64803	-0.6321	10	0.25751	T	0.34	-26.9448	16.3631	0.83280	0.0:0.0:0.0:1.0	.	706	P48736	PK3CG_HUMAN	P	706	ENSP00000392258:S706P;ENSP00000419260:S706P;ENSP00000352121:S706P	ENSP00000352121:S706P	S	+	1	0	PIK3CG	106300448	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.266000	0.75297	0.533000	0.62120	TCC		0.438	PIK3CG-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349294.1		
LAMB4	22798	hgsc.bcm.edu	37	7	107743551	107743551	+	Missense_Mutation	SNP	C	C	T			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:107743551C>T	ENST00000388781.3	-	10	1201	c.1118G>A	c.(1117-1119)cGc>cAc	p.R373H	LAMB4_ENST00000414450.2_Missense_Mutation_p.R373H|LAMB4_ENST00000418464.1_Missense_Mutation_p.R373H|LAMB4_ENST00000205386.4_Missense_Mutation_p.R373H|LAMB4_ENST00000388780.3_Missense_Mutation_p.R373H	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	373	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)				NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						GGGTCTGCAGCGGTCGCAGTG	0.612																																																	0			7											63.0	55.0	57.0					7																	107743551		2203	4300	6503	107530787	SO:0001583	missense	22798			AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"""Laminins"""	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.1118G>A	7.37:g.107743551C>T	ENSP00000373433:p.Arg373His		107530787	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Missense_Mutation	SNP	ENST00000388781.3	37	CCDS34732.1	.	.	.	.	.	.	.	.	.	.	C	7.750	0.703221	0.15172	.	.	ENSG00000091128	ENST00000205386;ENST00000388781;ENST00000388780;ENST00000418464;ENST00000414450	T;T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09;-0.09	4.02	-3.68	0.04463	EGF-like, laminin (4);	0.670359	0.13321	N	0.396717	T	0.45736	0.1357	L	0.58583	1.82	0.09310	N	1	B	0.25169	0.119	B	0.22386	0.039	T	0.35301	-0.9794	10	0.15066	T	0.55	.	4.0425	0.09758	0.105:0.2626:0.1038:0.5286	.	373	A4D0S4	LAMB4_HUMAN	H	373	ENSP00000205386:R373H;ENSP00000373433:R373H;ENSP00000373432:R373H;ENSP00000402353:R373H;ENSP00000402265:R373H	ENSP00000205386:R373H	R	-	2	0	LAMB4	107530787	0.000000	0.05858	0.002000	0.10522	0.829000	0.46940	-1.150000	0.03178	-0.752000	0.04728	-0.150000	0.13652	CGC		0.612	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857	
PRRT4	401399	hgsc.bcm.edu	37	7	127990957	127990957	+	Nonsense_Mutation	SNP	G	G	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:127990957G>A	ENST00000446477.2	-	6	2966	c.2653C>T	c.(2653-2655)Cga>Tga	p.R885*	PRRT4_ENST00000489835.2_3'UTR|PRRT4_ENST00000435512.1_Nonsense_Mutation_p.R679*|PRRT4_ENST00000535159.1_Nonsense_Mutation_p.R885*	NM_001174164.1	NP_001167635.1	C9JH25	PRRT4_HUMAN	proline-rich transmembrane protein 4	885						integral component of membrane (GO:0016021)				endometrium(4)|prostate(1)	5						TCGATCTGTCGGCAGGCGTCC	0.652																																																	0			7											10.0	12.0	11.0					7																	127990957		692	1588	2280	127778193	SO:0001587	stop_gained	0			BC063892	CCDS47698.1, CCDS47698.2, CCDS55160.1	7q32.1	2011-10-10			ENSG00000224940	ENSG00000224940		"""Proline-rich transmembrane proteins"""	37280	protein-coding gene	gene with protein product							Standard	NM_001114726		Approved		uc022aky.1	C9JH25	OTTHUMG00000157714	ENST00000446477.2:c.2653C>T	7.37:g.127990957G>A	ENSP00000415026:p.Arg885*		127778193	A4D0Z9|C9JVW7	Nonsense_Mutation	SNP	ENST00000446477.2	37	CCDS55160.1	.	.	.	.	.	.	.	.	.	.	G	39	7.609703	0.98387	.	.	ENSG00000224940	ENST00000446477;ENST00000480290;ENST00000535159;ENST00000435512	.	.	.	4.43	3.53	0.40419	.	.	.	.	.	.	.	.	.	.	.	0.54753	D	0.999984	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.4674	7.7267	0.28763	0.0:0.1804:0.633:0.1866	.	.	.	.	X	885;414;885;679	.	ENSP00000410779:R679X	R	-	1	2	PRRT4	127778193	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.768000	0.38511	1.207000	0.43291	0.655000	0.94253	CGA		0.652	PRRT4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001114726	
PARP12	64761	hgsc.bcm.edu	37	7	139724562	139724562	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:139724562A>G	ENST00000263549.3	-	12	2777	c.1904T>C	c.(1903-1905)gTc>gCc	p.V635A		NM_022750.2	NP_073587.1	Q9H0J9	PAR12_HUMAN	poly (ADP-ribose) polymerase family, member 12	635	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.					nucleus (GO:0005634)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(1)	19	Melanoma(164;0.0142)					CGGCGGACGGACAAAGGAGGC	0.582																																																	0			7											107.0	89.0	95.0					7																	139724562		2203	4300	6503	139371031	SO:0001583	missense	64761			AL136766	CCDS5857.1	7q34	2014-01-28	2005-06-02	2005-06-02	ENSG00000059378	ENSG00000059378		"""Zinc fingers, CCCH-type domain containing"", ""Poly (ADP-ribose) polymerases"""	21919	protein-coding gene	gene with protein product		612481	"""zinc finger CCCH-type domain containing 1"""	ZC3HDC1		11230166, 12851707	Standard	NM_022750		Approved	FLJ22693, PARP-12, ZC3H1	uc003vvl.1	Q9H0J9	OTTHUMG00000157315	ENST00000263549.3:c.1904T>C	7.37:g.139724562A>G	ENSP00000263549:p.Val635Ala		139371031	Q9H610|Q9NP36|Q9NTI3	Missense_Mutation	SNP	ENST00000263549.3	37	CCDS5857.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.115212	0.77210	.	.	ENSG00000059378	ENST00000263549;ENST00000541746	T	0.12672	2.66	5.18	5.18	0.71444	Poly(ADP-ribose) polymerase, catalytic domain (2);	0.145410	0.45606	D	0.000352	T	0.22475	0.0542	L	0.53561	1.675	0.42048	D	0.991108	P	0.39404	0.672	P	0.46110	0.504	T	0.01188	-1.1424	10	0.52906	T	0.07	.	15.0413	0.71793	1.0:0.0:0.0:0.0	.	635	Q9H0J9	PAR12_HUMAN	A	635;19	ENSP00000263549:V635A	ENSP00000263549:V635A	V	-	2	0	PARP12	139371031	0.446000	0.25665	0.967000	0.41034	0.546000	0.35178	4.154000	0.58125	1.958000	0.56883	0.533000	0.62120	GTC		0.582	PARP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348413.1	NM_022750	
BRAF	673	hgsc.bcm.edu	37	7	140453127	140453127	+	Missense_Mutation	SNP	C	C	A	rs372569965		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:140453127C>A	ENST00000288602.6	-	15	1868	c.1808G>T	c.(1807-1809)cGa>cTa	p.R603L		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	603	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.W604del(2)|p.T599_R603>I(2)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.V600_S605>EK(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	CCCACTCCATCGAGATTTCAC	0.383		61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												Colon(40;35 892 2973 5743 27438)			Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	7	Complex - deletion inframe(5)|Deletion - In frame(2)	thyroid(3)|small_intestine(2)|ovary(1)|skin(1)	7											107.0	100.0	102.0					7																	140453127		2203	4300	6503	140099596	SO:0001583	missense	673	Familial Cancer Database	CFC, CFCS	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1808G>T	7.37:g.140453127C>A	ENSP00000288602:p.Arg603Leu		140099596	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.0|22.0	4.234378|4.234378	0.79800|0.79800	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000496384|ENST00000288602	.|D	.|0.82803	.|-1.65	5.65|5.65	5.65|5.65	0.86999|0.86999	.|Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.76586|0.76586	0.4008|0.4008	N|N	0.20881|0.20881	0.62|0.62	0.80722|0.80722	D|D	1|1	.|B	.|0.27117	.|0.168	.|B	.|0.24701	.|0.055	T|T	0.74266|0.74266	-0.3721|-0.3721	5|10	.|0.87932	.|D	.|0	.|.	19.7917|19.7917	0.96461|0.96461	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|603	.|P15056	.|BRAF_HUMAN	Y|L	211|603	.|ENSP00000288602:R603L	.|ENSP00000288602:R603L	D|R	-|-	1|2	0|0	BRAF|BRAF	140099596|140099596	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.702000|7.702000	0.84576|0.84576	2.686000|2.686000	0.91538|0.91538	0.650000|0.650000	0.86243|0.86243	GAT|CGA		0.383	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333	
BRAF	673	hgsc.bcm.edu	37	7	140481406	140481406	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:140481406A>G	ENST00000288602.6	-	11	1462	c.1402T>C	c.(1402-1404)Ttt>Ctt	p.F468L		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	468	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		F -> S (in CFC1). {ECO:0000269|PubMed:16439621, ECO:0000269|PubMed:18042262}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)		SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	ACTGTTCCAAATGATCCAGAT	0.378		61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												Colon(40;35 892 2973 5743 27438)			Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	0			7											173.0	149.0	157.0					7																	140481406		2203	4300	6503	140127875	SO:0001583	missense	673	Familial Cancer Database	CFC, CFCS	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1402T>C	7.37:g.140481406A>G	ENSP00000288602:p.Phe468Leu		140127875	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	CCDS5863.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.124417	0.77436	.	.	ENSG00000157764	ENST00000288602	D	0.89196	-2.48	5.62	5.62	0.85841	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.095786	0.85682	D	0.000000	D	0.90345	0.6979	M	0.82716	2.605	0.80722	D	1	B	0.22080	0.064	B	0.28553	0.091	D	0.88758	0.3255	10	0.87932	D	0	.	14.394	0.66999	1.0:0.0:0.0:0.0	.	468	P15056	BRAF_HUMAN	L	468	ENSP00000288602:F468L	ENSP00000288602:F468L	F	-	1	0	BRAF	140127875	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.339000	0.96797	2.130000	0.65690	0.477000	0.44152	TTT		0.378	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333	
ZYX	7791	hgsc.bcm.edu	37	7	143080008	143080008	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:143080008T>C	ENST00000322764.5	+	5	961	c.616T>C	c.(616-618)Tcc>Ccc	p.S206P	ZYX_ENST00000477373.1_3'UTR|ZYX_ENST00000449423.2_Missense_Mutation_p.S119P|ZYX_ENST00000392910.2_Missense_Mutation_p.S49P|AC093673.5_ENST00000429630.1_RNA	NM_001010972.1|NM_003461.4	NP_001010972.1|NP_003452.1	Q15942	ZYX_HUMAN	zyxin	206					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|integrin-mediated signaling pathway (GO:0007229)|regulation of inflammatory response (GO:0050727)|signal transduction (GO:0007165)|stress fiber assembly (GO:0043149)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(8)|pancreas(1)	17	Melanoma(164;0.205)					CCCTTCCAGCTCCCAGCCTCT	0.642																																																	0			7											58.0	65.0	63.0					7																	143080008		2203	4300	6503	142790130	SO:0001583	missense	7791			X95735	CCDS5883.1	7q32	2010-02-26			ENSG00000159840	ENSG00000159840			13200	protein-coding gene	gene with protein product		602002				8917469, 8940160	Standard	XM_005250052		Approved		uc003wcx.3	Q15942	OTTHUMG00000023822	ENST00000322764.5:c.616T>C	7.37:g.143080008T>C	ENSP00000324422:p.Ser206Pro		142790130	A4D2G6|Q6I9S4	Missense_Mutation	SNP	ENST00000322764.5	37	CCDS5883.1	.	.	.	.	.	.	.	.	.	.	T	10.13	1.265038	0.23136	.	.	ENSG00000159840	ENST00000322764;ENST00000449630;ENST00000354434;ENST00000449423;ENST00000392910	T;T;T;T;T	0.54279	0.67;0.73;0.59;0.58;0.58	3.67	0.689	0.18033	.	0.589031	0.15010	N	0.285623	T	0.38612	0.1047	L	0.50919	1.6	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.18967	-1.0320	10	0.23302	T	0.38	.	4.4542	0.11635	0.0:0.152:0.3594:0.4886	.	119;206	B4DQR8;Q15942	.;ZYX_HUMAN	P	206;175;174;119;49	ENSP00000324422:S206P;ENSP00000413467:S175P;ENSP00000346417:S174P;ENSP00000394158:S119P;ENSP00000376642:S49P	ENSP00000324422:S206P	S	+	1	0	ZYX	142790130	0.001000	0.12720	0.425000	0.26659	0.818000	0.46254	0.035000	0.13797	0.370000	0.24538	0.459000	0.35465	TCC		0.642	ZYX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156296.2	NM_003461	
EPHA1	2041	hgsc.bcm.edu	37	7	143094439	143094439	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:143094439T>C	ENST00000275815.3	-	10	1815	c.1729A>G	c.(1729-1731)Agg>Ggg	p.R577G		NM_005232.4	NP_005223.4	P21709	EPHA1_HUMAN	EPH receptor A1	577					activation of Rho GTPase activity (GO:0032862)|angiogenesis (GO:0001525)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of cell migration (GO:0030336)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of stress fiber assembly (GO:0051496)|protein autophosphorylation (GO:0046777)|regulation of Rac GTPase activity (GO:0032314)|substrate adhesion-dependent cell spreading (GO:0034446)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(21)|ovary(4)|skin(1)|stomach(1)|urinary_tract(3)	51	Melanoma(164;0.205)	Myeloproliferative disorder(862;0.0255)				CTCTGCTGCCTCTGCCGCTGG	0.657																																																	0			7											23.0	16.0	19.0					7																	143094439		1995	3837	5832	142804561	SO:0001583	missense	2041			M18391	CCDS5884.1	7q32-q36	2013-02-11	2004-10-28		ENSG00000146904	ENSG00000146904	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3385	protein-coding gene	gene with protein product		179610	"""EphA1"""	EPHT, EPHT1		9267020	Standard	NM_005232		Approved	EPH	uc003wcz.3	P21709	OTTHUMG00000155894	ENST00000275815.3:c.1729A>G	7.37:g.143094439T>C	ENSP00000275815:p.Arg577Gly		142804561	A1L3V3|B5A966|B5A967|Q15405	Missense_Mutation	SNP	ENST00000275815.3	37	CCDS5884.1	.	.	.	.	.	.	.	.	.	.	T	9.124	1.009734	0.19277	.	.	ENSG00000146904	ENST00000275815	T	0.10668	2.85	5.96	0.208	0.15221	.	0.786081	0.10813	N	0.631358	T	0.08179	0.0204	L	0.35854	1.095	0.18873	N	0.999988	B	0.20887	0.049	B	0.19148	0.024	T	0.39187	-0.9626	10	0.25106	T	0.35	.	7.7353	0.28810	0.0836:0.0:0.2973:0.6191	.	577	P21709	EPHA1_HUMAN	G	577	ENSP00000275815:R577G	ENSP00000275815:R577G	R	-	1	2	EPHA1	142804561	0.002000	0.14202	0.075000	0.20258	0.311000	0.27955	0.401000	0.20948	0.341000	0.23771	-0.168000	0.13345	AGG		0.657	EPHA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342154.1		
KCNH2	3757	hgsc.bcm.edu	37	7	150649725	150649725	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:150649725A>G	ENST00000262186.5	-	6	1746	c.1345T>C	c.(1345-1347)Tgc>Cgc	p.C449R	KCNH2_ENST00000392968.2_Missense_Mutation_p.C353R|KCNH2_ENST00000330883.4_Missense_Mutation_p.C109R|KCNH2_ENST00000430723.3_Missense_Mutation_p.C449R	NM_000238.3	NP_000229.1	Q12809	KCNH2_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 2	449					cardiac muscle contraction (GO:0060048)|cellular response to drug (GO:0035690)|membrane depolarization during action potential (GO:0086010)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of potassium ion export (GO:1902303)|negative regulation of potassium ion transmembrane transport (GO:1901380)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|identical protein binding (GO:0042802)|inward rectifier potassium channel activity (GO:0005242)|phosphorelay sensor kinase activity (GO:0000155)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			NS(1)|cervix(1)|endometrium(10)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	42	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Alfuzosin(DB00346)|Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Cisapride(DB00604)|Dofetilide(DB00204)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Halofantrine(DB01218)|Ibutilide(DB00308)|Imipramine(DB00458)|Miconazole(DB01110)|Pimozide(DB01100)|Prazosin(DB00457)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terazosin(DB01162)|Thioridazine(DB00679)|Verapamil(DB00661)	AGCGGCTGGCAGGCGTAGCCA	0.587																																					GBM(137;110 1844 13671 20123 45161)												0			7											116.0	115.0	115.0					7																	150649725		2203	4300	6503	150280658	SO:0001583	missense	3757			U04270	CCDS5910.1, CCDS5911.1	7q36.1	2014-09-17			ENSG00000055118	ENSG00000055118		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6251	protein-coding gene	gene with protein product		152427		LQT2		18616963, 7842012, 8159766, 16382104	Standard	NM_000238		Approved	Kv11.1, HERG, erg1	uc003wic.3	Q12809	OTTHUMG00000158341	ENST00000262186.5:c.1345T>C	7.37:g.150649725A>G	ENSP00000262186:p.Cys449Arg		150280658	A5H1P7|C4PFH9|D3DX04|O75418|O75680|Q708S9|Q9BT72|Q9BUT7|Q9H3P0	Missense_Mutation	SNP	ENST00000262186.5	37	CCDS5910.1	.	.	.	.	.	.	.	.	.	.	A	19.88	3.908433	0.72868	.	.	ENSG00000055118	ENST00000330883;ENST00000392968;ENST00000262186;ENST00000350328;ENST00000430723	D;D;D;D	0.94537	-3.45;-3.45;-3.45;-3.45	4.8	4.8	0.61643	.	0.101742	0.64402	D	0.000001	D	0.97071	0.9043	M	0.85710	2.77	0.80722	D	1	D;D;P;D;P	0.89917	0.998;1.0;0.928;0.988;0.883	D;D;P;P;P	0.81914	0.982;0.995;0.573;0.837;0.681	D	0.97443	1.0023	10	0.66056	D	0.02	.	12.3181	0.54969	1.0:0.0:0.0:0.0	.	353;449;109;449;109	C4PFH9;G5E9I0;Q708S9;Q12809;Q12809-2	.;.;.;KCNH2_HUMAN;.	R	109;353;449;109;449	ENSP00000328531:C109R;ENSP00000376695:C353R;ENSP00000262186:C449R;ENSP00000387657:C449R	ENSP00000262186:C449R	C	-	1	0	KCNH2	150280658	1.000000	0.71417	1.000000	0.80357	0.726000	0.41606	7.185000	0.77714	1.812000	0.52913	0.448000	0.29417	TGC		0.587	KCNH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350741.2	NM_000238	
ATG9B	285973	hgsc.bcm.edu	37	7	150713872	150713872	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:150713872A>G	ENST00000377974.2	-	11	2399	c.2324T>C	c.(2323-2325)cTc>cCc	p.L775P	ATG9B_ENST00000605938.1_Missense_Mutation_p.S776P|ATG9B_ENST00000444312.1_Missense_Mutation_p.L261P|ATG9B_ENST00000494791.1_5'UTR			Q674R7	ATG9B_HUMAN	autophagy related 9B	776					autophagic vacuole assembly (GO:0000045)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(1)|ovary(4)|prostate(1)	14	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CGGAGGCAGGAGAGGGTGCAC	0.617																																																	0			7											40.0	45.0	43.0					7																	150713872		2041	4208	6249	150344805	SO:0001583	missense	285973			AK027791		7q36	2014-02-12	2012-06-06	2005-09-11	ENSG00000181652	ENSG00000181652			21899	protein-coding gene	gene with protein product		612205	"""nitric oxide synthase 3 antisense"", ""ATG9 autophagy related 9 homolog B (S. cerevisiae)"""	NOS3AS		15234981, 15755735	Standard	NM_173681		Approved	FLJ14885, APG9L2, SONE	uc011kvc.2	Q674R7	OTTHUMG00000158634	ENST00000377974.2:c.2324T>C	7.37:g.150713872A>G	ENSP00000475005:p.Leu775Pro		150344805	A1A5D3|Q6JRW5|Q8N8I8	Missense_Mutation	SNP	ENST00000377974.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	8.656|8.656	0.899512|0.899512	0.17686|0.17686	.|.	.|.	ENSG00000248602|ENSG00000248602	ENST00000377974;ENST00000444312|ENST00000397266	.|.	.|.	.|.	5.33|5.33	4.16|4.16	0.48862|0.48862	.|.	0.440664|.	0.24081|.	N|.	0.041725|.	T|T	0.53769|0.53769	0.1817|0.1817	.|.	.|.	.|.	.|.	.|.	.|.	P|.	0.49447|.	0.924|.	B|.	0.41619|.	0.361|.	T|T	0.62378|0.62378	-0.6867|-0.6867	7|3	0.33141|.	T|.	0.24|.	-6.9931|-6.9931	10.3366|10.3366	0.43854|0.43854	0.8274:0.1726:0.0:0.0|0.8274:0.1726:0.0:0.0	.|.	776|.	Q674R7|.	ATG9B_HUMAN|.	P|P	775;261|776	.|.	ENSP00000444232:L775P|.	L|S	-|-	2|1	0|0	AC010973.1|AC010973.1	150344805|150344805	0.001000|0.001000	0.12720|0.12720	0.057000|0.057000	0.19452|0.19452	0.347000|0.347000	0.29111|0.29111	0.383000|0.383000	0.20651|0.20651	0.837000|0.837000	0.34925|0.34925	0.459000|0.459000	0.35465|0.35465	CTC|TCC		0.617	ATG9B-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_173681	
KMT2C	58508	hgsc.bcm.edu	37	7	151845973	151845973	+	Missense_Mutation	SNP	G	G	T			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:151845973G>T	ENST00000262189.6	-	52	13257	c.13039C>A	c.(13039-13041)Ccg>Acg	p.P4347T	KMT2C_ENST00000355193.2_Missense_Mutation_p.P4404T	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	4347					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										TTATTGAGCGGCCTGCAATCT	0.468																																																	0			7											65.0	61.0	63.0					7																	151845973		2203	4300	6503	151476906	SO:0001583	missense	58508			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.13039C>A	7.37:g.151845973G>T	ENSP00000262189:p.Pro4347Thr		151476906	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.366|7.366	0.625793|0.625793	0.14257|0.14257	.|.	.|.	ENSG00000055609|ENSG00000055609	ENST00000360104|ENST00000262189;ENST00000355193;ENST00000424877	.|D;D;D	.|0.88818	.|-1.77;-1.75;-2.43	5.67|5.67	4.78|4.78	0.61160|0.61160	.|.	.|0.159293	.|0.29212	.|U	.|0.012816	D|D	0.88702|0.88702	0.6508|0.6508	M|M	0.69823|0.69823	2.125|2.125	0.80722|0.80722	D|D	1|1	.|P;P;P	.|0.42456	.|0.78;0.775;0.775	.|B;B;B	.|0.42282	.|0.335;0.382;0.382	D|D	0.88927|0.88927	0.3370|0.3370	5|10	.|0.66056	.|D	.|0.02	.|.	12.4842|12.4842	0.55863|0.55863	0.1393:0.0:0.8607:0.0|0.1393:0.0:0.8607:0.0	.|.	.|4347;3465;4404	.|Q8NEZ4;Q8NEZ4-2;Q8NEZ4-3	.|MLL3_HUMAN;.;.	D|T	1907|4347;4404;964	.|ENSP00000262189:P4347T;ENSP00000347325:P4404T;ENSP00000410411:P964T	.|ENSP00000262189:P4347T	A|P	-|-	2|1	0|0	MLL3|MLL3	151476906|151476906	1.000000|1.000000	0.71417|0.71417	0.481000|0.481000	0.27354|0.27354	0.034000|0.034000	0.12701|0.12701	6.333000|6.333000	0.72939|0.72939	1.384000|1.384000	0.46424|0.46424	0.650000|0.650000	0.86243|0.86243	GCC|CCG		0.468	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
TBC1D20	128637	hgsc.bcm.edu	37	20	419927	419927	+	Missense_Mutation	SNP	G	G	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr20:419927G>A	ENST00000354200.4	-	7	928	c.781C>T	c.(781-783)Cgc>Tgc	p.R261C	TBC1D20_ENST00000461188.1_5'UTR	NM_144628.2	NP_653229.1	Q96BZ9	TBC20_HUMAN	TBC1 domain family, member 20	261					acrosome assembly (GO:0001675)|cargo loading into COPII-coated vesicle (GO:0090110)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|lens fiber cell morphogenesis (GO:0070309)|lipid particle organization (GO:0034389)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|seminiferous tubule development (GO:0072520)|virion assembly (GO:0019068)	endoplasmic reticulum membrane (GO:0005789)|integral component of Golgi membrane (GO:0030173)|nuclear membrane (GO:0031965)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	12		all_epithelial(17;0.228)|Breast(17;0.231)				TCCTGCTCGCGATACAACACA	0.547																																																	0			20											119.0	104.0	109.0					20																	419927		2203	4300	6503	367927	SO:0001583	missense	128637			AK055573	CCDS13002.1	20p13	2013-07-10	2005-01-05	2005-01-05	ENSG00000125875	ENSG00000125875			16133	protein-coding gene	gene with protein product		611663	"""chromosome 20 open reading frame 140"""	C20orf140		17901050	Standard	XM_005260661		Approved	dJ852M4.2	uc002wds.3	Q96BZ9	OTTHUMG00000031637	ENST00000354200.4:c.781C>T	20.37:g.419927G>A	ENSP00000346139:p.Arg261Cys		367927	A8K6I3|B9A6M1|Q5JWQ7|Q6ZSY8|Q96NE1|Q9BYM7|Q9H140	Missense_Mutation	SNP	ENST00000354200.4	37	CCDS13002.1	.	.	.	.	.	.	.	.	.	.	G	15.19	2.760441	0.49468	.	.	ENSG00000125875	ENST00000354200;ENST00000246077	T	0.22134	1.97	5.54	4.57	0.56435	Rab-GAP/TBC domain (3);	0.000000	0.85682	D	0.000000	T	0.28566	0.0707	M	0.86420	2.815	0.80722	D	1	P	0.39847	0.691	B	0.34093	0.175	T	0.24154	-1.0168	10	0.48119	T	0.1	-12.238	12.6821	0.56928	0.0:0.0:0.7006:0.2994	.	261	Q96BZ9	TBC20_HUMAN	C	261;286	ENSP00000346139:R261C	ENSP00000246077:R286C	R	-	1	0	TBC1D20	367927	1.000000	0.71417	0.998000	0.56505	0.919000	0.55068	4.590000	0.61013	1.526000	0.49068	0.655000	0.94253	CGC		0.547	TBC1D20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251397.2	NM_144628	
CDS2	8760	hgsc.bcm.edu	37	20	5154229	5154229	+	Missense_Mutation	SNP	G	G	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr20:5154229G>A	ENST00000460006.1	+	2	425	c.118G>A	c.(118-120)Gaa>Aaa	p.E40K	CDS2_ENST00000379062.4_Intron	NM_003818.3	NP_003809.1	O95674	CDS2_HUMAN	CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 2	40					CDP-diacylglycerol biosynthetic process (GO:0016024)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)	phosphatidate cytidylyltransferase activity (GO:0004605)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|prostate(1)|stomach(1)	14						GAGCCGGGCAGAATCCGCACC	0.507																																																	0			20											159.0	161.0	160.0					20																	5154229		2203	4300	6503	5102229	SO:0001583	missense	8760			AF069532	CCDS13088.1	20p13	2006-03-28			ENSG00000101290	ENSG00000101290	2.7.7.41		1801	protein-coding gene	gene with protein product		603549				9806839, 9889000	Standard	NM_003818		Approved		uc002wls.3	O95674	OTTHUMG00000031801	ENST00000460006.1:c.118G>A	20.37:g.5154229G>A	ENSP00000419879:p.Glu40Lys		5102229	B2RDC6|D3DW04|Q5TDY2|Q5TDY3|Q5TDY4|Q5TDY5|Q9BYK5|Q9NTT2	Missense_Mutation	SNP	ENST00000460006.1	37	CCDS13088.1	.	.	.	.	.	.	.	.	.	.	G	12.17	1.858355	0.32791	.	.	ENSG00000101290	ENST00000460006	T	0.43294	0.95	5.39	5.39	0.77823	.	0.107189	0.64402	D	0.000006	T	0.32941	0.0846	L	0.38838	1.175	0.80722	D	1	B	0.02656	0.0	B	0.09377	0.004	T	0.16719	-1.0393	10	0.06891	T	0.86	-13.2875	18.0708	0.89405	0.0:0.0:1.0:0.0	.	40	O95674	CDS2_HUMAN	K	40	ENSP00000419879:E40K	ENSP00000419879:E40K	E	+	1	0	CDS2	5102229	1.000000	0.71417	0.095000	0.20976	0.165000	0.22458	8.174000	0.89682	2.676000	0.91093	0.655000	0.94253	GAA		0.507	CDS2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077858.2		
BPIFB2	80341	hgsc.bcm.edu	37	20	31600614	31600614	+	Missense_Mutation	SNP	G	G	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr20:31600614G>A	ENST00000170150.3	+	4	404	c.209G>A	c.(208-210)cGg>cAg	p.R70Q		NM_025227.1	NP_079503.1	Q8N4F0	BPIB2_HUMAN	BPI fold containing family B, member 2	70						extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)										TGCAGGATCCGGATTCTGAAT	0.522																																																	0			20											199.0	186.0	191.0					20																	31600614		2203	4300	6503	31064275	SO:0001583	missense	80341			AF465765	CCDS13210.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000078898	ENSG00000078898		"""BPI fold containing"""	16177	protein-coding gene	gene with protein product		614108	"""bactericidal/permeability-increasing protein-like 1"""	C20orf184, BPIL1		12185532, 21787333	Standard	NM_025227		Approved	dJ726C3.2, LPLUNC2	uc002wyj.4	Q8N4F0	OTTHUMG00000032232	ENST00000170150.3:c.209G>A	20.37:g.31600614G>A	ENSP00000170150:p.Arg70Gln		31064275	Q6UWN3|Q6ZME0|Q8NFQ7	Missense_Mutation	SNP	ENST00000170150.3	37	CCDS13210.1	.	.	.	.	.	.	.	.	.	.	G	1.932	-0.445795	0.04604	.	.	ENSG00000078898	ENST00000170150	T	0.05025	3.51	4.41	1.98	0.26296	.	0.703635	0.12548	N	0.459345	T	0.01835	0.0058	N	0.02247	-0.625	0.22050	N	0.999396	B	0.09022	0.002	B	0.04013	0.001	T	0.46925	-0.9156	10	0.02654	T	1	-6.1992	2.9411	0.05830	0.6653:0.0:0.1202:0.2145	.	70	Q8N4F0	BPIB2_HUMAN	Q	70	ENSP00000170150:R70Q	ENSP00000170150:R70Q	R	+	2	0	BPIFB2	31064275	0.999000	0.42202	0.998000	0.56505	0.537000	0.34900	1.188000	0.32102	0.848000	0.35191	-0.302000	0.09304	CGG		0.522	BPIFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078652.2	NM_025227	
CDK5RAP1	51654	hgsc.bcm.edu	37	20	31954784	31954784	+	Missense_Mutation	SNP	C	C	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr20:31954784C>A	ENST00000357886.4	-	13	1618	c.1465G>T	c.(1465-1467)Gat>Tat	p.D489Y	CDK5RAP1_ENST00000473997.1_Missense_Mutation_p.D385Y|CDK5RAP1_ENST00000346416.2_Missense_Mutation_p.D475Y|CDK5RAP1_ENST00000544843.1_3'UTR|CDK5RAP1_ENST00000339269.5_Missense_Mutation_p.D398Y			Q96SZ6	CK5P1_HUMAN	CDK5 regulatory subunit associated protein 1	489	CDK5R1-binding.				brain development (GO:0007420)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|regulation of neuron differentiation (GO:0045664)|tRNA modification (GO:0006400)	cytoplasm (GO:0005737)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|transferase activity (GO:0016740)	p.D475N(1)		endometrium(2)|kidney(2)|large_intestine(3)|lung(12)|ovary(3)|skin(3)|urinary_tract(1)	26						TCCGGGACATCATCCTTCAGC	0.418																																																	1	Substitution - Missense(1)	skin(1)	20											167.0	156.0	160.0					20																	31954784		2203	4300	6503	31418445	SO:0001583	missense	51654			AF152097	CCDS13219.1, CCDS63255.1	20q11.21	2012-09-20	2002-07-22	2002-07-26	ENSG00000101391	ENSG00000101391			15880	protein-coding gene	gene with protein product		608200	"""chromosome 20 open reading frame 34"""	C20orf34		10721722, 11882646, 15329498	Standard	NM_016408		Approved	CGI-05, HSPC167, C42	uc002wyy.4	Q96SZ6	OTTHUMG00000032256	ENST00000357886.4:c.1465G>T	20.37:g.31954784C>A	ENSP00000350558:p.Asp489Tyr		31418445	A8K7R0|Q5QP46|Q5QP47|Q5QP48|Q675N4|Q675N5|Q9BVG6|Q9BWZ5|Q9H859|Q9NZZ9|Q9Y3F0	Missense_Mutation	SNP	ENST00000357886.4	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.78|18.78	3.697846|3.697846	0.68386|0.68386	.|.	.|.	ENSG00000101391|ENSG00000101391	ENST00000346416;ENST00000357886;ENST00000339269;ENST00000452723;ENST00000375351|ENST00000427097	T;T;T;T|.	0.21543|.	2.0;2.0;2.0;2.0|.	5.17|5.17	4.23|4.23	0.50019|0.50019	Elongator protein 3/MiaB/NifB (1);Radical SAM, alpha/beta horseshoe (1);|.	0.150326|.	0.64402|.	D|.	0.000013|.	D|D	0.85826|0.85826	0.5787|0.5787	H|H	0.96365|0.96365	3.81|3.81	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D|.	0.89917|.	0.999;0.998;0.998;1.0;0.999;1.0;0.998|.	D;D;D;D;D;D;D|.	0.76071|.	0.944;0.95;0.95;0.979;0.97;0.987;0.964|.	D|D	0.89190|0.89190	0.3550|0.3550	10|5	0.87932|.	D|.	0|.	-7.0046|-7.0046	11.6915|11.6915	0.51519|0.51519	0.0:0.9144:0.0:0.0856|0.0:0.9144:0.0:0.0856	.|.	398;489;475;215;474;475;385|.	Q96SZ6-4;Q96SZ6;Q675N5;E9PF14;Q53H36;Q96SZ6-3;Q96SZ6-2|.	.;CK5P1_HUMAN;.;.;.;.;.|.	Y|I	475;489;398;385;215|143	ENSP00000217372:D475Y;ENSP00000350558:D489Y;ENSP00000341840:D398Y;ENSP00000408133:D385Y|.	ENSP00000341840:D398Y|.	D|M	-|-	1|3	0|0	CDK5RAP1|CDK5RAP1	31418445|31418445	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.884000|0.884000	0.51177|0.51177	4.180000|4.180000	0.58296|0.58296	1.403000|1.403000	0.46800|0.46800	0.655000|0.655000	0.94253|0.94253	GAT|ATG		0.418	CDK5RAP1-011	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000078697.1	NM_016408	
TRPC4AP	26133	hgsc.bcm.edu	37	20	33632316	33632316	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr20:33632316A>G	ENST00000252015.2	-	7	946	c.857T>C	c.(856-858)aTc>aCc	p.I286T	TRPC4AP_ENST00000451813.2_Missense_Mutation_p.I286T|TRPC4AP_ENST00000432634.2_Missense_Mutation_p.I247T			Q8TEL6	TP4AP_HUMAN	transient receptor potential cation channel, subfamily C, member 4 associated protein	286	Interaction with TNFRSF1A. {ECO:0000250}.				calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|protein ubiquitination (GO:0016567)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process (GO:0006511)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|plasma membrane (GO:0005886)	phosphatase binding (GO:0019902)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|skin(1)|stomach(1)|urinary_tract(1)	32			BRCA - Breast invasive adenocarcinoma(18;0.00936)			ACCTTGATTGATTTCAGCTGC	0.378																																																	0			20											93.0	95.0	94.0					20																	33632316		2203	4300	6503	33095977	SO:0001583	missense	26133			AF055022	CCDS13246.1, CCDS46591.1	20q11.23	2014-06-13	2003-10-06	2003-10-08	ENSG00000100991	ENSG00000100991			16181	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 158"""	608430	"""chromosome 20 open reading frame 188"""	C20orf188			Standard	NM_015638		Approved	DKFZP727M231, DKFZp586C1223, dJ756N5.2, TRRP4AP, PPP1R158	uc002xbk.3	Q8TEL6	OTTHUMG00000032319	ENST00000252015.2:c.857T>C	20.37:g.33632316A>G	ENSP00000252015:p.Ile286Thr		33095977	E1P5Q0|E1P5Q1|Q96H82|Q9BVB8|Q9H429|Q9UFS6	Missense_Mutation	SNP	ENST00000252015.2	37	CCDS13246.1	.	.	.	.	.	.	.	.	.	.	A	14.12	2.440645	0.43326	.	.	ENSG00000100991	ENST00000252015;ENST00000451813;ENST00000432634;ENST00000541994	T;T;T	0.28895	1.59;1.59;1.59	5.74	5.74	0.90152	.	0.191113	0.47852	D	0.000214	T	0.21631	0.0521	N	0.22421	0.69	0.80722	D	1	B;B;B	0.29716	0.118;0.156;0.255	B;B;B	0.19666	0.018;0.026;0.026	T	0.03673	-1.1014	10	0.30078	T	0.28	.	16.043	0.80698	1.0:0.0:0.0:0.0	.	247;286;286	B4E0Q1;E1P5Q0;Q8TEL6	.;.;TP4AP_HUMAN	T	286;286;247;271	ENSP00000252015:I286T;ENSP00000400614:I286T;ENSP00000400497:I247T	ENSP00000252015:I286T	I	-	2	0	TRPC4AP	33095977	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.035000	0.93752	2.187000	0.69744	0.477000	0.44152	ATC		0.378	TRPC4AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078832.2	NM_015638	
C20orf173	140873	hgsc.bcm.edu	37	20	34117013	34117013	+	5'UTR	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr20:34117013A>G	ENST00000246199.2	-	0	124				C20orf173_ENST00000444723.1_Missense_Mutation_p.S64P|RP3-477O4.5_ENST00000422009.1_RNA|C20orf173_ENST00000374345.4_Missense_Mutation_p.S64P			Q96LM9	CT173_HUMAN	chromosome 20 open reading frame 173											haematopoietic_and_lymphoid_tissue(1)|skin(1)	2						TGGCAGGAGGAGCAGTTGAGG	0.547																																																	0			20											100.0	94.0	96.0					20																	34117013		692	1591	2283	33580427	SO:0001623	5_prime_UTR_variant	140873			AL121586	CCDS46594.1	20q11.22	2012-10-30			ENSG00000125975	ENSG00000125975			16166	protein-coding gene	gene with protein product							Standard	NM_001145350		Approved	dJ477O4.4	uc010zvf.1	Q96LM9	OTTHUMG00000032340	ENST00000246199.2:c.-155T>C	20.37:g.34117013A>G			33580427	A6PVJ1|Q2M293|Q5JWS4|Q9H449	Missense_Mutation	SNP	ENST00000246199.2	37		.	.	.	.	.	.	.	.	.	.	A	21.9	4.221054	0.79464	.	.	ENSG00000125975	ENST00000444723;ENST00000374345	T	0.53206	0.63	4.48	3.39	0.38822	.	1.219700	0.05590	N	0.574540	T	0.62295	0.2416	M	0.61703	1.905	0.09310	N	1	P	0.50943	0.94	P	0.61328	0.887	T	0.46610	-0.9179	10	0.66056	D	0.02	-13.6709	6.1342	0.20221	0.8882:0.0:0.1118:0.0	.	64	E9PFA0	.	P	64	ENSP00000403566:S64P	ENSP00000363465:S64P	S	-	1	0	C20orf173	33580427	0.472000	0.25870	0.056000	0.19401	0.787000	0.44495	1.501000	0.35693	2.011000	0.59026	0.460000	0.39030	TCC		0.547	C20orf173-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000078874.6	NM_001145350	
RBM12	10137	hgsc.bcm.edu	37	20	34240740	34240740	+	Silent	SNP	A	A	G	rs376657170|rs201181145		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr20:34240740A>G	ENST00000374114.3	-	3	2768	c.2505T>C	c.(2503-2505)ccT>ccC	p.P835P	RBM12_ENST00000374104.3_Silent_p.P835P|CPNE1_ENST00000397445.1_Intron|CPNE1_ENST00000352393.4_Intron|CPNE1_ENST00000397443.1_Intron|RP1-309K20.6_ENST00000541176.2_Intron|CPNE1_ENST00000397442.1_Intron|CPNE1_ENST00000317619.3_Intron|CPNE1_ENST00000317677.5_Intron|CPNE1_ENST00000397446.1_Intron|RBM12_ENST00000359646.1_Silent_p.P835P	NM_001198838.1|NM_001198840.1|NM_006047.5	NP_001185767.1|NP_001185769.1|NP_006038.2	Q9NTZ6	RBM12_HUMAN	RNA binding motif protein 12	835	Gly-rich.|Pro-rich.					nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(7)|kidney(1)|large_intestine(3)|lung(14)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			GGATTgggccagggccggggc	0.597																																																	0			20											20.0	22.0	21.0					20																	34240740		2143	4252	6395	33704154	SO:0001819	synonymous_variant	10137			AJ289772	CCDS13261.1	20q11.21	2013-02-12			ENSG00000244462	ENSG00000244462		"""RNA binding motif (RRM) containing"""	9898	protein-coding gene	gene with protein product		607179				11435693	Standard	NM_006047		Approved	HRIHFB2091, KIAA0765, SWAN	uc021wcq.1	Q9NTZ6	OTTHUMG00000032350	ENST00000374114.3:c.2505T>C	20.37:g.34240740A>G			33704154	B3KRU2|E1P5R6|O94865|Q8N3B1|Q9H196	Silent	SNP	ENST00000374114.3	37	CCDS13261.1																																																																																				0.597	RBM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078894.1	NM_006047	
NFS1	9054	hgsc.bcm.edu	37	20	34286486	34286486	+	Missense_Mutation	SNP	C	C	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr20:34286486C>A	ENST00000374092.4	-	2	194	c.124G>T	c.(124-126)Gtt>Ttt	p.V42F	NFS1_ENST00000540053.1_5'UTR|NFS1_ENST00000306750.3_Missense_Mutation_p.V42F|ROMO1_ENST00000374072.1_5'Flank|NFS1_ENST00000541387.1_Missense_Mutation_p.V42F|ROMO1_ENST00000397416.1_5'Flank|ROMO1_ENST00000374078.1_5'Flank|NFS1_ENST00000397425.1_5'UTR|NFS1_ENST00000374085.1_5'UTR|ROMO1_ENST00000374077.3_5'Flank|ROMO1_ENST00000336695.4_5'Flank	NM_021100.4	NP_066923.3	Q9Y697	NFS1_HUMAN	NFS1 cysteine desulfurase	42					cysteine metabolic process (GO:0006534)|iron incorporation into metallo-sulfur cluster (GO:0018283)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|protein complex assembly (GO:0006461)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine desulfurase activity (GO:0031071)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	18	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.0886)		L-Alanine(DB00160)|L-Cysteine(DB00151)	TCTGCGGGAACCGCAGACTGA	0.532																																																	0			20											40.0	44.0	43.0					20																	34286486		2203	4300	6503	33749900	SO:0001583	missense	9054			AF097025	CCDS13262.1, CCDS56185.1	20q11.22	2013-08-06	2013-08-06		ENSG00000244005	ENSG00000244005	2.8.1.7		15910	protein-coding gene	gene with protein product		603485	"""nitrogen fixation 1 (S. cerevisiae, homolog)"", ""NFS1 nitrogen fixation 1 homolog (S. cerevisiae)"""			9885568, 16847322	Standard	NM_021100		Approved	NifS, IscS	uc002xdw.2	Q9Y697	OTTHUMG00000032361	ENST00000374092.4:c.124G>T	20.37:g.34286486C>A	ENSP00000363205:p.Val42Phe		33749900	B3KMA5|B4DXK9|E1P5R8|F5GYK5|Q6P0L8|Q9NTZ5|Q9Y481	Missense_Mutation	SNP	ENST00000374092.4	37	CCDS13262.1	.	.	.	.	.	.	.	.	.	.	C	13.43	2.236109	0.39498	.	.	ENSG00000244005	ENST00000374092;ENST00000541387;ENST00000537772;ENST00000306750	T;T;T	0.33216	1.87;1.85;1.42	5.09	1.94	0.25998	.	0.834306	0.11116	N	0.598001	T	0.15046	0.0363	N	0.08118	0	0.09310	N	0.999992	B;B;B	0.21309	0.018;0.046;0.054	B;B;B	0.17722	0.019;0.009;0.015	T	0.20472	-1.0274	10	0.72032	D	0.01	.	5.4787	0.16710	0.0:0.6552:0.1632:0.1816	.	42;42;42	F5GYK5;Q8WV90;Q9Y697	.;.;NFS1_HUMAN	F	42	ENSP00000363205:V42F;ENSP00000440897:V42F;ENSP00000304740:V42F	ENSP00000304740:V42F	V	-	1	0	NFS1	33749900	0.042000	0.20092	0.052000	0.19188	0.005000	0.04900	0.174000	0.16743	0.731000	0.32448	0.563000	0.77884	GTT		0.532	NFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078936.4	NM_021100	
PTPRT	11122	hgsc.bcm.edu	37	20	40730859	40730859	+	Nonsense_Mutation	SNP	G	G	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr20:40730859G>A	ENST00000373187.1	-	26	3618	c.3619C>T	c.(3619-3621)Cga>Tga	p.R1207*	PTPRT_ENST00000373201.1_Nonsense_Mutation_p.R1197*|PTPRT_ENST00000356100.2_Nonsense_Mutation_p.R1216*|PTPRT_ENST00000373190.1_Nonsense_Mutation_p.R1206*|PTPRT_ENST00000373198.4_Nonsense_Mutation_p.R1226*|PTPRT_ENST00000373184.1_Nonsense_Mutation_p.R1217*|PTPRT_ENST00000373193.3_Nonsense_Mutation_p.R1210*			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	1207	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)	p.R1229*(1)		NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				TCCATACTTCGATTCTTATCA	0.552																																																	1	Substitution - Nonsense(1)	large_intestine(1)	20											78.0	82.0	81.0					20																	40730859		2146	4269	6415	40164273	SO:0001587	stop_gained	11122			AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.3619C>T	20.37:g.40730859G>A	ENSP00000362283:p.Arg1207*		40164273	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Nonsense_Mutation	SNP	ENST00000373187.1	37	CCDS42874.1	.	.	.	.	.	.	.	.	.	.	G	45	11.689647	0.99591	.	.	ENSG00000196090	ENST00000373190;ENST00000373187;ENST00000373193;ENST00000356100;ENST00000373198;ENST00000373184;ENST00000373201	.	.	.	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.354	0.94404	0.0:0.0:1.0:0.0	.	.	.	.	X	1206;1207;1210;1216;1229;1217;1197	.	ENSP00000348408:R1216X	R	-	1	2	PTPRT	40164273	1.000000	0.71417	0.995000	0.50966	0.990000	0.78478	8.013000	0.88655	2.588000	0.87417	0.650000	0.86243	CGA		0.552	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1		
NCOA3	8202	hgsc.bcm.edu	37	20	46264449	46264450	+	Missense_Mutation	DNP	CT	CT	AC			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C|T	C|T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr20:46264449_46264450CT>AC	ENST00000371998.3	+	11	1687_1688	c.1496_1497CT>AC	c.(1495-1497)cCT>cAC	p.P499H	NCOA3_ENST00000341724.6_Missense_Mutation_p.P509H|NCOA3_ENST00000372004.3_Missense_Mutation_p.P499H|NCOA3_ENST00000371997.3_Missense_Mutation_p.P509H			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	499					androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.P499L(1)		breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						CAGTTTTCTCCTGTTGCAGGTA	0.361																																																	1	Substitution - Missense(1)	lung(1)	20																																								45697856|45697857	SO:0001583	missense	8202			AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7670	protein-coding gene	gene with protein product	"""receptor-associated coactivator 3"", ""thyroid hormone receptor activator molecule 1"""	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	Exception_encountered	20.37:g.46264449_46264450delinsAC	ENSP00000361066:p.Pro499His		45697856|45697857	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Missense_Mutation|Silent	SNP	ENST00000371998.3	37	CCDS13407.1																																																																																				0.361	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534	
ADRM1	11047	hgsc.bcm.edu	37	20	60882692	60882692	+	Missense_Mutation	SNP	A	A	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr20:60882692A>C	ENST00000253003.2	+	7	710	c.664A>C	c.(664-666)Acc>Ccc	p.T222P	RP11-157P1.4_ENST00000414042.1_RNA|LAMA5_ENST00000492698.1_5'Flank	NM_007002.2|NM_175573.1	NP_008933.2|NP_783163.1	Q16186	ADRM1_HUMAN	adhesion regulating molecule 1	222	Ser-rich.				positive regulation of endopeptidase activity (GO:0010950)|proteasome assembly (GO:0043248)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteasome complex (GO:0000502)	endopeptidase activator activity (GO:0061133)|protease binding (GO:0002020)|proteasome binding (GO:0070628)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|urinary_tract(1)	5	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;2.51e-06)			GTCATCCACCACCTCTTCCAC	0.697																																																	0			20											37.0	37.0	37.0					20																	60882692		2196	4296	6492	60316087	SO:0001583	missense	11047			D64154	CCDS13496.1, CCDS74747.1	20q13.33	2008-05-22			ENSG00000130706	ENSG00000130706			15759	protein-coding gene	gene with protein product		610650				8033103	Standard	NM_007002		Approved	GP110, Rpn13, ARM1	uc002yco.3	Q16186	OTTHUMG00000032904	ENST00000253003.2:c.664A>C	20.37:g.60882692A>C	ENSP00000253003:p.Thr222Pro		60316087	A0PKB1|Q96FJ7|Q9H1P2	Missense_Mutation	SNP	ENST00000253003.2	37	CCDS13496.1	.	.	.	.	.	.	.	.	.	.	A	15.61	2.883900	0.51908	.	.	ENSG00000130706	ENST00000370744;ENST00000253003	.	.	.	5.25	-2.74	0.05932	.	0.486350	0.24530	N	0.037739	T	0.45337	0.1337	L	0.53249	1.67	0.39955	D	0.974594	B	0.10296	0.003	B	0.15870	0.014	T	0.26189	-1.0110	9	0.72032	D	0.01	-13.293	7.4044	0.26983	0.7243:0.0:0.1684:0.1072	.	222	Q16186	ADRM1_HUMAN	P	201;222	.	ENSP00000253003:T222P	T	+	1	0	ADRM1	60316087	0.441000	0.25626	0.995000	0.50966	0.919000	0.55068	0.090000	0.15025	-0.274000	0.09232	0.459000	0.35465	ACC		0.697	ADRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080007.1		
CHRNA4	1137	hgsc.bcm.edu	37	20	61981238	61981238	+	Missense_Mutation	SNP	C	C	T	rs142137599		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr20:61981238C>T	ENST00000370263.4	-	5	1746	c.1525G>A	c.(1525-1527)Gcc>Acc	p.A509T	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)	509					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)	GAGGCCAGGGCGCCGGCAGCC	0.682																																																	0			20						C	THR/ALA	0,4374		0,0,2187	20.0	21.0	21.0		1525	1.0	0.0	20	dbSNP_134	21	1,8577		0,1,4288	no	missense	CHRNA4	NM_000744.5	58	0,1,6475	TT,TC,CC		0.0117,0.0,0.0077	benign	509/628	61981238	1,12951	2187	4289	6476	61451682	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.1525G>A	20.37:g.61981238C>T	ENSP00000359285:p.Ala509Thr		61451682	Q4JGR7|Q4VAQ5|Q4VAQ6	Missense_Mutation	SNP	ENST00000370263.4	37	CCDS13517.1	.	.	.	.	.	.	.	.	.	.	C	8.643	0.896519	0.17686	0.0	1.17E-4	ENSG00000101204	ENST00000370258;ENST00000370263;ENST00000539366	T	0.77877	-1.13	4.67	1.04	0.20106	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.580257	0.12578	U	0.456707	T	0.52403	0.1732	N	0.11560	0.145	0.28591	N	0.909628	P;B	0.39520	0.676;0.006	B;B	0.35413	0.202;0.002	T	0.45920	-0.9228	10	0.13108	T	0.6	.	7.6129	0.28142	0.4812:0.4414:0.0774:0.0	.	438;509	Q4VAQ5;P43681	.;ACHA4_HUMAN	T	415;509;438	ENSP00000359285:A509T	ENSP00000359280:A415T	A	-	1	0	CHRNA4	61451682	0.555000	0.26530	0.007000	0.13788	0.013000	0.08279	1.127000	0.31357	-0.099000	0.12263	-0.467000	0.05162	GCC		0.682	CHRNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080508.3		
SMARCB1	6598	hgsc.bcm.edu	37	22	24175874	24175874	+	Missense_Mutation	SNP	C	C	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr22:24175874C>A	ENST00000263121.7	+	8	1298	c.1102C>A	c.(1102-1104)Cag>Aag	p.Q368K	SMARCB1_ENST00000407422.3_Missense_Mutation_p.Q359K|SMARCB1_ENST00000407082.3_Missense_Mutation_p.Q322K|SMARCB1_ENST00000344921.6_Missense_Mutation_p.Q377K|DERL3_ENST00000464023.1_5'Flank	NM_003073.3	NP_003064.2	Q12824	SNF5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1	368					ATP-dependent chromatin remodeling (GO:0043044)|blastocyst hatching (GO:0001835)|cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|DNA integration (GO:0015074)|DNA repair (GO:0006281)|mitotic cell cycle phase transition (GO:0044772)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|XY body (GO:0001741)	p53 binding (GO:0002039)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)	p.?(2)|p.Q368*(2)|p.Q377*(1)|p.L266_*386del(1)		bone(4)|central_nervous_system(198)|endometrium(4)|haematopoietic_and_lymphoid_tissue(25)|kidney(3)|large_intestine(5)|liver(2)|lung(5)|meninges(5)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|soft_tissue(194)	458		Medulloblastoma(6;2.2e-09)|all_neural(6;2.73e-05)				GATCCGCGACCAGGACAGGAA	0.622			"""D, N, F, S"""		malignant rhabdoid	malignant rhabdoid																																	yes	Rec	yes	Rhabdoid predisposition syndrome	22	22q11	6598	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1"""		M	6	Substitution - Nonsense(3)|Unknown(2)|Deletion - In frame(1)	central_nervous_system(3)|kidney(2)|haematopoietic_and_lymphoid_tissue(1)	22											122.0	105.0	111.0					22																	24175874		2203	4300	6503	22505874	SO:0001583	missense	6598			U04847	CCDS13817.1, CCDS46671.1	22q11.23	2014-09-17			ENSG00000099956	ENSG00000099956			11103	protein-coding gene	gene with protein product	"""sucrose nonfermenting, yeast, homolog-like 1"", ""integrase interactor 1"", ""malignant rhabdoid tumor suppressor"", ""protein phosphatase 1, regulatory subunit 144"""	601607		SNF5L1		7801128, 10319872, 10365963	Standard	NM_003073		Approved	BAF47, Ini1, Snr1, hSNFS, Sfh1p, RDT, PPP1R144	uc002zyb.3	Q12824	OTTHUMG00000150737	ENST00000263121.7:c.1102C>A	22.37:g.24175874C>A	ENSP00000263121:p.Gln368Lys		22505874	O75784|O95474|Q17S11|Q38GA1|Q76N08|Q9UBH2	Missense_Mutation	SNP	ENST00000263121.7	37	CCDS13817.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.606407	0.87157	.	.	ENSG00000099956	ENST00000344921;ENST00000263121;ENST00000407422;ENST00000407082	T;T;T;T	0.75260	-0.92;-0.92;-0.92;-0.92	4.76	4.76	0.60689	.	0.108664	0.64402	D	0.000004	T	0.81861	0.4912	L	0.45228	1.405	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.91635	0.998;0.997;0.999	T	0.82141	-0.0604	10	0.46703	T	0.11	-31.4772	17.2148	0.86940	0.0:1.0:0.0:0.0	.	377;359;368	G5E975;Q17S11;Q12824	.;.;SNF5_HUMAN	K	377;368;359;322	ENSP00000340883:Q377K;ENSP00000263121:Q368K;ENSP00000383984:Q359K;ENSP00000385226:Q322K	ENSP00000263121:Q368K	Q	+	1	0	SMARCB1	22505874	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.569000	0.82380	2.387000	0.81309	0.543000	0.68304	CAG		0.622	SMARCB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319872.1	NM_003073	
DEPDC5	9681	hgsc.bcm.edu	37	22	32239741	32239741	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr22:32239741A>G	ENST00000382112.3	+	28	2787	c.2717A>G	c.(2716-2718)gAg>gGg	p.E906G	DEPDC5_ENST00000382105.2_Missense_Mutation_p.E837G|DEPDC5_ENST00000535622.1_Missense_Mutation_p.E837G|DEPDC5_ENST00000266091.3_Missense_Mutation_p.E915G|DEPDC5_ENST00000400249.2_Missense_Mutation_p.E906G|DEPDC5_ENST00000382111.2_Missense_Mutation_p.E915G|DEPDC5_ENST00000400246.1_Missense_Mutation_p.E915G|DEPDC5_ENST00000400248.2_Missense_Mutation_p.E906G	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	915					intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						CGGCTGGAGGAGTACAAGTGG	0.512																																																	0			22											83.0	80.0	81.0					22																	32239741		1881	4099	5980	30569741	SO:0001583	missense	9681			AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150			18423	protein-coding gene	gene with protein product		614191				23542697, 23542701	Standard	NM_001242896		Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000382112.3:c.2717A>G	22.37:g.32239741A>G	ENSP00000371546:p.Glu906Gly		30569741	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Missense_Mutation	SNP	ENST00000382112.3	37	CCDS46692.1	.	.	.	.	.	.	.	.	.	.	A	25.1	4.599602	0.87055	.	.	ENSG00000100150	ENST00000535622;ENST00000266091;ENST00000400249;ENST00000382109;ENST00000400246;ENST00000382105;ENST00000382112;ENST00000382111;ENST00000400248	T;T;T;T;T;T;T;T	0.34667	1.38;1.81;1.81;1.79;1.35;1.8;1.79;1.81	5.91	5.91	0.95273	.	0.104113	0.64402	D	0.000004	T	0.38558	0.1045	L	0.40543	1.245	0.80722	D	1	B;P;P;P;P;P	0.45396	0.054;0.856;0.857;0.787;0.536;0.799	B;B;P;B;B;B	0.46275	0.099;0.285;0.51;0.298;0.11;0.156	T	0.11916	-1.0568	10	0.45353	T	0.12	.	15.5312	0.75964	1.0:0.0:0.0:0.0	.	236;915;837;915;906;906	B4DSS1;B9EGN9;B4DH93;O75140-4;A8MPX9;O75140	.;.;.;.;.;DEPD5_HUMAN	G	837;915;906;837;915;837;906;915;906	ENSP00000440210:E837G;ENSP00000266091:E915G;ENSP00000383108:E906G;ENSP00000383105:E915G;ENSP00000371539:E837G;ENSP00000371546:E906G;ENSP00000371545:E915G;ENSP00000383107:E906G	ENSP00000266091:E915G	E	+	2	0	DEPDC5	30569741	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.327000	0.90012	2.270000	0.75569	0.528000	0.53228	GAG		0.512	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129087.1	NM_014662	
RTCB	51493	hgsc.bcm.edu	37	22	32792108	32792108	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr22:32792108T>C	ENST00000216038.5	-	8	1041	c.943A>G	c.(943-945)Aac>Gac	p.N315D	RTCB_ENST00000476619.1_5'Flank|RTCB_ENST00000451746.2_Intron	NM_014306.4	NP_055121.1			RNA 2',3'-cyclic phosphate and 5'-OH ligase																		CAGGCATAGTTCCCAGCAGCT	0.488																																																	0			22											233.0	221.0	225.0					22																	32792108		2203	4300	6503	31122108	SO:0001583	missense	51493			BC016707	CCDS13905.1	22q12.3	2013-05-22	2013-05-22	2013-05-22	ENSG00000100220	ENSG00000100220	6.5.1.3		26935	protein-coding gene	gene with protein product	"""focal adhesion-associated protein"""	613901	"""chromosome 22 open reading frame 28"""	C22orf28		11042152, 21209330, 21311021	Standard	NM_014306		Approved	HSPC117, FAAP		Q9Y3I0	OTTHUMG00000030300	ENST00000216038.5:c.943A>G	22.37:g.32792108T>C	ENSP00000216038:p.Asn315Asp		31122108		Missense_Mutation	SNP	ENST00000216038.5	37	CCDS13905.1	.	.	.	.	.	.	.	.	.	.	T	33	5.274181	0.95459	.	.	ENSG00000100220	ENST00000216038	T	0.32753	1.44	5.64	5.64	0.86602	.	0.080350	0.85682	D	0.000000	T	0.54046	0.1834	M	0.64170	1.965	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.56950	-0.7894	10	0.87932	D	0	-10.6085	15.8531	0.78952	0.0:0.0:0.0:1.0	.	315	Q9Y3I0	RTCB_HUMAN	D	315	ENSP00000216038:N315D	ENSP00000216038:N315D	N	-	1	0	C22orf28	31122108	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.995000	0.70631	2.149000	0.67028	0.459000	0.35465	AAC		0.488	RTCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075188.3	NM_014306	
DDX17	10521	hgsc.bcm.edu	37	22	38891910	38891910	+	Silent	SNP	G	G	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr22:38891910G>A	ENST00000396821.3	-	6	870	c.771C>T	c.(769-771)gcC>gcT	p.A257A	DDX17_ENST00000432525.1_5'UTR|DDX17_ENST00000381633.3_Silent_p.A178A	NM_001098504.1|NM_006386.4	NP_001091974|NP_006377.2	Q92841	DDX17_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 17	257	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of skeletal muscle cell differentiation (GO:2001014)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA helicase activity (GO:0003724)|RNA-dependent ATPase activity (GO:0008186)|transcription coactivator activity (GO:0003713)	p.A257A(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(6)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	25	Melanoma(58;0.0286)					GTACTTGCTGGGCAAGCTCTC	0.413																																					Ovarian(55;1085 1454 6392 21425)												1	Substitution - coding silent(1)	skin(1)	22											96.0	101.0	99.0					22																	38891910		2203	4300	6503	37221856	SO:0001819	synonymous_variant	10521			U59321	CCDS33646.1, CCDS46706.1	22q13.1	2012-02-23	2012-02-23		ENSG00000100201	ENSG00000100201		"""DEAD-boxes"""	2740	protein-coding gene	gene with protein product		608469	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 17 (72kD)"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 17"""			8871553, 17226766	Standard	NM_006386		Approved	P72	uc003avy.4	Q92841	OTTHUMG00000151136	ENST00000396821.3:c.771C>T	22.37:g.38891910G>A			37221856	B1AHM0|Q69YT1|Q6ICD6	Silent	SNP	ENST00000396821.3	37	CCDS46706.1																																																																																				0.413	DDX17-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321476.2	NM_030881	
SREBF2	6721	hgsc.bcm.edu	37	22	42269974	42269974	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr22:42269974A>G	ENST00000361204.4	+	5	1206	c.1040A>G	c.(1039-1041)aAt>aGt	p.N347S		NM_004599.2	NP_004590.2	Q12772	SRBP2_HUMAN	sterol regulatory element binding transcription factor 2	347	Interaction with LMNA. {ECO:0000250}.|bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.		N -> K (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cellular lipid metabolic process (GO:0044255)|cellular response to laminar fluid shear stress (GO:0071499)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cholesterol homeostasis (GO:2000188)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|response to low-density lipoprotein particle (GO:0055098)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SREBP-SCAP-Insig complex (GO:0032937)	E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(6)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	38						TCCTCCATCAATGACAAAATC	0.488																																																	0			22											93.0	78.0	83.0					22																	42269974		2203	4300	6503	40599920	SO:0001583	missense	6721			U02031	CCDS14023.1	22q13.2	2013-05-21			ENSG00000198911	ENSG00000198911		"""Basic helix-loop-helix proteins"""	11290	protein-coding gene	gene with protein product		600481				7903453	Standard	NM_004599		Approved	SREBP2, bHLHd2	uc003bbi.3	Q12772	OTTHUMG00000151261	ENST00000361204.4:c.1040A>G	22.37:g.42269974A>G	ENSP00000354476:p.Asn347Ser		40599920	Q05BD5|Q6GTH7|Q86V36|Q9UH04	Missense_Mutation	SNP	ENST00000361204.4	37	CCDS14023.1	.	.	.	.	.	.	.	.	.	.	A	32	5.162495	0.94727	.	.	ENSG00000198911	ENST00000361204;ENST00000444813;ENST00000457567	D	0.99369	-5.78	6.17	6.17	0.99709	Helix-loop-helix DNA-binding (5);	0.000000	0.85682	D	0.000000	D	0.99498	0.9821	M	0.88181	2.935	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.98496	1.0612	10	0.87932	D	0	-25.217	16.8222	0.85835	1.0:0.0:0.0:0.0	.	347	Q12772	SRBP2_HUMAN	S	347	ENSP00000354476:N347S	ENSP00000354476:N347S	N	+	2	0	SREBF2	40599920	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.329000	0.96413	2.371000	0.80710	0.533000	0.62120	AAT		0.488	SREBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321956.1	NM_004599	
GTSE1	51512	hgsc.bcm.edu	37	22	46704749	46704749	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr22:46704749A>G	ENST00000454366.1	+	4	883	c.671A>G	c.(670-672)cAg>cGg	p.Q224R		NM_016426.6	NP_057510	Q9NYZ3	GTSE1_HUMAN	G-2 and S-phase expressed 1	205					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|microtubule-based process (GO:0007017)	cytoplasmic microtubule (GO:0005881)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	27		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00462)		GCTGCAAGTCAGGCAGCGACT	0.642																																					GBM(153;542 1915 12487 29016 50495)												0			22											53.0	62.0	59.0					22																	46704749		2203	4299	6502	45083413	SO:0001583	missense	51512			AF223408	CCDS14074.2	22q13.2-q13.3	2008-06-10			ENSG00000075218	ENSG00000075218			13698	protein-coding gene	gene with protein product		607477				10974554, 10984615, 12750368	Standard	NM_016426		Approved	GTSE-1, B99	uc011aqy.2	Q9NYZ3	OTTHUMG00000150486	ENST00000454366.1:c.671A>G	22.37:g.46704749A>G	ENSP00000415430:p.Gln224Arg		45083413	B0QYM3|Q20WK2|Q53GX5|Q5R3I6|Q6DHX4|Q9BRE0|Q9UGZ9|Q9Y557	Missense_Mutation	SNP	ENST00000454366.1	37	CCDS14074.2	.	.	.	.	.	.	.	.	.	.	A	15.26	2.782093	0.49891	.	.	ENSG00000075218	ENST00000454366;ENST00000361934	T	0.07688	3.17	4.88	0.019	0.14119	.	1.133970	0.06283	N	0.697782	T	0.07369	0.0186	L	0.46157	1.445	0.09310	N	1	P	0.46142	0.873	B	0.43225	0.412	T	0.25641	-1.0126	10	0.10377	T	0.69	-1.276	1.857	0.03181	0.412:0.3343:0.0923:0.1614	.	205	Q9NYZ3	GTSE1_HUMAN	R	224;184	ENSP00000415430:Q224R	ENSP00000354634:Q184R	Q	+	2	0	GTSE1	45083413	0.036000	0.19791	0.017000	0.16124	0.026000	0.11368	0.239000	0.18023	-0.034000	0.13713	-0.313000	0.08912	CAG		0.642	GTSE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318360.2	NM_016426	
PLXNB2	23654	hgsc.bcm.edu	37	22	50721555	50721555	+	Missense_Mutation	SNP	T	T	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr22:50721555T>G	ENST00000449103.1	-	17	2880	c.2740A>C	c.(2740-2742)Acc>Ccc	p.T914P	PLXNB2_ENST00000496720.1_5'Flank|PLXNB2_ENST00000359337.4_Missense_Mutation_p.T914P			O15031	PLXB2_HUMAN	plexin B2	914	IPT/TIG 2.				brain development (GO:0007420)|neural tube closure (GO:0001843)|neuroblast proliferation (GO:0007405)|positive regulation of axonogenesis (GO:0050772)|regulation of cell shape (GO:0008360)|regulation of neuron migration (GO:2001222)|regulation of protein phosphorylation (GO:0001932)|regulation of Rho GTPase activity (GO:0032319)|semaphorin-plexin signaling pathway (GO:0071526)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	GTPase activator activity (GO:0005096)|semaphorin receptor activity (GO:0017154)			breast(2)|central_nervous_system(4)|cervix(2)|endometrium(11)|kidney(4)|large_intestine(3)|liver(1)|lung(20)|ovary(5)|prostate(6)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	66		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CCGTGGATGGTCAGTGTGGTG	0.687																																																	0			22											13.0	18.0	17.0					22																	50721555		1991	4133	6124	49063682	SO:0001583	missense	23654				CCDS43035.1	22q13.33	2008-06-12			ENSG00000196576	ENSG00000196576		"""Plexins"""	9104	protein-coding gene	gene with protein product		604293				10520995, 12183458	Standard	NM_012401		Approved	MM1, KIAA0315, PLEXB2	uc003bkv.4	O15031	OTTHUMG00000150219	ENST00000449103.1:c.2740A>C	22.37:g.50721555T>G	ENSP00000409171:p.Thr914Pro		49063682	A6QRH0|Q7KZU3|Q9BSU7	Missense_Mutation	SNP	ENST00000449103.1	37	CCDS43035.1	.	.	.	.	.	.	.	.	.	.	T	16.82	3.228434	0.58777	.	.	ENSG00000196576	ENST00000449103;ENST00000359337	D;D	0.84223	-1.82;-1.82	3.96	2.85	0.33270	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.265720	0.26631	N	0.023308	D	0.92348	0.7572	M	0.93763	3.455	0.49213	D	0.999762	D	0.71674	0.998	D	0.69824	0.966	D	0.91770	0.5427	10	0.72032	D	0.01	.	6.5693	0.22529	0.0:0.1326:0.0:0.8674	.	914	O15031	PLXB2_HUMAN	P	914	ENSP00000409171:T914P;ENSP00000352288:T914P	ENSP00000352288:T914P	T	-	1	0	PLXNB2	49063682	1.000000	0.71417	0.994000	0.49952	0.403000	0.30841	3.013000	0.49582	1.654000	0.50703	0.459000	0.35465	ACC		0.687	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401	
ADM2	79924	hgsc.bcm.edu	37	22	50921164	50921164	+	Silent	SNP	A	A	C	rs72438078|rs3840963	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr22:50921164A>C	ENST00000395738.2	+	2	571	c.279A>C	c.(277-279)cgA>cgC	p.R93R	ADM2_ENST00000362068.2_Missense_Mutation_p.E10A|ADM2_ENST00000395737.1_Silent_p.R93R	NM_001253845.1|NM_024866.5	NP_001240774.1|NP_079142.2	Q7Z4H4	ADM2_HUMAN	adrenomedullin 2	93					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|angiogenesis (GO:0001525)|digestion (GO:0007586)|feeding behavior (GO:0007631)|negative regulation of blood pressure (GO:0045776)|positive regulation of angiogenesis (GO:0045766)|positive regulation of gene expression (GO:0010628)|protein phosphorylation (GO:0006468)	extracellular region (GO:0005576)	protein complex binding (GO:0032403)	p.H95_R100delHSGPRR(1)		breast(1)|kidney(1)	2		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CGGGCCCCCGAAGACACTCGG	0.697																																																	1	Deletion - In frame(1)	breast(1)	22																																								49268030	SO:0001819	synonymous_variant	79924			AF529213	CCDS33682.1	22q13.33	2013-02-25			ENSG00000128165	ENSG00000128165		"""Endogenous ligands"""	28898	protein-coding gene	gene with protein product		608682				14706825	Standard	NM_024866		Approved	AM2, FLJ21135	uc003blj.3	Q7Z4H4	OTTHUMG00000150202	ENST00000395738.2:c.279A>C	22.37:g.50921164A>C			49268030	Q3LFQ0	Silent	SNP	ENST00000395738.2	37	CCDS33682.1	.	.	.	.	.	.	.	.	.	.	A	16.21	3.058801	0.55325	.	.	ENSG00000128165	ENST00000362068	.	.	.	4.21	-5.89	0.02282	.	.	.	.	.	T	0.08670	0.0215	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.35151	-0.9800	5	0.08381	T	0.77	.	0.8616	0.01194	0.2188:0.3176:0.2553:0.2083	.	.	.	.	A	10	.	ENSP00000354955:E10A	E	+	2	0	ADM2	49268030	0.000000	0.05858	0.002000	0.10522	0.479000	0.33129	-1.143000	0.03200	-0.430000	0.07318	0.368000	0.22195	GAA		0.697	ADM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316816.1	NM_024866	
C14orf119	55017	hgsc.bcm.edu	37	14	23567258	23567258	+	Missense_Mutation	SNP	C	C	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr14:23567258C>A	ENST00000319074.4	+	2	1247	c.391C>A	c.(391-393)Caa>Aaa	p.Q131K	C14orf119_ENST00000554203.1_Missense_Mutation_p.Q131K|ACIN1_ENST00000605057.1_5'Flank|ACIN1_ENST00000457657.1_5'Flank|ACIN1_ENST00000262710.1_5'Flank|ACIN1_ENST00000555053.1_5'Flank	NM_017924.3	NP_060394.1	Q9NWQ9	CN119_HUMAN	chromosome 14 open reading frame 119	131						mitochondrion (GO:0005739)				central_nervous_system(1)|endometrium(1)|lung(1)	3	all_cancers(95;4.6e-05)			GBM - Glioblastoma multiforme(265;0.00649)		AAAGTTTTACCAAGCAGTGGC	0.478																																																	0			14											77.0	78.0	78.0					14																	23567258		2203	4300	6503	22637098	SO:0001583	missense	55017				CCDS9588.1	14q11.2	2012-09-25			ENSG00000179933	ENSG00000179933			20270	protein-coding gene	gene with protein product							Standard	NM_017924		Approved	FLJ20671	uc001wiu.3	Q9NWQ9	OTTHUMG00000028717	ENST00000319074.4:c.391C>A	14.37:g.23567258C>A	ENSP00000322238:p.Gln131Lys		22637098	Q6IAA7	Missense_Mutation	SNP	ENST00000319074.4	37	CCDS9588.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.026283	0.75390	.	.	ENSG00000179933	ENST00000319074;ENST00000554203	T;T	0.45276	0.9;0.9	6.07	6.07	0.98685	.	0.265262	0.43919	D	0.000503	T	0.44393	0.1291	M	0.67953	2.075	0.33916	D	0.64027	B	0.16396	0.017	B	0.15484	0.013	T	0.52711	-0.8539	10	0.49607	T	0.09	-17.1923	15.0234	0.71650	0.0:0.8579:0.1421:0.0	.	131	Q9NWQ9	CN119_HUMAN	K	131	ENSP00000322238:Q131K;ENSP00000450861:Q131K	ENSP00000322238:Q131K	Q	+	1	0	C14orf119	22637098	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.725000	0.38074	2.902000	0.99343	0.650000	0.86243	CAA		0.478	C14orf119-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071713.3	NM_017924	
EFS	10278	hgsc.bcm.edu	37	14	23828606	23828606	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr14:23828606T>C	ENST00000216733.3	-	4	1688	c.1081A>G	c.(1081-1083)Atg>Gtg	p.M361V	RP11-124D2.3_ENST00000554010.1_RNA|EFS_ENST00000429593.2_Missense_Mutation_p.M192V|EFS_ENST00000351354.3_Missense_Mutation_p.M268V	NM_005864.2	NP_005855.1	O43281	EFS_HUMAN	embryonal Fyn-associated substrate	361			M -> I (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)			endometrium(2)|kidney(1)|large_intestine(1)|liver(1)|lung(5)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)	16	all_cancers(95;7.12e-06)			GBM - Glioblastoma multiforme(265;0.00649)		TCATCCTCCATCTCCCTGCCC	0.652																																																	0			14											78.0	70.0	72.0					14																	23828606		2201	4297	6498	22898446	SO:0001583	missense	10278			AB001466	CCDS9595.1, CCDS9596.1, CCDS61404.1	14q11.2-q12	2011-04-13			ENSG00000100842	ENSG00000100842		"""Cas scaffolding proteins"""	16898	protein-coding gene	gene with protein product	"""Cas scaffolding protein family member 3"""	609906				9349509	Standard	NM_005864		Approved	EFS2, EFS1, HEFS, SIN, CASS3	uc001wjo.4	O43281	OTTHUMG00000028741	ENST00000216733.3:c.1081A>G	14.37:g.23828606T>C	ENSP00000216733:p.Met361Val		22898446	B2RAJ7|B4DJ56|E9PGU2|O43282	Missense_Mutation	SNP	ENST00000216733.3	37	CCDS9595.1	.	.	.	.	.	.	.	.	.	.	T	0	-2.639489	0.00112	.	.	ENSG00000100842	ENST00000216733;ENST00000351354;ENST00000429593	T;T;T	0.54675	0.56;1.07;1.05	4.69	3.76	0.43208	.	0.920027	0.09175	N	0.838226	T	0.26484	0.0647	N	0.02539	-0.55	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.07290	-1.0780	10	0.08837	T	0.75	-1.8724	11.7367	0.51769	0.0:0.9118:0.0:0.0882	.	192;268;361	B4DJ56;O43281-2;O43281	.;.;EFS_HUMAN	V	361;268;192	ENSP00000216733:M361V;ENSP00000340607:M268V;ENSP00000416684:M192V	ENSP00000216733:M361V	M	-	1	0	EFS	22898446	0.026000	0.19158	0.003000	0.11579	0.019000	0.09904	1.697000	0.37784	1.188000	0.43014	-0.177000	0.13119	ATG		0.652	EFS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071770.2		
VRTN	55237	hgsc.bcm.edu	37	14	74825081	74825081	+	Missense_Mutation	SNP	G	G	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr14:74825081G>A	ENST00000256362.4	+	2	1836	c.1595G>A	c.(1594-1596)cGc>cAc	p.R532H		NM_018228.2	NP_060698.2	Q9H8Y1	VRTN_HUMAN	vertebrae development associated	532					transposition, DNA-mediated (GO:0006313)		sequence-specific DNA binding (GO:0043565)|transposase activity (GO:0004803)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(15)|ovary(5)|prostate(2)|skin(1)|urinary_tract(1)	41						TTCCGCCTCCGCTACCCCAGC	0.647																																																	0			14											71.0	73.0	72.0					14																	74825081		2203	4300	6503	73894834	SO:0001583	missense	0			AK001673	CCDS9830.1	14q24.2	2012-12-07	2012-12-07	2010-10-20	ENSG00000133980	ENSG00000133980			20223	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 115"", ""vertebrae development homolog (pig)"""	C14orf115		21232157	Standard	NM_018228		Approved	FLJ10811, vertnin	uc001xpw.4	Q9H8Y1	OTTHUMG00000171208	ENST00000256362.4:c.1595G>A	14.37:g.74825081G>A	ENSP00000256362:p.Arg532His		73894834	Q9NVC7	Missense_Mutation	SNP	ENST00000256362.4	37	CCDS9830.1	.	.	.	.	.	.	.	.	.	.	G	16.84	3.233517	0.58886	.	.	ENSG00000133980	ENST00000256362	T	0.54479	0.57	4.29	2.41	0.29592	.	0.167734	0.38272	U	0.001744	T	0.37404	0.1002	L	0.32530	0.975	0.36627	D	0.876102	B	0.23490	0.086	B	0.17098	0.017	T	0.33828	-0.9853	10	0.72032	D	0.01	-6.4676	7.2197	0.25979	0.0873:0.0:0.7451:0.1676	.	532	Q9H8Y1	VRTN_HUMAN	H	532	ENSP00000256362:R532H	ENSP00000256362:R532H	R	+	2	0	VRTN	73894834	1.000000	0.71417	1.000000	0.80357	0.558000	0.35554	3.062000	0.49971	0.428000	0.26173	-0.500000	0.04577	CGC		0.647	VRTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412339.1	NM_018228	
PSMC1	5700	hgsc.bcm.edu	37	14	90731462	90731462	+	Missense_Mutation	SNP	G	G	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr14:90731462G>A	ENST00000261303.8	+	7	746	c.643G>A	c.(643-645)Ggt>Agt	p.G215S	PSMC1_ENST00000543772.2_Missense_Mutation_p.G142S	NM_002802.2	NP_002793.2	P62191	PRS4_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 1	215					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(2)|upper_aerodigestive_tract(2)	6		all_cancers(154;0.142)		COAD - Colon adenocarcinoma(157;0.21)		TGAAGAGATGGGTATAAAGCC	0.433																																																	0			14											89.0	91.0	90.0					14																	90731462		2203	4297	6500	89801215	SO:0001583	missense	5700			L02426	CCDS32139.1	14q32.11	2010-04-21			ENSG00000100764	ENSG00000100764		"""Proteasome (prosome, macropain) subunits"", ""ATPases / AAA-type"""	9547	protein-coding gene	gene with protein product		602706				9473509	Standard	NM_002802		Approved	S4, p56	uc001xyf.3	P62191		ENST00000261303.8:c.643G>A	14.37:g.90731462G>A	ENSP00000261303:p.Gly215Ser		89801215	B4DR63|P49014|Q03527|Q6IAW0|Q6NW36|Q96AZ3	Missense_Mutation	SNP	ENST00000261303.8	37	CCDS32139.1	.	.	.	.	.	.	.	.	.	.	G	35	5.455305	0.96223	.	.	ENSG00000100764	ENST00000261303;ENST00000553835;ENST00000543772	D;D;D	0.95980	-3.75;-3.87;-3.75	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	D	0.98024	0.9349	M	0.86953	2.85	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98860	1.0762	10	0.87932	D	0	-18.7785	18.8979	0.92430	0.0:0.0:1.0:0.0	.	215	P62191	PRS4_HUMAN	S	215;52;142	ENSP00000261303:G215S;ENSP00000452049:G52S;ENSP00000445147:G142S	ENSP00000261303:G215S	G	+	1	0	PSMC1	89801215	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.802000	0.99131	2.546000	0.85860	0.561000	0.74099	GGT		0.433	PSMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411253.1	NM_002802	
EVL	51466	hgsc.bcm.edu	37	14	100589881	100589881	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr14:100589881T>C	ENST00000402714.2	+	4	962	c.358T>C	c.(358-360)Tcc>Ccc	p.S120P	EVL_ENST00000544450.2_Missense_Mutation_p.S126P|EVL_ENST00000392920.3_Missense_Mutation_p.S122P			Q9UI08	EVL_HUMAN	Enah/Vasp-like	120					actin filament organization (GO:0007015)|actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ruffle assembly (GO:1900028)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of stress fiber assembly (GO:0051496)|protein homotetramerization (GO:0051289)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|membrane (GO:0016020)	profilin binding (GO:0005522)|SH3 domain binding (GO:0017124)			cervix(1)|large_intestine(5)|lung(3)|ovary(3)|urinary_tract(2)	14		Melanoma(154;0.152)				CACAGGCCCCTCCAGCCAGCG	0.587																																																	0			14											42.0	39.0	40.0					14																	100589881		2203	4300	6503	99659634	SO:0001583	missense	51466			AF112209	CCDS9955.1	14q32.2	2014-08-13			ENSG00000196405	ENSG00000196405			20234	protein-coding gene	gene with protein product						10945997, 10993894	Standard	NM_016337		Approved	RNB6	uc001ygu.3	Q9UI08	OTTHUMG00000171530	ENST00000402714.2:c.358T>C	14.37:g.100589881T>C	ENSP00000384720:p.Ser120Pro		99659634	A8K105|O95884|Q7Z522|Q8TBV1|Q9UF25|Q9UIC2	Missense_Mutation	SNP	ENST00000402714.2	37		.	.	.	.	.	.	.	.	.	.	T	11.86	1.764720	0.31228	.	.	ENSG00000196405	ENST00000402714;ENST00000544450;ENST00000392920;ENST00000555706;ENST00000539470;ENST00000557153;ENST00000557384	T;T;T;T;T;T	0.77877	-0.57;-0.6;-0.58;-1.13;-0.5;0.92	5.22	4.09	0.47781	.	0.301734	0.30269	N	0.010012	T	0.49712	0.1573	N	0.05351	-0.065	0.34952	D	0.751376	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.08055	0.003;0.002;0.001	T	0.49790	-0.8902	10	0.09843	T	0.71	-24.7806	3.19	0.06614	0.0:0.1478:0.2483:0.6039	.	126;122;120	B7Z3I5;Q9UI08-2;Q9UI08	.;.;EVL_HUMAN	P	120;126;122;107;122;107;16	ENSP00000384720:S120P;ENSP00000437904:S126P;ENSP00000376652:S122P;ENSP00000450723:S107P;ENSP00000452327:S107P;ENSP00000450979:S16P	ENSP00000376652:S122P	S	+	1	0	EVL	99659634	0.999000	0.42202	1.000000	0.80357	0.996000	0.88848	0.594000	0.24014	1.968000	0.57251	0.459000	0.35465	TCC		0.587	EVL-006	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000413958.1		
WDR20	91833	hgsc.bcm.edu	37	14	102675499	102675499	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr14:102675499A>G	ENST00000342702.3	+	3	1023	c.992A>G	c.(991-993)gAt>gGt	p.D331G	WDR20_ENST00000299135.6_3'UTR|WDR20_ENST00000556511.2_Missense_Mutation_p.D270G|WDR20_ENST00000335263.5_Missense_Mutation_p.D331G|WDR20_ENST00000545563.1_Missense_Mutation_p.D158G|WDR20_ENST00000556807.1_Missense_Mutation_p.D270G|WDR20_ENST00000424963.2_Missense_Mutation_p.D207G|WDR20_ENST00000499851.2_Missense_Mutation_p.D74G|WDR20_ENST00000322340.5_Intron|WDR20_ENST00000454394.2_Missense_Mutation_p.D362G	NM_001242418.1|NM_144574.3	NP_001229347.1|NP_653175.2	Q8TBZ3	WDR20_HUMAN	WD repeat domain 20	331										breast(1)|large_intestine(2)|lung(4)|prostate(1)	8						AGTGGCAGCGATGAGGACTTC	0.517																																																	0			14											83.0	81.0	82.0					14																	102675499		2203	4300	6503	101745252	SO:0001583	missense	91833			BC028387	CCDS9968.1, CCDS9969.1, CCDS9970.1, CCDS55942.1, CCDS55943.1, CCDS55944.1, CCDS55945.1	14q32.31	2013-01-09				ENSG00000140153		"""WD repeat domain containing"""	19667	protein-coding gene	gene with protein product							Standard	NM_181291		Approved	DMR, MGC33177, FLJ33659	uc010txu.2	Q8TBZ3		ENST00000342702.3:c.992A>G	14.37:g.102675499A>G	ENSP00000341037:p.Asp331Gly		101745252	B4DN18|E7EUY8|F8W9S4|G3V2F8|G3V5R0|H0YJJ1|Q86TU2|Q8NCN7|Q8WXX2|Q9UF86	Missense_Mutation	SNP	ENST00000342702.3	37	CCDS9969.1	.	.	.	.	.	.	.	.	.	.	A	16.51	3.143467	0.57044	.	.	ENSG00000140153	ENST00000335263;ENST00000299135;ENST00000424963;ENST00000342702;ENST00000556807;ENST00000499851;ENST00000454394;ENST00000401892;ENST00000545563	T;T;T;T;T;T;T	0.74632	0.09;0.09;0.09;-0.12;1.32;-0.12;-0.86	5.56	5.56	0.83823	WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.83589	0.5287	L	0.59436	1.845	0.80722	D	1	D;D;D;D;D;D;P	0.89917	0.998;0.997;1.0;0.999;0.995;0.997;0.895	D;P;D;D;D;D;P	0.87578	0.947;0.89;0.998;0.945;0.931;0.98;0.579	T	0.83265	-0.0046	10	0.41790	T	0.15	.	15.722	0.77718	1.0:0.0:0.0:0.0	.	362;343;270;331;270;207;331	E7EUY8;Q5JPH5;G3V2F8;Q8TBZ3-2;F8W9S4;B3KR43;Q8TBZ3	.;.;.;.;.;.;WDR20_HUMAN	G	331;270;207;331;270;74;362;261;158	ENSP00000335434:D331G;ENSP00000395793:D207G;ENSP00000341037:D331G;ENSP00000450636:D270G;ENSP00000443641:D74G;ENSP00000406084:D362G;ENSP00000437927:D158G	ENSP00000299135:D270G	D	+	2	0	WDR20	101745252	1.000000	0.71417	0.991000	0.47740	0.943000	0.58893	8.953000	0.93041	2.133000	0.65898	0.533000	0.62120	GAT		0.517	WDR20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414963.1	NM_181291	
AHNAK2	113146	hgsc.bcm.edu	37	14	105418345	105418345	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr14:105418345T>C	ENST00000333244.5	-	7	3562	c.3443A>G	c.(3442-3444)gAa>gGa	p.E1148G	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1148						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CAGGGACAGTTCCCCCTCCAG	0.632																																																	0			14											162.0	184.0	177.0					14																	105418345		1971	4148	6119	104489390	SO:0001583	missense	113146			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.3443A>G	14.37:g.105418345T>C	ENSP00000353114:p.Glu1148Gly		104489390	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	t	12.99	2.102033	0.37048	.	.	ENSG00000185567	ENST00000333244	T	0.00711	5.8	4.22	4.22	0.49857	.	.	.	.	.	T	0.00998	0.0033	L	0.48877	1.53	0.09310	N	1	B	0.22146	0.065	B	0.22601	0.04	T	0.45891	-0.9230	9	0.26408	T	0.33	.	7.8851	0.29646	0.0:0.1024:0.0:0.8976	.	1148	Q8IVF2	AHNK2_HUMAN	G	1148	ENSP00000353114:E1148G	ENSP00000353114:E1148G	E	-	2	0	AHNAK2	104489390	0.033000	0.19621	0.004000	0.12327	0.002000	0.02628	1.169000	0.31871	1.542000	0.49330	0.402000	0.26972	GAA		0.632	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
MUC16	94025	hgsc.bcm.edu	37	19	9066829	9066829	+	Missense_Mutation	SNP	C	C	T			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr19:9066829C>T	ENST00000397910.4	-	3	20820	c.20617G>A	c.(20617-20619)Gac>Aac	p.D6873N		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	6875	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						GCTGTGGTGTCTTCATCTGTT	0.488																																																	0			19											199.0	188.0	192.0					19																	9066829		2106	4233	6339	8927829	SO:0001583	missense	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.20617G>A	19.37:g.9066829C>T	ENSP00000381008:p.Asp6873Asn		8927829	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	8.470	0.857363	0.17106	.	.	ENSG00000181143	ENST00000397910	T	0.24350	1.86	2.05	2.05	0.26809	.	.	.	.	.	T	0.14270	0.0345	N	0.22421	0.69	.	.	.	P	0.50710	0.938	B	0.37451	0.25	T	0.15407	-1.0438	8	0.87932	D	0	.	7.593	0.28031	0.0:1.0:0.0:0.0	.	6873	B5ME49	.	N	6873	ENSP00000381008:D6873N	ENSP00000381008:D6873N	D	-	1	0	MUC16	8927829	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-1.236000	0.02925	1.444000	0.47605	0.407000	0.27541	GAC		0.488	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ICAM5	7087	hgsc.bcm.edu	37	19	10403920	10403920	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr19:10403920A>G	ENST00000221980.4	+	6	1526	c.1463A>G	c.(1462-1464)gAg>gGg	p.E488G		NM_003259.3	NP_003250.3	Q9UMF0	ICAM5_HUMAN	intercellular adhesion molecule 5, telencephalin	488			E -> Q (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(20;2.64e-09)|Epithelial(33;4.31e-06)|all cancers(31;9.75e-06)			CTAACGGTGGAGTGTGAGTGG	0.607																																																	0			19											73.0	54.0	61.0					19																	10403920		2194	4289	6483	10264920	SO:0001583	missense	7087			U72671	CCDS12233.1	19p13.2	2013-01-14				ENSG00000105376		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5348	protein-coding gene	gene with protein product	"""telencephalin"""	601852		TLCN		8995416, 9828136	Standard	NM_003259		Approved	TLN	uc002mnu.4	Q9UMF0		ENST00000221980.4:c.1463A>G	19.37:g.10403920A>G	ENSP00000221980:p.Glu488Gly		10264920	Q9Y6F3	Missense_Mutation	SNP	ENST00000221980.4	37	CCDS12233.1	.	.	.	.	.	.	.	.	.	.	A	19.33	3.807692	0.70797	.	.	ENSG00000105376	ENST00000221980	T	0.15718	2.4	4.84	3.83	0.44106	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.207799	0.33572	N	0.004768	T	0.26195	0.0639	L	0.55990	1.75	0.36635	D	0.876495	D	0.67145	0.996	P	0.58331	0.837	T	0.15492	-1.0435	10	0.31617	T	0.26	-20.9806	6.9864	0.24731	0.8978:0.0:0.1022:0.0	.	488	Q9UMF0	ICAM5_HUMAN	G	488	ENSP00000221980:E488G	ENSP00000221980:E488G	E	+	2	0	ICAM5	10264920	1.000000	0.71417	1.000000	0.80357	0.554000	0.35429	3.210000	0.51129	0.891000	0.36235	0.402000	0.26972	GAG		0.607	ICAM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451217.1	NM_003259	
LDLR	3949	hgsc.bcm.edu	37	19	11230864	11230864	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr19:11230864T>C	ENST00000558518.1	+	13	2129	c.1942T>C	c.(1942-1944)Tcc>Ccc	p.S648P	LDLR_ENST00000558013.1_Missense_Mutation_p.S648P|LDLR_ENST00000545707.1_Missense_Mutation_p.S521P|LDLR_ENST00000557933.1_Missense_Mutation_p.S648P|LDLR_ENST00000535915.1_Missense_Mutation_p.S607P|LDLR_ENST00000455727.2_Missense_Mutation_p.S480P	NM_000527.4|NM_001195798.1	NP_000518.1|NP_001182727.1	P01130	LDLR_HUMAN	low density lipoprotein receptor	648					cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|intestinal cholesterol absorption (GO:0030299)|lipid metabolic process (GO:0006629)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|phototransduction, visible light (GO:0007603)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol homeostasis (GO:2000188)|regulation of phosphatidylcholine catabolic process (GO:0010899)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|low-density lipoprotein particle (GO:0034362)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|glycoprotein binding (GO:0001948)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|very-low-density lipoprotein particle receptor activity (GO:0030229)	p.?(1)		breast(2)|endometrium(2)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Porfimer(DB00707)	AAACCTACTGTCCCCAGAGGA	0.502																																					GBM(18;201 575 7820 21545)												1	Unknown(1)	lung(1)	19	GRCh37	CM074324	LDLR	M							117.0	89.0	98.0					19																	11230864		2203	4300	6503	11091864	SO:0001583	missense	3949			AY114155	CCDS12254.1, CCDS56083.1, CCDS56084.1, CCDS56085.1, CCDS58651.1	19p13.2	2014-09-17	2008-08-01		ENSG00000130164	ENSG00000130164		"""Low density lipoprotein receptors"""	6547	protein-coding gene	gene with protein product	"""familial hypercholesterolemia"""	606945					Standard	NM_000527		Approved	LDLCQ2	uc002mqk.4	P01130		ENST00000558518.1:c.1942T>C	19.37:g.11230864T>C	ENSP00000454071:p.Ser648Pro		11091864	B4DII3|B4DJZ8|B4DR00|B4DTQ3|C0JYY8|H0YLU8|H0YNT7|Q53ZD9|Q59FQ1|Q9UDH7	Missense_Mutation	SNP	ENST00000558518.1	37	CCDS12254.1	.	.	.	.	.	.	.	.	.	.	T	5.227	0.227401	0.09916	.	.	ENSG00000130164	ENST00000252444;ENST00000545707;ENST00000535915;ENST00000455727	D;D;D	0.96168	-3.93;-3.93;-3.93	5.37	4.35	0.52113	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.228496	0.29752	N	0.011284	D	0.96303	0.8794	M	0.66506	2.035	0.18873	N	0.999984	B;D;B;B;B;B	0.54964	0.018;0.969;0.049;0.043;0.018;0.018	B;P;B;B;B;B	0.61940	0.078;0.896;0.129;0.061;0.121;0.078	D	0.90836	0.4720	10	0.38643	T	0.18	.	10.3077	0.43691	0.0:0.0788:0.0:0.9212	.	480;521;527;607;660;648	B4DR00;B4DJZ8;B4DII3;B4DTQ3;Q59FQ1;P01130	.;.;.;.;.;LDLR_HUMAN	P	648;521;607;480	ENSP00000437639:S521P;ENSP00000440520:S607P;ENSP00000397829:S480P	ENSP00000252444:S648P	S	+	1	0	LDLR	11091864	0.015000	0.18098	0.017000	0.16124	0.011000	0.07611	1.737000	0.38197	0.900000	0.36469	-0.262000	0.10625	TCC		0.502	LDLR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415973.2		
RAD23A	5886	hgsc.bcm.edu	37	19	13059032	13059032	+	Silent	SNP	A	A	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr19:13059032A>C	ENST00000586534.1	+	3	337	c.276A>C	c.(274-276)tcA>tcC	p.S92S	RAD23A_ENST00000592268.1_Silent_p.S92S|RAD23A_ENST00000588826.2_3'UTR|RAD23A_ENST00000316856.3_Silent_p.S92S|RAD23A_ENST00000541222.1_5'UTR			P54725	RD23A_HUMAN	RAD23 homolog A (S. cerevisiae)	92					nucleotide-excision repair (GO:0006289)|positive regulation of viral genome replication (GO:0045070)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	damaged DNA binding (GO:0003684)|polyubiquitin binding (GO:0031593)|single-stranded DNA binding (GO:0003697)|ubiquitin-specific protease binding (GO:1990381)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)|skin(1)	12						CAGAGGCCTCACCCACAGCTG	0.627								Nucleotide excision repair (NER)																																									0			19											54.0	67.0	63.0					19																	13059032		2203	4300	6503	12920032	SO:0001819	synonymous_variant	5886				CCDS12289.1, CCDS59357.1, CCDS59358.1	19p13.2	2008-07-17	2001-11-28			ENSG00000179262			9812	protein-coding gene	gene with protein product	"""RAD23, yeast homolog, A"""	600061	"""RAD23 (S. cerevisiae) homolog A"""			7851894	Standard	NM_005053		Approved	HHR23A, MGC111083	uc002mvw.2	P54725		ENST00000586534.1:c.276A>C	19.37:g.13059032A>C			12920032	K7ESE3|Q59EU8|Q5M7Z1	Silent	SNP	ENST00000586534.1	37	CCDS12289.1																																																																																				0.627	RAD23A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452752.1	NM_005053	
NFIX	4784	hgsc.bcm.edu	37	19	13186419	13186419	+	Missense_Mutation	SNP	G	G	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr19:13186419G>A	ENST00000592199.1	+	6	889	c.889G>A	c.(889-891)Ggg>Agg	p.G297R	NFIX_ENST00000588228.1_Missense_Mutation_p.G250R|NFIX_ENST00000587260.1_Missense_Mutation_p.G296R|NFIX_ENST00000358552.3_Missense_Mutation_p.G296R|NFIX_ENST00000397661.2_Missense_Mutation_p.G297R|NFIX_ENST00000360105.4_Missense_Mutation_p.G300R|NFIX_ENST00000585575.1_Missense_Mutation_p.G289R|NFIX_ENST00000587760.1_Missense_Mutation_p.G289R			Q14938	NFIX_HUMAN	nuclear factor I/X (CCAAT-binding transcription factor)	297					astrocyte differentiation (GO:0048708)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell layer development (GO:0021680)|DNA replication (GO:0006260)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(1)|skin(1)|urinary_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(19;8.2e-22)			GTTCTATCCCGGGACAGGCCG	0.617																																																	0			19											44.0	50.0	48.0					19																	13186419		2052	4196	6248	13047419	SO:0001583	missense	4784			U18761	CCDS45996.1, CCDS59359.1	19p13.3	2008-02-05				ENSG00000008441			7788	protein-coding gene	gene with protein product		164005				8340106, 7590749	Standard	NM_001271043		Approved	NF1A	uc010xmx.2	Q14938		ENST00000592199.1:c.889G>A	19.37:g.13186419G>A	ENSP00000467512:p.Gly297Arg		13047419	B4DM25|O60413|Q0VG09|Q12859|Q13050|Q13052|Q5U094|Q9UPH1|Q9Y6R8	Missense_Mutation	SNP	ENST00000592199.1	37		.	.	.	.	.	.	.	.	.	.	G	20.4	3.977771	0.74360	.	.	ENSG00000008441	ENST00000397661;ENST00000360105;ENST00000264825;ENST00000358552	T;T	0.44482	0.92;0.97	4.69	4.69	0.59074	.	0.000000	0.64402	D	0.000016	T	0.58061	0.2096	L	0.51422	1.61	0.46823	D	0.999218	D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.996;0.999;0.999	T	0.53272	-0.8462	10	0.31617	T	0.26	.	16.5244	0.84327	0.0:0.0:1.0:0.0	.	305;296;300;297;297	B4DHW2;Q14938-5;F8W8H9;Q14938;Q14938-3	.;.;.;NFIX_HUMAN;.	R	297;297;300;296	ENSP00000380781:G297R;ENSP00000351354:G296R	ENSP00000264825:G300R	G	+	1	0	NFIX	13047419	1.000000	0.71417	0.980000	0.43619	0.814000	0.46013	6.453000	0.73488	2.440000	0.82611	0.561000	0.74099	GGG		0.617	NFIX-013	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000452763.1	NM_002501	
SUGP2	10147	hgsc.bcm.edu	37	19	19115059	19115059	+	Silent	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr19:19115059A>G	ENST00000601879.1	-	7	3144	c.2847T>C	c.(2845-2847)ccT>ccC	p.P949P	SUGP2_ENST00000600377.1_Silent_p.P963P|SUGP2_ENST00000456085.2_Silent_p.P718P|SUGP2_ENST00000452918.2_Silent_p.P949P|SUGP2_ENST00000337018.6_Silent_p.P949P			Q8IX01	SUGP2_HUMAN	SURP and G patch domain containing 2	949					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						TCCTCTTCCGAGGGAAGCAGG	0.622																																																	0			19											70.0	70.0	70.0					19																	19115059		2203	4300	6503	18976059	SO:0001819	synonymous_variant	0			AB002363	CCDS12392.1	19p13	2013-01-28	2010-08-10	2010-08-10	ENSG00000064607	ENSG00000064607		"""G patch domain containing"""	18641	protein-coding gene	gene with protein product		607993	"""splicing factor, arginine/serine-rich 14"""	SFRS14		12594045	Standard	NM_014884		Approved	KIAA0365	uc002nkx.2	Q8IX01		ENST00000601879.1:c.2847T>C	19.37:g.19115059A>G			18976059	C9JI71|O15071|O60369|Q5JPH7|Q8WUF7	Silent	SNP	ENST00000601879.1	37	CCDS12392.1																																																																																				0.622	SUGP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464627.1	NM_001017392	
ZNF568	374900	hgsc.bcm.edu	37	19	37416131	37416131	+	Missense_Mutation	SNP	G	G	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr19:37416131G>A	ENST00000333987.7	+	4	612	c.106G>A	c.(106-108)Gag>Aag	p.E36K	ZNF568_ENST00000415168.1_Intron|ZNF568_ENST00000427117.1_Missense_Mutation_p.E36K|ZNF568_ENST00000455427.2_5'UTR	NM_001204835.1|NM_198539.3	NP_001191764.1|NP_940941.2	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	36					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(9)|ovary(1)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TGCCCTTTCCGAGGAAGAAGA	0.413																																																	0			19											141.0	126.0	131.0					19																	37416131		1878	4112	5990	42107971	SO:0001583	missense	374900			BX640681	CCDS42558.1, CCDS56092.1, CCDS56093.1, CCDS74351.1	19q13.12	2013-09-20			ENSG00000198453	ENSG00000198453		"""Zinc fingers, C2H2-type"", ""-"""	25392	protein-coding gene	gene with protein product							Standard	NM_198539		Approved	DKFZp686B0797	uc002ofc.3	Q3ZCX4	OTTHUMG00000048160	ENST00000333987.7:c.106G>A	19.37:g.37416131G>A	ENSP00000334685:p.Glu36Lys		42107971	B4DS92|E7ER33|Q6N060|Q8NA64	Missense_Mutation	SNP	ENST00000333987.7	37	CCDS42558.1	.	.	.	.	.	.	.	.	.	.	G	8.439	0.850363	0.17034	.	.	ENSG00000198453	ENST00000427117;ENST00000333987;ENST00000444991	T;T;T	0.06449	5.83;3.51;3.3	3.74	-7.48	0.01360	.	.	.	.	.	T	0.02455	0.0075	N	0.08118	0	0.09310	N	1	B;B	0.14438	0.01;0.0	B;B	0.04013	0.001;0.0	T	0.47497	-0.9113	9	0.09338	T	0.73	.	9.6374	0.39817	0.186:0.2588:0.5552:0.0	.	36;36	C9JZ58;Q3ZCX4	.;ZN568_HUMAN	K	36	ENSP00000407012:E36K;ENSP00000334685:E36K;ENSP00000389794:E36K	ENSP00000334685:E36K	E	+	1	0	ZNF568	42107971	0.000000	0.05858	0.000000	0.03702	0.137000	0.21094	-3.302000	0.00520	-2.153000	0.00793	-0.796000	0.03273	GAG		0.413	ZNF568-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109572.2	NM_198539	
SIPA1L3	23094	hgsc.bcm.edu	37	19	38590741	38590741	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr19:38590741T>C	ENST00000222345.6	+	5	2314	c.1805T>C	c.(1804-1806)cTc>cCc	p.L602P		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	602					hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			CGGCTGGCCCTCAACACCCCC	0.647																																																	0			19											52.0	47.0	49.0					19																	38590741		2203	4300	6503	43282581	SO:0001583	missense	23094			AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738			23801	protein-coding gene	gene with protein product							Standard	XM_005258671		Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.1805T>C	19.37:g.38590741T>C	ENSP00000222345:p.Leu602Pro		43282581	Q2TV87	Missense_Mutation	SNP	ENST00000222345.6	37	CCDS33007.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.380306	0.82682	.	.	ENSG00000105738	ENST00000222345	D	0.94457	-3.43	5.88	5.88	0.94601	.	0.062740	0.64402	D	0.000004	D	0.93220	0.7840	M	0.61703	1.905	0.80722	D	1	B	0.15141	0.012	B	0.17098	0.017	D	0.90301	0.4330	10	0.56958	D	0.05	-40.9922	15.2813	0.73787	0.0:0.0:0.0:1.0	.	602	O60292	SI1L3_HUMAN	P	602	ENSP00000222345:L602P	ENSP00000222345:L602P	L	+	2	0	SIPA1L3	43282581	0.992000	0.36948	1.000000	0.80357	0.988000	0.76386	4.966000	0.63715	2.257000	0.74773	0.459000	0.35465	CTC		0.647	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278	
IRGQ	126298	hgsc.bcm.edu	37	19	44097454	44097454	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr19:44097454T>C	ENST00000602269.1	-	2	781	c.596A>G	c.(595-597)gAg>gGg	p.E199G	L34079.2_ENST00000594374.1_5'Flank|IRGQ_ENST00000422989.1_Missense_Mutation_p.E199G|IRGQ_ENST00000601520.1_5'Flank			Q8WZA9	IRGQ_HUMAN	immunity-related GTPase family, Q	199										endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(3)	18		Prostate(69;0.0199)				CTCAAAGGCCTCACGCACAGC	0.667																																																	0			19											37.0	37.0	37.0					19																	44097454		2203	4297	6500	48789294	SO:0001583	missense	126298			AF322648	CCDS33040.1	19q13.31	2013-07-03	2005-10-31	2005-10-31		ENSG00000167378			24868	protein-coding gene	gene with protein product			"""immunity-related GTPase family, Q1"""	IRGQ1		16277747	Standard	NM_001007561		Approved	FKSG27	uc010eiv.2	Q8WZA9		ENST00000602269.1:c.596A>G	19.37:g.44097454T>C	ENSP00000472250:p.Glu199Gly		48789294	B2RNP3	Missense_Mutation	SNP	ENST00000602269.1	37	CCDS33040.1	.	.	.	.	.	.	.	.	.	.	T	17.67	3.446635	0.63178	.	.	ENSG00000167378	ENST00000422989	T	0.51071	0.72	5.14	5.14	0.70334	.	0.000000	0.64402	D	0.000001	T	0.60301	0.2258	M	0.64997	1.995	0.31376	N	0.679564	D	0.76494	0.999	D	0.68943	0.961	T	0.63545	-0.6613	10	0.33141	T	0.24	-5.9844	9.3454	0.38104	0.0:0.0:0.1803:0.8197	.	199	Q8WZA9	IRGQ_HUMAN	G	199	ENSP00000387535:E199G	ENSP00000387535:E199G	E	-	2	0	IRGQ	48789294	1.000000	0.71417	0.994000	0.49952	0.627000	0.37826	3.612000	0.54142	2.291000	0.77112	0.533000	0.62120	GAG		0.667	IRGQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463205.1	NM_001007561	
EPS8L1	54869	hgsc.bcm.edu	37	19	55597841	55597841	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr19:55597841T>C	ENST00000201647.6	+	17	1788	c.1732T>C	c.(1732-1734)Tgg>Cgg	p.W578R	EPS8L1_ENST00000586329.1_Intron|EPS8L1_ENST00000245618.5_Missense_Mutation_p.W451R|EPS8L1_ENST00000540810.1_Missense_Mutation_p.W514R|EPS8L1_ENST00000588359.1_Missense_Mutation_p.W264R	NM_133180.2	NP_573441.2	Q8TE68	ES8L1_HUMAN	EPS8-like 1	578					positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|T cell receptor binding (GO:0042608)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|prostate(1)	12			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		CAGGCCCCGCTGGGACAGCTG	0.682																																					Ovarian(149;255 1863 3636 27051 29647)												0			19											23.0	19.0	21.0					19																	55597841		2043	4009	6052	60289653	SO:0001583	missense	54869			AK057052	CCDS12914.1, CCDS12915.1	19q13.42	2008-02-05				ENSG00000131037			21295	protein-coding gene	gene with protein product		614987				12620401	Standard	NM_133180		Approved	FLJ20258, DRC3, MGC23164, MGC4642	uc002qis.4	Q8TE68		ENST00000201647.6:c.1732T>C	19.37:g.55597841T>C	ENSP00000201647:p.Trp578Arg		60289653	Q71RE2|Q8NC10|Q96BB7|Q9BSQ2|Q9GZQ2|Q9NXH0	Missense_Mutation	SNP	ENST00000201647.6	37	CCDS12914.1	.	.	.	.	.	.	.	.	.	.	T	9.529	1.110275	0.20714	.	.	ENSG00000131037	ENST00000201647;ENST00000540810;ENST00000245618;ENST00000539118	T;T;T	0.05081	3.75;3.51;3.5	3.97	2.93	0.34026	.	3.431930	0.02776	U	0.120307	T	0.04679	0.0127	N	0.14661	0.345	0.25758	N	0.984976	B;B;B	0.14805	0.011;0.002;0.0	B;B;B	0.12156	0.007;0.006;0.001	T	0.41179	-0.9523	10	0.10377	T	0.69	-6.0143	6.9123	0.24342	0.2187:0.0:0.0:0.7813	.	357;451;578	Q8TE68-4;Q8TE68-2;Q8TE68	.;.;ES8L1_HUMAN	R	578;514;451;264	ENSP00000201647:W578R;ENSP00000437541:W514R;ENSP00000245618:W451R	ENSP00000201647:W578R	W	+	1	0	EPS8L1	60289653	0.264000	0.24093	0.974000	0.42286	0.574000	0.36063	0.373000	0.20484	0.663000	0.31027	0.240000	0.17902	TGG		0.682	EPS8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451713.1	NM_017729	
TEX15	56154	hgsc.bcm.edu	37	8	30704020	30704020	+	Silent	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr8:30704020T>C	ENST00000256246.2	-	1	2588	c.2514A>G	c.(2512-2514)aaA>aaG	p.K838K	TEX15_ENST00000523186.1_5'Flank	NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	838					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)					NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		TATTATCAACTTTATCTTCAC	0.363																																																	0			8											64.0	60.0	62.0					8																	30704020		2203	4299	6502	30823562	SO:0001819	synonymous_variant	56154			AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"""cancer/testis antigen 42"""	605795	"""testis expressed sequence 15"""			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.2514A>G	8.37:g.30704020T>C			30823562		Silent	SNP	ENST00000256246.2	37	CCDS6080.1																																																																																				0.363	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1		
SGK3	23678	hgsc.bcm.edu	37	8	67726110	67726110	+	Silent	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr8:67726110A>G	ENST00000396596.1	+	5	490	c.276A>G	c.(274-276)gcA>gcG	p.A92A	SGK3_ENST00000345714.4_Silent_p.A92A|SGK3_ENST00000520976.1_Silent_p.A92A|SGK3_ENST00000521198.2_Silent_p.A92A|C8orf44-SGK3_ENST00000519289.1_Silent_p.A92A|SGK3_ENST00000522398.1_Silent_p.A92A	NM_013257.4	NP_037389.4	Q96BR1	SGK3_HUMAN	serum/glucocorticoid regulated kinase family, member 3	92	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.		A -> V (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		ion transmembrane transport (GO:0034220)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|response to stress (GO:0006950)|transmembrane transport (GO:0055085)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|phosphatidylinositol binding (GO:0035091)|potassium channel regulator activity (GO:0015459)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	18	Breast(64;0.186)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0046)|OV - Ovarian serous cystadenocarcinoma(28;0.0112)|all cancers(69;0.0141)|BRCA - Breast invasive adenocarcinoma(89;0.206)			AAAGACGAGCAGGACTAAACG	0.303																																																	0			8											70.0	74.0	73.0					8																	67726110		2202	4292	6494	67888664	SO:0001819	synonymous_variant	23678				CCDS6195.1, CCDS6196.1	8q12	2008-07-28	2005-09-13	2005-09-13		ENSG00000104205			10812	protein-coding gene	gene with protein product		607591	"""serum/glucocorticoid regulated kinase-like"""	SGK2, SGKL		10585774, 10548550	Standard	NM_013257		Approved		uc003xwr.3	Q96BR1		ENST00000396596.1:c.276A>G	8.37:g.67726110A>G			67888664	A8K5W3|B3KQC2|Q9P1Q7|Q9UKG5	Silent	SNP	ENST00000396596.1	37	CCDS6195.1																																																																																				0.303	SGK3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379232.3		
KCNB2	9312	hgsc.bcm.edu	37	8	73848940	73848940	+	Silent	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr8:73848940T>C	ENST00000523207.1	+	3	1938	c.1350T>C	c.(1348-1350)gtT>gtC	p.V450V		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	450			V -> I (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	GAAGCATCGTTTCTATGAACT	0.478																																																	0			8											77.0	82.0	80.0					8																	73848940		2203	4300	6503	74011494	SO:0001819	synonymous_variant	9312			U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.1350T>C	8.37:g.73848940T>C			74011494	Q7Z7D0|Q9BXD3	Silent	SNP	ENST00000523207.1	37	CCDS6209.1																																																																																				0.478	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770	
NBN	4683	hgsc.bcm.edu	37	8	90990529	90990529	+	Missense_Mutation	SNP	C	C	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr8:90990529C>A	ENST00000265433.3	-	5	657	c.503G>T	c.(502-504)gGa>gTa	p.G168V	NBN_ENST00000409330.1_Missense_Mutation_p.G86V	NM_002485.4	NP_002476.2	O60934	NBN_HUMAN	nibrin	168	BRCT.|Mediates interaction with SP100. {ECO:0000250}.				blastocyst growth (GO:0001832)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|DNA damage checkpoint (GO:0000077)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intrinsic apoptotic signaling pathway (GO:0097193)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mitotic cell cycle checkpoint (GO:0007093)|mitotic G2 DNA damage checkpoint (GO:0007095)|neuromuscular process controlling balance (GO:0050885)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|telomere maintenance (GO:0000723)	Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nuclear inclusion body (GO:0042405)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|replication fork (GO:0005657)|site of double-strand break (GO:0035861)	damaged DNA binding (GO:0003684)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27			BRCA - Breast invasive adenocarcinoma(11;0.0344)			AATTGGACGTCCACAAATGAG	0.303								Homologous recombination																																									0			8											78.0	78.0	78.0					8																	90990529		2203	4300	6503	91059705	SO:0001583	missense	9048			AF058696	CCDS6249.1	8q21-q24	2014-09-17	2005-06-02	2005-06-02	ENSG00000104320	ENSG00000104320			7652	protein-coding gene	gene with protein product		602667	"""Nijmegen breakage syndrome 1 (nibrin)"""	NBS, NBS1		9590181, 9590180	Standard	XM_005250923		Approved	ATV, AT-V2, AT-V1	uc003yej.1	O60934	OTTHUMG00000153546	ENST00000265433.3:c.503G>T	8.37:g.90990529C>A	ENSP00000265433:p.Gly168Val		91059705	B2R626|B2RNC5|O60672|Q32NF7|Q53FM6|Q63HR6|Q7LDM2	Missense_Mutation	SNP	ENST00000265433.3	37	CCDS6249.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.983360	0.74474	.	.	ENSG00000104320	ENST00000265433;ENST00000409330;ENST00000452387;ENST00000517772;ENST00000517337	T;T;D;T	0.82255	0.47;0.47;-1.59;0.47	5.96	5.96	0.96718	BRCT (2);	0.046520	0.85682	D	0.000000	D	0.88581	0.6475	M	0.61703	1.905	0.58432	D	0.999999	D;D	0.65815	0.995;0.995	P;P	0.59595	0.86;0.86	D	0.88006	0.2759	10	0.51188	T	0.08	-29.2814	17.3038	0.87189	0.0:0.8751:0.1249:0.0	.	168;168	A6H8Y5;O60934	.;NBN_HUMAN	V	168;86;168;86;86	ENSP00000265433:G168V;ENSP00000386924:G86V;ENSP00000428717:G86V;ENSP00000429971:G86V	ENSP00000265433:G168V	G	-	2	0	NBN	91059705	0.999000	0.42202	0.991000	0.47740	0.998000	0.95712	2.505000	0.45424	2.826000	0.97356	0.655000	0.94253	GGA		0.303	NBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331583.3	NM_001024688	
PDP1	54704	hgsc.bcm.edu	37	8	94934247	94934247	+	5'UTR	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr8:94934247T>C	ENST00000297598.4	+	0	229				PDP1_ENST00000396200.3_Missense_Mutation_p.I12T|PDP1_ENST00000517764.1_5'UTR|PDP1_ENST00000520728.1_5'UTR	NM_001161781.1|NM_018444.3	NP_001155253.1|NP_060914.2	Q9P0J1	PDP1_HUMAN	pyruvate dehyrogenase phosphatase catalytic subunit 1						cellular metabolic process (GO:0044237)|peptidyl-threonine dephosphorylation (GO:0035970)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	[pyruvate dehydrogenase (lipoamide)] phosphatase activity (GO:0004741)|metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|liver(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)	18						TGTCTAGGAATCCCAGTCAGA	0.413																																																	0			8											86.0	87.0	86.0					8																	94934247		2203	4300	6503	95003423	SO:0001623	5_prime_UTR_variant	54704			AF155661	CCDS6259.1, CCDS55262.1	8q22.1	2012-04-17	2009-06-12	2009-06-12	ENSG00000164951	ENSG00000164951	3.1.3.43	"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	9279	protein-coding gene	gene with protein product		605993	"""protein phosphatase 2C, magnesium-dependent, catalytic subunit"""	PPM2C		8396421	Standard	NM_001161779		Approved	PDP, PDH	uc003ygf.3	Q9P0J1		ENST00000297598.4:c.-41T>C	8.37:g.94934247T>C			95003423	B3KX71|J3KPU0|Q5U5K1	Missense_Mutation	SNP	ENST00000297598.4	37	CCDS6259.1	.	.	.	.	.	.	.	.	.	.	T	12.70	2.017187	0.35606	.	.	ENSG00000164951	ENST00000396200	T	0.49139	0.79	5.45	5.45	0.79879	.	.	.	.	.	T	0.29556	0.0737	N	0.08118	0	0.34064	D	0.657619	B	0.30482	0.281	B	0.22753	0.041	T	0.44802	-0.9304	9	0.52906	T	0.07	-12.0246	15.6958	0.77494	0.0:0.0:0.0:1.0	.	38	B4DYX8	.	T	12	ENSP00000379503:I12T	ENSP00000379503:I12T	I	+	2	0	PDP1	95003423	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.030000	0.49720	2.288000	0.76882	0.528000	0.53228	ATC		0.413	PDP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378415.2	NM_018444	
RAD21	5885	hgsc.bcm.edu	37	8	117864237	117864237	+	Missense_Mutation	SNP	G	G	T			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr8:117864237G>T	ENST00000297338.2	-	11	1707	c.1420C>A	c.(1420-1422)Cag>Aag	p.Q474K	RAD21_ENST00000517749.1_5'Flank|RAD21_ENST00000523986.1_5'UTR|RAD21_ENST00000518055.1_Missense_Mutation_p.Q19K	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:0001583	missense	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>A	8.37:g.117864237G>T	ENSP00000297338:p.Gln474Lys		117933418	A8K0E0|Q15001|Q99568	Missense_Mutation	SNP	ENST00000297338.2	37	CCDS6321.1	.	.	.	.	.	.	.	.	.	.	G	16.61	3.171209	0.57584	.	.	ENSG00000164754	ENST00000297338;ENST00000518055	T;T	0.65178	0.7;-0.14	5.71	5.71	0.89125	.	0.108239	0.64402	D	0.000005	T	0.54334	0.1852	L	0.44542	1.39	0.42186	D	0.991704	B	0.06786	0.001	B	0.04013	0.001	T	0.53725	-0.8398	10	0.07175	T	0.84	-21.6355	19.8625	0.96789	0.0:0.0:1.0:0.0	.	474	O60216	RAD21_HUMAN	K	474;19	ENSP00000297338:Q474K;ENSP00000428003:Q19K	ENSP00000297338:Q474K	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		0.473	RAD21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381184.1	NM_006265	
HHLA1	10086	hgsc.bcm.edu	37	8	133092020	133092020	+	Silent	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr8:133092020A>G	ENST00000414222.1	-	10	869	c.870T>C	c.(868-870)ctT>ctC	p.L290L	HHLA1_ENST00000434736.2_Silent_p.L326L|OC90_ENST00000262283.5_Intron	NM_001145095.1	NP_001138567.1	C9JL84	HHLA1_HUMAN	HERV-H LTR-associating 1	290						extracellular region (GO:0005576)				endometrium(6)|kidney(1)|lung(2)|skin(1)|stomach(2)	12						CCCTGGCTGGAAGCTCAGGAG	0.582																																																	0			8											56.0	60.0	59.0					8																	133092020		692	1591	2283	133161202	SO:0001819	synonymous_variant	10086			AF110315		8q24	2011-03-01			ENSG00000132297	ENSG00000132297			4904	protein-coding gene	gene with protein product		604109		PLA2L		10329003	Standard	NM_001145095		Approved		uc011liy.1	C9JL84	OTTHUMG00000140390	ENST00000414222.1:c.870T>C	8.37:g.133092020A>G			133161202		Silent	SNP	ENST00000414222.1	37																																																																																					0.582	HHLA1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XR_017860	
MROH5	389690	hgsc.bcm.edu	37	8	142476614	142476614	+	RNA	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr8:142476614A>G	ENST00000430863.1	-	0	2452					NM_207414.2	NP_997297.2	Q6ZUA9	MROH5_HUMAN	maestro heat-like repeat family member 5																		GGCTTGCGGGATGTGGACAGA	0.652																																																	0			8											72.0	83.0	80.0					8																	142476614		2128	4230	6358	142545796			389690					8q24.3	2012-12-20			ENSG00000226807	ENSG00000226807		"""maestro heat-like repeat containing"""	42976	protein-coding gene	gene with protein product							Standard	NM_207414		Approved	FLJ43860	uc003ywi.2	Q6ZUA9	OTTHUMG00000155944		8.37:g.142476614A>G			142545796		Missense_Mutation	SNP	ENST00000430863.1	37																																																																																					0.652	MROH5-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000342412.4	NM_207414	
EPPK1	83481	hgsc.bcm.edu	37	8	144946730	144946730	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr8:144946730A>G	ENST00000525985.1	-	2	763	c.692T>C	c.(691-693)cTc>cCc	p.L231P				P58107	EPIPL_HUMAN	epiplakin 1	231						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GGTGATCTTGAGGGGCAGCAA	0.677																																																	0			8											17.0	21.0	20.0					8																	144946730		2133	4223	6356	145018718	SO:0001583	missense	83481			AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"""epidermal autoantigen 450K"""	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.692T>C	8.37:g.144946730A>G	ENSP00000436337:p.Leu231Pro		145018718	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	37		.	.	.	.	.	.	.	.	.	.	A	10.29	1.308701	0.23821	.	.	ENSG00000227184	ENST00000525985	T	0.70749	-0.51	4.23	4.23	0.50019	.	.	.	.	.	T	0.81034	0.4739	M	0.76727	2.345	0.51012	D	0.999904	D	0.89917	1.0	D	0.70716	0.97	T	0.80374	-0.1409	9	0.36615	T	0.2	.	11.575	0.50856	1.0:0.0:0.0:0.0	.	231	E9PPU0	.	P	231	ENSP00000436337:L231P	ENSP00000436337:L231P	L	-	2	0	EPPK1	145018718	0.910000	0.30920	0.626000	0.29213	0.016000	0.09150	7.710000	0.84655	1.895000	0.54865	0.334000	0.21626	CTC		0.677	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
SLC52A2	79581	hgsc.bcm.edu	37	8	145584592	145584592	+	Missense_Mutation	SNP	G	G	A	rs397514658		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr8:145584592G>A	ENST00000532887.1	+	5	1838	c.1255G>A	c.(1255-1257)Ggc>Agc	p.G419S	SLC52A2_ENST00000540505.1_Missense_Mutation_p.G331S|SLC52A2_ENST00000527078.1_Missense_Mutation_p.G419S|SLC52A2_ENST00000402965.1_Missense_Mutation_p.G419S|FBXL6_ENST00000455319.2_5'Flank|SLC52A2_ENST00000329994.2_Missense_Mutation_p.G419S|SLC52A2_ENST00000530047.1_Missense_Mutation_p.G419S|FBXL6_ENST00000331890.5_5'Flank|SLC52A2_ENST00000526752.1_Missense_Mutation_p.R87Q			Q9HAB3	S52A2_HUMAN	solute carrier family 52 (riboflavin transporter), member 2	419					riboflavin transport (GO:0032218)	integral component of plasma membrane (GO:0005887)	riboflavin transporter activity (GO:0032217)|virus receptor activity (GO:0001618)									Gamma Hydroxybutyric Acid(DB01440)	CTCTCTGCTCGGCGCTGTTGC	0.652																																																	0			8											111.0	104.0	106.0					8																	145584592		2203	4300	6503	145555400	SO:0001583	missense	79581			AY070774	CCDS6423.1	8q24.3	2013-07-17	2013-07-17	2012-02-29		ENSG00000185803		"""Solute carriers"""	30224	protein-coding gene	gene with protein product		607882	"""G protein-coupled receptor 172A"""	GPR172A		12740431	Standard	NM_024531		Approved	FLJ11856, PAR1, GPCR41, D15Ertd747e, RFVT2, hRFT3	uc003zcd.2	Q9HAB3		ENST00000532887.1:c.1255G>A	8.37:g.145584592G>A	ENSP00000436768:p.Gly419Ser		145555400	A8K6B6|D3DWL8|G1UCY1|Q86UT1	Missense_Mutation	SNP	ENST00000532887.1	37	CCDS6423.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	27.2|27.2	4.810462|4.810462	0.90707|0.90707	.|.	.|.	ENSG00000185803|ENSG00000185803	ENST00000530047;ENST00000527078;ENST00000402965;ENST00000532887;ENST00000329994;ENST00000540505|ENST00000526752	D;D;D;D;D;D|D	0.86956|0.90504	-2.19;-2.19;-2.19;-2.19;-2.19;-1.94|-2.68	5.25|5.25	5.25|5.25	0.73442|0.73442	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.94142|0.94142	0.8121|0.8121	M|M	0.86502|0.86502	2.82|2.82	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	D|D	0.92514|0.92514	0.6019|0.6019	10|7	0.87932|0.13470	D|T	0|0.59	.|.	16.4138|16.4138	0.83727|0.83727	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	419|.	Q9HAB3|.	RFT3_HUMAN|.	S|Q	419;419;419;419;419;331|87	ENSP00000435820:G419S;ENSP00000434728:G419S;ENSP00000385961:G419S;ENSP00000436768:G419S;ENSP00000333638:G419S;ENSP00000440400:G331S|ENSP00000433796:R87Q	ENSP00000333638:G419S|ENSP00000433796:R87Q	G|R	+|+	1|2	0|0	GPR172A|GPR172A	145555400|145555400	1.000000|1.000000	0.71417|0.71417	0.190000|0.190000	0.23270|0.23270	0.731000|0.731000	0.41821|0.41821	7.543000|7.543000	0.82106|0.82106	2.480000|2.480000	0.83734|0.83734	0.456000|0.456000	0.33151|0.33151	GGC|CGG		0.652	SLC52A2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382405.1	NM_024531	
TNFRSF9	3604	hgsc.bcm.edu	37	1	7980913	7980913	+	Silent	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:7980913T>C	ENST00000377507.3	-	8	916	c.750A>G	c.(748-750)gaA>gaG	p.E250E		NM_001561.5	NP_001552.2	Q07011	TNR9_HUMAN	tumor necrosis factor receptor superfamily, member 9	250	Interaction with LRR-1.		E -> G (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)			NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19	Ovarian(185;0.0634)|all_lung(157;0.151)	all_epithelial(116;9.63e-21)|all_lung(118;1.29e-06)|Lung NSC(185;7.5e-06)|Renal(390;0.000147)|Breast(348;0.000625)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;2.93e-71)|GBM - Glioblastoma multiforme(8;3.72e-37)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;7.71e-06)|Kidney(185;5.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000419)|KIRC - Kidney renal clear cell carcinoma(229;0.000979)|STAD - Stomach adenocarcinoma(132;0.00103)|READ - Rectum adenocarcinoma(331;0.0649)		CACATCCTCCTTCTTCTTCTT	0.378																																																	0			1											137.0	142.0	140.0					1																	7980913		2203	4300	6503	7903500	SO:0001819	synonymous_variant	3604			L12964	CCDS92.1	1p36	2008-02-05			ENSG00000049249	ENSG00000049249		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11924	protein-coding gene	gene with protein product		602250		ILA		8262389, 8639902	Standard	NM_001561		Approved	CD137, 4-1BB	uc001aot.3	Q07011	OTTHUMG00000001223	ENST00000377507.3:c.750A>G	1.37:g.7980913T>C			7903500		Silent	SNP	ENST00000377507.3	37	CCDS92.1																																																																																				0.378	TNFRSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003622.1		
CASZ1	54897	hgsc.bcm.edu	37	1	10699176	10699176	+	Missense_Mutation	SNP	G	G	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:10699176G>C	ENST00000377022.3	-	21	5420	c.5103C>G	c.(5101-5103)gaC>gaG	p.D1701E	RP4-734G22.3_ENST00000606802.1_RNA	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	1701	Asp-rich.|Glu-rich.				multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		cctcgtcgtcgtcgtcctcgt	0.731																																																	0			1											6.0	6.0	6.0					1																	10699176		1801	3652	5453	10621763	SO:0001583	missense	54897			AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"""Zinc fingers, C2H2-type"""	26002	protein-coding gene	gene with protein product	"""zinc finger protein 693"", ""survival related gene"""	609895	"""castor homolog 1, zinc finger (Drosophila)"""			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.5103C>G	1.37:g.10699176G>C	ENSP00000366221:p.Asp1701Glu		10621763	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Missense_Mutation	SNP	ENST00000377022.3	37	CCDS41246.1	.	.	.	.	.	.	.	.	.	.	G	14.95	2.689008	0.48097	.	.	ENSG00000130940	ENST00000377022	T	0.20463	2.07	2.95	-2.01	0.07410	.	0.000000	0.41500	U	0.000865	T	0.09379	0.0231	N	0.14661	0.345	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.09058	-1.0692	10	0.62326	D	0.03	-11.0431	5.6169	0.17436	0.3393:0.4577:0.203:0.0	.	1701	Q86V15	CASZ1_HUMAN	E	1701	ENSP00000366221:D1701E	ENSP00000366221:D1701E	D	-	3	2	CASZ1	10621763	0.017000	0.18338	0.885000	0.34714	0.524000	0.34500	-1.781000	0.01774	-0.050000	0.13356	0.195000	0.17529	GAC		0.731	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766	
MTOR	2475	hgsc.bcm.edu	37	1	11188061	11188061	+	Splice_Site	SNP	C	C	T			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:11188061C>T	ENST00000361445.4	-	43	6109	c.6033G>A	c.(6031-6033)atG>atA	p.M2011I	MTOR_ENST00000376838.1_Splice_Site_p.M216I	NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	2011			M -> V (in an ovarian mucinous carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	TCCGACCCACCATCATGGCCT	0.557																																																	0			1											105.0	106.0	106.0					1																	11188061		2203	4300	6503	11110648	SO:0001630	splice_region_variant	2475			L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"""FK506 binding protein 12-rapamycin associated protein 2"", ""rapamycin target protein"", ""FKBP12-rapamycin complex-associated protein 1"", ""FKBP-rapamycin associated protein"", ""rapamycin associated protein FRAP2"", ""dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)"", ""rapamycin and FKBP12 target 1"", ""mammalian target of rapamycin"""	601231	"""FK506 binding protein 12-rapamycin associated protein 1"""	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.6033+1G>A	1.37:g.11188061C>T			11110648	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Missense_Mutation	SNP	ENST00000361445.4	37	CCDS127.1	.	.	.	.	.	.	.	.	.	.	C	19.48	3.835988	0.71373	.	.	ENSG00000198793	ENST00000361445;ENST00000376838	T;T	0.09630	3.21;2.96	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.11922	0.0290	L	0.37561	1.115	0.80722	D	1	B	0.28880	0.226	B	0.28709	0.093	T	0.15435	-1.0437	9	.	.	.	-20.5682	20.063	0.97692	0.0:1.0:0.0:0.0	.	2011	P42345	MTOR_HUMAN	I	2011;216	ENSP00000354558:M2011I;ENSP00000366034:M216I	.	M	-	3	0	MTOR	11110648	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	7.431000	0.80335	2.735000	0.93741	0.655000	0.94253	ATG		0.557	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958	Missense_Mutation
VPS13D	55187	hgsc.bcm.edu	37	1	12387773	12387773	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:12387773T>C	ENST00000358136.3	+	36	8189	c.8059T>C	c.(8059-8061)Tcc>Ccc	p.S2687P	VPS13D_ENST00000356315.4_Missense_Mutation_p.S2687P	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)											NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		TTCCTTGGCCTCCACCAGCCG	0.483																																																	0			1											159.0	161.0	160.0					1																	12387773		2203	4300	6503	12310360	SO:0001583	missense	55187			AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"""vacuolar protein sorting 13D (yeast)"""				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.8059T>C	1.37:g.12387773T>C	ENSP00000350854:p.Ser2687Pro		12310360		Missense_Mutation	SNP	ENST00000358136.3	37	CCDS30588.1	.	.	.	.	.	.	.	.	.	.	T	12.00	1.805632	0.31961	.	.	ENSG00000048707	ENST00000356315;ENST00000358136	T;T	0.43688	0.94;0.94	5.51	0.127	0.14727	.	2.095450	0.01699	N	0.027116	T	0.43500	0.1250	L	0.57536	1.79	0.27388	N	0.955214	B;P;B	0.36315	0.0;0.547;0.412	B;B;B	0.41088	0.001;0.347;0.188	T	0.17471	-1.0368	9	.	.	.	.	4.0221	0.09670	0.1182:0.0651:0.2468:0.5698	.	594;2687;2687	B1AJZ2;Q5THJ4-2;Q5THJ4	.;.;VP13D_HUMAN	P	2687	ENSP00000348666:S2687P;ENSP00000350854:S2687P	.	S	+	1	0	VPS13D	12310360	0.000000	0.05858	0.530000	0.27963	0.382000	0.30200	0.030000	0.13688	-0.152000	0.11156	0.533000	0.62120	TCC		0.483	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378	
NBL1	4681	hgsc.bcm.edu	37	1	19983484	19983484	+	Silent	SNP	G	G	T			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:19983484G>T	ENST00000375136.3	+	4	711	c.408G>T	c.(406-408)gtG>gtT	p.V136V	NBL1_ENST00000548815.1_Silent_p.V135V|NBL1_ENST00000289749.2_Silent_p.V171V|MINOS1-NBL1_ENST00000602662.1_Silent_p.V136V	NM_001204085.1|NM_001204089.1|NM_001278164.1|NM_001278166.1	NP_001191014.1|NP_001191018.1|NP_001265093.1|NP_001265095.1	P41271	NBL1_HUMAN	neuroblastoma 1, DAN family BMP antagonist	136					determination of dorsal identity (GO:0048263)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of monocyte chemotaxis (GO:0090027)|nervous system development (GO:0007399)|neuron projection morphogenesis (GO:0048812)|positive regulation of neuron differentiation (GO:0045666)|sequestering of BMP from receptor via BMP binding (GO:0038098)|sequestering of BMP in extracellular matrix (GO:0035582)	extracellular space (GO:0005615)	BMP binding (GO:0036122)|morphogen activity (GO:0016015)|protein homodimerization activity (GO:0042803)			lung(2)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00043)|Ovarian(437;0.00373)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;5.9e-05)|Kidney(64;0.000173)|GBM - Glioblastoma multiforme(114;0.0012)|KIRC - Kidney renal clear cell carcinoma(64;0.0026)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GCGTCTATGTGCAGGGCGAGG	0.697																																																	0			1											42.0	37.0	39.0					1																	19983484		2197	4299	6496	19856071	SO:0001819	synonymous_variant	4681				CCDS196.1, CCDS41278.1, CCDS196.2, CCDS72720.1	1p36.3-p36.2	2013-02-26	2013-02-26		ENSG00000158747	ENSG00000158747			7650	protein-coding gene	gene with protein product	"""neuroblastoma candidate region, suppression of tumorigenicity 1"", ""neuroblastoma suppressor of tumorigenicity 1"", ""differential screening-selected gene aberrant in neuroblastoma"""	600613	"""neuroblastoma, suppression of tumorigenicity 1"""			7633401	Standard	NM_182744		Approved	D1S1733E, NB, DAN, NO3, DAND1	uc001bcj.2	P41271	OTTHUMG00000002700	ENST00000375136.3:c.408G>T	1.37:g.19983484G>T			19856071	A3KFI7|Q5TGZ2|Q5U0N4|Q96L68	Silent	SNP	ENST00000375136.3	37	CCDS196.2																																																																																				0.697	NBL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000007681.4	NM_005380	
SEPN1	57190	hgsc.bcm.edu	37	1	26138348	26138348	+	Missense_Mutation	SNP	T	T	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:26138348T>G	ENST00000374315.1	+	8	1195	c.1157T>G	c.(1156-1158)gTg>gGg	p.V386G	SEPN1_ENST00000361547.2_Missense_Mutation_p.V420G|SEPN1_ENST00000354177.4_Missense_Mutation_p.V386G|RP1-317E23.6_ENST00000527604.1_5'Flank	NM_206926.1	NP_996809.1	Q9NZV5	SELN_HUMAN	selenoprotein N, 1	420						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	19		Colorectal(325;3.46e-05)|Lung NSC(340;0.00038)|all_lung(284;0.00051)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0505)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0421)|OV - Ovarian serous cystadenocarcinoma(117;1.26e-25)|Colorectal(126;3.01e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000751)|BRCA - Breast invasive adenocarcinoma(304;0.00099)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0143)|READ - Rectum adenocarcinoma(331;0.0649)		CGCCTGGAGGTGGCCATGTAC	0.652																																																	0			1											16.0	17.0	17.0					1																	26138348		2091	4219	6310	26010935	SO:0001583	missense	57190			AF166125	CCDS41282.1, CCDS41283.1	1p36.13	2014-09-17	2004-02-13		ENSG00000162430	ENSG00000162430		"""EF-hand domain containing"""	15999	protein-coding gene	gene with protein product		606210	"""rigid spine muscular dystrophy 1"""	RSMD1, MDRS1		10608886	Standard	NM_020451		Approved	selN, RSS	uc021ojl.1	Q9NZV5	OTTHUMG00000007375	ENST00000374315.1:c.1157T>G	1.37:g.26138348T>G	ENSP00000363434:p.Val386Gly		26010935	A6NJG8|A8MQ64|Q6PI70|Q969F6|Q9NUI6	Missense_Mutation	SNP	ENST00000374315.1	37	CCDS41283.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.560498	0.86335	.	.	ENSG00000162430	ENST00000361547;ENST00000354177;ENST00000374315	D;D;D	0.89415	-2.51;-2.49;-2.49	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	D	0.92711	0.7683	M	0.65975	2.015	0.80722	D	1	D;D	0.71674	0.996;0.998	D;P	0.63877	0.919;0.897	D	0.92752	0.6217	10	0.48119	T	0.1	-27.4748	14.7338	0.69402	0.0:0.0:0.0:1.0	.	386;420	Q9NZV5-2;Q9NZV5	.;SELN_HUMAN	G	420;386;386	ENSP00000355141:V420G;ENSP00000346109:V386G;ENSP00000363434:V386G	ENSP00000346109:V386G	V	+	2	0	SEPN1	26010935	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.008000	0.88588	1.888000	0.54679	0.254000	0.18369	GTG		0.652	SEPN1-002	KNOWN	basic|appris_candidate_longest|CCDS|seleno	protein_coding	protein_coding	OTTHUMT00000019315.2	NM_020451	
ARID1A	8289	hgsc.bcm.edu	37	1	27101398	27101398	+	Silent	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:27101398T>C	ENST00000324856.7	+	18	5051	c.4680T>C	c.(4678-4680)ccT>ccC	p.P1560P	ARID1A_ENST00000374152.2_Silent_p.P1177P|ARID1A_ENST00000457599.2_Intron|ARID1A_ENST00000540690.1_Intron	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1560					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		CCTCTGCCCCTGTGCCCCCCA	0.617			"""Mis, N, F, S, D"""		"""clear cell ovarian carcinoma, RCC"""																																			Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	0			1											38.0	39.0	39.0					1																	27101398		2203	4300	6503	26973985	SO:0001819	synonymous_variant	8289			AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"""-"""	11110	protein-coding gene	gene with protein product		603024	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1"", ""AT rich interactive domain 1A (SWI- like)"""	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.4680T>C	1.37:g.27101398T>C			26973985	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Silent	SNP	ENST00000324856.7	37	CCDS285.1	.	.	.	.	.	.	.	.	.	.	T	1.713	-0.498624	0.04291	.	.	ENSG00000117713	ENST00000430799	.	.	.	5.18	-4.79	0.03200	.	.	.	.	.	T	0.51635	0.1686	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52793	-0.8528	4	.	.	.	-8.5123	9.4962	0.38989	0.0962:0.32:0.0:0.5838	.	.	.	.	R	457	.	.	C	+	1	0	ARID1A	26973985	0.002000	0.14202	0.800000	0.32199	0.788000	0.44548	-1.665000	0.01965	-0.707000	0.05022	-1.556000	0.00890	TGT		0.617	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135	
THEMIS2	9473	hgsc.bcm.edu	37	1	28209271	28209271	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:28209271A>G	ENST00000373921.3	+	4	1440	c.1436A>G	c.(1435-1437)gAg>gGg	p.E479G	THEMIS2_ENST00000373927.3_Intron|THEMIS2_ENST00000328928.7_Missense_Mutation_p.E350G|THEMIS2_ENST00000373925.1_Intron	NM_001105556.1	NP_001099026.1	Q5TEJ8	THMS2_HUMAN	thymocyte selection associated family member 2	479	CABIT 2.				cell adhesion (GO:0007155)|inflammatory response (GO:0006954)|T cell receptor signaling pathway (GO:0050852)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											CGGCTGGAGGAGAAGATCACA	0.597																																																	0			1											81.0	82.0	82.0					1																	28209271		2084	4209	6293	28081858	SO:0001583	missense	9473			AF044896	CCDS30653.1, CCDS30654.1, CCDS41290.1, CCDS65461.1	1p35.2	2012-07-10	2012-07-10	2012-07-10	ENSG00000130775	ENSG00000130775			16839	protein-coding gene	gene with protein product	"""induced by contact to basement membrane 1"""		"""chromosome 1 open reading frame 38"""	C1orf38		16219472	Standard	XM_005246041		Approved	ICB-1, Icb-1	uc001bpc.4	Q5TEJ8	OTTHUMG00000003735	ENST00000373921.3:c.1436A>G	1.37:g.28209271A>G	ENSP00000363031:p.Glu479Gly		28081858	A2RTZ3|B4DZT9|B4DZY3|O60560|Q5TEJ1|Q5TEJ9|Q5TEK1|Q68DP4|Q9BYB6|Q9NS90	Missense_Mutation	SNP	ENST00000373921.3	37	CCDS41290.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.33|17.33	3.363391|3.363391	0.61513|0.61513	.|.	.|.	ENSG00000130775|ENSG00000130775	ENST00000328928;ENST00000373921|ENST00000456990	T;T|.	0.14266|.	2.52;2.52|.	4.98|4.98	4.98|4.98	0.66077|0.66077	.|.	0.297287|.	0.36555|.	N|.	0.002538|.	T|T	0.61324|0.61324	0.2338|0.2338	M|M	0.81341|0.81341	2.54|2.54	0.24955|0.24955	N|N	0.991766|0.991766	D;P;B|.	0.63880|.	0.993;0.607;0.4|.	P;B;B|.	0.55871|.	0.786;0.299;0.212|.	T|T	0.57277|0.57277	-0.7839|-0.7839	10|5	0.72032|.	D|.	0.01|.	-34.0508|-34.0508	11.1673|11.1673	0.48550|0.48550	0.8004:0.1996:0.0:0.0|0.8004:0.1996:0.0:0.0	.|.	350;283;479|.	Q5TEJ8-5;Q5TEJ8-6;Q5TEJ8|.	.;.;THMS2_HUMAN|.	G|G	350;479|227	ENSP00000329862:E350G;ENSP00000363031:E479G|.	ENSP00000329862:E350G|.	E|R	+|+	2|1	0|2	C1orf38|C1orf38	28081858|28081858	0.975000|0.975000	0.34042|0.34042	1.000000|1.000000	0.80357|0.80357	0.926000|0.926000	0.56050|0.56050	2.280000|2.280000	0.43443|0.43443	2.014000|2.014000	0.59158|0.59158	0.454000|0.454000	0.30748|0.30748	GAG|AGA		0.597	THEMIS2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011148.1	NM_004848	
PHC2	1912	hgsc.bcm.edu	37	1	33836171	33836171	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:33836171A>G	ENST00000257118.5	-	4	480	c.427T>C	c.(427-429)Tcc>Ccc	p.S143P	PHC2_ENST00000373416.1_5'UTR|PHC2_ENST00000431992.1_Missense_Mutation_p.S143P|PHC2_ENST00000419414.2_Missense_Mutation_p.S143P	NM_198040.2	NP_932157.1	Q8IXK0	PHC2_HUMAN	polyhomeotic homolog 2 (Drosophila)	143					multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				GCTGCTGGGGAGGCTGCCAGG	0.582																																																	0			1											47.0	39.0	42.0					1																	33836171		2203	4300	6503	33608758	SO:0001583	missense	1912			AJ419231	CCDS378.1, CCDS379.1	1p34.3	2013-01-10	2006-09-12	2002-11-15	ENSG00000134686	ENSG00000134686		"""Sterile alpha motif (SAM) domain containing"""	3183	protein-coding gene	gene with protein product		602979	"""early development regulator 2 (homolog of polyhomeotic 2)"", ""polyhomeotic-like 2 (Drosophila)"""	EDR2		9121482, 12384788	Standard	NM_198040		Approved	HPH2	uc001bxg.1	Q8IXK0	OTTHUMG00000004133	ENST00000257118.5:c.427T>C	1.37:g.33836171A>G	ENSP00000257118:p.Ser143Pro		33608758	A1L4Q1|A8KA40|D3DPR2|Q2TAL3|Q5T0C1|Q6NUJ6|Q6ZQR1|Q8N306|Q8TAG8|Q96BL4|Q9Y4Y7	Missense_Mutation	SNP	ENST00000257118.5	37	CCDS378.1	.	.	.	.	.	.	.	.	.	.	A	16.64	3.179624	0.57800	.	.	ENSG00000134686	ENST00000431992;ENST00000257118;ENST00000419414	T;T;T	0.39229	1.38;1.09;1.49	4.84	4.84	0.62591	.	0.066272	0.64402	D	0.000008	T	0.44008	0.1273	M	0.75777	2.31	0.80722	D	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.08055	0.003;0.003;0.001	T	0.41088	-0.9528	10	0.45353	T	0.12	-19.2188	12.3836	0.55322	1.0:0.0:0.0:0.0	.	143;143;143	A8KA40;B7ZLY0;Q8IXK0	.;.;PHC2_HUMAN	P	143	ENSP00000389436:S143P;ENSP00000257118:S143P;ENSP00000391440:S143P	ENSP00000257118:S143P	S	-	1	0	PHC2	33608758	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.576000	0.67437	1.801000	0.52704	0.460000	0.39030	TCC		0.582	PHC2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000011895.1	NM_198040	
PPT1	5538	hgsc.bcm.edu	37	1	40536642	40536642	+	IGR	SNP	C	C	A	rs377481764		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:40536642C>A	ENST00000433473.3	-	0	2740				CAP1_ENST00000372797.3_Silent_p.G445G|CAP1_ENST00000372792.2_Silent_p.G445G|CAP1_ENST00000479759.1_3'UTR|CAP1_ENST00000340450.3_Silent_p.G444G|CAP1_ENST00000372802.1_Silent_p.G444G|PPT1_ENST00000372775.2_5'Flank|CAP1_ENST00000372798.1_Silent_p.G444G|CAP1_ENST00000372805.3_Silent_p.G445G	NM_000310.3	NP_000301.1	P50897	PPT1_HUMAN	palmitoyl-protein thioesterase 1						adult locomotory behavior (GO:0008344)|associative learning (GO:0008306)|brain development (GO:0007420)|cell death (GO:0008219)|cellular protein catabolic process (GO:0044257)|cofactor metabolic process (GO:0051186)|cofactor transport (GO:0051181)|grooming behavior (GO:0007625)|lipid catabolic process (GO:0016042)|lysosomal lumen acidification (GO:0007042)|membrane raft organization (GO:0031579)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)|neuron development (GO:0048666)|neurotransmitter secretion (GO:0007269)|pinocytosis (GO:0006907)|positive regulation of pinocytosis (GO:0048549)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein catabolic process (GO:0030163)|protein depalmitoylation (GO:0002084)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|regulation of phospholipase A2 activity (GO:0032429)|regulation of synapse structure and activity (GO:0050803)|sphingolipid catabolic process (GO:0030149)|visual perception (GO:0007601)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)	palmitoyl-(protein) hydrolase activity (GO:0008474)|palmitoyl-CoA hydrolase activity (GO:0016290)			endometrium(5)|large_intestine(1)|lung(3)|ovary(1)|stomach(1)	11	Lung NSC(20;3.43e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1e-18)|Epithelial(16;3.6e-17)|all cancers(16;1.1e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			CTACAGAAGGCGGTGACTTTG	0.398																																																	0			1											149.0	136.0	140.0					1																	40536642		1853	4100	5953	40309229	SO:0001628	intergenic_variant	10487			U44772	CCDS447.1, CCDS44119.1	1p32	2014-09-17	2008-07-31		ENSG00000131238	ENSG00000131238	3.1.2.22		9325	protein-coding gene	gene with protein product	"""ceroid-lipofuscinosis, neuronal 1, infantile"""	600722		PPT		7637805, 8325646	Standard	NM_000310		Approved	CLN1, INCL	uc001cfb.2	P50897	OTTHUMG00000004495		1.37:g.40536642C>A			40309229	B4DY24|Q6FGQ4	Silent	SNP	ENST00000433473.3	37	CCDS447.1																																																																																				0.398	PPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000013126.2	NM_000310	
SLFNL1	200172	hgsc.bcm.edu	37	1	41481833	41481833	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:41481833A>G	ENST00000359345.1	-	4	3745	c.1169T>C	c.(1168-1170)cTc>cCc	p.L390P	SLFNL1_ENST00000302946.8_Missense_Mutation_p.L390P|SLFNL1_ENST00000439569.2_Missense_Mutation_p.L390P|SLFNL1_ENST00000372611.1_Missense_Mutation_p.L331P|SLFNL1_ENST00000397197.2_Missense_Mutation_p.L342P|SLFNL1_ENST00000372613.2_Missense_Mutation_p.L342P	NM_144990.3	NP_659427.3	Q499Z3	SLNL1_HUMAN	schlafen-like 1	390							ATP binding (GO:0005524)			endometrium(3)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	10	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Breast(333;0.1)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0393)				CTGCTGCTGGAGCTGCTCCTT	0.632																																																	0			1											86.0	79.0	81.0					1																	41481833		2203	4300	6503	41254420	SO:0001583	missense	200172			BC022037	CCDS460.1, CCDS72766.1	1p34.2	2008-02-05			ENSG00000171790	ENSG00000171790			26313	protein-coding gene	gene with protein product							Standard	NM_144990		Approved	FLJ23878	uc001cgm.2	Q499Z3	OTTHUMG00000005719	ENST00000359345.1:c.1169T>C	1.37:g.41481833A>G	ENSP00000352299:p.Leu390Pro		41254420	A8K8D1|Q49AG8|Q5VW72|Q5VW74|Q8N7V7|Q8TCH6|Q8WVZ8	Missense_Mutation	SNP	ENST00000359345.1	37	CCDS460.1	.	.	.	.	.	.	.	.	.	.	A	19.30	3.800276	0.70567	.	.	ENSG00000171790	ENST00000302946;ENST00000372613;ENST00000372611;ENST00000359345;ENST00000439569;ENST00000397197	T;T;T;T;T;T	0.52526	0.66;1.63;1.01;0.66;0.66;1.63	5.25	5.25	0.73442	.	0.000000	0.44483	D	0.000460	T	0.56601	0.1996	L	0.34521	1.04	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.997	T	0.60291	-0.7292	10	0.87932	D	0	-46.1824	11.5599	0.50769	1.0:0.0:0.0:0.0	.	342;331;390	Q499Z3-3;Q499Z3-2;Q499Z3	.;.;SLNL1_HUMAN	P	390;342;331;390;390;342	ENSP00000304401:L390P;ENSP00000361696:L342P;ENSP00000361694:L331P;ENSP00000352299:L390P;ENSP00000398938:L390P;ENSP00000380381:L342P	ENSP00000304401:L390P	L	-	2	0	SLFNL1	41254420	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	5.308000	0.65768	1.991000	0.58162	0.459000	0.35465	CTC		0.632	SLFNL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015650.1	NM_144990	
MPL	4352	hgsc.bcm.edu	37	1	43815006	43815006	+	Missense_Mutation	SNP	G	G	T			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:43815006G>T	ENST00000372470.3	+	10	1583	c.1541G>T	c.(1540-1542)aGg>aTg	p.R514M	MPL_ENST00000413998.2_Missense_Mutation_p.R514M	NM_005373.2	NP_005364.1	P40238	TPOR_HUMAN	MPL proto-oncogene, thrombopoietin receptor	514					blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|homeostasis of number of cells (GO:0048872)|platelet activation (GO:0030168)|regulation of chemokine production (GO:0032642)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|transmembrane signaling receptor activity (GO:0004888)	p.R514K(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(551)|large_intestine(3)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	567	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			Eltrombopag(DB06210)|Romiplostim(DB05332)	CTGCTGCTGAGGTGGCAGTTT	0.617			Mis		MPD	MPD	congenital amegakaryocytic thrombocytopenia																														NSCLC(52;534 1204 10016 41452 44427)		yes	Dom	yes	Familial essential thrombocythemia	1	p34	4352	"""myeloproliferative leukemia virus oncogene, thrombopoietin receptor"""	yes	L	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	1											99.0	99.0	99.0					1																	43815006		2203	4300	6503	43587593	SO:0001583	missense	4352			M90102	CCDS483.1	1p34	2014-09-17	2014-06-26		ENSG00000117400	ENSG00000117400		"""CD molecules"", ""Fibronectin type III domain containing"""	7217	protein-coding gene	gene with protein product		159530	"""myeloproliferative leukemia virus oncogene"""			1608974	Standard	NM_005373		Approved	CD110, TPOR	uc001ciw.3	P40238	OTTHUMG00000007429	ENST00000372470.3:c.1541G>T	1.37:g.43815006G>T	ENSP00000361548:p.Arg514Met		43587593	Q5JUZ0	Missense_Mutation	SNP	ENST00000372470.3	37	CCDS483.1	.	.	.	.	.	.	.	.	.	.	g	20.4	3.987670	0.74589	.	.	ENSG00000117400	ENST00000372470;ENST00000413998	D;T	0.81659	-1.52;-1.25	4.53	2.58	0.30949	.	1.779270	0.02274	N	0.068782	D	0.83450	0.5257	L	0.53249	1.67	0.22354	N	0.99918	P;P;D	0.63046	0.468;0.528;0.992	B;B;P	0.52710	0.079;0.116;0.707	T	0.63444	-0.6636	10	0.56958	D	0.05	-0.0063	6.2546	0.20867	0.1053:0.1891:0.7057:0.0	.	507;514;514	Q308M1;P40238;Q5JUY5	.;TPOR_HUMAN;.	M	514	ENSP00000361548:R514M;ENSP00000414004:R514M	ENSP00000361548:R514M	R	+	2	0	MPL	43587593	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	2.240000	0.43088	0.424000	0.26061	0.430000	0.28490	AGG		0.617	MPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019522.1	NM_005373	
ST6GALNAC5	81849	hgsc.bcm.edu	37	1	77334298	77334298	+	Silent	SNP	G	G	A	rs554217920	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:77334298G>A	ENST00000477717.1	+	2	367	c.132G>A	c.(130-132)caG>caA	p.Q44Q	ST6GALNAC5_ENST00000496845.1_3'UTR	NM_030965.1	NP_112227.1	Q9BVH7	SIA7E_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	44	Poly-Gln.				glycosphingolipid biosynthetic process (GO:0006688)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	integral component of Golgi membrane (GO:0030173)	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity (GO:0001665)|sialyltransferase activity (GO:0008373)			endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	18						agcagcagcagcaacagcagc	0.711													G|||	2	0.000399361	0.0	0.0	5008	,	,		11676	0.002		0.0	False		,,,				2504	0.0																0			1											12.0	12.0	12.0					1																	77334298		2054	3972	6026	77106886	SO:0001819	synonymous_variant	81849				CCDS673.1	1p31.1	2013-03-01	2005-02-07	2005-02-07	ENSG00000117069	ENSG00000117069		"""Sialyltransferases"""	19342	protein-coding gene	gene with protein product		610134	"""sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) E"""	SIAT7E		10521438, 10601645	Standard	NM_030965		Approved	MGC3184, ST6GalNAcV	uc001dhi.3	Q9BVH7	OTTHUMG00000009687	ENST00000477717.1:c.132G>A	1.37:g.77334298G>A			77106886	B1AK82	Silent	SNP	ENST00000477717.1	37	CCDS673.1																																																																																				0.711	ST6GALNAC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026692.2	NM_030965	
RHOC	389	hgsc.bcm.edu	37	1	113244242	113244242	+	Missense_Mutation	SNP	G	G	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:113244242G>A	ENST00000285735.2	-	6	1711	c.502C>T	c.(502-504)Cgg>Tgg	p.R168W	RHOC_ENST00000369633.2_Missense_Mutation_p.R168W|RHOC_ENST00000369642.3_Missense_Mutation_p.R168W|RHOC_ENST00000369632.2_Missense_Mutation_p.R168W|RHOC_ENST00000369637.1_Missense_Mutation_p.R168W|RHOC_ENST00000369636.2_Silent_p.C147C|RP11-426L16.10_ENST00000471038.2_5'Flank|RHOC_ENST00000369638.2_Missense_Mutation_p.R168W|RHOC_ENST00000339083.7_Missense_Mutation_p.R168W			P08134	RHOC_HUMAN	ras homolog family member C	168					apical junction assembly (GO:0043297)|axon guidance (GO:0007411)|cytokinesis (GO:0000910)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cleavage furrow (GO:0032154)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|signal transducer activity (GO:0004871)			endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	9	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		AACACCTCCCGCACTCCCTCC	0.607																																																	0			1											123.0	108.0	113.0					1																	113244242		2203	4300	6503	113045765	SO:0001583	missense	389			BC052808	CCDS854.1	1p13.1	2012-02-27	2012-02-27	2004-03-24	ENSG00000155366	ENSG00000155366			669	protein-coding gene	gene with protein product		165380	"""ras homolog gene family, member C"""	ARH9, ARHC		3283705	Standard	NM_001042678		Approved	RhoC	uc001ecp.1	P08134	OTTHUMG00000011905	ENST00000285735.2:c.502C>T	1.37:g.113244242G>A	ENSP00000285735:p.Arg168Trp		113045765	B3KSW1|Q6ICN3	Missense_Mutation	SNP	ENST00000285735.2	37	CCDS854.1	.	.	.	.	.	.	.	.	.	.	G	16.78	3.217183	0.58560	.	.	ENSG00000155366	ENST00000339083;ENST00000369633;ENST00000369642;ENST00000285735;ENST00000369638;ENST00000369637;ENST00000369632;ENST00000484054;ENST00000425265;ENST00000534717	T;T;T;T;T;T;T;T;T;T	0.77489	-1.1;-1.1;-1.1;-1.1;-1.1;-1.1;-1.1;-1.1;-1.1;-1.1	5.13	3.17	0.36434	.	.	.	.	.	T	0.81678	0.4873	M	0.71206	2.165	0.80722	D	1	D	0.76494	0.999	D	0.71184	0.972	D	0.83633	0.0146	9	0.87932	D	0	10.5575	12.5942	0.56459	0.0:0.0:0.5395:0.4605	.	168	P08134	RHOC_HUMAN	W	168;168;168;168;168;168;168;205;168;168	ENSP00000345236:R168W;ENSP00000358647:R168W;ENSP00000358656:R168W;ENSP00000285735:R168W;ENSP00000358652:R168W;ENSP00000358651:R168W;ENSP00000358646:R168W;ENSP00000434877:R205W;ENSP00000390823:R168W;ENSP00000436240:R168W	ENSP00000285735:R168W	R	-	1	2	RHOC	113045765	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	2.972000	0.49256	0.498000	0.27948	0.563000	0.77884	CGG		0.607	RHOC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032904.2	NM_175744	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144994637	144994637	+	Missense_Mutation	SNP	C	C	T	rs372978033		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:144994637C>T	ENST00000369354.3	-	1	284	c.95G>A	c.(94-96)cGc>cAc	p.R32H	PDE4DIP_ENST00000369349.3_Missense_Mutation_p.R32H|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.R169H|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.R32H|PDE4DIP_ENST00000369348.3_Missense_Mutation_p.R169H|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.R98H|PDE4DIP_ENST00000369347.4_Missense_Mutation_p.R32H|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.R169H|PDE4DIP_ENST00000369351.3_Missense_Mutation_p.R32H			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	32					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		CTGTTGCATGCGCTCCTCCAG	0.587			T	PDGFRB	MPD																																			Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	0			1						C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,	0,4406		0,0,2203	162.0	140.0	148.0		95,95,104,293,95,95,506,	4.9	1.0	1		148	2,8598		0,2,4298	no	missense,missense,missense,missense,missense,missense,missense,utr-5	PDE4DIP	NM_001002810.3,NM_001002812.1,NM_001195261.1,NM_001198832.1,NM_001198834.2,NM_014644.4,NM_022359.5,NM_001195260.1	29,29,29,29,29,29,29,	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,	32/174,32/970,35/177,98/2241,32/2363,32/2347,169/311,	144994637	2,13004	2203	4300	6503	143705994	SO:0001583	missense	9659			AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.95G>A	1.37:g.144994637C>T	ENSP00000358360:p.Arg32His		143705994	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.985239	0.93044	0.0	2.33E-4	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359;ENST00000369351;ENST00000369349;ENST00000530078;ENST00000534536;ENST00000369347;ENST00000369348;ENST00000531369	T;T;T;T;T;T;T;T;T;T;T	0.79940	1.79;1.79;1.79;1.79;1.79;1.79;1.79;1.79;1.79;1.79;-1.32	5.78	4.86	0.63082	Spindle associated (1);	.	.	.	.	D	0.85843	0.5791	M	0.70275	2.135	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.87578	0.966;0.985;0.991;0.998;0.995;0.996;0.992	D	0.86795	0.1988	9	0.87932	D	0	.	11.8519	0.52415	0.0:0.9164:0.0:0.0836	.	32;98;32;169;98;35;32	Q5VU43-7;Q5VU43-3;Q5VU43;E9PJ64;E9PQH9;E9PS60;Q5VU43-10	.;.;MYOME_HUMAN;.;.;.;.	H	98;32;32;169;169;32;32;98;35;32;169;99	ENSP00000327209:R98H;ENSP00000358360:R32H;ENSP00000358363:R32H;ENSP00000435654:R169H;ENSP00000358366:R169H;ENSP00000358357:R32H;ENSP00000358355:R32H;ENSP00000435920:R35H;ENSP00000358353:R32H;ENSP00000358354:R169H;ENSP00000435616:R99H	ENSP00000327209:R98H	R	-	2	0	PDE4DIP	143705994	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.196000	0.51020	2.731000	0.93534	0.650000	0.86243	CGC		0.587	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
RBM8A	9939	hgsc.bcm.edu	37	1	145509017	145509017	+	Missense_Mutation	SNP	G	G	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:145509017G>C	ENST00000330165.8	+	5	513	c.444G>C	c.(442-444)tgG>tgC	p.W148C	RP11-315I20.1_ENST00000448561.1_RNA|RP11-315I20.1_ENST00000599469.1_RNA|RBM8A_ENST00000369307.3_Missense_Mutation_p.W147C|GNRHR2_ENST00000312753.5_RNA|RP11-315I20.1_ENST00000597144.1_RNA|RP11-315I20.1_ENST00000599147.1_RNA|RP11-315I20.1_ENST00000595518.1_RNA|RP11-315I20.1_ENST00000595494.1_RNA|RP11-315I20.1_ENST00000598354.1_RNA|RP11-315I20.1_ENST00000437797.1_RNA|RP11-315I20.1_ENST00000596355.1_RNA|RP11-315I20.1_ENST00000412239.1_RNA|RP11-315I20.1_ENST00000447686.2_RNA|RP11-315I20.1_ENST00000599626.1_RNA|RP11-315I20.1_ENST00000601726.1_RNA|RP11-315I20.1_ENST00000600340.1_RNA|RP11-315I20.1_ENST00000598103.1_RNA|RP11-315I20.1_ENST00000421764.1_RNA	NM_005105.3	NP_005096.1	Q9Y5S9	RBM8A_HUMAN	RNA binding motif protein 8A	148	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			kidney(2)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	6	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GCGTTGACTGGTGTTTTGTTC	0.473																																																	0			1											107.0	107.0	107.0					1																	145509017		2203	4300	6503	144220374	SO:0001583	missense	9939			AF127761	CCDS72872.1	1q21.1	2013-02-12			ENSG00000131795			"""RNA binding motif (RRM) containing"""	9905	protein-coding gene	gene with protein product		605313		RBM8		11004516, 11013075	Standard	NM_005105		Approved	ZNRP, BOV-1A, BOV-1B, BOV-1C, RBM8B, Y14	uc001ent.2	Q9Y5S9	OTTHUMG00000013736	ENST00000330165.8:c.444G>C	1.37:g.145509017G>C	ENSP00000333001:p.Trp148Cys		144220374	B3KQI9|Q6FHD1|Q6IQ40|Q9GZX8|Q9NZI4	Missense_Mutation	SNP	ENST00000330165.8	37	CCDS916.1	.	.	.	.	.	.	.	.	.	.	G	17.76	3.468310	0.63625	.	.	ENSG00000131795	ENST00000330165;ENST00000369307	T;T	0.75367	-0.93;-0.93	4.02	3.09	0.35607	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (1);	0.000000	0.85682	D	0.000000	D	0.85057	0.5610	M	0.93898	3.47	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.995	D	0.87017	0.2126	9	.	.	.	-6.6545	9.8054	0.40791	0.1048:0.0:0.8952:0.0	.	147;148	Q9Y5S9-2;Q9Y5S9	.;RBM8A_HUMAN	C	148;147	ENSP00000333001:W148C;ENSP00000358313:W147C	.	W	+	3	0	RBM8A	144220374	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.883000	0.75595	0.880000	0.35969	0.561000	0.74099	TGG		0.473	RBM8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038503.2	NM_005105	
FLG	2312	hgsc.bcm.edu	37	1	152282812	152282812	+	Missense_Mutation	SNP	T	T	G	rs146433981	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:152282812T>G	ENST00000368799.1	-	3	4585	c.4550A>C	c.(4549-4551)tAc>tCc	p.Y1517S	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1517	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCTGTGATGGTACCCTGAGTG	0.562									Ichthyosis				t|||	21	0.00419329	0.0159	0.0	5008	,	,		19489	0.0		0.0	False		,,,				2504	0.0																0			1						T	SER/TYR	60,4346	56.8+/-93.2	0,60,2143	324.0	307.0	313.0		4550	0.0	0.0	1	dbSNP_134	313	0,8600		0,0,4300	no	missense	FLG	NM_002016.1	144	0,60,6443	GG,GT,TT		0.0,1.3618,0.4613	benign	1517/4062	152282812	60,12946	2203	4300	6503	150549436	SO:0001583	missense	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.4550A>C	1.37:g.152282812T>G	ENSP00000357789:p.Tyr1517Ser		150549436	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	21	0.009615384615384616	9	0.018292682926829267	1	0.0027624309392265192	5	0.008741258741258742	6	0.0079155672823219	t	8.034	0.762413	0.15914	0.013618	0.0	ENSG00000143631	ENST00000368799	T	0.04454	3.62	3.26	1.16E-4	0.14041	.	.	.	.	.	T	0.00241	0.0007	N	0.00034	-2.555	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38564	-0.9655	9	0.10636	T	0.68	.	5.727	0.18018	0.0:0.192:0.4108:0.3973	.	1517	P20930	FILA_HUMAN	S	1517	ENSP00000357789:Y1517S	ENSP00000357789:Y1517S	Y	-	2	0	FLG	150549436	0.000000	0.05858	0.000000	0.03702	0.037000	0.13140	-0.173000	0.09854	-0.085000	0.12573	-0.343000	0.07986	TAC		0.562	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
FLG	2312	hgsc.bcm.edu	37	1	152284628	152284628	+	Missense_Mutation	SNP	G	G	A	rs147145635		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:152284628G>A	ENST00000368799.1	-	3	2769	c.2734C>T	c.(2734-2736)Cgt>Tgt	p.R912C	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	912	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCATGGTGACGTGACCCTGAG	0.567									Ichthyosis				-|||	1	0.000199681	0.0	0.0	5008	,	,		21118	0.0		0.001	False		,,,				2504	0.0																0			1						G	CYS/ARG	1,4405		0,1,2202	385.0	363.0	370.0		2734	-2.3	0.0	1	dbSNP_134	370	17,8583		0,17,4283	yes	missense	FLG	NM_002016.1	180	0,18,6485	AA,AG,GG		0.1977,0.0227,0.1384	probably-damaging	912/4062	152284628	18,12988	2203	4300	6503	150551252	SO:0001583	missense	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.2734C>T	1.37:g.152284628G>A	ENSP00000357789:p.Arg912Cys		150551252	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	-	4.416	0.076815	0.08485	2.27E-4	0.001977	ENSG00000143631	ENST00000368799	T	0.02446	4.29	2.3	-2.27	0.06846	.	.	.	.	.	T	0.01835	0.0058	M	0.65975	2.015	0.09310	N	1	D	0.76494	0.999	P	0.46659	0.523	T	0.40701	-0.9549	9	0.41790	T	0.15	.	9.1447	0.36925	0.0:0.6868:0.3132:0.0	.	912	P20930	FILA_HUMAN	C	912	ENSP00000357789:R912C	ENSP00000357789:R912C	R	-	1	0	FLG	150551252	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.326000	0.07965	-0.352000	0.08237	0.479000	0.44913	CGT		0.567	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
IVL	3713	hgsc.bcm.edu	37	1	152883253	152883253	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:152883253A>G	ENST00000368764.3	+	2	1044	c.980A>G	c.(979-981)gAg>gGg	p.E327G	IVL_ENST00000392667.2_Missense_Mutation_p.E181G			P07476	INVO_HUMAN	involucrin	327	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].				isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			aagcatctggagcagcaggag	0.642																																																	0			1											17.0	17.0	17.0					1																	152883253		2114	4160	6274	151149877	SO:0001583	missense	3713			BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.980A>G	1.37:g.152883253A>G	ENSP00000357753:p.Glu327Gly		151149877	Q5T7P4	Missense_Mutation	SNP	ENST00000368764.3	37	CCDS1030.1	.	.	.	.	.	.	.	.	.	.	A	9.475	1.096584	0.20552	.	.	ENSG00000163207	ENST00000368764;ENST00000392667	T;T	0.10477	3.04;2.87	3.82	-0.483	0.12075	.	.	.	.	.	T	0.01730	0.0055	N	0.14661	0.345	0.09310	N	1	B	0.27286	0.174	B	0.29176	0.099	T	0.46261	-0.9204	9	0.51188	T	0.08	.	4.3193	0.11009	0.5239:0.0:0.1122:0.3639	.	327	P07476	INVO_HUMAN	G	327;181	ENSP00000357753:E327G;ENSP00000376435:E181G	ENSP00000357753:E327G	E	+	2	0	IVL	151149877	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.366000	0.20365	-0.360000	0.08138	-0.648000	0.03929	GAG		0.642	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547	
NPR1	4881	hgsc.bcm.edu	37	1	153657499	153657499	+	Missense_Mutation	SNP	T	T	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:153657499T>G	ENST00000368680.3	+	8	2016	c.1544T>G	c.(1543-1545)gTt>gGt	p.V515G		NM_000906.3	NP_000897.3	P16066	ANPRA_HUMAN	natriuretic peptide receptor 1	515					body fluid secretion (GO:0007589)|cell surface receptor signaling pathway (GO:0007166)|cGMP biosynthetic process (GO:0006182)|dopamine metabolic process (GO:0042417)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cGMP biosynthetic process (GO:0030828)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|regulation of blood vessel size (GO:0050880)|regulation of vascular permeability (GO:0043114)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|G-protein coupled peptide receptor activity (GO:0008528)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(17)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)		Amyl Nitrite(DB01612)|Erythrityl Tetranitrate(DB01613)|Isosorbide Dinitrate(DB00883)|Nesiritide(DB04899)|Nitroglycerin(DB00727)|Nitroprusside(DB00325)	TGGGAGGACGTTGAGCCCAGT	0.627																																					Pancreas(141;1349 1870 15144 15830 40702)												0			1											62.0	60.0	60.0					1																	153657499		2203	4300	6503	151924123	SO:0001583	missense	4881			BC063304	CCDS1051.1	1q21-q22	2014-03-03	2014-03-03		ENSG00000169418	ENSG00000169418			7943	protein-coding gene	gene with protein product	"""guanylate cyclase A"""	108960	"""atrionatriuretic peptide receptor A"", ""natriuretic peptide receptor A"""	ANPRA, NPRA		1979052	Standard	NM_000906		Approved	GUCY2A, ANPa	uc001fcs.4	P16066	OTTHUMG00000037085	ENST00000368680.3:c.1544T>G	1.37:g.153657499T>G	ENSP00000357669:p.Val515Gly		151924123	B0ZBF0|Q5SR08|Q6P4Q3	Missense_Mutation	SNP	ENST00000368680.3	37	CCDS1051.1	.	.	.	.	.	.	.	.	.	.	T	16.57	3.161524	0.57368	.	.	ENSG00000169418	ENST00000368680;ENST00000428723	T	0.57107	0.42	4.86	4.86	0.63082	.	0.633338	0.14462	N	0.318124	T	0.41511	0.1162	L	0.46819	1.47	0.80722	D	1	P;P	0.49185	0.92;0.547	P;B	0.46543	0.52;0.282	T	0.47522	-0.9111	10	0.87932	D	0	.	12.4638	0.55747	0.0:0.0:0.0:1.0	.	20;515	B7Z4Y7;P16066	.;ANPRA_HUMAN	G	515;20	ENSP00000357669:V515G	ENSP00000357669:V515G	V	+	2	0	NPR1	151924123	1.000000	0.71417	0.444000	0.26895	0.252000	0.25951	7.496000	0.81526	2.043000	0.60533	0.533000	0.62120	GTT		0.627	NPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090034.1	NM_000906	
SHC1	6464	hgsc.bcm.edu	37	1	154942755	154942755	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:154942755T>C	ENST00000368445.5	-	1	462	c.248A>G	c.(247-249)gAg>gGg	p.E83G	SHC1_ENST00000606391.1_Intron|SHC1_ENST00000368453.4_Intron|SHC1_ENST00000368449.4_Intron|SHC1_ENST00000448116.2_Missense_Mutation_p.E83G|SHC1_ENST00000368450.1_Intron	NM_183001.4	NP_892113.4	P29353	SHC1_HUMAN	SHC (Src homology 2 domain containing) transforming protein 1	83					actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|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)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet activation (GO:0030168)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|Ras protein signal transduction (GO:0007265)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of growth (GO:0040008)|single organismal cell-cell adhesion (GO:0016337)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|Shc-EGFR complex (GO:0070435)	ephrin receptor binding (GO:0046875)|epidermal growth factor receptor binding (GO:0005154)|insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phospholipid binding (GO:0005543)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)			breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	20	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			CCTTCCTGGCTCCCCCTTAGA	0.652																																					NSCLC(4;32 234 1864 2492 3259 13747 17376)												0			1											24.0	29.0	28.0					1																	154942755		2203	4299	6502	153209379	SO:0001583	missense	6464			U73377	CCDS1076.1, CCDS30881.1, CCDS44233.1, CCDS44234.1	1q21	2013-02-14	2002-01-14		ENSG00000160691	ENSG00000160691		"""SH2 domain containing"""	10840	protein-coding gene	gene with protein product		600560	"""SHC (Src homology 2 domain-containing) transforming protein 1"""	SHC		1623525	Standard	NM_003029		Approved	p66	uc001ffw.3	P29353	OTTHUMG00000037295	ENST00000368445.5:c.248A>G	1.37:g.154942755T>C	ENSP00000357430:p.Glu83Gly		153209379	B5BU19|D3DV78|O15290|Q5T180|Q5T183|Q5T184|Q5T185|Q5T186|Q8N4K5|Q96CL1	Missense_Mutation	SNP	ENST00000368445.5	37	CCDS30881.1	.	.	.	.	.	.	.	.	.	.	T	10.79	1.449519	0.26074	.	.	ENSG00000160691	ENST00000368445;ENST00000448116;ENST00000368443	T;T	0.50548	0.74;0.74	4.27	4.27	0.50696	.	0.226724	0.42420	D	0.000713	T	0.19886	0.0478	L	0.51422	1.61	0.80722	D	1	B;B	0.09022	0.002;0.0	B;B	0.04013	0.001;0.0	T	0.08513	-1.0718	10	0.15499	T	0.54	.	7.5658	0.27879	0.0:0.0975:0.0:0.9025	.	83;83	P29353-6;P29353	.;SHC1_HUMAN	G	83;83;19	ENSP00000357430:E83G;ENSP00000401303:E83G	ENSP00000357428:E19G	E	-	2	0	SHC1	153209379	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.539000	0.36104	1.922000	0.55676	0.454000	0.30748	GAG		0.652	SHC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090781.2	NM_183001	
RUSC1	23623	hgsc.bcm.edu	37	1	155291183	155291183	+	Intron	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:155291183A>G	ENST00000368352.5	+	2	65				RUSC1_ENST00000368354.3_Intron|RUSC1_ENST00000368347.4_5'Flank|RUSC1-AS1_ENST00000543656.1_RNA|RUSC1-AS1_ENST00000443642.1_RNA|RUSC1-AS1_ENST00000446880.1_RNA|RUSC1-AS1_ENST00000450199.1_RNA	NM_001105203.1	NP_001098673.1	Q9BVN2	RUSC1_HUMAN	RUN and SH3 domain containing 1						positive regulation of signal transduction (GO:0009967)|protein polyubiquitination (GO:0000209)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	actin binding (GO:0003779)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(2)|skin(1)|urinary_tract(1)	21	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;1.55e-10)|all cancers(21;4.15e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)			GGCAGCAGGGACCTGGAGGTC	0.677																																																	0			1											14.0	16.0	15.0					1																	155291183		1850	4087	5937	153557807	SO:0001627	intron_variant	284618			AB026894	CCDS1112.1, CCDS41410.1, CCDS41411.1, CCDS41412.1	1q21-q22	2011-04-28			ENSG00000160753	ENSG00000160753			17153	protein-coding gene	gene with protein product						10760598	Standard	NM_001105203		Approved	NESCA	uc001fkj.2	Q9BVN2	OTTHUMG00000013910	ENST00000368352.5:c.-86-296A>G	1.37:g.155291183A>G			153557807	B3KWM9|Q5T9U9|Q5T9V0|Q5T9V1|Q5T9V2|Q9UPY4|Q9Y4T5	Missense_Mutation	SNP	ENST00000368352.5	37	CCDS41410.1																																																																																				0.677	RUSC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039071.1		
ASTN1	460	hgsc.bcm.edu	37	1	176998807	176998807	+	Silent	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:176998807A>G	ENST00000367654.3	-	5	1294	c.1083T>C	c.(1081-1083)ttT>ttC	p.F361F	ASTN1_ENST00000281881.3_5'UTR|ASTN1_ENST00000424564.2_Silent_p.F361F|ASTN1_ENST00000361833.2_Silent_p.F361F|MIR488_ENST00000365739.2_RNA|ASTN1_ENST00000367657.3_Silent_p.F361F	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	361					locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						GATCCGTGTAAAAGGTCAGCT	0.542																																																	0			1											70.0	66.0	67.0					1																	176998807		2203	4300	6503	175265430	SO:0001819	synonymous_variant	460			AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"""astrotactin"""	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.1083T>C	1.37:g.176998807A>G			175265430	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Silent	SNP	ENST00000367654.3	37																																																																																					0.542	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319	
B3GALT2	8707	hgsc.bcm.edu	37	1	193150027	193150027	+	Silent	SNP	A	A	G	rs376102979	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:193150027A>G	ENST00000367434.4	-	2	1421	c.666T>C	c.(664-666)gaT>gaC	p.D222D	CDC73_ENST00000367435.3_Intron	NM_003783.3	NP_003774.1	O43825	B3GT2_HUMAN	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2	222					oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity (GO:0008499)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(4)|ovary(2)	16						TATAGTACGTATCTAAGTATT	0.348													A|||	4	0.000798722	0.0	0.0	5008	,	,		20480	0.004		0.0	False		,,,				2504	0.0																0			1											123.0	122.0	122.0					1																	193150027		2203	4299	6502	191416650	SO:0001819	synonymous_variant	8707			Y15060	CCDS1383.1	1q31	2013-02-19			ENSG00000162630	ENSG00000162630		"""Beta 3-glycosyltransferases"""	917	protein-coding gene	gene with protein product		603018				9582303, 9417100	Standard	NM_003783		Approved	beta3Gal-T2	uc001gtc.4	O43825	OTTHUMG00000035687	ENST00000367434.4:c.666T>C	1.37:g.193150027A>G			191416650	B2RAB1|Q9BZQ9	Silent	SNP	ENST00000367434.4	37	CCDS1383.1																																																																																				0.348	B3GALT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086759.1	NM_003783	
NFASC	23114	hgsc.bcm.edu	37	1	204985634	204985634	+	Silent	SNP	G	G	A	rs143897854	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:204985634G>A	ENST00000401399.1	+	29	3889	c.3690G>A	c.(3688-3690)acG>acA	p.T1230T	NFASC_ENST00000513543.1_Silent_p.T1159T|NFASC_ENST00000539706.1_Silent_p.T1164T|NFASC_ENST00000339876.6_Silent_p.T1230T|NFASC_ENST00000367170.4_Silent_p.T1258T|NFASC_ENST00000367171.4_Silent_p.T1322T|NFASC_ENST00000338515.6_Silent_p.T1247T|NFASC_ENST00000367169.4_Silent_p.T1061T|NFASC_ENST00000338586.6_Silent_p.T1214T|NFASC_ENST00000404907.1_Silent_p.T1164T|NFASC_ENST00000404076.1_Silent_p.T1147T|NFASC_ENST00000360049.4_Silent_p.T1159T|NFASC_ENST00000495396.1_3'UTR|NFASC_ENST00000367172.4_Silent_p.T1337T			O94856	NFASC_HUMAN	neurofascin	1337					axon guidance (GO:0007411)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|myelination (GO:0042552)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|synapse organization (GO:0050808)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|node of Ranvier (GO:0033268)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	81	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			CAGAGGCCACGTCACCTGTCA	0.562													G|||	18	0.00359425	0.0015	0.0043	5008	,	,		19173	0.0		0.005	False		,,,				2504	0.0082																0			1						G	,,,	5,4401	9.9+/-24.2	0,5,2198	163.0	142.0	149.0		3690,3537,3492,3477	-4.4	0.5	1	dbSNP_134	149	54,8546	34.3+/-88.2	0,54,4246	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NFASC	NM_001005388.2,NM_001160331.1,NM_001160332.1,NM_015090.3	,,,	0,59,6444	AA,AG,GG		0.6279,0.1135,0.4536	,,,	1230/1241,1179/1190,1164/1175,1159/1170	204985634	59,12947	2203	4300	6503	203252257	SO:0001819	synonymous_variant	23114			AK027553	CCDS30982.1, CCDS53460.1, CCDS53461.1, CCDS53462.1	1q32.1	2013-02-11	2010-06-24		ENSG00000163531	ENSG00000163531		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	29866	protein-coding gene	gene with protein product		609145	"""neurofascin homolog (chicken)"""			1377696, 8672144	Standard	NM_015090		Approved	NRCAML, KIAA0756, FLJ46866, NF	uc001hbj.3	O94856	OTTHUMG00000151697	ENST00000401399.1:c.3690G>A	1.37:g.204985634G>A			203252257	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Silent	SNP	ENST00000401399.1	37	CCDS53460.1	9	0.004120879120879121	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	G	9.318	1.057210	0.19907	0.001135	0.006279	ENSG00000163531	ENST00000367173;ENST00000425360	.	.	.	5.34	-4.44	0.03557	.	.	.	.	.	T	0.43942	0.1270	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49504	-0.8933	4	.	.	.	.	9.6176	0.39701	0.6087:0.1038:0.2874:0.0	.	.	.	.	H	1031;288	.	.	R	+	2	0	NFASC	203252257	0.001000	0.12720	0.522000	0.27862	0.993000	0.82548	-1.532000	0.02217	-0.900000	0.03896	-0.251000	0.11542	CGT		0.562	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388	
MAPKAPK2	9261	hgsc.bcm.edu	37	1	206902139	206902139	+	Missense_Mutation	SNP	G	G	T			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:206902139G>T	ENST00000367103.3	+	2	557	c.364G>T	c.(364-366)Gat>Tat	p.D122Y	MAPKAPK2_ENST00000294981.4_Missense_Mutation_p.D122Y	NM_004759.4|NM_032960.3	NP_004750.1|NP_116584.2	P49137	MAPK2_HUMAN	mitogen-activated protein kinase-activated protein kinase 2	122	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|activation of MAPK activity (GO:0000187)|arachidonic acid metabolic process (GO:0019369)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|G2 DNA damage checkpoint (GO:0031572)|gene expression (GO:0010467)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|leukotriene metabolic process (GO:0006691)|macropinocytosis (GO:0044351)|MAPK cascade (GO:0000165)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of interleukin-6 production (GO:0032675)|regulation of tumor necrosis factor production (GO:0032680)|response to cytokine (GO:0034097)|response to lipopolysaccharide (GO:0032496)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|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)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	19	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.211)			ACGGATCGTGGATGTGTACGA	0.612																																																	0			1											52.0	58.0	56.0					1																	206902139		2203	4300	6503	204968762	SO:0001583	missense	9261			U12779	CCDS1466.1, CCDS31001.1	1q32	2008-02-05			ENSG00000162889	ENSG00000162889			6887	protein-coding gene	gene with protein product		602006				8179591, 8280084	Standard	NM_004759		Approved		uc001hem.2	P49137	OTTHUMG00000036342	ENST00000367103.3:c.364G>T	1.37:g.206902139G>T	ENSP00000356070:p.Asp122Tyr		204968762	Q5SY30|Q5SY41|Q8IYD6	Missense_Mutation	SNP	ENST00000367103.3	37	CCDS31001.1	.	.	.	.	.	.	.	.	.	.	G	31	5.064922	0.93898	.	.	ENSG00000162889	ENST00000294981;ENST00000367103	T;T	0.55234	0.53;0.53	5.58	5.58	0.84498	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.71451	0.3341	L	0.61387	1.9	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.73442	-0.3981	9	0.87932	D	0	-26.8459	18.1381	0.89627	0.0:0.0:1.0:0.0	.	122;122	P49137;P49137-2	MAPK2_HUMAN;.	Y	122	ENSP00000294981:D122Y;ENSP00000356070:D122Y	ENSP00000294981:D122Y	D	+	1	0	MAPKAPK2	204968762	1.000000	0.71417	0.993000	0.49108	0.971000	0.66376	9.869000	0.99810	2.611000	0.88343	0.655000	0.94253	GAT		0.612	MAPKAPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088465.1	NM_004759	
CCDC185	164127	hgsc.bcm.edu	37	1	223568115	223568115	+	Missense_Mutation	SNP	G	G	A	rs560005249		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:223568115G>A	ENST00000366875.3	+	1	1401	c.1298G>A	c.(1297-1299)cGg>cAg	p.R433Q		NM_152610.2	NP_689823.2	Q8N715	CC185_HUMAN		433										breast(4)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|skin(3)	29				GBM - Glioblastoma multiforme(131;0.0704)		TACCAGGCCCGGAAGGTCCTC	0.602													G|||	1	0.000199681	0.0	0.0	5008	,	,		18052	0.0		0.0	False		,,,				2504	0.001																0			1											39.0	34.0	36.0					1																	223568115		2203	4299	6502	221634738	SO:0001583	missense	164127																														ENST00000366875.3:c.1298G>A	1.37:g.223568115G>A	ENSP00000355840:p.Arg433Gln		221634738	Q8N746|Q8NA93	Missense_Mutation	SNP	ENST00000366875.3	37	CCDS1537.1	.	.	.	.	.	.	.	.	.	.	G	18.92	3.724736	0.68959	.	.	ENSG00000178395	ENST00000366875	T	0.26518	1.73	5.59	3.69	0.42338	.	.	.	.	.	T	0.36580	0.0972	M	0.66939	2.045	0.32537	N	0.534194	D	0.71674	0.998	P	0.57371	0.819	T	0.47420	-0.9119	9	0.39692	T	0.17	.	4.2902	0.10874	0.0845:0.1579:0.5942:0.1634	.	433	Q8N715	CA065_HUMAN	Q	433	ENSP00000355840:R433Q	ENSP00000355840:R433Q	R	+	2	0	C1orf65	221634738	0.999000	0.42202	0.845000	0.33349	0.984000	0.73092	4.841000	0.62824	0.695000	0.31675	0.655000	0.94253	CGG		0.602	C1orf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092718.1		
TRIM11	81559	hgsc.bcm.edu	37	1	228588858	228588858	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:228588858T>C	ENST00000284551.6	-	3	820	c.542A>G	c.(541-543)gAg>gGg	p.E181G	TRIM11_ENST00000460651.1_5'UTR|TRIM11_ENST00000493030.2_Missense_Mutation_p.E56G|TRIM11_ENST00000366699.3_Missense_Mutation_p.E181G	NM_145214.2	NP_660215.1	Q96F44	TRI11_HUMAN	tripartite motif containing 11	181					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of neurogenesis (GO:0050768)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of viral entry into host cell (GO:0046598)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|skin(1)	18		Prostate(94;0.0724)				ACGCTCGAACTCACCCAGCAC	0.662																																																	0			1											33.0	34.0	33.0					1																	228588858		2203	4300	6503	226655481	SO:0001583	missense	81559			AF220125	CCDS31048.1	1q42.13	2013-01-09	2011-01-25		ENSG00000154370	ENSG00000154370		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16281	protein-coding gene	gene with protein product		607868	"""tripartite motif-containing 11"""			11331580	Standard	NM_145214		Approved	RNF92, BIA1	uc001hss.3	Q96F44	OTTHUMG00000039773	ENST00000284551.6:c.542A>G	1.37:g.228588858T>C	ENSP00000284551:p.Glu181Gly		226655481	A6NKE2|B2RB82|B3KUS3|B4DX88|Q5VSU1|Q8NCA6|Q9C022	Missense_Mutation	SNP	ENST00000284551.6	37	CCDS31048.1	.	.	.	.	.	.	.	.	.	.	t	14.89	2.669573	0.47677	.	.	ENSG00000154370	ENST00000284551;ENST00000366699	T;T	0.05025	3.51;3.51	4.86	4.86	0.63082	.	0.336267	0.21519	N	0.073242	T	0.20455	0.0492	M	0.70108	2.13	0.27717	N	0.94525	D;D;D	0.89917	0.998;1.0;0.983	D;D;P	0.74348	0.957;0.983;0.862	T	0.03259	-1.1055	10	0.52906	T	0.07	.	9.0393	0.36307	0.0:0.0:0.1859:0.8141	.	180;181;181	Q96F44-3;Q96F44-2;Q96F44	.;.;TRI11_HUMAN	G	181	ENSP00000284551:E181G;ENSP00000355660:E181G	ENSP00000284551:E181G	E	-	2	0	TRIM11	226655481	1.000000	0.71417	0.980000	0.43619	0.062000	0.15995	6.626000	0.74253	1.958000	0.56883	0.255000	0.18592	GAG		0.662	TRIM11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095995.3	NM_145214	
COG2	22796	hgsc.bcm.edu	37	1	230827217	230827217	+	Silent	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:230827217T>C	ENST00000366669.4	+	17	2137	c.2022T>C	c.(2020-2022)acT>acC	p.T674T	COG2_ENST00000546013.1_Silent_p.T363T|COG2_ENST00000366668.3_Silent_p.T673T|COG2_ENST00000534989.1_Silent_p.T615T|COG2_ENST00000535166.1_Silent_p.T558T	NM_001145036.1|NM_007357.2	NP_001138508.1|NP_031383.1	Q14746	COG2_HUMAN	component of oligomeric golgi complex 2	674					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	cytosol (GO:0005829)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|Golgi transport complex (GO:0017119)	protein transporter activity (GO:0008565)			NS(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|urinary_tract(3)	27	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				GAAAAACCACTCCCGCCAACC	0.498																																																	0			1											67.0	69.0	69.0					1																	230827217		2203	4300	6503	228893840	SO:0001819	synonymous_variant	22796			Z34975	CCDS1584.1, CCDS44329.1	1q42.2	2008-02-05	2002-05-28	2002-05-31	ENSG00000135775	ENSG00000135775		"""Components of oligomeric golgi complex"""	6546	protein-coding gene	gene with protein product		606974	"""low density lipoprotein receptor defect C complementing"""	LDLC		7962052	Standard	NM_007357		Approved		uc001htw.3	Q14746	OTTHUMG00000037753	ENST00000366669.4:c.2022T>C	1.37:g.230827217T>C			228893840	Q86U99	Silent	SNP	ENST00000366669.4	37	CCDS1584.1																																																																																				0.498	COG2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092087.1	NM_007357	
B4GALNT4	338707	hgsc.bcm.edu	37	11	379598	379598	+	Silent	SNP	A	A	G	rs1134699	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:379598A>G	ENST00000329962.6	+	15	2385	c.2385A>G	c.(2383-2385)gaA>gaG	p.E795E		NM_178537.4	NP_848632.2	Q76KP1	B4GN4_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 4	795					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)		AAAGTCCCGAACCCGCTCCCG	0.731													.|||	2497	0.498602	0.6664	0.464	5008	,	,		10232	0.4911		0.4026	False		,,,				2504	0.4029																0			11						G		2237,1841		675,887,477	5.0	7.0	7.0		2385	2.7	0.3	11	dbSNP_86	7	2925,5275		621,1683,1796	no	coding-synonymous	B4GALNT4	NM_178537.4		1296,2570,2273	GG,GA,AA		35.6707,45.1447,42.0427		795/1040	379598	5162,7116	2039	4100	6139	369598	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.2385A>G	11.37:g.379598A>G			369598	Q96LV2	Silent	SNP	ENST00000329962.6	37	CCDS7694.1																																																																																				0.731	B4GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239289.2	NM_178537	
MUC5B	727897	hgsc.bcm.edu	37	11	1253733	1253733	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:1253733T>C	ENST00000529681.1	+	16	1955	c.1897T>C	c.(1897-1899)Tcg>Ccg	p.S633P	MUC5B_ENST00000447027.1_Missense_Mutation_p.S636P	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	633	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CAGTGCCTTCTCGCGCTGCCA	0.667																																																	0			11											38.0	44.0	42.0					11																	1253733		2108	4208	6316	1210309	SO:0001583	missense	727897			U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.1897T>C	11.37:g.1253733T>C	ENSP00000436812:p.Ser633Pro		1210309	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	T	10.32	1.318377	0.23994	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.78707	-1.2;-1.2	4.32	-1.52	0.08637	von Willebrand factor, type D domain (1);Uncharacterised domain, cysteine-rich (2);	.	.	.	.	D	0.85890	0.5802	M	0.83312	2.635	0.09310	N	1	D;D;D	0.76494	0.984;0.999;0.999	P;D;D	0.72338	0.825;0.977;0.977	T	0.76121	-0.3075	9	0.87932	D	0	.	8.862	0.35263	0.0921:0.0:0.5806:0.3274	.	633;1292;636	Q9HC84;A7Y9J9;E9PBJ0	MUC5B_HUMAN;.;.	P	633;636;634;669	ENSP00000436812:S633P;ENSP00000415793:S636P	ENSP00000343037:S634P	S	+	1	0	MUC5B	1210309	0.002000	0.14202	0.000000	0.03702	0.017000	0.09413	-0.074000	0.11450	-0.320000	0.08640	0.379000	0.24179	TCG		0.667	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
MUC5B	727897	hgsc.bcm.edu	37	11	1270938	1270938	+	Silent	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:1270938T>C	ENST00000529681.1	+	31	12886	c.12828T>C	c.(12826-12828)gcT>gcC	p.A4276A	MUC5B_ENST00000447027.1_Silent_p.A4279A|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4276	23 X approximate tandem repeats, Ser/Thr- rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CGGGAACAGCTCCCCCTCCCA	0.637																																																	0			11											122.0	142.0	136.0					11																	1270938		2103	4198	6301	1227514	SO:0001819	synonymous_variant	727897			U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.12828T>C	11.37:g.1270938T>C			1227514	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																				0.637	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
KRTAP5-1	387264	hgsc.bcm.edu	37	11	1606443	1606443	+	Missense_Mutation	SNP	T	T	C	rs541535366		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:1606443T>C	ENST00000382171.2	-	1	70	c.37A>G	c.(37-39)Agc>Ggc	p.S13G	KRTAP5-AS1_ENST00000424148.1_RNA|KRTAP5-AS1_ENST00000524947.1_RNA|KRTAP5-AS1_ENST00000532922.1_RNA|KRTAP5-AS1_ENST00000534077.1_RNA	NM_001005922.1	NP_001005922.1	Q6L8H4	KRA51_HUMAN	keratin associated protein 5-1	13						keratin filament (GO:0045095)				endometrium(3)|kidney(1)|lung(9)|skin(2)|upper_aerodigestive_tract(1)	16		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		CCCCCACAGCTGGAGCCACAG	0.672													T|||	1	0.000199681	0.0	0.0	5008	,	,		10249	0.001		0.0	False		,,,				2504	0.0																0			11											50.0	59.0	56.0					11																	1606443		2191	4292	6483	1563019	SO:0001583	missense	387264			AB126070	CCDS31330.1	11p15.5	2008-02-05			ENSG00000205869	ENSG00000205869		"""Keratin associated proteins"""	23596	protein-coding gene	gene with protein product		148022	"""keratin, cuticle, ultrahigh sulphur 1-like"""	KRN1L		15144888	Standard	NM_001005922		Approved	KRTAP5.1	uc001ltu.1	Q6L8H4	OTTHUMG00000057557	ENST00000382171.2:c.37A>G	11.37:g.1606443T>C	ENSP00000371606:p.Ser13Gly		1563019		Missense_Mutation	SNP	ENST00000382171.2	37	CCDS31330.1	.	.	.	.	.	.	.	.	.	.	T	0.020	-1.442712	0.01089	.	.	ENSG00000205869	ENST00000382171	T	0.05786	3.39	3.68	-0.313	0.12754	.	.	.	.	.	T	0.04363	0.0120	N	0.21448	0.665	0.09310	N	0.999997	B	0.11235	0.004	B	0.09377	0.004	T	0.39522	-0.9610	9	0.62326	D	0.03	.	5.381	0.16192	0.1575:0.1056:0.0:0.7369	.	13	Q6L8H4	KRA51_HUMAN	G	13	ENSP00000371606:S13G	ENSP00000371606:S13G	S	-	1	0	KRTAP5-1	1563019	0.013000	0.17824	0.972000	0.41901	0.013000	0.08279	-1.124000	0.03260	-0.420000	0.07427	-0.748000	0.03510	AGC		0.672	KRTAP5-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127922.1	NM_001005922	
TSPAN32	10077	hgsc.bcm.edu	37	11	2337867	2337867	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:2337867A>G	ENST00000182290.4	+	8	826	c.689A>G	c.(688-690)gAc>gGc	p.D230G	TSPAN32_ENST00000451520.2_Missense_Mutation_p.D219G|TSPAN32_ENST00000381121.3_Missense_Mutation_p.D230G	NM_139022.2	NP_620591.3	Q96QS1	TSN32_HUMAN	tetraspanin 32	230					cell-cell signaling (GO:0007267)|cytoskeleton organization (GO:0007010)|defense response to protozoan (GO:0042832)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of cell proliferation (GO:0008285)|negative regulation of myeloid dendritic cell activation (GO:0030886)|platelet aggregation (GO:0070527)|regulation of defense response to virus (GO:0050688)	cell surface (GO:0009986)|integrin alphaIIb-beta3 complex (GO:0070442)|intracellular (GO:0005622)				breast(1)|central_nervous_system(1)|lung(4)|ovary(1)|skin(1)	8		all_epithelial(84;4.89e-05)|Breast(177;0.000962)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|all_neural(188;0.00791)|Lung NSC(207;0.209)		BRCA - Breast invasive adenocarcinoma(625;0.000533)|LUSC - Lung squamous cell carcinoma(625;0.082)|Lung(200;0.153)		TGCAGCTTGGACCGCAAGGGC	0.662																																																	0			11											107.0	86.0	93.0					11																	2337867		2202	4299	6501	2294443	SO:0001583	missense	10077			AF176070	CCDS7733.1	11p15	2013-02-14	2005-08-16	2005-08-16	ENSG00000064201	ENSG00000064201		"""Tetraspanins"""	13410	protein-coding gene	gene with protein product		603853	"""pan-hematopoietic expression"""	TSSC6, PHEMX		10072438, 10950922	Standard	NM_139022		Approved		uc001lvy.1	Q96QS1	OTTHUMG00000009762	ENST00000182290.4:c.689A>G	11.37:g.2337867A>G	ENSP00000182290:p.Asp230Gly		2294443	Q96KX4|Q9HC50|Q9HC51|Q9Y5U1	Missense_Mutation	SNP	ENST00000182290.4	37	CCDS7733.1	.	.	.	.	.	.	.	.	.	.	.	12.28	1.891076	0.33348	.	.	ENSG00000064201	ENST00000182290;ENST00000381121;ENST00000451520;ENST00000444307;ENST00000381117	T;T;T	0.51071	0.73;0.8;0.72	3.5	3.5	0.40072	.	0.501194	0.16044	U	0.232280	T	0.51584	0.1683	L	0.27053	0.805	0.27197	N	0.960276	D;D;D;D	0.89917	1.0;0.998;1.0;0.997	D;D;D;P	0.87578	0.964;0.943;0.998;0.878	T	0.33979	-0.9847	10	0.41790	T	0.15	-12.9163	8.7151	0.34405	1.0:0.0:0.0:0.0	.	219;175;230;230	D3YTD1;G3XAG6;Q96QS1-3;Q96QS1	.;.;.;TSN32_HUMAN	G	230;230;219;166;175	ENSP00000182290:D230G;ENSP00000370513:D230G;ENSP00000405205:D219G	ENSP00000182290:D230G	D	+	2	0	TSPAN32	2294443	0.964000	0.33143	0.688000	0.30117	0.041000	0.13682	2.369000	0.44231	1.389000	0.46526	0.260000	0.18958	GAC		0.662	TSPAN32-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026912.2	NM_139024	
NAV2	89797	hgsc.bcm.edu	37	11	19968013	19968013	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:19968013A>G	ENST00000396087.3	+	10	2381	c.2282A>G	c.(2281-2283)gAg>gGg	p.E761G	NAV2_ENST00000349880.4_Missense_Mutation_p.E738G|NAV2_ENST00000527559.2_Missense_Mutation_p.E690G|NAV2_ENST00000540292.1_Missense_Mutation_p.E692G|NAV2_ENST00000396085.1_Missense_Mutation_p.E738G|NAV2_ENST00000360655.4_Missense_Mutation_p.E674G	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	761					glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						CAGAATTTGGAGGAAACCATG	0.458																																																	0			11											91.0	82.0	85.0					11																	19968013		2199	4293	6492	19924589	SO:0001583	missense	89797			AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 2"", ""retinoic acid inducible gene in neuroblastoma 1"", ""helicase, APC down-regulated 1"""	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.2282A>G	11.37:g.19968013A>G	ENSP00000379396:p.Glu761Gly		19924589	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Missense_Mutation	SNP	ENST00000396087.3	37	CCDS58126.1	.	.	.	.	.	.	.	.	.	.	A	32	5.187293	0.94923	.	.	ENSG00000166833	ENST00000360655;ENST00000396085;ENST00000349880;ENST00000396087;ENST00000527559;ENST00000540292	T;T;T;T;T;T	0.15834	2.39;2.39;2.39;2.39;2.39;2.39	5.92	5.92	0.95590	.	0.000000	0.64402	D	0.000002	T	0.42607	0.1210	M	0.71206	2.165	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	T	0.18023	-1.0350	9	.	.	.	.	16.3668	0.83335	1.0:0.0:0.0:0.0	.	738;674	Q8IVL1-3;Q8IVL1-4	.;.	G	674;738;738;761;690;692	ENSP00000353871:E674G;ENSP00000379394:E738G;ENSP00000309577:E738G;ENSP00000379396:E761G;ENSP00000435395:E690G;ENSP00000443489:E692G	.	E	+	2	0	NAV2	19924589	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.268000	0.75426	0.454000	0.30748	GAG		0.458	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117	
MYRF	745	hgsc.bcm.edu	37	11	61539374	61539374	+	Silent	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:61539374T>C	ENST00000278836.5	+	7	1161	c.1065T>C	c.(1063-1065)ccT>ccC	p.P355P	TMEM258_ENST00000535042.1_Intron|MYRF_ENST00000327797.1_5'Flank|MYRF_ENST00000265460.5_Silent_p.P346P	NM_001127392.1	NP_001120864.1	Q9Y2G1	MRF_HUMAN	myelin regulatory factor	355					central nervous system myelin maintenance (GO:0032286)|central nervous system myelination (GO:0022010)|oligodendrocyte development (GO:0014003)|oligodendrocyte differentiation (GO:0048709)|positive regulation of myelination (GO:0031643)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)										AGTGGCAGCCTCATCAGCAGA	0.612																																																	0			11											152.0	148.0	150.0					11																	61539374		2202	4299	6501	61295950	SO:0001819	synonymous_variant	745				CCDS31579.1, CCDS44622.1	11q12-q13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000124920	ENSG00000124920			1181	protein-coding gene	gene with protein product	"""myelin gene regulatory factor"""	608329	"""chromosome 11 open reading frame 9"""	C11orf9		10828591, 12384578	Standard	NM_001127392		Approved	Ndt80, pqn-47, MRF	uc001nsc.1	Q9Y2G1	OTTHUMG00000168161	ENST00000278836.5:c.1065T>C	11.37:g.61539374T>C			61295950	O43582|Q9P1Q6	Silent	SNP	ENST00000278836.5	37	CCDS44622.1																																																																																				0.612	MYRF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398519.2	NM_013279	
ROM1	6094	hgsc.bcm.edu	37	11	62381295	62381295	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:62381295A>G	ENST00000278833.3	+	1	1083	c.542A>G	c.(541-543)cAg>cGg	p.Q181R	EML3_ENST00000494176.2_5'Flank|ROM1_ENST00000534093.1_Intron|EML3_ENST00000278845.4_5'Flank|EML3_ENST00000529309.1_5'Flank|EML3_ENST00000531557.1_5'Flank|EML3_ENST00000394773.2_5'Flank	NM_000327.3	NP_000318	Q03395	ROM1_HUMAN	retinal outer segment membrane protein 1	181					camera-type eye photoreceptor cell differentiation (GO:0060219)|cell adhesion (GO:0007155)|regulation of gene expression (GO:0010468)|retina vasculature development in camera-type eye (GO:0061298)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)				central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	8						TTTGGGGTCCAGTGGGTCAGC	0.622																																																	0			11											71.0	81.0	78.0					11																	62381295		2202	4299	6501	62137871	SO:0001583	missense	6094			L07894	CCDS8024.1	11q13	2013-02-14				ENSG00000149489		"""Tetraspanins"""	10254	protein-coding gene	gene with protein product		180721				8504299	Standard	NM_000327		Approved	TSPAN23, ROM	uc001ntv.3	Q03395		ENST00000278833.3:c.542A>G	11.37:g.62381295A>G	ENSP00000278833:p.Gln181Arg		62137871	B2R978	Missense_Mutation	SNP	ENST00000278833.3	37	CCDS8024.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.289141	0.80914	.	.	ENSG00000149489	ENST00000278833	T	0.80123	-1.34	4.74	4.74	0.60224	Tetraspanin, EC2 domain (1);	0.000000	0.85682	D	0.000000	D	0.89371	0.6696	M	0.82823	2.61	0.58432	D	0.999998	D	0.76494	0.999	D	0.87578	0.998	D	0.90627	0.4564	10	0.72032	D	0.01	-28.5236	12.2478	0.54581	1.0:0.0:0.0:0.0	.	181	Q03395	ROM1_HUMAN	R	181	ENSP00000278833:Q181R	ENSP00000278833:Q181R	Q	+	2	0	ROM1	62137871	1.000000	0.71417	1.000000	0.80357	0.847000	0.48162	5.610000	0.67668	1.994000	0.58287	0.260000	0.18958	CAG		0.622	ROM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394929.1	NM_000327	
RPS6KA4	8986	hgsc.bcm.edu	37	11	64129168	64129168	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:64129168T>C	ENST00000334205.4	+	7	771	c.706T>C	c.(706-708)Tcg>Ccg	p.S236P	RPS6KA4_ENST00000528057.1_Missense_Mutation_p.S236P|RPS6KA4_ENST00000294261.4_Missense_Mutation_p.S236P	NM_003942.2	NP_003933.1	O75676	KS6A4_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 4	236	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.		S -> L (in a breast infiltrating ductal carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		axon guidance (GO:0007411)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-S28 phosphorylation (GO:0043988)|histone phosphorylation (GO:0016572)|inflammatory response (GO:0006954)|interleukin-1-mediated signaling pathway (GO:0070498)|intracellular signal transduction (GO:0035556)|negative regulation of cytokine production (GO:0001818)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|mitogen-activated protein kinase p38 binding (GO:0048273)|protein serine/threonine kinase activity (GO:0004674)|ribosomal protein S6 kinase activity (GO:0004711)			breast(1)|endometrium(3)|lung(7)|ovary(1)|prostate(1)	13						GACGGGGGCCTCGCCCTTCAC	0.697																																																	0			11											21.0	22.0	22.0					11																	64129168		2199	4294	6493	63885744	SO:0001583	missense	8986			AJ010119	CCDS8073.1, CCDS73313.1	11q11-q13	2011-04-05	2002-08-29		ENSG00000162302	ENSG00000162302			10433	protein-coding gene	gene with protein product		603606	"""ribosomal protein S6 kinase, 90kD, polypeptide 4"""			9792677, 9687510	Standard	XM_005274379		Approved	RSK-B, MSK2	uc001oae.3	O75676	OTTHUMG00000046094	ENST00000334205.4:c.706T>C	11.37:g.64129168T>C	ENSP00000333896:p.Ser236Pro		63885744	A8K7Z8|O75585|Q53ES8	Missense_Mutation	SNP	ENST00000334205.4	37	CCDS8073.1	.	.	.	.	.	.	.	.	.	.	N	11.25	1.583050	0.28268	.	.	ENSG00000162302	ENST00000528057;ENST00000334205;ENST00000294261;ENST00000530504	T;T;T;T	0.20463	2.07;2.07;2.07;2.07	4.12	2.98	0.34508	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.155416	0.43747	D	0.000523	T	0.12944	0.0314	N	0.00507	-1.42	0.49915	D	0.999836	B;D;D;D	0.89917	0.011;0.995;1.0;0.999	B;D;D;D	0.85130	0.003;0.964;0.997;0.99	T	0.37103	-0.9720	10	0.32370	T	0.25	.	7.8104	0.29228	0.0:0.1028:0.0:0.8972	.	236;236;236;236	G3XAA9;E9PJN1;O75676;O75676-2	.;.;KS6A4_HUMAN;.	P	236;236;236;220	ENSP00000435580:S236P;ENSP00000333896:S236P;ENSP00000294261:S236P;ENSP00000432945:S220P	ENSP00000294261:S236P	S	+	1	0	RPS6KA4	63885744	0.999000	0.42202	0.520000	0.27837	0.524000	0.34500	3.456000	0.53000	0.743000	0.32719	0.418000	0.28097	TCG		0.697	RPS6KA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106246.2	NM_003942	
SPTBN2	6712	hgsc.bcm.edu	37	11	66466117	66466117	+	Missense_Mutation	SNP	A	A	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:66466117A>C	ENST00000533211.1	-	20	4338	c.4007T>G	c.(4006-4008)gTg>gGg	p.V1336G	SPTBN2_ENST00000529997.1_Missense_Mutation_p.V1336G|SPTBN2_ENST00000309996.2_Missense_Mutation_p.V1336G			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	1336					actin filament capping (GO:0051693)|adult behavior (GO:0030534)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|cell death (GO:0008219)|cerebellar Purkinje cell layer morphogenesis (GO:0021692)|multicellular organism growth (GO:0035264)|synapse assembly (GO:0007416)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|spectrin (GO:0008091)	actin binding (GO:0003779)|phospholipid binding (GO:0005543)|structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(15)|liver(1)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	74						CACCTTGTCCACCTTGTCCAG	0.602																																																	0			11											83.0	79.0	80.0					11																	66466117		2200	4295	6495	66222693	SO:0001583	missense	6712			AB008567, AF026487, AF026488, AF079569	CCDS8150.1	11q13.2	2013-01-10			ENSG00000173898	ENSG00000173898		"""Pleckstrin homology (PH) domain containing"""	11276	protein-coding gene	gene with protein product		604985	"""spinocerebellar ataxia 5"""	SCA5		9826670, 16429157	Standard	NM_006946		Approved		uc001ojd.3	O15020	OTTHUMG00000167262	ENST00000533211.1:c.4007T>G	11.37:g.66466117A>C	ENSP00000432568:p.Val1336Gly		66222693	O14872|O14873	Missense_Mutation	SNP	ENST00000533211.1	37	CCDS8150.1	.	.	.	.	.	.	.	.	.	.	A	16.16	3.044054	0.55110	.	.	ENSG00000173898	ENST00000533211;ENST00000309996;ENST00000529997	T;T;T	0.55234	0.53;0.53;0.53	4.72	4.72	0.59763	.	0.077294	0.53938	D	0.000042	T	0.66499	0.2795	M	0.80616	2.505	0.80722	D	1	P	0.50272	0.933	P	0.53313	0.723	T	0.72959	-0.4133	10	0.87932	D	0	.	13.341	0.60545	1.0:0.0:0.0:0.0	.	1336	O15020	SPTN2_HUMAN	G	1336	ENSP00000432568:V1336G;ENSP00000311489:V1336G;ENSP00000433593:V1336G	ENSP00000311489:V1336G	V	-	2	0	SPTBN2	66222693	1.000000	0.71417	1.000000	0.80357	0.704000	0.40688	9.081000	0.94049	1.981000	0.57761	0.533000	0.62120	GTG		0.602	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946	
MYEOV	26579	hgsc.bcm.edu	37	11	69063156	69063156	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:69063156T>C	ENST00000308946.3	+	3	689	c.239T>C	c.(238-240)cTc>cCc	p.L80P	MYEOV_ENST00000441339.2_Missense_Mutation_p.L80P|MYEOV_ENST00000535407.1_Missense_Mutation_p.L22P	NM_138768.2	NP_620123.2	Q96EZ4	MYEOV_HUMAN	myeloma overexpressed	80										endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(1)|lung(12)|prostate(2)|skin(1)|urinary_tract(1)	24	all_lung(4;2.21e-19)|Lung NSC(4;6.13e-19)|Melanoma(5;0.00128)		LUSC - Lung squamous cell carcinoma(11;3.33e-11)|STAD - Stomach adenocarcinoma(18;0.00654)|LUAD - Lung adenocarcinoma(13;0.0713)	Kidney(183;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(183;3.23e-08)|Lung(977;0.00361)|LUSC - Lung squamous cell carcinoma(976;0.0153)		CGGGGCCGCCTCTGTCTCTCC	0.617																																																	0			11											59.0	67.0	64.0					11																	69063156		2200	4294	6494	68819732	SO:0001583	missense	26579			AJ223366	CCDS8190.1, CCDS73340.1	11q13.2	2013-03-27	2013-03-27			ENSG00000172927			7563	protein-coding gene	gene with protein product		605625	"""myeloma overexpressed (in a subset of t(11;14) positive multiple myelomas)"""			10753852	Standard	XM_005273908		Approved	OCIM	uc001oov.3	Q96EZ4		ENST00000308946.3:c.239T>C	11.37:g.69063156T>C	ENSP00000308330:p.Leu80Pro		68819732	Q9UGN6|Q9UGN7	Missense_Mutation	SNP	ENST00000308946.3	37	CCDS8190.1	.	.	.	.	.	.	.	.	.	.	T	8.387	0.838868	0.16891	.	.	ENSG00000172927	ENST00000441339;ENST00000308946;ENST00000535407	T;T;T	0.27402	1.68;1.68;1.67	1.69	-0.752	0.11072	.	.	.	.	.	T	0.13415	0.0325	N	0.08118	0	0.09310	N	0.999999	B	0.23540	0.087	B	0.19148	0.024	T	0.21621	-1.0240	9	0.87932	D	0	.	4.1942	0.10435	0.0:0.4299:0.0:0.5701	.	80	Q96EZ4	MYEOV_HUMAN	P	80;80;22	ENSP00000412482:L80P;ENSP00000308330:L80P;ENSP00000438100:L22P	ENSP00000308330:L80P	L	+	2	0	MYEOV	68819732	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	0.018000	0.13422	-0.214000	0.10078	0.402000	0.26972	CTC		0.617	MYEOV-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396548.1		
FAM86C1	55199	hgsc.bcm.edu	37	11	71498591	71498591	+	Silent	SNP	C	C	G	rs12270466	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:71498591C>G	ENST00000359244.4	+	1	32	c.9C>G	c.(7-9)ccC>ccG	p.P3P	FAM86C1_ENST00000346333.6_Silent_p.P3P|FAM86C1_ENST00000426628.2_Silent_p.P3P	NM_018172.2	NP_060642.2	Q9NVL1	FA86C_HUMAN	family with sequence similarity 86, member C1	3										lung(1)	1						TCATGGCGCCCGAGGAGAACG	0.746													.|||	2240	0.447284	0.3328	0.3458	5008	,	,		9232	0.3403		0.5646	False		,,,				2504	0.6636																0			11											4.0	4.0	4.0					11																	71498591		1963	3674	5637	71176239	SO:0001819	synonymous_variant	55199			AK130709	CCDS8202.1, CCDS41686.1, CCDS44664.1	11q13.4	2011-07-07	2011-07-07	2011-07-07	ENSG00000158483	ENSG00000158483			25561	protein-coding gene	gene with protein product			"""family with sequence similarity 86, member C"""	FAM86C		12477932	Standard	NM_152563		Approved	FLJ10661, FLJ27199	uc001oqv.4	Q9NVL1	OTTHUMG00000160552	ENST00000359244.4:c.9C>G	11.37:g.71498591C>G			71176239	Q8N5D3	Silent	SNP	ENST00000359244.4	37	CCDS41686.1																																																																																				0.746	FAM86C1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000361120.1	NM_152563	
FAM86C1	55199	hgsc.bcm.edu	37	11	71498601	71498601	+	Missense_Mutation	SNP	G	G	T	rs12283300	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:71498601G>T	ENST00000359244.4	+	1	42	c.19G>T	c.(19-21)Gcg>Tcg	p.A7S	FAM86C1_ENST00000346333.6_Missense_Mutation_p.A7S|FAM86C1_ENST00000426628.2_Missense_Mutation_p.A7S	NM_018172.2	NP_060642.2	Q9NVL1	FA86C_HUMAN	family with sequence similarity 86, member C1	7			A -> S (in dbSNP:rs12283300). {ECO:0000269|PubMed:14702039}.							lung(1)	1						CGAGGAGAACGCGGGGAGCGA	0.736													.|||	2243	0.447883	0.3328	0.3458	5008	,	,		9168	0.3423		0.5646	False		,,,				2504	0.6646																0			11											5.0	5.0	5.0					11																	71498601		2022	3792	5814	71176249	SO:0001583	missense	55199			AK130709	CCDS8202.1, CCDS41686.1, CCDS44664.1	11q13.4	2011-07-07	2011-07-07	2011-07-07	ENSG00000158483	ENSG00000158483			25561	protein-coding gene	gene with protein product			"""family with sequence similarity 86, member C"""	FAM86C		12477932	Standard	NM_152563		Approved	FLJ10661, FLJ27199	uc001oqv.4	Q9NVL1	OTTHUMG00000160552	ENST00000359244.4:c.19G>T	11.37:g.71498601G>T	ENSP00000352182:p.Ala7Ser		71176249	Q8N5D3	Missense_Mutation	SNP	ENST00000359244.4	37	CCDS41686.1	838	0.3836996336996337	160	0.3252032520325203	130	0.35911602209944754	166	0.2902097902097902	382	0.503957783641161	.	11.43	1.635370	0.29068	.	.	ENSG00000158483	ENST00000346333;ENST00000359244;ENST00000426628;ENST00000528685	T;T;T;T	0.19394	2.15;2.15;2.15;2.15	1.78	0.792	0.18625	.	.	.	.	.	T	0.00012	0.0000	L	0.43152	1.355	0.80722	P	0.0	D;D;P	0.61080	0.961;0.989;0.561	P;D;B	0.74674	0.537;0.984;0.053	T	0.47611	-0.9104	8	0.72032	D	0.01	.	3.6282	0.08121	0.2602:0.0:0.7398:0.0	rs12283300;rs12283300	7;7;7	G3V0F7;Q9NVL1-2;Q9NVL1	.;.;FA86C_HUMAN	S	7	ENSP00000325662:A7S;ENSP00000352182:A7S;ENSP00000391329:A7S;ENSP00000436598:A7S	ENSP00000325662:A7S	A	+	1	0	FAM86C1	71176249	0.000000	0.05858	0.001000	0.08648	0.022000	0.10575	0.154000	0.16343	0.968000	0.38212	0.184000	0.17185	GCG		0.736	FAM86C1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000361120.1	NM_152563	
RPS3	6188	hgsc.bcm.edu	37	11	75115084	75115084	+	Missense_Mutation	SNP	G	G	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:75115084G>A	ENST00000531188.1	+	5	433	c.371G>A	c.(370-372)cGg>cAg	p.R124Q	SNORD15B_ENST00000384714.1_RNA|RPS3_ENST00000534440.1_Intron|RPS3_ENST00000527446.1_Missense_Mutation_p.R124Q|RPS3_ENST00000529285.1_Intron|RPS3_ENST00000526608.1_Missense_Mutation_p.R112Q|RPS3_ENST00000278572.6_Missense_Mutation_p.R140Q|RPS3_ENST00000524851.1_Missense_Mutation_p.R124Q	NM_001005.4|NM_001260506.1|NM_001260507.1	NP_000996.2|NP_001247435.1|NP_001247436.1	P23396	RS3_HUMAN	ribosomal protein S3	124					cellular protein metabolic process (GO:0044267)|cellular response to DNA damage stimulus (GO:0006974)|cytoplasmic translation (GO:0002181)|DNA catabolic process, endonucleolytic (GO:0000737)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|negative regulation of DNA repair (GO:0045738)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of DNA N-glycosylase activity (GO:1902546)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|ruffle membrane (GO:0032587)	damaged DNA binding (GO:0003684)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|enzyme binding (GO:0019899)|iron-sulfur cluster binding (GO:0051536)|mRNA binding (GO:0003729)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase A binding (GO:0051018)|protein kinase binding (GO:0019901)|structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(1)|large_intestine(2)|lung(2)	6						GGTGTGCTGCGGTTCATCATG	0.488																																																	0			11											106.0	101.0	103.0					11																	75115084		2200	4293	6493	74792732	SO:0001583	missense	6188				CCDS8236.1, CCDS58161.1	11q13.3-q13.5	2011-04-05				ENSG00000149273		"""S ribosomal proteins"""	10420	protein-coding gene	gene with protein product	"""IMR-90 ribosomal protein S3"", ""40S ribosomal protein S3"""	600454				1712897, 7789996	Standard	NM_001005		Approved	FLJ26283, FLJ27450, MGC87870, S3	uc031qcs.1	P23396		ENST00000531188.1:c.371G>A	11.37:g.75115084G>A	ENSP00000434643:p.Arg124Gln		74792732	B2R7N5|J3KN86|Q498B5|Q8NI95	Missense_Mutation	SNP	ENST00000531188.1	37	CCDS8236.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	18.35|18.35	3.605329|3.605329	0.66445|0.66445	.|.	.|.	ENSG00000149273|ENSG00000149273	ENST00000525933|ENST00000531188;ENST00000530689;ENST00000278572;ENST00000527446;ENST00000526608;ENST00000524851	.|.	.|.	.|.	5.01|5.01	4.1|4.1	0.47936|0.47936	.|Ribosomal protein S3, C-terminal (3);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.63105|0.63105	0.2483|0.2483	M|M	0.78637|0.78637	2.42|2.42	0.80722|0.80722	D|D	1|1	.|B	.|0.21753	.|0.06	.|B	.|0.23419	.|0.046	T|T	0.65541|0.65541	-0.6143|-0.6143	5|9	.|0.87932	.|D	.|0	-4.3954|-4.3954	11.3838|11.3838	0.49773|0.49773	0.0881:0.0:0.9119:0.0|0.0881:0.0:0.9119:0.0	.|.	.|124	.|P23396	.|RS3_HUMAN	S|Q	52|124;124;140;124;112;124	.|.	.|ENSP00000278572:R140Q	G|R	+|+	1|2	0|0	RPS3|RPS3	74792732|74792732	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.801000|0.801000	0.45260|0.45260	9.626000|9.626000	0.98410|0.98410	1.353000|1.353000	0.45828|0.45828	-0.162000|-0.162000	0.13425|0.13425	GGT|CGG		0.488	RPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384158.2	NM_001005	
KLHL35	283212	hgsc.bcm.edu	37	11	75137623	75137623	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:75137623T>C	ENST00000539798.1	-	3	1126	c.1127A>G	c.(1126-1128)aAg>aGg	p.K376R	KLHL35_ENST00000376292.4_Missense_Mutation_p.K156R	NM_001039548.2	NP_001034637.2	Q6PF15	KLH35_HUMAN	kelch-like family member 35	376										lung(2)|stomach(1)	3						AGAGGCTACCTTGATCCAGGT	0.577																																					Colon(77;683 1691 18820 23811)												0			11											43.0	45.0	44.0					11																	75137623		2085	4227	6312	74815271	SO:0001583	missense	283212				CCDS44685.1, CCDS44685.2	11q13.4	2013-02-22	2013-02-22		ENSG00000149243	ENSG00000149243		"""Kelch-like"", ""BTB/POZ domain containing"""	26597	protein-coding gene	gene with protein product			"""kelch-like 35 (Drosophila)"""				Standard	NM_001039548		Approved	FLJ33790	uc001owm.2	Q6PF15	OTTHUMG00000133573	ENST00000539798.1:c.1127A>G	11.37:g.75137623T>C	ENSP00000438526:p.Lys376Arg		74815271	A2RU06|F5H412|Q86XM7|Q8NBB1	Missense_Mutation	SNP	ENST00000539798.1	37	CCDS44685.2	.	.	.	.	.	.	.	.	.	.	T	7.387	0.630027	0.14257	.	.	ENSG00000149243	ENST00000376292;ENST00000539798	T;T	0.78595	-1.19;-1.19	5.23	4.09	0.47781	Kelch-type beta propeller (1);	0.141052	0.46442	D	0.000291	T	0.54095	0.1837	N	0.13272	0.32	0.35672	D	0.813373	B	0.16396	0.017	B	0.19666	0.026	T	0.52638	-0.8549	10	0.08599	T	0.76	.	5.1321	0.14915	0.0:0.1911:0.0:0.8088	.	156	Q6PF15	KLH35_HUMAN	R	156;376	ENSP00000365469:K156R;ENSP00000438526:K376R	ENSP00000365469:K156R	K	-	2	0	KLHL35	74815271	0.998000	0.40836	1.000000	0.80357	0.999000	0.98932	1.860000	0.39428	2.191000	0.70037	0.533000	0.62120	AAG		0.577	KLHL35-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_173583	
CCDC81	60494	hgsc.bcm.edu	37	11	86126334	86126334	+	Missense_Mutation	SNP	T	T	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:86126334T>A	ENST00000445632.2	+	13	1942	c.1670T>A	c.(1669-1671)aTg>aAg	p.M557K	CCDC81_ENST00000278487.3_Missense_Mutation_p.M292K|CCDC81_ENST00000354755.1_Missense_Mutation_p.M467K|CCDC81_ENST00000528728.1_Missense_Mutation_p.M292K	NM_001156474.1	NP_001149946.1	Q6ZN84	CCD81_HUMAN	coiled-coil domain containing 81	557										kidney(3)|large_intestine(8)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	20		Acute lymphoblastic leukemia(157;5.51e-06)|all_hematologic(158;0.00535)				GATTTGCAAATGCTTCAGAGG	0.483																																																	0			11											66.0	67.0	67.0					11																	86126334		2202	4299	6501	85803982	SO:0001583	missense	60494			AK131331	CCDS8276.1, CCDS53691.1	11q14.2	2006-03-09			ENSG00000149201	ENSG00000149201			26281	protein-coding gene	gene with protein product							Standard	NM_001156474		Approved	FLJ16339, FLJ23514	uc001pbx.2	Q6ZN84	OTTHUMG00000167213	ENST00000445632.2:c.1670T>A	11.37:g.86126334T>A	ENSP00000415528:p.Met557Lys		85803982	A0AVL7|Q53FW3|Q9H5E5	Missense_Mutation	SNP	ENST00000445632.2	37	CCDS53691.1	.	.	.	.	.	.	.	.	.	.	T	17.42	3.385379	0.61956	.	.	ENSG00000149201	ENST00000354755;ENST00000278487;ENST00000445632;ENST00000528728	T;T;T;T	0.30714	1.52;1.52;1.52;1.52	5.56	4.43	0.53597	.	0.326334	0.36374	N	0.002638	T	0.51312	0.1667	M	0.74258	2.255	0.40019	D	0.975386	P;P;D	0.71674	0.908;0.887;0.998	B;P;D	0.68943	0.436;0.638;0.961	T	0.52434	-0.8576	9	.	.	.	-10.3624	10.2948	0.43618	0.0:0.0792:0.0:0.9208	.	292;557;467	Q6ZN84-3;Q6ZN84;Q6ZN84-2	.;CCD81_HUMAN;.	K	467;292;557;292	ENSP00000346800:M467K;ENSP00000278487:M292K;ENSP00000415528:M557K;ENSP00000437165:M292K	.	M	+	2	0	CCDC81	85803982	1.000000	0.71417	0.934000	0.37439	0.763000	0.43281	3.128000	0.50492	0.940000	0.37473	0.528000	0.53228	ATG		0.483	CCDC81-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393756.1	NM_021827	
ATM	472	hgsc.bcm.edu	37	11	108139301	108139301	+	Missense_Mutation	SNP	A	A	G	rs35813135		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:108139301A>G	ENST00000452508.2	+	19	2992	c.2803A>G	c.(2803-2805)Acg>Gcg	p.T935A	ATM_ENST00000278616.4_Missense_Mutation_p.T935A|AP001925.1_ENST00000596081.1_5'Flank			Q13315	ATM_HUMAN	ATM serine/threonine kinase	935			T -> A. {ECO:0000269|PubMed:17344846}.|T -> M (in dbSNP:rs3218708).		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)			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)	TGATTCTAGCACGCTAGAACC	0.393			"""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)			A|||	1	0.000199681	0.0	0.0	5008	,	,		18115	0.001		0.0	False		,,,				2504	0.0						yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"""L, O"""	0			11											159.0	146.0	150.0					11																	108139301		2201	4298	6499	107644511	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.2803A>G	11.37:g.108139301A>G	ENSP00000388058:p.Thr935Ala		107644511	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	A	0.012	-1.655957	0.00779	.	.	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	T;T;T	0.70516	-0.49;-0.49;-0.49	5.5	3.14	0.36123	Armadillo-type fold (1);	0.774747	0.12455	N	0.467361	T	0.43010	0.1228	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.28933	-1.0028	10	0.08179	T	0.78	.	4.8104	0.13340	0.6646:0.0:0.2072:0.1282	rs35813135	935	Q13315	ATM_HUMAN	A	935	ENSP00000435747:T935A;ENSP00000278616:T935A;ENSP00000388058:T935A	ENSP00000278616:T935A	T	+	1	0	ATM	107644511	0.654000	0.27367	0.559000	0.28332	0.132000	0.20833	1.343000	0.33930	0.375000	0.24679	-0.333000	0.08304	ACG		0.393	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	
ATM	472	hgsc.bcm.edu	37	11	108180983	108180983	+	Silent	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:108180983A>G	ENST00000452508.2	+	40	6048	c.5859A>G	c.(5857-5859)acA>acG	p.T1953T	C11orf65_ENST00000525729.1_Intron|ATM_ENST00000278616.4_Silent_p.T1953T			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1953			T -> R (in B-cell chronic lymphocytic leukemia). {ECO:0000269|PubMed:10397742}.		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)			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)	CTCACTTTACAGCTTTACTCT	0.328			"""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"""	0			11											84.0	86.0	85.0					11																	108180983		2201	4297	6498	107686193	SO:0001819	synonymous_variant	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.5859A>G	11.37:g.108180983A>G			107686193	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Silent	SNP	ENST00000452508.2	37	CCDS31669.1																																																																																				0.328	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	
PDZD3	79849	hgsc.bcm.edu	37	11	119059156	119059156	+	Missense_Mutation	SNP	G	G	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:119059156G>A	ENST00000531114.1	+	6	1702	c.1153G>A	c.(1153-1155)Gtg>Atg	p.V385M	PDZD3_ENST00000525131.1_Missense_Mutation_p.V306M|PDZD3_ENST00000392817.2_Missense_Mutation_p.V385M|PDZD3_ENST00000322712.4_Missense_Mutation_p.V305M|PDZD3_ENST00000355547.5_Missense_Mutation_p.V319M			Q86UT5	NHRF4_HUMAN	PDZ domain containing 3	385	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cGMP-mediated signaling (GO:0019934)|ion transport (GO:0006811)|negative regulation of cGMP biosynthetic process (GO:0030827)|negative regulation of guanylate cyclase activity (GO:0031283)|receptor guanylyl cyclase signaling pathway (GO:0007168)|response to toxic substance (GO:0009636)|water transport (GO:0006833)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytosol (GO:0005829)|subapical complex (GO:0035003)	guanylate cyclase inhibitor activity (GO:0030251)|ion channel inhibitor activity (GO:0008200)|protein C-terminus binding (GO:0008022)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)	14	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0523)|Breast(348;0.174)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;7.52e-05)		TGGGGAGAGCGTGGAGGGGCT	0.672																																																	0			11											40.0	41.0	40.0					11																	119059156		2199	4294	6493	118564366	SO:0001583	missense	79849			AK091966	CCDS8417.1, CCDS53719.1	11q23.3	2008-02-05	2006-01-24	2006-01-24	ENSG00000172367	ENSG00000172367			19891	protein-coding gene	gene with protein product		607146	"""PDZ domain containing 2"""	PDZK2		11950846	Standard	NM_024791		Approved	FLJ22756, IKEPP	uc001pvz.3	Q86UT5	OTTHUMG00000166224	ENST00000531114.1:c.1153G>A	11.37:g.119059156G>A	ENSP00000431164:p.Val385Met		118564366	Q8N6R4|Q8NAW7|Q8NEX7|Q9H5Z3	Missense_Mutation	SNP	ENST00000531114.1	37		.	.	.	.	.	.	.	.	.	.	G	19.08	3.758644	0.69763	.	.	ENSG00000172367	ENST00000525131;ENST00000531114;ENST00000355547;ENST00000322712;ENST00000454065;ENST00000392817	T;T;T;T;T	0.33216	1.42;1.42;1.42;1.42;1.42	5.66	2.59	0.31030	PDZ/DHR/GLGF (4);	0.501532	0.20802	N	0.085402	T	0.40222	0.1108	M	0.76328	2.33	0.39671	D	0.970752	D;D;P;P	0.56035	0.974;0.974;0.942;0.953	P;P;B;B	0.51135	0.66;0.532;0.25;0.365	T	0.37596	-0.9699	10	0.62326	D	0.03	-12.5467	7.2772	0.26292	0.2225:0.1245:0.653:0.0	.	306;385;319;305	E9PPZ1;Q86UT5;Q86UT5-2;B0YJ61	.;NHRF4_HUMAN;.;.	M	306;385;319;305;319;385	ENSP00000434559:V306M;ENSP00000431164:V385M;ENSP00000347742:V319M;ENSP00000327107:V305M;ENSP00000376564:V385M	ENSP00000327107:V305M	V	+	1	0	PDZD3	118564366	1.000000	0.71417	0.972000	0.41901	0.933000	0.57130	4.672000	0.61597	0.742000	0.32697	-0.208000	0.12717	GTG		0.672	PDZD3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000388471.1	NM_024791	
CBL	867	hgsc.bcm.edu	37	11	119149245	119149245	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:119149245T>C	ENST00000264033.4	+	9	1629	c.1253T>C	c.(1252-1254)tTc>tCc	p.F418S		NM_005188.3	NP_005179.2	P22681	CBL_HUMAN	Cbl proto-oncogene, E3 ubiquitin protein ligase	418	Asp/Glu-rich (acidic).				cell surface receptor signaling pathway (GO:0007166)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|flotillin complex (GO:0016600)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ephrin receptor binding (GO:0046875)|ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.F418S(4)|p.G397_I429del(1)|p.E366_K477del(1)		breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(194)|kidney(3)|large_intestine(9)|lung(30)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	251		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)		GGCTGTCCTTTCTGCCGATGT	0.433			"""T, Mis S, O"""	MLL	"""AML, JMML, MDS"""				Noonan syndrome;CBL gene-associated Juvenile Myelomonocytic Leukemia and Developmental Anomalies																															"""Dom, Rec"""	yes		11	11q23.3	867	Cas-Br-M (murine) ecotropic retroviral transforming		L	6	Substitution - Missense(4)|Deletion - In frame(2)	haematopoietic_and_lymphoid_tissue(6)	11											126.0	123.0	124.0					11																	119149245		2199	4295	6494	118654455	SO:0001583	missense	867	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CBL-associated JMML	X57110	CCDS8418.1	11q23.3	2014-09-17	2012-02-23		ENSG00000110395	ENSG00000110395		"""RING-type (C3HC4) zinc fingers"""	1541	protein-coding gene	gene with protein product	"""oncogene CBL2"""	165360	"""Cas-Br-M (murine) ecotropic retroviral transforming sequence"""	CBL2		2013228	Standard	NM_005188		Approved	RNF55, c-Cbl	uc001pwe.4	P22681	OTTHUMG00000166170	ENST00000264033.4:c.1253T>C	11.37:g.119149245T>C	ENSP00000264033:p.Phe418Ser		118654455	A3KMP8	Missense_Mutation	SNP	ENST00000264033.4	37	CCDS8418.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.040706	0.75732	.	.	ENSG00000110395	ENST00000264033	D	0.95788	-3.81	5.96	5.96	0.96718	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.000000	0.85682	D	0.000000	D	0.97090	0.9049	L	0.58810	1.83	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.97729	1.0201	10	0.87932	D	0	-26.8748	16.4484	0.83959	0.0:0.0:0.0:1.0	.	418	P22681	CBL_HUMAN	S	418	ENSP00000264033:F418S	ENSP00000264033:F418S	F	+	2	0	CBL	118654455	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	2.285000	0.76669	0.533000	0.62120	TTC		0.433	CBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388219.4	NM_005188	
SCN3B	55800	hgsc.bcm.edu	37	11	123516432	123516432	+	Nonsense_Mutation	SNP	C	C	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:123516432C>A	ENST00000392770.2	-	2	884	c.82G>T	c.(82-84)Gaa>Taa	p.E28*	SCN3B_ENST00000299333.3_Nonsense_Mutation_p.E28*|SCN3B_ENST00000530277.1_Nonsense_Mutation_p.E28*	NM_018400.3	NP_060870.1	Q9NY72	SCN3B_HUMAN	sodium channel, voltage-gated, type III, beta subunit	28					atrial cardiac muscle cell action potential (GO:0086014)|axon guidance (GO:0007411)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|positive regulation of heart rate (GO:0010460)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|ventricular cardiac muscle cell action potential (GO:0086005)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	ion channel binding (GO:0044325)|sodium channel regulator activity (GO:0017080)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(16)|ovary(2)|skin(2)	26		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0227)	Valproic Acid(DB00313)|Zonisamide(DB00909)	GAGGGCACTTCCACACACACA	0.607																																																	0			11											90.0	86.0	88.0					11																	123516432		2202	4299	6501	123021642	SO:0001587	stop_gained	55800			AJ243396	CCDS8442.1	11q24.1	2014-09-17	2012-02-28		ENSG00000166257	ENSG00000166257		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"", ""Immunoglobulin superfamily / V-set domain containing"""	20665	protein-coding gene	gene with protein product		608214	"""sodium channel, voltage-gated, type III, beta"""			10688874	Standard	XR_428980		Approved	HSA243396	uc001pzb.1	Q9NY72	OTTHUMG00000166006	ENST00000392770.2:c.82G>T	11.37:g.123516432C>A	ENSP00000376523:p.Glu28*		123021642	A5H1I5|Q17RL3|Q9ULR2	Nonsense_Mutation	SNP	ENST00000392770.2	37	CCDS8442.1	.	.	.	.	.	.	.	.	.	.	C	41	8.829637	0.98970	.	.	ENSG00000166257	ENST00000392770;ENST00000299333;ENST00000530277;ENST00000527836;ENST00000528267	.	.	.	5.96	5.96	0.96718	.	0.086699	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.24483	T	0.36	-4.3832	20.4182	0.99029	0.0:1.0:0.0:0.0	.	.	.	.	X	28	.	ENSP00000299333:E28X	E	-	1	0	SCN3B	123021642	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.481000	0.81124	2.820000	0.97059	0.609000	0.83330	GAA		0.607	SCN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387412.1	NM_018400	
ETS1	2113	hgsc.bcm.edu	37	11	128354817	128354817	+	Nonsense_Mutation	SNP	G	G	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:128354817G>A	ENST00000319397.6	-	5	940	c.631C>T	c.(631-633)Cga>Tga	p.R211*	ETS1_ENST00000392668.4_Nonsense_Mutation_p.R255*|ETS1_ENST00000526145.2_Nonsense_Mutation_p.R211*|ETS1_ENST00000345075.4_Nonsense_Mutation_p.R211*|ETS1_ENST00000531611.1_Nonsense_Mutation_p.R211*|ETS1_ENST00000535549.1_Intron	NM_005238.3	NP_005229.1	P14921	ETS1_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog 1	211	Activation domain; required for transcription activation.				angiogenesis involved in wound healing (GO:0060055)|cell motility (GO:0048870)|cellular response to hydrogen peroxide (GO:0070301)|estrous cycle phase (GO:0060206)|female pregnancy (GO:0007565)|hypothalamus development (GO:0021854)|immune response (GO:0006955)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|pituitary gland development (GO:0021983)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of angiogenesis (GO:0045765)|regulation of apoptotic process (GO:0042981)|regulation of extracellular matrix disassembly (GO:0010715)|response to antibiotic (GO:0046677)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to laminar fluid shear stress (GO:0034616)|response to mechanical stimulus (GO:0009612)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.R211*(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|pleura(1)|prostate(1)|upper_aerodigestive_tract(3)	35	all_hematologic(175;0.0537)	Lung NSC(97;0.000542)|all_lung(97;0.000665)|Breast(109;0.00765)|all_neural(223;0.0351)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.47e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0174)|LUSC - Lung squamous cell carcinoma(976;0.0815)|Lung(307;0.0833)		AGAGGGTCTCGGAGAATGACC	0.532																																																	1	Substitution - Nonsense(1)	pleura(1)	11											140.0	125.0	130.0					11																	128354817		2201	4297	6498	127860027	SO:0001587	stop_gained	2113				CCDS8475.1, CCDS44767.1, CCDS53724.1	11q23.3	2013-07-09	2013-07-09		ENSG00000134954	ENSG00000134954			3488	protein-coding gene	gene with protein product	"""Avian erythroblastosis virus E26 (v-ets) oncogene homolog-1"", ""ets protein"""	164720		EWSR2		1522903	Standard	NM_005238		Approved	FLJ10768, ETS-1	uc001qej.2	P14921	OTTHUMG00000165799	ENST00000319397.6:c.631C>T	11.37:g.128354817G>A	ENSP00000324578:p.Arg211*		127860027	A9UL17|F5GYX9|Q14278|Q16080|Q6N087|Q96AC5	Nonsense_Mutation	SNP	ENST00000319397.6	37	CCDS8475.1	.	.	.	.	.	.	.	.	.	.	G	39	7.648207	0.98409	.	.	ENSG00000134954	ENST00000345075;ENST00000392668;ENST00000531611;ENST00000319397;ENST00000526145	.	.	.	5.67	4.68	0.58851	.	0.250164	0.40818	N	0.001002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.15499	T	0.54	.	17.3427	0.87301	0.0:0.0:0.8664:0.1336	.	.	.	.	X	211;255;211;211;211	.	ENSP00000324578:R211X	R	-	1	2	ETS1	127860027	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.876000	0.87215	2.673000	0.90976	0.561000	0.74099	CGA		0.532	ETS1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386269.2	NM_005238	
IER3	8870	hgsc.bcm.edu	37	6	30709588	30709588	+	IGR	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr6:30709588A>G	ENST00000259874.5	-	0	1244				FLOT1_ENST00000470643.1_5'UTR|FLOT1_ENST00000376389.3_Missense_Mutation_p.C34R|XXbac-BPG252P9.10_ENST00000607333.1_RNA|FLOT1_ENST00000456573.2_Missense_Mutation_p.C34R	NM_003897.3	NP_003888.2	P46695	IEX1_HUMAN	immediate early response 3						anatomical structure morphogenesis (GO:0009653)|apoptotic process (GO:0006915)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glycolytic process (GO:0045820)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901029)|negative regulation of systemic arterial blood pressure (GO:0003085)|positive regulation of protein catabolic process (GO:0045732)|regulation of DNA repair (GO:0006282)|regulation of nucleocytoplasmic transport (GO:0046822)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of response to DNA damage stimulus (GO:2001020)|response to protozoan (GO:0001562)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)				NS(1)	1						TGTTGGATGCAGGGCAGGACA	0.562																																																	0			6											66.0	66.0	66.0					6																	30709588		1509	2708	4217	30817567	SO:0001628	intergenic_variant	10211			AF083421	CCDS4689.1	6p21.3	2010-02-17			ENSG00000137331	ENSG00000137331			5392	protein-coding gene	gene with protein product		602996				8603392, 9703517	Standard	NM_003897		Approved	IEX-1, DIF-2, PRG1, IEX-1L	uc003nrn.3	P46695	OTTHUMG00000031265		6.37:g.30709588A>G			30817567	Q5SU30|Q92691|Q93044	Missense_Mutation	SNP	ENST00000259874.5	37	CCDS4689.1	.	.	.	.	.	.	.	.	.	.	A	15.29	2.789314	0.49997	.	.	ENSG00000137312	ENST00000376389;ENST00000456573;ENST00000438162;ENST00000445853;ENST00000416018;ENST00000454845	D;T;D;D;D;D	0.94417	-3.42;1.05;-3.42;-3.42;-3.42;-3.42	4.27	4.27	0.50696	.	0.000000	0.85682	D	0.000000	D	0.91935	0.7446	L	0.49350	1.555	0.80722	D	1	B;D	0.58620	0.26;0.983	B;P	0.50860	0.163;0.652	D	0.92272	0.5826	10	0.56958	D	0.05	-13.5039	11.6627	0.51356	1.0:0.0:0.0:0.0	.	34;34	B4DVY7;O75955	.;FLOT1_HUMAN	R	34	ENSP00000365569:C34R;ENSP00000394375:C34R;ENSP00000400615:C34R;ENSP00000398834:C34R;ENSP00000412058:C34R;ENSP00000391341:C34R	ENSP00000365569:C34R	C	-	1	0	FLOT1	30817567	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	6.082000	0.71318	1.909000	0.55274	0.379000	0.24179	TGC		0.562	IER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076578.2		
DPCR1	135656	hgsc.bcm.edu	37	6	30918665	30918665	+	Silent	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr6:30918665T>C	ENST00000462446.1	+	2	2452	c.2424T>C	c.(2422-2424)acT>acC	p.T808T	HCG21_ENST00000419481.1_RNA|DPCR1_ENST00000304311.2_5'UTR			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	0						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						CAGAAAGGACTCCACTGGCCA	0.488																																																	0			6											62.0	62.0	62.0					6																	30918665		692	1591	2283	31026644	SO:0001819	synonymous_variant	135656			AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.2424T>C	6.37:g.30918665T>C			31026644	C9IZC0|Q658M7|Q8WYN2	Silent	SNP	ENST00000462446.1	37	CCDS4692.2																																																																																				0.488	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870	
HLA-B	3106	hgsc.bcm.edu	37	6	31323116	31323116	+	Silent	SNP	C	C	T	rs1131446	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr6:31323116C>T	ENST00000412585.2	-	4	901	c.873G>A	c.(871-873)ccG>ccA	p.P291P		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	291	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						TGAGGGGCTTCGGCAGCCCCT	0.577									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				C|||	485	0.096845	0.0749	0.0922	5008	,	,		21693	0.0754		0.1074	False		,,,				2504	0.1411																0			6											60.0	57.0	58.0					6																	31323116		2203	4300	6503	31431095	SO:0001819	synonymous_variant	3106	Familial Cancer Database	;Lichen Sclerosis, Familial	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.873G>A	6.37:g.31323116C>T			31431095	Q29764	Silent	SNP	ENST00000412585.2	37	CCDS34394.1																																																																																				0.577	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
SLC39A7	7922	hgsc.bcm.edu	37	6	33171369	33171369	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr6:33171369T>C	ENST00000374677.3	+	7	1562	c.1189T>C	c.(1189-1191)Tgt>Cgt	p.C397R	SLC39A7_ENST00000463972.1_3'UTR|RXRB_ENST00000374685.4_5'Flank|HSD17B8_ENST00000374662.3_5'Flank|SLC39A7_ENST00000374675.3_Missense_Mutation_p.C397R|RXRB_ENST00000374680.3_5'Flank|RXRB_ENST00000544186.1_5'Flank|RXRB_ENST00000413614.2_5'Flank	NM_006979.2	NP_008910.2	Q92504	S39A7_HUMAN	solute carrier family 39 (zinc transporter), member 7	397				CALLTEGGAVGSEIAGGAGPGWVLPFTAGGFIYVATVSVLP ELLREASPLQSLLEVLGLLGGVIMMVLIAHLE -> VPFSL KEEQWTVKLQVVQVLAGSCHLLQVALST (in Ref. 1; BAA11528 and 2; AAD12305). {ECO:0000305}.	transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metal ion transmembrane transporter activity (GO:0046873)			NS(1)|breast(3)|endometrium(2)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	18						AGGCACAGCCTGTGCCCTTCT	0.532																																																	0			6											67.0	71.0	70.0					6																	33171369		2028	4167	6195	33279347	SO:0001583	missense	7922			AF117221	CCDS43453.1	6p21.3	2014-01-28		2003-10-27	ENSG00000112473	ENSG00000112473		"""Solute carriers"""	4927	protein-coding gene	gene with protein product		601416	"""HLA class II region expressed gene KE4"""	HKE4		8812499, 1855816, 19246244, 15705588	Standard	NM_006979		Approved	H2-KE4, D6S2244E, KE4, RING5, ZIP7	uc003odf.3	Q92504	OTTHUMG00000031238	ENST00000374677.3:c.1189T>C	6.37:g.33171369T>C	ENSP00000363809:p.Cys397Arg		33279347	B0UXF6|Q5STP8|Q9UIQ0	Missense_Mutation	SNP	ENST00000374677.3	37	CCDS43453.1	.	.	.	.	.	.	.	.	.	.	T	18.20	3.570233	0.65765	.	.	ENSG00000112473	ENST00000374675;ENST00000446283;ENST00000445037;ENST00000374677	T;T	0.47528	0.84;0.84	4.79	4.79	0.61399	.	0.105696	0.64402	D	0.000003	T	0.34279	0.0892	M	0.63843	1.955	0.80722	D	1	B;P	0.49090	0.072;0.919	B;B	0.41723	0.028;0.365	T	0.44329	-0.9335	10	0.87932	D	0	-22.1958	12.3302	0.55035	0.0:0.0:0.0:1.0	.	378;397	B4DVK8;Q92504	.;S39A7_HUMAN	R	397;378;302;397	ENSP00000363807:C397R;ENSP00000363809:C397R	ENSP00000363807:C397R	C	+	1	0	SLC39A7	33279347	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.050000	0.71063	2.018000	0.59344	0.448000	0.29417	TGT		0.532	SLC39A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076499.2	NM_006979	
ANKS1A	23294	hgsc.bcm.edu	37	6	35048831	35048831	+	Missense_Mutation	SNP	C	C	T	rs541932194		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr6:35048831C>T	ENST00000360359.3	+	17	2743	c.2605C>T	c.(2605-2607)Cgg>Tgg	p.R869W	ANKS1A_ENST00000535627.1_Intron	NM_015245.2	NP_056060.2	Q92625	ANS1A_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1A	869					ephrin receptor signaling pathway (GO:0048013)|neuron remodeling (GO:0016322)|substrate-dependent cell migration (GO:0006929)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nucleus (GO:0005634)				cervix(2)|endometrium(3)|large_intestine(4)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						CTGCACTGGGCGGTCGGCAGA	0.607													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19518	0.0		0.0	False		,,,				2504	0.0																0			6											118.0	101.0	107.0					6																	35048831		2203	4300	6503	35156809	SO:0001583	missense	23294			D86982	CCDS4798.1	6p21.31	2013-01-10	2006-02-17	2006-02-17	ENSG00000064999	ENSG00000064999		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	20961	protein-coding gene	gene with protein product		608994	"""ankyrin repeat and SAM domain containing 1"", ""ankyrin repeat and sterile alpha motif domain containing 1"""	ANKS1		9039502	Standard	NM_015245		Approved	KIAA0229	uc003ojx.4	Q92625	OTTHUMG00000014559	ENST00000360359.3:c.2605C>T	6.37:g.35048831C>T	ENSP00000353518:p.Arg869Trp		35156809	A2RUC1|B4DQW8|Q5JYI9|Q5SYR2|Q86WQ7	Missense_Mutation	SNP	ENST00000360359.3	37	CCDS4798.1	.	.	.	.	.	.	.	.	.	.	C	14.66	2.600636	0.46423	.	.	ENSG00000064999	ENST00000360359;ENST00000373990	T	0.39056	1.1	5.28	0.668	0.17912	.	0.163313	0.28119	N	0.016535	T	0.40322	0.1112	M	0.66939	2.045	0.80722	D	1	D;D;D	0.76494	0.999;0.998;0.999	P;P;P	0.58266	0.836;0.676;0.781	T	0.39121	-0.9629	10	0.56958	D	0.05	-11.4128	9.5806	0.39486	0.5006:0.4004:0.099:0.0	.	195;195;869	Q49AR9;E7EM84;Q92625	.;.;ANS1A_HUMAN	W	869;195	ENSP00000353518:R869W	ENSP00000353518:R869W	R	+	1	2	ANKS1A	35156809	0.558000	0.26554	0.003000	0.11579	0.127000	0.20565	0.958000	0.29227	0.175000	0.19841	-0.181000	0.13052	CGG		0.607	ANKS1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040262.1	XM_166478	
FOXP4	116113	hgsc.bcm.edu	37	6	41556431	41556431	+	Missense_Mutation	SNP	C	C	T			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr6:41556431C>T	ENST00000307972.4	+	8	1039	c.1027C>T	c.(1027-1029)Cgg>Tgg	p.R343W	FOXP4_ENST00000373063.3_Missense_Mutation_p.R342W|FOXP4_ENST00000373060.1_Missense_Mutation_p.R343W|FOXP4_ENST00000409208.1_Missense_Mutation_p.R343W|FOXP4_ENST00000373057.3_Missense_Mutation_p.R341W			Q8IVH2	FOXP4_HUMAN	forkhead box P4	343					embryonic foregut morphogenesis (GO:0048617)|heart development (GO:0007507)|lung secretory cell differentiation (GO:0061140)|negative regulation of lung goblet cell differentiation (GO:1901250)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	16	Ovarian(28;0.0327)|Colorectal(47;0.196)					AGCCCAGTGCCGGGTACAGAT	0.627																																																	0			6											139.0	123.0	128.0					6																	41556431		2203	4300	6503	41664409	SO:0001583	missense	116113			AB080747	CCDS4856.1, CCDS34447.1, CCDS34448.1	6p21.1	2008-02-05			ENSG00000137166	ENSG00000137166		"""Forkhead boxes"""	20842	protein-coding gene	gene with protein product		608924					Standard	XM_006714991		Approved	FLJ40908	uc003oql.3	Q8IVH2	OTTHUMG00000014679	ENST00000307972.4:c.1027C>T	6.37:g.41556431C>T	ENSP00000309823:p.Arg343Trp		41664409	Q5W098|Q7Z7F8|Q8IW55|Q96E19	Missense_Mutation	SNP	ENST00000307972.4	37	CCDS34447.1	.	.	.	.	.	.	.	.	.	.	C	13.66	2.303430	0.40795	.	.	ENSG00000137166	ENST00000373060;ENST00000373063;ENST00000409208;ENST00000373057;ENST00000307972	T;T;T;T;T	0.21191	2.02;2.02;2.02;2.02;2.02	4.92	3.04	0.35103	.	0.000000	0.64402	D	0.000001	T	0.37517	0.1006	M	0.84948	2.725	0.80722	D	1	D;D;P	0.89917	1.0;0.999;0.878	D;D;B	0.72075	0.965;0.976;0.261	T	0.43925	-0.9361	10	0.66056	D	0.02	.	13.0015	0.58679	0.2947:0.7052:0.0:0.0	.	342;341;343	Q8IW55;Q7Z7F8;Q8IVH2	.;.;FOXP4_HUMAN	W	343;342;343;341;343	ENSP00000362151:R343W;ENSP00000362154:R342W;ENSP00000386958:R343W;ENSP00000362148:R341W;ENSP00000309823:R343W	ENSP00000309823:R343W	R	+	1	2	FOXP4	41664409	0.997000	0.39634	0.999000	0.59377	0.997000	0.91878	1.282000	0.33226	0.432000	0.26286	0.561000	0.74099	CGG		0.627	FOXP4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000106767.1	NM_138457	
EYS	346007	hgsc.bcm.edu	37	6	64436546	64436546	+	Missense_Mutation	SNP	C	C	T			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr6:64436546C>T	ENST00000370621.3	-	43	8688	c.8162G>A	c.(8161-8163)aGa>aAa	p.R2721K	EYS_ENST00000370616.2_Missense_Mutation_p.R2721K|EYS_ENST00000503581.1_Missense_Mutation_p.R2700K			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	2721	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						CTCATTGCTTCTGAAAGATGG	0.383																																																	0			6											64.0	53.0	56.0					6																	64436546		692	1591	2283	64494505	SO:0001583	missense	346007				CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"""chromosome 6 open reading frame 180"", ""EGF-like-domain, multiple 11"", ""retinitis pigmentosa 25 (autosomal recessive)"", ""EGF-like-domain, multiple 10"", ""chromosome 6 open reading frame 178"", ""chromosome 6 open reading frame 179"""	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.8162G>A	6.37:g.64436546C>T	ENSP00000359655:p.Arg2721Lys		64494505	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	37		.	.	.	.	.	.	.	.	.	.	C	12.55	1.972146	0.34754	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	T;T;T	0.78816	-1.21;-0.35;-0.35	3.55	2.62	0.31277	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	.	.	.	.	T	0.37461	0.1004	N	0.08118	0	0.80722	D	1	B;B	0.19331	0.035;0.005	B;B	0.20767	0.031;0.014	T	0.12889	-1.0530	9	0.29301	T	0.29	.	8.3091	0.32060	0.0:0.8784:0.0:0.1216	.	2700;2721	Q5T1H1-1;Q5T1H1	.;EYS_HUMAN	K	2700;2721;2721	ENSP00000424243:R2700K;ENSP00000359655:R2721K;ENSP00000359650:R2721K	ENSP00000359650:R2721K	R	-	2	0	EYS	64494505	1.000000	0.71417	0.995000	0.50966	0.708000	0.40852	4.791000	0.62460	0.416000	0.25844	0.491000	0.48974	AGA		0.383	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
CD109	135228	hgsc.bcm.edu	37	6	74517810	74517810	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr6:74517810A>G	ENST00000287097.5	+	26	3306	c.3194A>G	c.(3193-3195)aAc>aGc	p.N1065S	CD109_ENST00000422508.2_Missense_Mutation_p.N988S|CD109_ENST00000437994.2_Missense_Mutation_p.N1065S			Q6YHK3	CD109_HUMAN	CD109 molecule	1065			N -> K (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TCCAAGCCTAACATTGATGTG	0.313																																																	0			6											66.0	63.0	64.0					6																	74517810		2203	4300	6503	74574531	SO:0001583	missense	135228			AF410459	CCDS4982.1, CCDS55038.1, CCDS55039.1	6q14.1	2008-02-05	2006-03-28		ENSG00000156535	ENSG00000156535		"""CD molecules"""	21685	protein-coding gene	gene with protein product		608859	"""CD109 antigen (Gov platelet alloantigens)"""			11861284, 11861285	Standard	XM_005248659		Approved	FLJ38569, DKFZp762L1111, CPAMD7	uc003php.3	Q6YHK3	OTTHUMG00000015040	ENST00000287097.5:c.3194A>G	6.37:g.74517810A>G	ENSP00000287097:p.Asn1065Ser		74574531	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Missense_Mutation	SNP	ENST00000287097.5	37	CCDS4982.1	.	.	.	.	.	.	.	.	.	.	A	8.192	0.796197	0.16327	.	.	ENSG00000156535	ENST00000437994;ENST00000422508;ENST00000287097	T;T;T	0.31510	1.49;1.49;1.49	5.02	3.86	0.44501	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);A-macroglobulin complement component (1);	0.659654	0.16401	N	0.216016	T	0.04543	0.0124	N	0.03224	-0.385	0.26399	N	0.976458	B;B;B	0.13594	0.004;0.008;0.001	B;B;B	0.15052	0.008;0.012;0.01	T	0.35001	-0.9806	10	0.13108	T	0.6	.	11.448	0.50136	0.7456:0.2544:0.0:0.0	.	988;1065;1065	Q6YHK3-2;Q6YHK3-4;Q6YHK3	.;.;CD109_HUMAN	S	1065;988;1065	ENSP00000388062:N1065S;ENSP00000404475:N988S;ENSP00000287097:N1065S	ENSP00000287097:N1065S	N	+	2	0	CD109	74574531	0.998000	0.40836	1.000000	0.80357	0.806000	0.45545	1.090000	0.30902	2.110000	0.64415	0.528000	0.53228	AAC		0.313	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493	
SENP6	26054	hgsc.bcm.edu	37	6	76373083	76373083	+	Silent	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr6:76373083A>G	ENST00000447266.2	+	9	1321	c.843A>G	c.(841-843)gaA>gaG	p.E281E	SENP6_ENST00000370010.2_Silent_p.E274E|SENP6_ENST00000327284.8_Silent_p.E274E|SENP6_ENST00000370014.3_Silent_p.E281E	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	281					protein desumoylation (GO:0016926)|protein modification by small protein removal (GO:0070646)|protein sumoylation (GO:0016925)|regulation of kinetochore assembly (GO:0090234)|regulation of spindle assembly (GO:0090169)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	SUMO-specific protease activity (GO:0016929)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(105;0.189)				ACAATGTGGAAAAGGTTCCAA	0.348																																																	0			6											119.0	114.0	115.0					6																	76373083		1851	4099	5950	76429803	SO:0001819	synonymous_variant	26054				CCDS43483.1, CCDS47454.1	6q13-q14.3	2008-02-05	2005-08-17		ENSG00000112701	ENSG00000112701			20944	protein-coding gene	gene with protein product		605003	"""SUMO1/sentrin specific protease 6"""				Standard	NM_015571		Approved	SUSP1, KIAA0797	uc003pid.4	Q9GZR1	OTTHUMG00000015060	ENST00000447266.2:c.843A>G	6.37:g.76373083A>G			76429803	A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	Silent	SNP	ENST00000447266.2	37	CCDS47454.1																																																																																				0.348	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041272.2	NM_015571	
REV3L	5980	hgsc.bcm.edu	37	6	111634650	111634650	+	Missense_Mutation	SNP	C	C	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr6:111634650C>A	ENST00000358835.3	-	29	8963	c.8509G>T	c.(8509-8511)Ggt>Tgt	p.G2837C	REV3L_ENST00000462119.1_5'UTR|REV3L_ENST00000435970.1_Missense_Mutation_p.G2759C|REV3L_ENST00000368802.3_Missense_Mutation_p.G2837C|REV3L_ENST00000368805.1_Missense_Mutation_p.G2837C|RP5-1112D6.8_ENST00000607434.1_RNA			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	2837					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)	p.G2759S(1)		NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		TACATGTAACCCACATACCTC	0.378								DNA polymerases (catalytic subunits)																																									1	Substitution - Missense(1)	skin(1)	6											108.0	106.0	107.0					6																	111634650		2203	4300	6503	111741343	SO:0001583	missense	5980			AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"""DNA polymerases"""	9968	protein-coding gene	gene with protein product	"""polymerase, DNA, zeta"""	602776	"""REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta"", ""REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"""			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.8509G>T	6.37:g.111634650C>A	ENSP00000351697:p.Gly2837Cys		111741343	O43214|Q5TC33	Missense_Mutation	SNP	ENST00000358835.3	37	CCDS5091.2	.	.	.	.	.	.	.	.	.	.	C	28.0	4.884216	0.91814	.	.	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970	T;T;T;T	0.22336	1.96;1.96;1.96;1.96	5.29	5.29	0.74685	DNA polymerase, palm domain (1);DNA-directed DNA polymerase, family B, multifunctional domain (1);	0.244012	0.42172	D	0.000753	T	0.52837	0.1759	M	0.92970	3.365	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.64546	-0.6382	10	0.87932	D	0	-8.722	19.1263	0.93386	0.0:1.0:0.0:0.0	.	2837	O60673	DPOLZ_HUMAN	C	2837;2837;2837;2759	ENSP00000357792:G2837C;ENSP00000357795:G2837C;ENSP00000351697:G2837C;ENSP00000402003:G2759C	ENSP00000351697:G2837C	G	-	1	0	REV3L	111741343	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.610000	0.82949	2.736000	0.93811	0.650000	0.86243	GGT		0.378	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912	
SHPRH	257218	hgsc.bcm.edu	37	6	146276034	146276034	+	Missense_Mutation	SNP	C	C	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr6:146276034C>A	ENST00000367505.2	-	2	689	c.425G>T	c.(424-426)aGt>aTt	p.S142I	SHPRH_ENST00000438092.2_Missense_Mutation_p.S142I|SHPRH_ENST00000367503.3_Missense_Mutation_p.S142I|SHPRH_ENST00000275233.7_Missense_Mutation_p.S142I			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	142					DNA repair (GO:0006281)|nucleosome assembly (GO:0006334)|protein polyubiquitination (GO:0000209)	nucleosome (GO:0000786)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(33)|ovary(3)|pancreas(2)|prostate(7)|skin(1)|urinary_tract(1)	79		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		TGACTCTGAACTCATCAATGT	0.343																																																	0			6											77.0	70.0	72.0					6																	146276034		1828	4084	5912	146317727	SO:0001583	missense	257218			AB095943	CCDS43513.1, CCDS47496.1, CCDS43513.2	6q24.2	2012-02-23	2012-02-23		ENSG00000146414	ENSG00000146414		"""RING-type (C3HC4) zinc fingers"""	19336	protein-coding gene	gene with protein product		608048	"""SNF2 histone linker PHD RING helicase"""			12837266	Standard	NM_001042683		Approved	FLJ90837, KIAA2023, bA545I5.2	uc003qlf.3	Q149N8	OTTHUMG00000015750	ENST00000367505.2:c.425G>T	6.37:g.146276034C>A	ENSP00000356475:p.Ser142Ile		146317727	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Missense_Mutation	SNP	ENST00000367505.2	37	CCDS43513.2	.	.	.	.	.	.	.	.	.	.	C	11.68	1.712070	0.30322	.	.	ENSG00000146414	ENST00000367505;ENST00000367503;ENST00000438092;ENST00000275233	T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29	5.66	1.55	0.23275	.	0.349704	0.28901	N	0.013764	T	0.33847	0.0877	L	0.44542	1.39	0.09310	N	1	B;B	0.32071	0.242;0.355	B;B	0.32864	0.074;0.154	T	0.16364	-1.0405	10	0.38643	T	0.18	-4.1426	6.8362	0.23937	0.0:0.4926:0.238:0.2695	.	142;142	Q149N8;Q149N8-4	SHPRH_HUMAN;.	I	142	ENSP00000356475:S142I;ENSP00000356473:S142I;ENSP00000412797:S142I;ENSP00000275233:S142I	ENSP00000275233:S142I	S	-	2	0	SHPRH	146317727	1.000000	0.71417	0.351000	0.25721	0.976000	0.68499	1.015000	0.29963	0.329000	0.23460	0.655000	0.94253	AGT		0.343	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082	
SYNE1	23345	hgsc.bcm.edu	37	6	152461141	152461141	+	Missense_Mutation	SNP	G	G	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr6:152461141G>A	ENST00000367255.5	-	140	26003	c.25402C>T	c.(25402-25404)Cgt>Tgt	p.R8468C	SYNE1_ENST00000423061.1_Missense_Mutation_p.R8420C|SYNE1_ENST00000341594.5_Missense_Mutation_p.R8080C|SYNE1_ENST00000539504.1_Missense_Mutation_p.R623C|SYNE1_ENST00000265368.4_Missense_Mutation_p.R8468C|SYNE1_ENST00000356820.4_Missense_Mutation_p.R2992C|SYNE1_ENST00000347037.5_5'UTR|SYNE1_ENST00000448038.1_Missense_Mutation_p.R8420C|SYNE1_ENST00000354674.4_Missense_Mutation_p.R646C	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	8468			R -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		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)		AGTTCCAGACGCTGGAGCTGT	0.557										HNSCC(10;0.0054)																																							0			6											121.0	99.0	106.0					6																	152461141		2203	4300	6503	152502834	SO:0001583	missense	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.25402C>T	6.37:g.152461141G>A	ENSP00000356224:p.Arg8468Cys		152502834	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	G	7.411	0.634666	0.14322	.	.	ENSG00000131018	ENST00000367255;ENST00000539504;ENST00000367257;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820;ENST00000313630;ENST00000367247;ENST00000367251;ENST00000354674	T;T;T;T;T;T;T;T;T;T	0.51071	0.72;0.72;0.72;0.72;0.72;0.72;0.72;0.72;0.72;0.72	5.92	5.04	0.67666	.	0.227351	0.31156	N	0.008147	T	0.27063	0.0663	M	0.64997	1.995	0.09310	N	0.999999	B;B;B;B;B	0.19073	0.033;0.033;0.027;0.033;0.008	B;B;B;B;B	0.17433	0.018;0.018;0.011;0.018;0.013	T	0.20739	-1.0266	10	0.51188	T	0.08	.	10.5768	0.45231	0.0683:0.0:0.7974:0.1342	.	8468;8468;8420;8420;670	Q8NF91;E7EQI5;Q8NF91-4;E9PEL9;B7Z9Y6	SYNE1_HUMAN;.;.;.;.	C	8468;623;1114;8420;8468;8420;8080;2992;653;648;1413;646	ENSP00000356224:R8468C;ENSP00000441052:R623C;ENSP00000356226:R1114C;ENSP00000396024:R8420C;ENSP00000265368:R8468C;ENSP00000390975:R8420C;ENSP00000341887:R8080C;ENSP00000349276:R2992C;ENSP00000356220:R1413C;ENSP00000346701:R646C	ENSP00000265368:R8468C	R	-	1	0	SYNE1	152502834	0.000000	0.05858	0.037000	0.18230	0.206000	0.24218	0.727000	0.25999	1.465000	0.48006	0.561000	0.74099	CGT		0.557	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
SYNE1	23345	hgsc.bcm.edu	37	6	152674796	152674796	+	Silent	SNP	G	G	A	rs143673038		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr6:152674796G>A	ENST00000367255.5	-	68	11611	c.11010C>T	c.(11008-11010)caC>caT	p.H3670H	SYNE1_ENST00000423061.1_Silent_p.H3655H|SYNE1_ENST00000341594.5_Silent_p.H3641H|SYNE1_ENST00000265368.4_Silent_p.H3670H|SYNE1_ENST00000448038.1_Silent_p.H3655H	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	3670					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)		TGCTGTTCACGTGGCTCTCGT	0.527										HNSCC(10;0.0054)																																							0			6											155.0	127.0	137.0					6																	152674796		2203	4300	6503	152716489	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.11010C>T	6.37:g.152674796G>A			152716489	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																																																																																				0.527	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
SYNE1	23345	hgsc.bcm.edu	37	6	152737961	152737961	+	Missense_Mutation	SNP	C	C	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr6:152737961C>A	ENST00000367255.5	-	41	6212	c.5611G>T	c.(5611-5613)Gca>Tca	p.A1871S	SYNE1_ENST00000423061.1_Missense_Mutation_p.A1878S|SYNE1_ENST00000341594.5_Missense_Mutation_p.A1908S|SYNE1_ENST00000265368.4_Missense_Mutation_p.A1871S|SYNE1_ENST00000448038.1_Missense_Mutation_p.A1878S	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1871					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)		AGGAATTCTGCCAAATGGGAC	0.562										HNSCC(10;0.0054)																																							0			6											81.0	79.0	80.0					6																	152737961		2203	4300	6503	152779654	SO:0001583	missense	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.5611G>T	6.37:g.152737961C>A	ENSP00000356224:p.Ala1871Ser		152779654	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	10.82	1.457586	0.26161	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.52754	0.74;0.74;0.65;0.7;0.82	6.16	2.92	0.33932	.	0.566781	0.17102	N	0.186955	T	0.09598	0.0236	N	0.22421	0.69	0.09310	N	1	B;B;B;B	0.22003	0.02;0.025;0.025;0.063	B;B;B;B	0.20767	0.016;0.015;0.015;0.031	T	0.34650	-0.9820	10	0.06236	T	0.91	.	7.0183	0.24900	0.0:0.5632:0.1355:0.3014	.	1854;1871;1871;1878	B3W695;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	S	1871;1878;1871;1878;1908	ENSP00000356224:A1871S;ENSP00000396024:A1878S;ENSP00000265368:A1871S;ENSP00000390975:A1878S;ENSP00000341887:A1908S	ENSP00000265368:A1871S	A	-	1	0	SYNE1	152779654	0.001000	0.12720	0.653000	0.29593	0.970000	0.65996	0.942000	0.29017	0.875000	0.35847	0.650000	0.86243	GCA		0.562	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
TP53	7157	hgsc.bcm.edu	37	17	7577094	7577094	+	Missense_Mutation	SNP	G	G	A	rs28934574		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr17:7577094G>A	ENST00000269305.4	-	8	1033	c.844C>T	c.(844-846)Cgg>Tgg	p.R282W	TP53_ENST00000413465.2_Intron|TP53_ENST00000420246.2_Missense_Mutation_p.R282W|TP53_ENST00000455263.2_Missense_Mutation_p.R282W|TP53_ENST00000445888.2_Missense_Mutation_p.R282W|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.R282W	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	282	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		DR -> EW (in sporadic cancers; somatic mutation).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in a sporadic cancer; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|Ref.22}.|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; dbSNP:rs28934574). {ECO:0000269|PubMed:8829627}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R282W(401)|p.R282G(29)|p.0?(8)|p.R282fs*24(4)|p.R282R(3)|p.?(2)|p.D281fs*63(2)|p.D281_R282>EW(2)|p.A276_R283delACPGRDRR(1)|p.D281_R282insXX(1)|p.C275fs*20(1)|p.R282_E287delRRTEEE(1)|p.L265_K305del41(1)|p.D281_R282delDR(1)|p.G279fs*59(1)|p.R280fs*62(1)|p.S269fs*21(1)|p.R282fs*63(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(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)	TCTGTGCGCCGGTCTCTCCCA	0.557		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"""	463	Substitution - Missense(430)|Whole gene deletion(8)|Deletion - In frame(6)|Deletion - Frameshift(5)|Insertion - Frameshift(4)|Substitution - coding silent(3)|Unknown(2)|Complex - frameshift(2)|Complex - compound substitution(2)|Insertion - In frame(1)	large_intestine(136)|oesophagus(49)|upper_aerodigestive_tract(43)|stomach(33)|central_nervous_system(29)|breast(29)|lung(26)|ovary(21)|skin(20)|urinary_tract(16)|haematopoietic_and_lymphoid_tissue(16)|pancreas(10)|biliary_tract(5)|liver(5)|bone(5)|vulva(4)|prostate(4)|endometrium(3)|peritoneum(2)|thyroid(2)|NS(2)|autonomic_ganglia(1)|soft_tissue(1)|salivary_gland(1)	17	GRCh37	CM056413|CM920678	TP53	M	rs28934574	G	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	83.0	71.0	75.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	844,844,844,844,448,448,448	1.5	0.3	17	dbSNP_125	75	2,8598	2.2+/-6.3	1,0,4299	no	missense,missense,missense,missense,missense,missense,missense	TP53	NM_000546.4,NM_001126112.1,NM_001126113.1,NM_001126114.1,NM_001126115.1,NM_001126116.1,NM_001126117.1	101,101,101,101,101,101,101	1,0,6502	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	282/394,282/394,282/347,282/342,150/262,150/210,150/215	7577094	2,13004	2203	4300	6503	7517819	SO:0001583	missense	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.844C>T	17.37:g.7577094G>A	ENSP00000269305:p.Arg282Trp		7517819	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.057525	0.76074	0.0	2.33E-4	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99869	-7.34;-7.34;-7.34;-7.34;-7.34;-7.34	4.75	1.49	0.22878	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99825	0.9922	M	0.89968	3.075	0.58432	A	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.998;1.0;0.999	D	0.97713	1.0192	9	0.87932	D	0	-12.0909	8.7508	0.34613	0.0:0.1376:0.5833:0.2792	rs28934574	282;282;282;282	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	W	282;282;282;282;282;271;150	ENSP00000352610:R282W;ENSP00000269305:R282W;ENSP00000398846:R282W;ENSP00000391127:R282W;ENSP00000391478:R282W;ENSP00000425104:R150W	ENSP00000269305:R282W	R	-	1	2	TP53	7517819	1.000000	0.71417	0.327000	0.25402	0.901000	0.52897	4.477000	0.60223	0.174000	0.19809	0.462000	0.41574	CGG		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
KDM6B	23135	hgsc.bcm.edu	37	17	7749471	7749471	+	Silent	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr17:7749471A>G	ENST00000448097.2	+	6	643	c.312A>G	c.(310-312)ccA>ccG	p.P104P	KDM6B_ENST00000254846.5_Silent_p.P104P			O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	104					cardiac muscle cell differentiation (GO:0055007)|cellular response to hydrogen peroxide (GO:0070301)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|mesodermal cell differentiation (GO:0048333)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|skin(5)	37						TCCGGGAGCCAGCCCAGCCAG	0.627																																																	0			17											42.0	42.0	42.0					17																	7749471		2203	4300	6503	7690196	SO:0001819	synonymous_variant	23135			AB002344	CCDS32552.1	17p13.1	2011-07-01	2009-04-17	2009-04-17		ENSG00000132510		"""Chromatin-modifying enzymes / K-demethylases"""	29012	protein-coding gene	gene with protein product		611577	"""jumonji domain containing 3"", ""jumonji domain containing 3, histone lysine demethylase"""	JMJD3		10662545, 9205841	Standard	NM_001080424		Approved	KIAA0346	uc002giw.1	O15054		ENST00000448097.2:c.312A>G	17.37:g.7749471A>G			7690196	C9IZ40|Q96G33	Silent	SNP	ENST00000448097.2	37																																																																																					0.627	KDM6B-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000440248.1	XM_043272	
NF1	4763	hgsc.bcm.edu	37	17	29527558	29527558	+	Missense_Mutation	SNP	G	G	T			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr17:29527558G>T	ENST00000358273.4	+	9	1390	c.1007G>T	c.(1006-1008)tGg>tTg	p.W336L	NF1_ENST00000356175.3_Missense_Mutation_p.W336L|NF1_ENST00000431387.4_Missense_Mutation_p.W336L	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	336					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.W336*(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)		TACATCAATTGGGAAGATAAC	0.393			"""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	17	Whole gene deletion(8)|Unknown(6)|Substitution - Nonsense(3)	soft_tissue(8)|lung(3)|autonomic_ganglia(3)|central_nervous_system(3)	17	GRCh37	CM003946|CS001840	NF1	M|S							122.0	107.0	112.0					17																	29527558		2203	4300	6503	26551684	SO:0001583	missense	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.1007G>T	17.37:g.29527558G>T	ENSP00000351015:p.Trp336Leu		26551684	O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	ENST00000358273.4	37	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.836698	0.91117	.	.	ENSG00000196712	ENST00000431387;ENST00000358273;ENST00000356175;ENST00000456735	T;T;T;T	0.62364	3.04;0.03;0.03;3.08	5.39	5.39	0.77823	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.73369	0.3578	L	0.54323	1.7	0.80722	D	1	B;D;B;P;B	0.57899	0.038;0.981;0.011;0.782;0.397	B;D;B;B;B	0.70487	0.013;0.969;0.011;0.423;0.24	T	0.66106	-0.6006	10	0.09843	T	0.71	.	19.1503	0.93485	0.0:0.0:1.0:0.0	.	336;336;336;336;336	E1P657;P21359-2;P21359;Q14931;P21359-3	.;.;NF1_HUMAN;.;.	L	336;336;336;2	ENSP00000412921:W336L;ENSP00000351015:W336L;ENSP00000348498:W336L;ENSP00000389907:W2L	ENSP00000348498:W336L	W	+	2	0	NF1	26551684	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.082000	0.94059	2.542000	0.85734	0.591000	0.81541	TGG		0.393	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267	
NF1	4763	hgsc.bcm.edu	37	17	29664408	29664408	+	Silent	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr17:29664408A>G	ENST00000358273.4	+	43	6833	c.6450A>G	c.(6448-6450)agA>agG	p.R2150R	NF1_ENST00000356175.3_Silent_p.R2129R|NF1_ENST00000444181.2_5'Flank|NF1_ENST00000417592.2_5'Flank	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	2150					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)|p.R2150S(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)		AAGTTTTGAGACTCAGTCTGA	0.368			"""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	12	Whole gene deletion(8)|Unknown(3)|Substitution - Missense(1)	soft_tissue(8)|autonomic_ganglia(2)|lung(1)|central_nervous_system(1)	17											86.0	75.0	79.0					17																	29664408		2203	4300	6503	26688534	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.6450A>G	17.37:g.29664408A>G			26688534	O00662|Q14284|Q14930|Q14931|Q9UMK3	Silent	SNP	ENST00000358273.4	37	CCDS42292.1																																																																																				0.368	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267	
TUBG2	27175	hgsc.bcm.edu	37	17	40811902	40811902	+	Nonsense_Mutation	SNP	G	G	T			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr17:40811902G>T	ENST00000251412.7	+	2	299	c.100G>T	c.(100-102)Gag>Tag	p.E34*		NM_016437.2	NP_057521.1	Q9NRH3	TBG2_HUMAN	tubulin, gamma 2	34					cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|gamma-tubulin complex (GO:0000930)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|pericentriolar material (GO:0000242)|spindle microtubule (GO:0005876)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	15		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.141)		TATCAGCCCCGAGGGCATCGT	0.652																																																	0			17											43.0	55.0	51.0					17																	40811902		2203	4298	6501	38065428	SO:0001587	stop_gained	27175			AF225971	CCDS32658.1	17q21.2	2014-09-04			ENSG00000037042	ENSG00000037042		"""Tubulins"""	12419	protein-coding gene	gene with protein product		605785					Standard	NM_016437		Approved		uc010wgr.2	Q9NRH3	OTTHUMG00000180640	ENST00000251412.7:c.100G>T	17.37:g.40811902G>T	ENSP00000251412:p.Glu34*		38065428	A6NDI4|Q32NB2	Nonsense_Mutation	SNP	ENST00000251412.7	37	CCDS32658.1	.	.	.	.	.	.	.	.	.	.	G	38	6.768235	0.97825	.	.	ENSG00000037042	ENST00000251412	.	.	.	5.15	4.15	0.48705	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-32.4097	13.162	0.59550	0.0:0.0:0.84:0.16	.	.	.	.	X	34	.	ENSP00000251412:E34X	E	+	1	0	TUBG2	38065428	1.000000	0.71417	0.999000	0.59377	0.811000	0.45836	6.404000	0.73268	1.254000	0.44035	0.655000	0.94253	GAG		0.652	TUBG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452326.1	NM_016437	
WNT3	7473	hgsc.bcm.edu	37	17	44851144	44851144	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr17:44851144T>C	ENST00000225512.5	-	2	374	c.212A>G	c.(211-213)gAg>gGg	p.E71G		NM_030753.4	NP_110380.1	P56703	WNT3_HUMAN	wingless-type MMTV integration site family, member 3	71					anterior/posterior axis specification (GO:0009948)|axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation (GO:0044338)|canonical Wnt signaling pathway involved in osteoblast differentiation (GO:0044339)|cell fate commitment (GO:0045165)|cell morphogenesis (GO:0000902)|cellular response to retinoic acid (GO:0071300)|dorsal/ventral axis specification (GO:0009950)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|gamete generation (GO:0007276)|head morphogenesis (GO:0060323)|limb bud formation (GO:0060174)|mammary gland epithelium development (GO:0061180)|mesoderm formation (GO:0001707)|negative regulation of axon extension involved in axon guidance (GO:0048843)|neuron differentiation (GO:0030182)|positive regulation of collateral sprouting in absence of injury (GO:0048697)|positive regulation of gene expression (GO:0010628)|Spemann organizer formation at the anterior end of the primitive streak (GO:0060064)	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)			endometrium(2)|large_intestine(6)|lung(4)|prostate(1)	13			BRCA - Breast invasive adenocarcinoma(9;0.0257)			CTTCACGCCCTCGGCCACGCT	0.652																																																	0			17											52.0	56.0	55.0					17																	44851144		2203	4300	6503	42206307	SO:0001583	missense	7473			AY009397	CCDS11505.1	17q21-q22	2013-02-28				ENSG00000108379		"""Wingless-type MMTV integration sites"", ""Endogenous ligands"""	12782	protein-coding gene	gene with protein product	"""WNT-3 proto-oncogene protein"""	165330		INT4		8244403	Standard	NM_030753		Approved	MGC131950, MGC138321, MGC138323	uc002ikv.3	P56703		ENST00000225512.5:c.212A>G	17.37:g.44851144T>C	ENSP00000225512:p.Glu71Gly		42206307	Q2M237|Q9H1J9	Missense_Mutation	SNP	ENST00000225512.5	37	CCDS11505.1	.	.	.	.	.	.	.	.	.	.	T	31	5.098801	0.94197	.	.	ENSG00000108379	ENST00000225512	T	0.77358	-1.09	4.42	4.42	0.53409	.	0.000000	0.85682	D	0.000000	D	0.83801	0.5333	M	0.77313	2.365	0.80722	D	1	D	0.53151	0.958	P	0.54174	0.744	D	0.85399	0.1130	10	0.49607	T	0.09	.	13.8223	0.63329	0.0:0.0:0.0:1.0	.	71	P56703	WNT3_HUMAN	G	71	ENSP00000225512:E71G	ENSP00000225512:E71G	E	-	2	0	WNT3	42206307	1.000000	0.71417	0.782000	0.31804	0.991000	0.79684	5.923000	0.70045	1.852000	0.53769	0.379000	0.24179	GAG		0.652	WNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440427.1	NM_030753	
EVPL	2125	hgsc.bcm.edu	37	17	74014586	74014586	+	Silent	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr17:74014586A>G	ENST00000301607.3	-	12	1633	c.1380T>C	c.(1378-1380)gcT>gcC	p.A460A	EVPL_ENST00000586740.1_Silent_p.A460A	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	460	Globular 1.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						AGGCGGCGGGAGCACGCTTGG	0.662																																																	0			17											20.0	20.0	20.0					17																	74014586		2202	4300	6502	71526181	SO:0001819	synonymous_variant	2125			U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.1380T>C	17.37:g.74014586A>G			71526181	A0AUV5	Silent	SNP	ENST00000301607.3	37	CCDS11737.1																																																																																				0.662	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988	
CANT1	124583	hgsc.bcm.edu	37	17	76993398	76993398	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr17:76993398T>C	ENST00000302345.2	-	2	801	c.307A>G	c.(307-309)Att>Gtt	p.I103V	CANT1_ENST00000591732.1_5'Flank|CANT1_ENST00000392446.5_Missense_Mutation_p.I103V|CANT1_ENST00000591773.1_Missense_Mutation_p.I103V	NM_001159773.1|NM_138793.3	NP_001153245.1|NP_620148.1	Q8WVQ1	CANT1_HUMAN	calcium activated nucleotidase 1	103					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|proteoglycan biosynthetic process (GO:0030166)|signal transduction (GO:0007165)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|signal transducer activity (GO:0004871)|uridine-diphosphatase activity (GO:0045134)		CANT1/ETV4(3)	cervix(1)|endometrium(1)|large_intestine(2)|lung(10)|prostate(1)|skin(1)	16			BRCA - Breast invasive adenocarcinoma(99;0.0362)|OV - Ovarian serous cystadenocarcinoma(97;0.139)			CGATACCGAATCCCAGCCGGT	0.577			T	ETV4	prostate																																			Dom	yes		17	17q25	124583	calcium activated nucleotidase 1		E	0			17											105.0	115.0	112.0					17																	76993398		2203	4300	6503	74504993	SO:0001583	missense	124583			AJ312208	CCDS11760.1	17q25.3	2008-02-05	2004-10-12	2004-10-15		ENSG00000171302			19721	protein-coding gene	gene with protein product	"""Soluble Ca-Activated Nucleotidase, isozyme 1"""	613165				12167635	Standard	NM_138793		Approved	SHAPY, SCAN-1	uc002jwk.3	Q8WVQ1		ENST00000302345.2:c.307A>G	17.37:g.76993398T>C	ENSP00000307674:p.Ile103Val		74504993	B4DJ54|Q7Z2J7|Q8NG05|Q8NHP0|Q9BSD5	Missense_Mutation	SNP	ENST00000302345.2	37	CCDS11760.1	.	.	.	.	.	.	.	.	.	.	T	0.421	-0.908095	0.02434	.	.	ENSG00000171302	ENST00000302345;ENST00000392446;ENST00000537282;ENST00000339300	D;D	0.85484	-1.99;-1.99	5.17	-0.112	0.13572	.	0.646879	0.16807	N	0.198759	T	0.64182	0.2575	N	0.10809	0.05	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48833	-0.9000	10	0.13853	T	0.58	-2.1482	5.5721	0.17202	0.0:0.2459:0.5215:0.2326	.	103	Q8WVQ1	CANT1_HUMAN	V	103;103;103;52	ENSP00000307674:I103V;ENSP00000376241:I103V	ENSP00000307674:I103V	I	-	1	0	CANT1	74504993	0.010000	0.17322	0.050000	0.19076	0.163000	0.22366	0.886000	0.28241	0.278000	0.22164	0.459000	0.35465	ATT		0.577	CANT1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437723.2	NM_138793	
ASPSCR1	79058	hgsc.bcm.edu	37	17	79974392	79974392	+	Missense_Mutation	SNP	A	A	G	rs112054193		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr17:79974392A>G	ENST00000306739.4	+	13	1491	c.1394A>G	c.(1393-1395)gAg>gGg	p.E465G	ASPSCR1_ENST00000582404.1_3'UTR|STRA13_ENST00000583767.1_5'Flank|ASPSCR1_ENST00000306729.7_Missense_Mutation_p.E559G|ASPSCR1_ENST00000580534.1_Missense_Mutation_p.E413G	NM_024083.3	NP_076988.1	Q9BZE9	ASPC1_HUMAN	alveolar soft part sarcoma chromosome region, candidate 1	465					glucose homeostasis (GO:0042593)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|regulation of glucose import (GO:0046324)	cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)			ASPSCR1/TFE3(167)	breast(2)|large_intestine(2)	4	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191)			TTGGGAGCCGAGGAGCCGGCA	0.706			T	TFE3	alveolar soft part sarcoma																																			Dom	yes		17	17q25	79058	"""alveolar soft part sarcoma chromosome region, candidate 1"""		M	0			17											20.0	22.0	21.0					17																	79974392		2060	4087	6147	77567681	SO:0001583	missense	79058			AF324219	CCDS11796.1, CCDS58611.1	17q25	2011-06-28				ENSG00000169696		"""UBX domain containing"""	13825	protein-coding gene	gene with protein product	"""UBX domain protein 9"""	606236				11244503, 10506710	Standard	NM_024083		Approved	ASPS, ASPL, UBXD9, UBXN9	uc002kcy.3	Q9BZE9		ENST00000306739.4:c.1394A>G	17.37:g.79974392A>G	ENSP00000302176:p.Glu465Gly		77567681	A8K3K9|Q7Z6N7|Q8WV59|Q96LS5|Q96M40	Missense_Mutation	SNP	ENST00000306739.4	37	CCDS11796.1	.	.	.	.	.	.	.	.	.	.	A	5.720	0.317268	0.10845	.	.	ENSG00000169696	ENST00000306739;ENST00000306729	T;T	0.30182	1.77;1.54	3.76	2.62	0.31277	.	0.633971	0.15827	N	0.242716	T	0.35682	0.0940	M	0.63428	1.95	0.19300	N	0.999978	D;D;D	0.57257	0.979;0.978;0.974	P;P;B	0.50109	0.631;0.546;0.422	T	0.12116	-1.0560	9	.	.	.	-16.2532	7.1134	0.25403	0.8866:0.0:0.1134:0.0	.	413;559;465	Q9BZE9-3;Q9BZE9-2;Q9BZE9	.;.;ASPC1_HUMAN	G	465;559	ENSP00000302176:E465G;ENSP00000306625:E559G	.	E	+	2	0	ASPSCR1	77567681	0.479000	0.25925	0.348000	0.25681	0.074000	0.17049	2.581000	0.46077	1.581000	0.49865	0.460000	0.39030	GAG		0.706	ASPSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441972.1	NM_024083	
CD7	924	hgsc.bcm.edu	37	17	80274179	80274179	+	Silent	SNP	A	A	G	rs560319694		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr17:80274179A>G	ENST00000312648.3	-	3	610	c.504T>C	c.(502-504)tcT>tcC	p.S168S	CD7_ENST00000583376.1_Silent_p.S68S|CD7_ENST00000578509.1_Silent_p.S68S|CD7_ENST00000584284.1_Silent_p.S168S	NM_006137.6	NP_006128.1	P09564	CD7_HUMAN	CD7 molecule	168	4 X 9 AA tandem repeats, potential spacer function.				homeostasis of number of cells within a tissue (GO:0048873)|immune response (GO:0006955)|T cell activation (GO:0042110)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			endometrium(1)|large_intestine(1)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	8	Breast(20;0.000675)|all_neural(118;0.0804)|Lung NSC(278;0.128)|all_lung(278;0.145)|Ovarian(332;0.249)		OV - Ovarian serous cystadenocarcinoma(97;0.00463)|BRCA - Breast invasive adenocarcinoma(99;0.0667)			CAGGGAGGGCAGAGGCTGTCT	0.716																																					Pancreas(45;804 1068 19702 28207 28798)												0			17											14.0	17.0	16.0					17																	80274179		2168	4265	6433	77867468	SO:0001819	synonymous_variant	924			X06180	CCDS11807.1	17q25.2-q25.3	2013-01-11	2006-03-28			ENSG00000173762		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1695	protein-coding gene	gene with protein product	"""p41 protein"", ""T-cell antigen CD7"", ""T-cell leukemia antigen"""	186820	"""CD7 antigen (p41)"""			1695199, 3501369	Standard	NM_006137		Approved	GP40, LEU-9, TP41, Tp40	uc002kel.1	P09564		ENST00000312648.3:c.504T>C	17.37:g.80274179A>G			77867468		Silent	SNP	ENST00000312648.3	37	CCDS11807.1																																																																																				0.716	CD7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442826.1	NM_006137	
CD7	924	hgsc.bcm.edu	37	17	80274183	80274183	+	Missense_Mutation	SNP	G	G	C	rs199986856		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr17:80274183G>C	ENST00000312648.3	-	3	606	c.500C>G	c.(499-501)gCc>gGc	p.A167G	CD7_ENST00000583376.1_Missense_Mutation_p.A67G|CD7_ENST00000578509.1_Missense_Mutation_p.A67G|CD7_ENST00000584284.1_Missense_Mutation_p.A167G	NM_006137.6	NP_006128.1	P09564	CD7_HUMAN	CD7 molecule	167	4 X 9 AA tandem repeats, potential spacer function.				homeostasis of number of cells within a tissue (GO:0048873)|immune response (GO:0006955)|T cell activation (GO:0042110)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			endometrium(1)|large_intestine(1)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	8	Breast(20;0.000675)|all_neural(118;0.0804)|Lung NSC(278;0.128)|all_lung(278;0.145)|Ovarian(332;0.249)		OV - Ovarian serous cystadenocarcinoma(97;0.00463)|BRCA - Breast invasive adenocarcinoma(99;0.0667)			GAGGGCAGAGGCTGTCTGCGG	0.711																																					Pancreas(45;804 1068 19702 28207 28798)												0			17																																								77867472	SO:0001583	missense	924			X06180	CCDS11807.1	17q25.2-q25.3	2013-01-11	2006-03-28			ENSG00000173762		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1695	protein-coding gene	gene with protein product	"""p41 protein"", ""T-cell antigen CD7"", ""T-cell leukemia antigen"""	186820	"""CD7 antigen (p41)"""			1695199, 3501369	Standard	NM_006137		Approved	GP40, LEU-9, TP41, Tp40	uc002kel.1	P09564		ENST00000312648.3:c.500C>G	17.37:g.80274183G>C	ENSP00000312027:p.Ala167Gly		77867472		Missense_Mutation	SNP	ENST00000312648.3	37	CCDS11807.1	.	.	.	.	.	.	.	.	.	.	G	1.766	-0.485462	0.04352	.	.	ENSG00000173762	ENST00000312648	T	0.25912	1.77	0.122	-0.245	0.13027	.	.	.	.	.	T	0.08537	0.0212	N	0.08118	0	0.20926	N	0.999825	P;P	0.38110	0.618;0.618	B;B	0.28638	0.092;0.092	T	0.27088	-1.0084	9	0.21540	T	0.41	.	4.5003	0.11860	0.3195:0.0:0.6805:0.0	.	167;167	Q29VG3;P09564	.;CD7_HUMAN	G	167	ENSP00000312027:A167G	ENSP00000312027:A167G	A	-	2	0	CD7	77867472	0.013000	0.17824	0.007000	0.13788	0.007000	0.05969	0.000000	0.12993	-1.039000	0.03275	-1.031000	0.02408	GCC		0.711	CD7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442826.1	NM_006137	
ZNF750	79755	hgsc.bcm.edu	37	17	80789936	80789936	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr17:80789936A>G	ENST00000269394.3	-	2	1228	c.395T>C	c.(394-396)cTc>cCc	p.L132P	ZNF750_ENST00000572562.1_Intron|TBCD_ENST00000355528.4_Intron|TBCD_ENST00000397466.2_Intron|TBCD_ENST00000539345.2_Intron	NM_024702.2	NP_078978.2	Q32MQ0	ZN750_HUMAN	zinc finger protein 750	132					cell differentiation (GO:0030154)|epidermis development (GO:0008544)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(3)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(4)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	31	Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0514)|all_epithelial(8;0.0748)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.149)			TGCCCTGTGGAGGGCTGGCTT	0.632																																																	0			17											33.0	35.0	34.0					17																	80789936		2203	4300	6503	78383225	SO:0001583	missense	79755			AK023903	CCDS11819.1	17q25.3	2008-05-02				ENSG00000141579			25843	protein-coding gene	gene with protein product		610226				16751772	Standard	NM_024702		Approved	FLJ13841, Zfp750	uc002kga.3	Q32MQ0		ENST00000269394.3:c.395T>C	17.37:g.80789936A>G	ENSP00000269394:p.Leu132Pro		78383225	Q9H899	Missense_Mutation	SNP	ENST00000269394.3	37	CCDS11819.1	.	.	.	.	.	.	.	.	.	.	A	5.038	0.192741	0.09599	.	.	ENSG00000141579	ENST00000269394	T	0.25085	1.82	5.86	0.873	0.19118	.	0.693133	0.13492	N	0.383930	T	0.16514	0.0397	L	0.29908	0.895	0.09310	N	1	B	0.14438	0.01	B	0.14023	0.01	T	0.27502	-1.0072	9	.	.	.	-21.9099	9.3124	0.37912	0.6777:0.0:0.3223:0.0	.	132	Q32MQ0	ZN750_HUMAN	P	132	ENSP00000269394:L132P	.	L	-	2	0	ZNF750	78383225	0.014000	0.17966	0.004000	0.12327	0.023000	0.10783	1.466000	0.35310	0.380000	0.24823	0.533000	0.62120	CTC		0.632	ZNF750-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439074.2	NM_024702	
KRTAP6-3	337968	hgsc.bcm.edu	37	21	31964985	31964985	+	Missense_Mutation	SNP	G	G	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr21:31964985G>A	ENST00000391624.1	+	1	227	c.200G>A	c.(199-201)aGa>aAa	p.R67K	KRTAP22-2_ENST00000382830.2_5'Flank	NM_181605.3	NP_853636.3	Q3LI67	KRA63_HUMAN	keratin associated protein 6-3	67						intermediate filament (GO:0005882)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(7)	10						tgtggctacagaggcctggac	0.607																																																	0			21											52.0	64.0	60.0					21																	31964985		2203	4300	6503	30886856	SO:0001583	missense	337968			AP001708		21q22.1	2012-04-19			ENSG00000212938	ENSG00000212938		"""Keratin associated proteins"""	18933	protein-coding gene	gene with protein product						12359730	Standard	NM_181605		Approved	KAP6.3	uc002yom.3	Q3LI67	OTTHUMG00000057791	ENST00000391624.1:c.200G>A	21.37:g.31964985G>A	ENSP00000375482:p.Arg67Lys		30886856	A4IF26	Missense_Mutation	SNP	ENST00000391624.1	37		.	.	.	.	.	.	.	.	.	.	G	3.589	-0.083957	0.07141	.	.	ENSG00000212938	ENST00000391624	T	0.34072	1.38	3.62	2.74	0.32292	.	.	.	.	.	T	0.27027	0.0662	L	0.39898	1.24	0.09310	N	1	B	0.31290	0.318	B	0.26770	0.073	T	0.21143	-1.0254	9	0.87932	D	0	.	7.3391	0.26627	0.12:0.0:0.88:0.0	.	67	Q3LI67	KRA63_HUMAN	K	67	ENSP00000375482:R67K	ENSP00000375482:R67K	R	+	2	0	KRTAP6-3	30886856	0.002000	0.14202	0.035000	0.18076	0.022000	0.10575	1.139000	0.31504	1.097000	0.41459	0.650000	0.86243	AGA		0.607	KRTAP6-3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000128243.2	NM_181605	
RUNX1	861	hgsc.bcm.edu	37	21	36259150	36259150	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr21:36259150A>G	ENST00000344691.4	-	1	1837	c.260T>C	c.(259-261)aTc>aCc	p.I87T	RUNX1_ENST00000300305.3_Missense_Mutation_p.I114T|RUNX1_ENST00000325074.5_Missense_Mutation_p.I102T|RUNX1_ENST00000358356.5_Missense_Mutation_p.I87T|RUNX1_ENST00000437180.1_Missense_Mutation_p.I114T|RUNX1_ENST00000399240.1_Missense_Mutation_p.I87T|RUNX1_ENST00000486278.2_Missense_Mutation_p.I90T	NM_001001890.2	NP_001001890.1	Q01196	RUNX1_HUMAN	runt-related transcription factor 1	87	Runt. {ECO:0000255|PROSITE- ProRule:PRU00399}.				behavioral response to pain (GO:0048266)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system development (GO:0007417)|definitive hemopoiesis (GO:0060216)|embryonic hemopoiesis (GO:0035162)|hair follicle morphogenesis (GO:0031069)|hematopoietic stem cell proliferation (GO:0071425)|hemopoiesis (GO:0030097)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|myeloid cell differentiation (GO:0030099)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of granulocyte differentiation (GO:0030853)|peripheral nervous system neuron development (GO:0048935)|positive regulation of angiogenesis (GO:0045766)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of progesterone secretion (GO:2000872)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hair follicle cell proliferation (GO:0071336)|regulation of signal transduction (GO:0009966)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	basement membrane (GO:0005604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.V90_K117del(1)		breast(5)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(428)|large_intestine(3)|lung(6)|oesophagus(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	452						CTTGAAAGCGATGGGCAGGGT	0.726			T	"""RPL22, MDS1, EVI1, CBFA2T3, CBFA2T1, ETV6, LAF4"""	"""AML, preB- ALL, T-ALL"""																																			Dom	yes		21	21q22.3	861	runt-related transcription factor 1  (AML1)		L	1	Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)	21											53.0	51.0	51.0					21																	36259150		2203	4300	6503	35181020	SO:0001583	missense	861			X79549	CCDS13639.1, CCDS42922.1, CCDS46646.1	21q22.3	2014-09-17	2008-07-29		ENSG00000159216	ENSG00000159216			10471	protein-coding gene	gene with protein product	"""aml1 oncogene"""	151385	"""acute myeloid leukemia 1"""	AML1, CBFA2		1427868, 7835892	Standard	NM_001001890		Approved	PEBP2A2, AMLCR1	uc010gmv.3	Q01196	OTTHUMG00000086299	ENST00000344691.4:c.260T>C	21.37:g.36259150A>G	ENSP00000340690:p.Ile87Thr		35181020	A8MV94|B2RMS4|D3DSG1|O60472|O60473|O76047|O76089|Q13081|Q13755|Q13756|Q13757|Q13758|Q13759|Q15341|Q15343|Q16122|Q16284|Q16285|Q16286|Q16346|Q16347|Q92479	Missense_Mutation	SNP	ENST00000344691.4	37	CCDS42922.1	.	.	.	.	.	.	.	.	.	.	A	15.64	2.892310	0.52121	.	.	ENSG00000159216	ENST00000344691;ENST00000300305;ENST00000437180;ENST00000325074;ENST00000399240;ENST00000399245;ENST00000358356;ENST00000399237;ENST00000486278;ENST00000455571	D;D;D;D;D;D;D;D;D	0.99462	-5.94;-5.94;-5.94;-5.94;-5.94;-5.94;-5.94;-5.94;-5.94	4.45	4.45	0.53987	Acute myeloid leukemia 1 (AML 1)/Runt (2);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.98966	0.9648	L	0.29908	0.895	0.80722	D	1	D;B;D;P;D	0.71674	0.987;0.413;0.998;0.807;0.966	D;B;D;P;D	0.87578	0.946;0.272;0.998;0.565;0.925	D	0.99802	1.1036	10	0.87932	D	0	-23.3958	13.8867	0.63712	1.0:0.0:0.0:0.0	.	114;87;114;102;87	Q2TAM6;Q01196-3;Q01196-8;Q01196-10;Q01196	.;.;.;.;RUNX1_HUMAN	T	87;114;114;102;87;90;87;102;90;101	ENSP00000340690:I87T;ENSP00000300305:I114T;ENSP00000409227:I114T;ENSP00000319459:I102T;ENSP00000382184:I87T;ENSP00000351123:I87T;ENSP00000382182:I102T;ENSP00000438019:I90T;ENSP00000388189:I101T	ENSP00000300305:I114T	I	-	2	0	RUNX1	35181020	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.587000	0.90810	1.862000	0.54008	0.460000	0.39030	ATC		0.726	RUNX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000194230.1		
TSPEAR	54084	hgsc.bcm.edu	37	21	45924704	45924704	+	Silent	SNP	G	G	T			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr21:45924704G>T	ENST00000323084.4	-	11	1880	c.1815C>A	c.(1813-1815)tcC>tcA	p.S605S	TSPEAR-AS1_ENST00000451035.1_RNA	NM_001272037.1|NM_144991.2	NP_001258966.1|NP_659428.2	Q8WU66	TSEAR_HUMAN	thrombospondin-type laminin G domain and EAR repeats	605					sensory perception of sound (GO:0007605)	cell surface (GO:0009986)|ciliary membrane (GO:0060170)|extracellular region (GO:0005576)|stereocilium (GO:0032420)				breast(1)|central_nervous_system(6)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	37						GCCCATCGAAGGAGTTGGCCA	0.537																																																	0			21											88.0	83.0	85.0					21																	45924704		2203	4300	6503	44749132	SO:0001819	synonymous_variant	54084			AJ487962	CCDS13712.1, CCDS74801.1	21q22.3	2012-10-30	2011-01-25	2011-01-25	ENSG00000175894	ENSG00000175894			1268	protein-coding gene	gene with protein product		612920	"""chromosome 21 open reading frame 29"", ""deafness, autosomal recessive 98"""	C21orf29, DFNB98		12095917, 22678063	Standard	NM_144991		Approved	MGC11251, TSP-EAR	uc002zfe.1	Q8WU66	OTTHUMG00000041215	ENST00000323084.4:c.1815C>A	21.37:g.45924704G>T			44749132		Silent	SNP	ENST00000323084.4	37	CCDS13712.1																																																																																				0.537	TSPEAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098761.1	NM_144991	
UBE2G2	7327	hgsc.bcm.edu	37	21	46207991	46207991	+	Silent	SNP	C	C	A	rs546573694		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr21:46207991C>A	ENST00000345496.2	-	2	333	c.63G>T	c.(61-63)ccG>ccT	p.P21P	UBE2G2_ENST00000330942.5_5'UTR|UBE2G2_ENST00000477954.1_5'UTR	NM_003343.5	NP_003334.2	P60604	UB2G2_HUMAN	ubiquitin-conjugating enzyme E2G 2	21					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein K48-linked ubiquitination (GO:0070936)|protein N-linked glycosylation via asparagine (GO:0018279)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			breast(3)|central_nervous_system(1)|lung(1)	5				Colorectal(79;0.0638)		CAATTCCTTCCGGAGGATTCA	0.269																																																	0			21											44.0	47.0	46.0					21																	46207991		2201	4300	6501	45032419	SO:0001819	synonymous_variant	7327			BC008351	CCDS13714.1, CCDS33586.1	21q22.3	2011-05-19	2011-05-19		ENSG00000184787	ENSG00000184787		"""Ubiquitin-conjugating enzymes E2"""	12483	protein-coding gene	gene with protein product		603124	"""ubiquitin-conjugating enzyme E2G 2 (homologous to yeast UBC7)"", ""ubiquitin-conjugating enzyme E2G 2 (UBC7 homolog, yeast)"""			9693041, 9925943	Standard	NM_003343		Approved	UBC7	uc002zfy.3	P60604	OTTHUMG00000089179	ENST00000345496.2:c.63G>T	21.37:g.46207991C>A			45032419	A6NMQ7|A8K3L4|D3DSL7|P56554	Silent	SNP	ENST00000345496.2	37	CCDS13714.1																																																																																				0.269	UBE2G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202647.2	NM_182688	
COL6A2	1292	hgsc.bcm.edu	37	21	47544566	47544566	+	Splice_Site	SNP	C	C	T	rs376303610		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr21:47544566C>T	ENST00000300527.4	+	22	1777	c.1673C>T	c.(1672-1674)gCg>gTg	p.A558V	COL6A2_ENST00000357838.4_Splice_Site_p.A558V|COL6A2_ENST00000310645.5_Splice_Site_p.A558V|COL6A2_ENST00000409416.1_Splice_Site_p.A558V|COL6A2_ENST00000397763.1_Splice_Site_p.A558V	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	558	Triple-helical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)		p.A558V(1)		NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	43	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		CCTTCTCAGGCGGATCCTGGT	0.672																																																	1	Substitution - Missense(1)	central_nervous_system(1)	21						C	VAL/ALA,VAL/ALA,VAL/ALA	0,4406		0,0,2203	49.0	59.0	55.0		1673,1673,1673	4.1	1.0	21		55	1,8599	1.2+/-3.3	0,1,4299	no	missense-near-splice,missense-near-splice,missense-near-splice	COL6A2	NM_001849.3,NM_058174.2,NM_058175.2	64,64,64	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	558/1020,558/919,558/829	47544566	1,13005	2203	4300	6503	46368994	SO:0001630	splice_region_variant	1292			M20777	CCDS13728.1, CCDS13729.1, CCDS13730.1	21q22.3	2014-09-17			ENSG00000142173	ENSG00000142173		"""Collagens"""	2212	protein-coding gene	gene with protein product		120240					Standard	NM_001849		Approved		uc002zia.1	P12110	OTTHUMG00000090489	ENST00000300527.4:c.1672-1C>T	21.37:g.47544566C>T			46368994	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Missense_Mutation	SNP	ENST00000300527.4	37	CCDS13728.1	.	.	.	.	.	.	.	.	.	.	C	18.62	3.662467	0.67700	0.0	1.16E-4	ENSG00000142173	ENST00000300527;ENST00000357838;ENST00000310645;ENST00000409416;ENST00000397763;ENST00000413758	D;D;D;D;D;D	0.93906	-3.31;-2.48;-3.31;-3.31;-2.48;-3.27	4.08	4.08	0.47627	.	0.055737	0.64402	D	0.000001	D	0.90573	0.7045	N	0.19112	0.55	0.40611	D	0.981674	D;D;D	0.56035	0.974;0.968;0.968	P;P;P	0.53185	0.72;0.598;0.598	D	0.90399	0.4401	10	0.39692	T	0.17	-9.0304	12.5266	0.56089	0.0:0.6896:0.3104:0.0	.	558;558;558	P12110;P12110-2;P12110-3	CO6A2_HUMAN;.;.	V	558;558;558;558;558;99	ENSP00000300527:A558V;ENSP00000350497:A558V;ENSP00000312529:A558V;ENSP00000387115:A558V;ENSP00000380870:A558V;ENSP00000395751:A99V	ENSP00000300527:A558V	A	+	2	0	COL6A2	46368994	1.000000	0.71417	0.993000	0.49108	0.607000	0.37147	4.099000	0.57755	1.852000	0.53769	0.585000	0.79938	GCG		0.672	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1		Missense_Mutation
TMEM8A	58986	hgsc.bcm.edu	37	16	425425	425425	+	Missense_Mutation	SNP	C	C	T	rs370004240		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr16:425425C>T	ENST00000431232.2	-	7	1395	c.1235G>A	c.(1234-1236)cGg>cAg	p.R412Q	TMEM8A_ENST00000250930.3_Missense_Mutation_p.R219Q|TMEM8A_ENST00000476735.1_5'Flank	NM_021259.2	NP_067082.2	Q9HCN3	TMM8A_HUMAN	transmembrane protein 8A	412					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)				central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	14						GGTCTCGTTCCGCATCTCTGT	0.637																																																	0			16						C	GLN/ARG	0,4402		0,0,2201	95.0	78.0	84.0		1235	-3.3	0.0	16		84	1,8595	1.2+/-3.3	0,1,4297	no	missense	TMEM8A	NM_021259.2	43	0,1,6498	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	412/772	425425	1,12997	2201	4298	6499	365426	SO:0001583	missense	58986			AB045292	CCDS10407.1	16p13.3	2009-06-12	2009-06-12	2009-06-12	ENSG00000129925	ENSG00000129925			17205	protein-coding gene	gene with protein product			"""transmembrane protein 6"", ""transmembrane protein 8 (five membrane-spanning domains)"""	TMEM6, TMEM8		11006113	Standard	NM_021259		Approved	M83	uc002cgu.4	Q9HCN3	OTTHUMG00000047996	ENST00000431232.2:c.1235G>A	16.37:g.425425C>T	ENSP00000401338:p.Arg412Gln		365426	D3DU49|Q4TT35|Q8WU24|Q96S25|Q9BR03|Q9BT97|Q9H7B9	Missense_Mutation	SNP	ENST00000431232.2	37	CCDS10407.1	.	.	.	.	.	.	.	.	.	.	C	5.338	0.247696	0.10130	0.0	1.16E-4	ENSG00000129925	ENST00000431232;ENST00000250930	T;T	0.29655	1.97;1.56	4.17	-3.31	0.04988	.	2.138010	0.01884	N	0.038028	T	0.15565	0.0375	N	0.11427	0.14	0.09310	N	1	B	0.18166	0.026	B	0.06405	0.002	T	0.19289	-1.0310	10	0.12766	T	0.61	0.7189	9.039	0.36305	0.0:0.3632:0.3138:0.323	.	412	Q9HCN3	TMM8A_HUMAN	Q	412;219	ENSP00000401338:R412Q;ENSP00000250930:R219Q	ENSP00000250930:R219Q	R	-	2	0	TMEM8A	365426	0.014000	0.17966	0.000000	0.03702	0.000000	0.00434	0.638000	0.24674	-0.373000	0.07979	-1.751000	0.00678	CGG		0.637	TMEM8A-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000109257.2	NM_021259	
ZP2	7783	hgsc.bcm.edu	37	16	21213466	21213466	+	Missense_Mutation	SNP	G	G	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr16:21213466G>A	ENST00000574002.1	-	12	1728	c.1246C>T	c.(1246-1248)Cgg>Tgg	p.R416W	ZP2_ENST00000219593.4_Missense_Mutation_p.R416W|ZP2_ENST00000574091.1_Missense_Mutation_p.R416W|AF001550.7_ENST00000572747.1_RNA			Q05996	ZP2_HUMAN	zona pellucida glycoprotein 2 (sperm receptor)	416	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				binding of sperm to zona pellucida (GO:0007339)|intracellular protein transport (GO:0006886)|multicellular organism reproduction (GO:0032504)|prevention of polyspermy (GO:0060468)|signal transduction (GO:0007165)|single fertilization (GO:0007338)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	acrosin binding (GO:0032190)|coreceptor activity (GO:0015026)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(16)|ovary(1)|prostate(1)|stomach(1)	41				GBM - Glioblastoma multiforme(48;0.0573)		ATGTGGAACCGTACCAGCCCC	0.507																																																	0			16											88.0	78.0	81.0					16																	21213466		2200	4300	6500	21120967	SO:0001583	missense	7783			M90366	CCDS10596.1, CCDS73843.1	16p12	2014-07-04			ENSG00000103310	ENSG00000103310		"""Zona pellucida glycoproteins"""	13188	protein-coding gene	gene with protein product		182888				8385033	Standard	XM_005255562		Approved	ZPA	uc002dii.2	Q05996	OTTHUMG00000090681	ENST00000574002.1:c.1246C>T	16.37:g.21213466G>A	ENSP00000460971:p.Arg416Trp		21120967	B2R7J2|Q4VAN9|Q4VAP0|Q4VAP1	Missense_Mutation	SNP	ENST00000574002.1	37	CCDS10596.1	.	.	.	.	.	.	.	.	.	.	G	10.56	1.384048	0.25031	.	.	ENSG00000103310	ENST00000219593	D	0.82984	-1.67	5.83	-0.0239	0.13941	Zona pellucida sperm-binding protein (3);	0.917115	0.09272	N	0.824992	T	0.70159	0.3192	L	0.38531	1.155	0.09310	N	1	P;B	0.35844	0.524;0.205	B;B	0.28916	0.096;0.096	T	0.54622	-0.8266	10	0.36615	T	0.2	0.2289	6.6004	0.22697	0.1381:0.0:0.3582:0.5037	.	416;416	Q4VAP1;Q05996	.;ZP2_HUMAN	W	416	ENSP00000219593:R416W	ENSP00000219593:R416W	R	-	1	2	ZP2	21120967	0.000000	0.05858	0.000000	0.03702	0.665000	0.39181	0.200000	0.17257	-0.203000	0.10251	0.467000	0.42956	CGG		0.507	ZP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207365.2		
ATP2A1	487	hgsc.bcm.edu	37	16	28912087	28912087	+	Silent	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr16:28912087T>C	ENST00000357084.3	+	15	2217	c.1950T>C	c.(1948-1950)gaT>gaC	p.D650D	ATP2A1_ENST00000536376.1_Silent_p.D525D|ATP2A1_ENST00000395503.4_Silent_p.D650D	NM_173201.3	NP_775293.1	O14983	AT2A1_HUMAN	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	650					apoptotic mitochondrial changes (GO:0008637)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|ion transmembrane transport (GO:0034220)|maintenance of mitochondrion location (GO:0051659)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|negative regulation of striated muscle contraction (GO:0045988)|positive regulation of endoplasmic reticulum calcium ion concentration (GO:0032470)|positive regulation of fast-twitch skeletal muscle fiber contraction (GO:0031448)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|regulation of striated muscle contraction (GO:0006942)|relaxation of skeletal muscle (GO:0090076)|response to endoplasmic reticulum stress (GO:0034976)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|H zone (GO:0031673)|I band (GO:0031674)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-transporting ATPase activity (GO:0005388)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(2)	38						AGGTGGCCGATCGCGCCTACA	0.647																																																	0			16											90.0	73.0	79.0					16																	28912087		2197	4300	6497	28819588	SO:0001819	synonymous_variant	487				CCDS10643.1, CCDS42139.1, CCDS66997.1	16p12.1	2012-10-22			ENSG00000196296	ENSG00000196296	3.6.3.8	"""ATPases / P-type"""	811	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 1"", ""calcium pump 1"""	108730		ATP2A			Standard	NM_004320		Approved	SERCA1	uc002dro.1	O14983	OTTHUMG00000131760	ENST00000357084.3:c.1950T>C	16.37:g.28912087T>C			28819588	A8K5J9|B3KY17|O14984	Silent	SNP	ENST00000357084.3	37	CCDS10643.1																																																																																				0.647	ATP2A1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254686.2	NM_004320	
CA7	766	hgsc.bcm.edu	37	16	66885460	66885460	+	Splice_Site	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr16:66885460A>G	ENST00000338437.2	+	4	561	c.452A>G	c.(451-453)gAg>gGg	p.E151G	CA7_ENST00000394069.3_Splice_Site_p.E95G|RP11-61A14.1_ENST00000551187.1_RNA	NM_005182.2	NP_005173.1	P43166	CAH7_HUMAN	carbonic anhydrase VII	151					bicarbonate transport (GO:0015701)|one-carbon metabolic process (GO:0006730)|positive regulation of cellular pH reduction (GO:0032849)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|regulation of chloride transport (GO:2001225)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(1)|lung(4)	6		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.088)|Epithelial(162;0.204)	Acetazolamide(DB00819)|Diclofenamide(DB01144)|Methazolamide(DB00703)|Zonisamide(DB00909)	GTTTTTTTGGAGGTGAGTGGT	0.592																																																	0			16											167.0	154.0	158.0					16																	66885460		2200	4300	6500	65442961	SO:0001630	splice_region_variant	766				CCDS10821.1, CCDS42173.1	16q22.1	2008-02-05			ENSG00000168748	ENSG00000168748	4.2.1.1	"""Carbonic anhydrases"""	1381	protein-coding gene	gene with protein product		114770				1783392	Standard	XM_005256135		Approved		uc002eqi.3	P43166	OTTHUMG00000137524	ENST00000338437.2:c.453+1A>G	16.37:g.66885460A>G			65442961	Q541F0|Q86YU0	Missense_Mutation	SNP	ENST00000338437.2	37	CCDS10821.1	.	.	.	.	.	.	.	.	.	.	A	17.21	3.332686	0.60853	.	.	ENSG00000168748	ENST00000338437;ENST00000394069	T;T	0.66815	-0.23;-0.23	5.87	5.87	0.94306	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.000000	0.85682	D	0.000000	D	0.84197	0.5419	M	0.90369	3.11	0.80722	D	1	D	0.76494	0.999	D	0.66847	0.947	D	0.87565	0.2474	10	0.87932	D	0	-28.3879	15.1012	0.72279	1.0:0.0:0.0:0.0	.	151	P43166	CAH7_HUMAN	G	151;95	ENSP00000345659:E151G;ENSP00000377632:E95G	ENSP00000345659:E151G	E	+	2	0	CA7	65442961	1.000000	0.71417	1.000000	0.80357	0.513000	0.34164	9.026000	0.93700	2.247000	0.74100	0.528000	0.53228	GAG		0.592	CA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268847.1		Missense_Mutation
CDH1	999	hgsc.bcm.edu	37	16	68844110	68844110	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr16:68844110A>G	ENST00000261769.5	+	6	889	c.698A>G	c.(697-699)cAc>cGc	p.H233R	CDH1_ENST00000562836.1_3'UTR|CDH1_ENST00000422392.2_Missense_Mutation_p.H233R	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	233	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)	p.?(4)		NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		CTCTTCTCTCACGCTGTGTCA	0.532			"""Mis, N, F, S"""		"""lobular breast, gastric"""	gastric			Hereditary Diffuse Gastric Cancer																														yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"""cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"""		E	4	Unknown(4)	breast(4)	16											154.0	144.0	148.0					16																	68844110		2198	4300	6498	67401611	SO:0001583	missense	51343	Familial Cancer Database	HDGC	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"""CD molecules"", ""Cadherins / Major cadherins"""	1748	protein-coding gene	gene with protein product	"""E-Cadherin"""	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.698A>G	16.37:g.68844110A>G	ENSP00000261769:p.His233Arg		67401611	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Missense_Mutation	SNP	ENST00000261769.5	37	CCDS10869.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.243615	0.79912	.	.	ENSG00000039068	ENST00000261769;ENST00000379120;ENST00000268794;ENST00000422392	T;T	0.68765	-0.35;-0.35	5.22	5.22	0.72569	Cadherin (4);Cadherin-like (1);	0.000000	0.51477	D	0.000100	T	0.74696	0.3750	L	0.39467	1.215	0.80722	D	1	D;P	0.89917	1.0;0.941	D;B	0.73708	0.981;0.441	T	0.77159	-0.2690	10	0.66056	D	0.02	.	14.391	0.66978	1.0:0.0:0.0:0.0	.	233;233	Q9UII8;P12830	.;CADH1_HUMAN	R	233	ENSP00000261769:H233R;ENSP00000414946:H233R	ENSP00000261769:H233R	H	+	2	0	CDH1	67401611	1.000000	0.71417	0.996000	0.52242	0.885000	0.51271	8.671000	0.91174	2.096000	0.63516	0.455000	0.32223	CAC		0.532	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360	
ADAMTS18	170692	hgsc.bcm.edu	37	16	77389967	77389967	+	Missense_Mutation	SNP	T	T	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr16:77389967T>G	ENST00000282849.5	-	9	1748	c.1330A>C	c.(1330-1332)Atg>Ctg	p.M444L		NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	444	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						TCGTGAATCATACCAAAGCTG	0.403																																																	0			16											96.0	88.0	91.0					16																	77389967		2198	4300	6498	75947468	SO:0001583	missense	170692			AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17110	protein-coding gene	gene with protein product		607512	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"""	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.1330A>C	16.37:g.77389967T>G	ENSP00000282849:p.Met444Leu		75947468	Q6P4R5|Q6ZWJ9	Missense_Mutation	SNP	ENST00000282849.5	37	CCDS10926.1	.	.	.	.	.	.	.	.	.	.	T	18.72	3.683950	0.68157	.	.	ENSG00000140873	ENST00000282849	T	0.61980	0.06	5.19	5.19	0.71726	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.85682	D	0.000000	T	0.77922	0.4203	M	0.76170	2.325	0.58432	D	0.999999	P;D	0.60575	0.909;0.988	P;D	0.70227	0.646;0.968	T	0.80654	-0.1286	10	0.72032	D	0.01	.	14.6804	0.69012	0.0:0.0:0.0:1.0	.	444;444	Q8TE60-2;Q8TE60	.;ATS18_HUMAN	L	444	ENSP00000282849:M444L	ENSP00000282849:M444L	M	-	1	0	ADAMTS18	75947468	1.000000	0.71417	1.000000	0.80357	0.253000	0.25986	7.825000	0.86693	2.311000	0.77944	0.533000	0.62120	ATG		0.403	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1		
BANP	54971	hgsc.bcm.edu	37	16	88039785	88039785	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr16:88039785A>G	ENST00000393207.1	+	6	766	c.545A>G	c.(544-546)gAg>gGg	p.E182G	BANP_ENST00000355022.4_Missense_Mutation_p.E151G|BANP_ENST00000286122.7_Missense_Mutation_p.E182G|BANP_ENST00000393208.2_Missense_Mutation_p.E151G|BANP_ENST00000355163.5_Missense_Mutation_p.E157G|BANP_ENST00000538234.1_Missense_Mutation_p.E190G|BANP_ENST00000479780.2_Missense_Mutation_p.E151G	NM_001173543.1	NP_001167014.1	Q8N9N5	BANP_HUMAN	BTG3 associated nuclear protein	182	Interaction with CUX1 and HDAC1. {ECO:0000250}.				cell cycle (GO:0007049)|chromatin modification (GO:0016568)|multicellular organismal development (GO:0007275)|negative regulation of protein catabolic process (GO:0042177)|protein localization to nucleus (GO:0034504)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)	12				BRCA - Breast invasive adenocarcinoma(80;0.00551)		AGCGGCTCGGAGGCCAGCGAC	0.652																																																	0			16											71.0	70.0	70.0					16																	88039785		2198	4299	6497	86597286	SO:0001583	missense	54971			AK094158	CCDS10966.2, CCDS42215.1, CCDS54052.1, CCDS54053.1, CCDS54054.1	16q24	2012-11-22			ENSG00000172530	ENSG00000172530		"""BEN domain containing"""	13450	protein-coding gene	gene with protein product	"""BEN domain containing 1"""	611564				10940556, 10950932	Standard	NM_017869		Approved	SMARBP1, SMAR1, FLJ20538, DKFZp761H172, FLJ10177, BEND1	uc010vow.2	Q8N9N5	OTTHUMG00000137678	ENST00000393207.1:c.545A>G	16.37:g.88039785A>G	ENSP00000376902:p.Glu182Gly		86597286	A8MU25|A8MX25|B2RCF7|B4DNJ9|F5GZM0|Q96GJ7|Q9NWY1	Missense_Mutation	SNP	ENST00000393207.1	37	CCDS54054.1	.	.	.	.	.	.	.	.	.	.	A	27.6	4.846486	0.91277	.	.	ENSG00000172530	ENST00000439677;ENST00000286122;ENST00000355163;ENST00000289484;ENST00000479780;ENST00000393208;ENST00000540932;ENST00000355022;ENST00000538234;ENST00000393207	T;T;T;T;T;T;T;T	0.25579	1.79;1.79;1.79;1.79;1.79;1.79;1.79;1.79	5.43	5.43	0.79202	.	0.045450	0.85682	D	0.000000	T	0.38852	0.1056	L	0.27053	0.805	0.58432	D	0.999999	D;D;P;D;D;D	0.89917	0.993;1.0;0.948;0.994;0.969;1.0	D;D;P;D;P;D	0.85130	0.968;0.993;0.452;0.979;0.556;0.997	T	0.28776	-1.0033	10	0.72032	D	0.01	.	14.9579	0.71131	1.0:0.0:0.0:0.0	.	190;157;151;182;151;151	B4DE54;B4DNJ9;B2RCF7;Q8N9N5;Q8N9N5-2;Q8N9N5-4	.;.;.;BANP_HUMAN;.;.	G	157;182;157;147;151;151;151;151;190;182	ENSP00000411479:E157G;ENSP00000286122:E182G;ENSP00000347290:E157G;ENSP00000432508:E151G;ENSP00000376903:E151G;ENSP00000347125:E151G;ENSP00000444352:E190G;ENSP00000376902:E182G	ENSP00000286122:E182G	E	+	2	0	BANP	86597286	1.000000	0.71417	1.000000	0.80357	0.736000	0.42039	8.101000	0.89546	2.186000	0.69663	0.533000	0.62120	GAG		0.652	BANP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269166.1	NM_017869	
ATP5A1	498	hgsc.bcm.edu	37	18	43669870	43669870	+	Silent	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr18:43669870T>C	ENST00000398752.6	-	4	523	c.402A>G	c.(400-402)acA>acG	p.T134T	ATP5A1_ENST00000593152.2_Silent_p.T84T|ATP5A1_ENST00000282050.2_Silent_p.T134T|ATP5A1_ENST00000590665.1_Silent_p.T134T	NM_001001935.2|NM_004046.5	NP_001001935.1|NP_004037.1	P25705	ATPA_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle	134					ATP biosynthetic process (GO:0006754)|ATP catabolic process (GO:0006200)|ATP hydrolysis coupled proton transport (GO:0015991)|cellular metabolic process (GO:0044237)|embryo development (GO:0009790)|lipid metabolic process (GO:0006629)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|negative regulation of endothelial cell proliferation (GO:0001937)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|proton-transporting ATP synthase complex, catalytic core F(1) (GO:0045261)	ATP binding (GO:0005524)|MHC class I protein binding (GO:0042288)|poly(A) RNA binding (GO:0044822)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transmembrane transporter activity (GO:0022857)			breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(8)|skin(1)|urinary_tract(1)	22						CAATGGCTCCTGTCCTCTTCA	0.433																																																	0			18											127.0	98.0	108.0					18																	43669870		2203	4300	6503	41923868	SO:0001819	synonymous_variant	498			D14710	CCDS11927.1, CCDS58620.1, CCDS59315.1	18q21	2012-10-12	2006-01-13		ENSG00000152234	ENSG00000152234	3.6.1.14	"""Mitochondrial respiratory chain complex / Complex V"", ""ATPases / F-type"""	823	protein-coding gene	gene with protein product		164360	"""ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 2, non-cardiac muscle-like 2"", ""ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 1, cardiac muscle"""	ATP5AL2, ATPM		1830491	Standard	NM_001257334		Approved	ATP5A, hATP1, OMR, ORM	uc002lbr.2	P25705	OTTHUMG00000132637	ENST00000398752.6:c.402A>G	18.37:g.43669870T>C			41923868	A8K092|B4DY56|K7ENP3|Q53XX6|Q8IXV2|Q96FB4|Q96HW2|Q96IR6|Q9BTV8	Silent	SNP	ENST00000398752.6	37	CCDS11927.1																																																																																				0.433	ATP5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255884.1	NM_004046	
SMAD4	4089	hgsc.bcm.edu	37	18	48591827	48591827	+	Silent	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr18:48591827A>G	ENST00000342988.3	+	9	1528	c.990A>G	c.(988-990)gaA>gaG	p.E330E	SMAD4_ENST00000398417.2_Silent_p.E330E|SMAD4_ENST00000588745.1_Silent_p.E234E	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	330	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.		E -> G (in JPS; dbSNP:rs281875324). {ECO:0000269|PubMed:12417513}.		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)		CTTACTTTGAAATGGATGTTC	0.423																																																	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											259.0	224.0	236.0					18																	48591827		2203	4300	6503	46845825	SO:0001819	synonymous_variant	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.990A>G	18.37:g.48591827A>G			46845825	A8K405	Silent	SNP	ENST00000342988.3	37	CCDS11950.1																																																																																				0.423	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359	
CDH7	1005	hgsc.bcm.edu	37	18	63489414	63489414	+	Silent	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr18:63489414A>G	ENST00000397968.2	+	5	1149	c.723A>G	c.(721-723)ggA>ggG	p.G241G	CDH7_ENST00000536984.2_Silent_p.G241G|CDH7_ENST00000323011.3_Silent_p.G241G	NM_004361.2	NP_004352.2	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2	241	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(43)|ovary(3)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	80		Esophageal squamous(42;0.129)				AAAATGGAGGACTGTCAGGAA	0.443																																																	0			18											171.0	124.0	140.0					18																	63489414		2203	4300	6503	61640394	SO:0001819	synonymous_variant	28513			AB035301	CCDS11993.1	18q22.1	2010-01-26			ENSG00000081138	ENSG00000081138		"""Cadherins / Major cadherins"""	1766	protein-coding gene	gene with protein product		605806				9615235	Standard	NM_033646		Approved		uc002ljz.3	Q9ULB5	OTTHUMG00000132800	ENST00000397968.2:c.723A>G	18.37:g.63489414A>G			61640394	Q9H157	Silent	SNP	ENST00000397968.2	37	CCDS11993.1																																																																																				0.443	CDH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256217.2	NM_033646	
CNDP2	55748	hgsc.bcm.edu	37	18	72178204	72178204	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr18:72178204T>C	ENST00000324262.4	+	6	929	c.613T>C	c.(613-615)Tgc>Cgc	p.C205R	CNDP2_ENST00000324301.8_Missense_Mutation_p.C121R|CNDP2_ENST00000579847.1_Missense_Mutation_p.C205R	NM_018235.2	NP_060705.2	Q96KP4	CNDP2_HUMAN	CNDP dipeptidase 2 (metallopeptidase M20 family)	205					cellular nitrogen compound metabolic process (GO:0034641)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|tripeptidase activity (GO:0034701)			breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(5)|ovary(2)|skin(2)|stomach(3)	24		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.22)		GAAGAAGCCCTGCATCACCTA	0.493																																																	0			18											121.0	102.0	109.0					18																	72178204		2203	4300	6503	70329184	SO:0001583	missense	55748			AK001692	CCDS12006.1, CCDS54190.1	18q22.3	2014-07-14	2004-07-12		ENSG00000133313	ENSG00000133313	3.4.13.18		24437	protein-coding gene	gene with protein product	"""cytosolic nonspecific dipeptidase"""	169800	"""peptidase A"""	PEPA		12473676	Standard	NM_018235		Approved	FLJ10830, CN2, HsT2298, CPGL	uc002llm.2	Q96KP4	OTTHUMG00000132853	ENST00000324262.4:c.613T>C	18.37:g.72178204T>C	ENSP00000325548:p.Cys205Arg		70329184	B3KUG4|Q8WY59|Q9BQ94|Q9NVB4	Missense_Mutation	SNP	ENST00000324262.4	37	CCDS12006.1	.	.	.	.	.	.	.	.	.	.	T	13.20	2.165232	0.38217	.	.	ENSG00000133313	ENST00000324262;ENST00000324301	T	0.20598	2.06	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.61073	0.2318	H	0.95365	3.66	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	T	0.73547	-0.3948	10	0.87932	D	0	0.0	16.8222	0.85835	0.0:0.0:0.0:1.0	.	110;121;205	B4DPF1;Q96KP4-2;Q96KP4	.;.;CNDP2_HUMAN	R	205;121	ENSP00000325548:C205R	ENSP00000325548:C205R	C	+	1	0	CNDP2	70329184	1.000000	0.71417	0.988000	0.46212	0.702000	0.40608	6.222000	0.72249	2.371000	0.80710	0.533000	0.62120	TGC		0.493	CNDP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256327.1	NM_018235	
VHL	7428	hgsc.bcm.edu	37	3	10188214	10188214	+	Missense_Mutation	SNP	C	C	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:10188214C>A	ENST00000256474.2	+	2	1197	c.357C>A	c.(355-357)ttC>ttA	p.F119L	VHL_ENST00000345392.2_Intron|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	119	Involved in binding to CCT complex.		F -> L (in pheochromocytoma and VHLD; type II). {ECO:0000269|PubMed:12000816}.|F -> S (in VHLD; type II). {ECO:0000269|PubMed:8825918}.		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.F119L(3)|p.?(1)|p.L118_G123>P(1)|p.W117fs*1(1)|p.F119fs*40(1)|p.F119fs*11(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		TTTGGCTCTTCAGAGATGCAG	0.502		1	"""D, Mis, N, F, S"""		"""renal, hemangioma, pheochromocytoma"""	"""renal, hemangioma, pheochromocytoma"""			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																														yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"""E, M, O"""	8	Substitution - Missense(3)|Deletion - Frameshift(3)|Unknown(1)|Complex - deletion inframe(1)	kidney(8)	3	GRCh37	CM951287	VHL	M							178.0	165.0	170.0					3																	10188214		2203	4300	6503	10163214	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.357C>A	3.37:g.10188214C>A	ENSP00000256474:p.Phe119Leu		10163214	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.988860	0.74589	.	.	ENSG00000134086	ENST00000256474;ENST00000450183	D	0.99677	-6.37	5.07	5.07	0.68467	von Hippel-Lindau disease tumor suppressor,  beta domain (1);von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);	0.000000	0.85682	D	0.000000	D	0.99515	0.9827	L	0.56340	1.77	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.98181	1.0457	10	0.66056	D	0.02	-6.0328	16.3181	0.82935	0.0:1.0:0.0:0.0	.	119	P40337	VHL_HUMAN	L	119;37	ENSP00000256474:F119L	ENSP00000256474:F119L	F	+	3	2	VHL	10163214	1.000000	0.71417	1.000000	0.80357	0.377000	0.30045	5.803000	0.69129	2.530000	0.85305	0.563000	0.77884	TTC		0.502	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551	
VHL	7428	hgsc.bcm.edu	37	3	10188240	10188240	+	Missense_Mutation	SNP	T	T	C	rs5030649		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:10188240T>C	ENST00000256474.2	+	2	1223	c.383T>C	c.(382-384)cTt>cCt	p.L128P	VHL_ENST00000345392.2_Intron|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	128	Involved in binding to CCT complex.		L -> F (in VHLD; type II).		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.L128H(4)|p.L128P(4)|p.L128R(2)|p.H125fs*27(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		CACGATGGGCTTCTGGTTAAC	0.488		1	"""D, Mis, N, F, S"""		"""renal, hemangioma, pheochromocytoma"""	"""renal, hemangioma, pheochromocytoma"""			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																														yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"""E, M, O"""	11	Substitution - Missense(10)|Deletion - Frameshift(1)	kidney(11)	3	GRCh37	CM040270	VHL	M							204.0	188.0	194.0					3																	10188240		2203	4300	6503	10163240	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.383T>C	3.37:g.10188240T>C	ENSP00000256474:p.Leu128Pro		10163240	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	T	14.37	2.515896	0.44763	.	.	ENSG00000134086	ENST00000256474;ENST00000450183	D	0.99848	-7.14	5.07	5.07	0.68467	von Hippel-Lindau disease tumor suppressor,  beta domain (1);von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);	0.070012	0.64402	D	0.000019	D	0.99729	0.9894	M	0.73962	2.25	0.80722	D	1	D	0.89917	1.0	D	0.72625	0.978	D	0.97047	0.9761	10	0.87932	D	0	-11.7092	13.0887	0.59156	0.0:0.0:0.0:1.0	.	128	P40337	VHL_HUMAN	P	128;46	ENSP00000256474:L128P	ENSP00000256474:L128P	L	+	2	0	VHL	10163240	1.000000	0.71417	1.000000	0.80357	0.171000	0.22731	5.965000	0.70387	2.047000	0.60756	0.460000	0.39030	CTT		0.488	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551	
VHL	7428	hgsc.bcm.edu	37	3	10188309	10188309	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:10188309T>C	ENST00000256474.2	+	2	1292	c.452T>C	c.(451-453)aTc>aCc	p.I151T	VHL_ENST00000345392.2_Intron|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	151	Involved in binding to CCT complex.				cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.I151T(7)|p.I151S(6)|p.I151N(3)|p.I151>?(1)|p.?(1)|p.N150fs*7(1)|p.I151_T152del(1)|p.I151fs*8(1)|p.G144fs*19(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		TTTGCCAATATCACACTGCCA	0.398		1	"""D, Mis, N, F, S"""		"""renal, hemangioma, pheochromocytoma"""	"""renal, hemangioma, pheochromocytoma"""			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																														yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"""E, M, O"""	22	Substitution - Missense(16)|Deletion - Frameshift(3)|Complex(1)|Deletion - In frame(1)|Unknown(1)	kidney(22)	3	GRCh37	CM994244	VHL	M							195.0	182.0	187.0					3																	10188309		2203	4300	6503	10163309	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.452T>C	3.37:g.10188309T>C	ENSP00000256474:p.Ile151Thr		10163309	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	T	19.92	3.915471	0.73098	.	.	ENSG00000134086	ENST00000256474;ENST00000450183	D	0.99876	-7.41	4.89	4.89	0.63831	von Hippel-Lindau disease tumor suppressor,  beta domain (1);von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);	0.000000	0.85682	D	0.000000	D	0.99796	0.9913	M	0.76574	2.34	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96623	0.9461	10	0.87932	D	0	0.0775	12.7607	0.57363	0.0:0.0:0.0:1.0	.	151	P40337	VHL_HUMAN	T	151;69	ENSP00000256474:I151T	ENSP00000256474:I151T	I	+	2	0	VHL	10163309	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	5.968000	0.70413	1.966000	0.57179	0.460000	0.39030	ATC		0.398	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551	
VHL	7428	hgsc.bcm.edu	37	3	10188318	10188318	+	Missense_Mutation	SNP	C	C	T			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:10188318C>T	ENST00000256474.2	+	2	1301	c.461C>T	c.(460-462)cCa>cTa	p.P154L	VHL_ENST00000345392.2_Intron|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	154	Involved in binding to CCT complex.		P -> L (in VHLD; type II).		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.?(2)|p.P154L(2)|p.P154fs*5(1)|p.L153fs*4(1)|p.?fs(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		ATCACACTGCCAGGTACTGAC	0.403		1	"""D, Mis, N, F, S"""		"""renal, hemangioma, pheochromocytoma"""	"""renal, hemangioma, pheochromocytoma"""			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																														yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"""E, M, O"""	7	Substitution - Missense(2)|Unknown(2)|Deletion - Frameshift(2)|Insertion - Frameshift(1)	kidney(7)	3	GRCh37	CM941378	VHL	M							173.0	164.0	167.0					3																	10188318		2203	4300	6503	10163318	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.461C>T	3.37:g.10188318C>T	ENSP00000256474:p.Pro154Leu		10163318	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.511774	0.85389	.	.	ENSG00000134086	ENST00000256474;ENST00000450183	D	0.99841	-7.09	4.79	4.79	0.61399	von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);von Hippel-Lindau disease tumor suppressor, alpha domain (1);	0.055625	0.64402	D	0.000001	D	0.99757	0.9902	M	0.75777	2.31	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96868	0.9637	10	0.87932	D	0	-3.2366	15.7004	0.77538	0.0:1.0:0.0:0.0	.	154	P40337	VHL_HUMAN	L	154;72	ENSP00000256474:P154L	ENSP00000256474:P154L	P	+	2	0	VHL	10163318	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	5.806000	0.69150	2.380000	0.81148	0.563000	0.77884	CCA		0.403	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551	
TSEN2	80746	hgsc.bcm.edu	37	3	12558136	12558136	+	Silent	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:12558136A>G	ENST00000284995.6	+	7	1323	c.936A>G	c.(934-936)ggA>ggG	p.G312G	TSEN2_ENST00000314571.7_Silent_p.G286G|C3orf83_ENST00000567514.1_Intron|TSEN2_ENST00000454502.2_Silent_p.G253G|TSEN2_ENST00000444864.1_Silent_p.G286G|TSEN2_ENST00000415684.1_Silent_p.G286G|RNU6-377P_ENST00000515965.1_RNA|TSEN2_ENST00000383797.5_Intron|TSEN2_ENST00000402228.3_Silent_p.G312G	NM_025265.3	NP_079541.1	Q8NCE0	SEN2_HUMAN	TSEN2 tRNA splicing endonuclease subunit	312					mRNA processing (GO:0006397)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|tRNA-intron endonuclease complex (GO:0000214)	lyase activity (GO:0016829)|nucleic acid binding (GO:0003676)|tRNA-intron endonuclease activity (GO:0000213)			central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(7)	19						ATGCTCTGGGATGTTTAAGTA	0.328																																																	0			3											158.0	133.0	141.0					3																	12558136		2203	4299	6502	12533136	SO:0001819	synonymous_variant	80746			BC019582	CCDS2611.1, CCDS46757.1, CCDS46758.1, CCDS46759.1	3p25.2	2013-08-06	2013-08-06		ENSG00000154743	ENSG00000154743		"""tRNA splicing endonuclease subunits"""	28422	protein-coding gene	gene with protein product		608753	"""tRNA splicing endonuclease 2 homolog (SEN2, S. cerevisiae)"", ""tRNA splicing endonuclease 2 homolog (S. cerevisiae)"""			15109492	Standard	NM_025265		Approved	SEN2, SEN2L, MGC2776	uc003bxb.3	Q8NCE0	OTTHUMG00000129765	ENST00000284995.6:c.936A>G	3.37:g.12558136A>G			12533136	B7Z6K1|C9IZI7|G5E9Q3|Q8WTW7|Q9BPU7	Silent	SNP	ENST00000284995.6	37	CCDS2611.1																																																																																				0.328	TSEN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251981.1	NM_025265	
MLH1	4292	hgsc.bcm.edu	37	3	37053590	37053590	+	Splice_Site	SNP	G	G	A	rs63751711|rs587779032|rs587779033|rs267607779		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:37053590G>A	ENST00000231790.2	+	8	893	c.677G>A	c.(676-678)cGa>cAa	p.R226Q	MLH1_ENST00000539477.1_5'UTR|MLH1_ENST00000455445.2_5'UTR|MLH1_ENST00000435176.1_Splice_Site_p.R128Q|MLH1_ENST00000458205.2_5'UTR|MLH1_ENST00000536378.1_5'UTR	NM_000249.3|NM_001258273.1	NP_000240.1|NP_001245202.1	P40692	MLH1_HUMAN	mutL homolog 1	226			Missing (in HNPCC2).|R -> L (in HNPCC2). {ECO:0000269|PubMed:8566964}.		ATP catabolic process (GO:0006200)|double-strand break repair via nonhomologous end joining (GO:0006303)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|male meiosis chromosome segregation (GO:0007060)|meiotic metaphase I plate congression (GO:0043060)|mismatch repair (GO:0006298)|negative regulation of mitotic recombination (GO:0045950)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|oogenesis (GO:0048477)|resolution of meiotic recombination intermediates (GO:0000712)|somatic hypermutation of immunoglobulin genes (GO:0016446)|spermatogenesis (GO:0007283)|spindle midzone assembly involved in meiosis (GO:0051257)|synapsis (GO:0007129)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|guanine/thymine mispair binding (GO:0032137)	p.0?(1)		NS(1)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(54)|lung(13)|oesophagus(7)|ovary(6)|pancreas(5)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	127						GCTGTTAGTCGGTATGTCGAT	0.348		1	"""D, Mis, N, F, S"""		"""colorectal, endometrial, ovarian, CNS"""	"""colorectal, endometrial, ovarian, CNS"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																														yes	Rec	yes	"""Hereditary non-polyposis colorectal cancer, Turcot syndrome"""	3	3p21.3	4292	E.coli MutL homolog gene		"""E, O"""	1	Whole gene deletion(1)	ovary(1)	3	GRCh37	CM045463|CM082944|CS951471|CS961616	MLH1	M|S							111.0	101.0	105.0					3																	37053590		2203	4300	6503	37028594	SO:0001630	splice_region_variant	4292	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	U07418	CCDS2663.1, CCDS54562.1, CCDS54563.1	3p22.3	2014-09-17	2013-09-12		ENSG00000076242	ENSG00000076242			7127	protein-coding gene	gene with protein product		120436	"""mutL (E. coli) homolog 1 (colon cancer, nonpolyposis type 2)"", ""mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)"""	COCA2		7903889	Standard	NM_000249		Approved	HNPCC, FCC2, HNPCC2	uc003cgl.3	P40692	OTTHUMG00000130797	ENST00000231790.2:c.677+1G>A	3.37:g.37053590G>A			37028594	B4DI13|B4DQ11|E9PCU2	Missense_Mutation	SNP	ENST00000231790.2	37	CCDS2663.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	37|37	6.267885|6.267885	0.97426|0.97426	.|.	.|.	ENSG00000076242|ENSG00000076242	ENST00000456676|ENST00000231790;ENST00000436867;ENST00000537937;ENST00000383761;ENST00000435176	.|D;D	.|0.90788	.|-2.73;-2.73	5.46|5.46	5.46|5.46	0.80206|0.80206	.|Ribosomal protein S5 domain 2-type fold (1);DNA mismatch repair protein, N-terminal (1);Ribosomal protein S5 domain 2-type fold, subgroup (1);DNA mismatch repair protein, C-terminal (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.93223|0.93223	0.7841|0.7841	L|L	0.49126|0.49126	1.545|1.545	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.67145	.|0.996;0.989;0.991	.|P;P;P	.|0.59643	.|0.861;0.832;0.832	D|D	0.93288|0.93288	0.6666|0.6666	5|10	.|0.62326	.|D	.|0.03	-5.9319|-5.9319	19.6609|19.6609	0.95871|0.95871	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|128;226;226	.|E9PCU2;Q53GX1;P40692	.|.;.;MLH1_HUMAN	K|Q	218|226;192;192;90;128	.|ENSP00000231790:R226Q;ENSP00000402564:R128Q	.|ENSP00000231790:R226Q	E|R	+|+	1|2	0|0	MLH1|MLH1	37028594|37028594	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.976000|0.976000	0.68499|0.68499	9.270000|9.270000	0.95690|0.95690	2.736000|2.736000	0.93811|0.93811	0.655000|0.655000	0.94253|0.94253	GAG|CGA		0.348	MLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253337.2	NM_000249	Missense_Mutation
DLEC1	9940	hgsc.bcm.edu	37	3	38104250	38104250	+	Missense_Mutation	SNP	C	C	T			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:38104250C>T	ENST00000308059.6	+	5	1073	c.1052C>T	c.(1051-1053)cCa>cTa	p.P351L	DLEC1_ENST00000346219.3_Missense_Mutation_p.P351L|DLEC1_ENST00000452631.2_Missense_Mutation_p.P351L					deleted in lung and esophageal cancer 1									p.P351R(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		CCAAAGAAGCCAGCACCGATA	0.463																																																	1	Substitution - Missense(1)	breast(1)	3											77.0	74.0	75.0					3																	38104250		1846	4093	5939	38079254	SO:0001583	missense	9940			AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 81"""	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.1052C>T	3.37:g.38104250C>T	ENSP00000308597:p.Pro351Leu		38079254		Missense_Mutation	SNP	ENST00000308059.6	37	CCDS2672.2	.	.	.	.	.	.	.	.	.	.	C	6.499	0.460334	0.12342	.	.	ENSG00000008226	ENST00000308059;ENST00000346219;ENST00000452631	T;T;T	0.05649	3.42;3.41;3.65	4.67	3.8	0.43715	.	0.850025	0.10774	N	0.635668	T	0.07863	0.0197	L	0.56769	1.78	0.27107	N	0.962483	B;P;B;P	0.34864	0.344;0.473;0.335;0.473	B;B;B;B	0.31751	0.054;0.088;0.135;0.088	T	0.23190	-1.0195	10	0.26408	T	0.33	-3.0099	8.914	0.35570	0.0:0.8974:0.0:0.1026	.	351;351;351;351	A1L305;F8W6T4;Q9Y238-3;Q9Y238	.;.;.;DLEC1_HUMAN	L	351	ENSP00000308597:P351L;ENSP00000315914:P351L;ENSP00000410427:P351L	ENSP00000308597:P351L	P	+	2	0	DLEC1	38079254	0.071000	0.21146	0.175000	0.22980	0.200000	0.23975	0.735000	0.26115	1.324000	0.45282	-0.140000	0.14226	CCA		0.463	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337	
CTNNB1	1499	hgsc.bcm.edu	37	3	41266135	41266135	+	Silent	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:41266135T>C	ENST00000349496.5	+	3	412	c.132T>C	c.(130-132)ccT>ccC	p.P44P	CTNNB1_ENST00000405570.1_Silent_p.P44P|CTNNB1_ENST00000396185.3_Silent_p.P44P|CTNNB1_ENST00000396183.3_Silent_p.P44P|CTNNB1_ENST00000453024.1_Silent_p.P37P	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	44					adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|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 cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.D32_S47del(2)|p.P44_S45del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.Q28_Q61del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.P44_S45insAP(1)|p.P44_N51del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.T42_G48del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.T40_L46del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S45del(1)|p.H24_M131del(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.A21_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.P44del(1)|p.A20_S111del(1)|p.T42_K49>Q(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		CCACAGCTCCTTCTCTGAGTG	0.502		15	"""H, Mis, T"""	PLAG1	"""colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"""				Pilomatrixoma, Familial Clustering of																												Colon(6;3 56 14213 18255)			Dom	yes		3	3p22-p21.3	1499	"""catenin (cadherin-associated protein), beta 1"""		"""E, M, O"""	124	Deletion - In frame(98)|Complex - deletion inframe(18)|Unknown(7)|Insertion - In frame(1)	liver(88)|large_intestine(17)|stomach(7)|adrenal_gland(3)|soft_tissue(2)|small_intestine(2)|skin(2)|kidney(2)|haematopoietic_and_lymphoid_tissue(1)	3											85.0	75.0	78.0					3																	41266135		2203	4300	6503	41241139	SO:0001819	synonymous_variant	1499	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"""Armadillo repeat containing"""	2514	protein-coding gene	gene with protein product		116806	"""catenin (cadherin-associated protein), beta 1 (88kD)"""	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.132T>C	3.37:g.41266135T>C			41241139	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Silent	SNP	ENST00000349496.5	37	CCDS2694.1																																																																																				0.502	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210	
BSN	8927	hgsc.bcm.edu	37	3	49698674	49698674	+	Silent	SNP	T	T	C	rs146469841		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:49698674T>C	ENST00000296452.4	+	6	9510	c.9396T>C	c.(9394-9396)ttT>ttC	p.F3132F		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	3132					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		GCACCCTTTTTCCAGTCCCCG	0.607																																																	0			3											64.0	53.0	57.0					3																	49698674		2203	4300	6503	49673678	SO:0001819	synonymous_variant	8927			AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"""zinc finger protein 231"", ""neuronal double zinc finger protein"""	604020	"""bassoon (presynaptic cytomatrix protein)"""	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.9396T>C	3.37:g.49698674T>C			49673678	O43161|Q7LGH3	Silent	SNP	ENST00000296452.4	37	CCDS2800.1																																																																																				0.607	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458	
TMEM115	11070	hgsc.bcm.edu	37	3	50396032	50396032	+	Missense_Mutation	SNP	C	C	T			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:50396032C>T	ENST00000266025.3	-	1	1009	c.463G>A	c.(463-465)Gac>Aac	p.D155N	XXcos-LUCA11.5_ENST00000606589.1_Intron	NM_007024.4	NP_008955.1	Q12893	TM115_HUMAN	transmembrane protein 115	155					negative regulation of cell proliferation (GO:0008285)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(2)|endometrium(1)|lung(1)|prostate(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		ACCACACAGTCCCCCATGGTT	0.637																																																	0			3											36.0	34.0	35.0					3																	50396032		2202	4300	6502	50371036	SO:0001583	missense	11070			BC011948	CCDS2828.1	3p21.31	2008-11-04			ENSG00000126062	ENSG00000126062			30055	protein-coding gene	gene with protein product	"""placental protein 6"""	607069				11085536	Standard	NM_007024		Approved	PL6	uc003dan.1	Q12893	OTTHUMG00000044212	ENST00000266025.3:c.463G>A	3.37:g.50396032C>T	ENSP00000266025:p.Asp155Asn		50371036	A2IDB7|O14568|Q6IAY4|Q9UIX3	Missense_Mutation	SNP	ENST00000266025.3	37	CCDS2828.1	.	.	.	.	.	.	.	.	.	.	C	36	5.708013	0.96821	.	.	ENSG00000126062	ENST00000266025	T	0.10860	2.83	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.33847	0.0877	M	0.75884	2.315	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.01330	-1.1383	10	0.27785	T	0.31	-0.1149	18.3837	0.90459	0.0:1.0:0.0:0.0	.	155	Q12893	TM115_HUMAN	N	155	ENSP00000266025:D155N	ENSP00000266025:D155N	D	-	1	0	TMEM115	50371036	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.708000	0.84633	2.622000	0.88805	0.563000	0.77884	GAC		0.637	TMEM115-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102784.3	NM_007024	
ABHD14B	84836	hgsc.bcm.edu	37	3	52004110	52004110	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:52004110T>C	ENST00000483233.1	-	4	808	c.302A>G	c.(301-303)gAg>gGg	p.E101G	PCBP4_ENST00000355852.2_5'Flank|PCBP4_ENST00000395013.3_5'Flank|PCBP4_ENST00000428823.2_5'Flank|ABHD14B_ENST00000461108.1_Missense_Mutation_p.E101G|PCBP4_ENST00000461554.1_5'Flank|ABHD14B_ENST00000315877.10_Missense_Mutation_p.E99G|ABHD14B_ENST00000395008.2_Missense_Mutation_p.E101G|RP11-155D18.14_ENST00000489595.2_Intron|ABHD14B_ENST00000525795.1_Missense_Mutation_p.E101G|RP11-155D18.12_ENST00000488257.1_RNA|ABHD14B_ENST00000487005.1_5'UTR|ABHD14B_ENST00000361143.5_Missense_Mutation_p.E101G|PCBP4_ENST00000484633.1_5'Flank			Q96IU4	ABHEB_HUMAN	abhydrolase domain containing 14B	101					metabolic process (GO:0008152)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleus (GO:0005634)	hydrolase activity (GO:0016787)			large_intestine(2)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000548)|KIRC - Kidney renal clear cell carcinoma(197;0.00072)		GGGGCCCAGCTCCAAGGCATC	0.662																																																	0			3											39.0	41.0	40.0					3																	52004110		2203	4300	6503	51979150	SO:0001583	missense	84836			AK075112	CCDS2842.1	3p21.2	2009-01-12			ENSG00000114779	ENSG00000114779		"""Abhydrolase domain containing"""	28235	protein-coding gene	gene with protein product							Standard	NM_032750		Approved	MGC15429, CIB	uc011bdy.2	Q96IU4	OTTHUMG00000157816	ENST00000483233.1:c.302A>G	3.37:g.52004110T>C	ENSP00000420065:p.Glu101Gly		51979150	Q86VK8|Q8N8W5	Missense_Mutation	SNP	ENST00000483233.1	37	CCDS2842.1	.	.	.	.	.	.	.	.	.	.	T	10.28	1.307142	0.23821	.	.	ENSG00000114779	ENST00000483233;ENST00000315877;ENST00000395008;ENST00000361143;ENST00000439982;ENST00000461108;ENST00000525795	T;T;T;T;T;T	0.61392	2.1;2.1;2.1;2.1;0.11;2.1	5.58	1.82	0.25136	.	0.780131	0.12732	N	0.443770	T	0.19406	0.0466	N	0.00707	-1.245	0.09310	N	0.999995	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.30357	-0.9981	10	0.02654	T	1	-5.9318	7.7429	0.28851	0.0:0.0695:0.2631:0.6674	.	101;101	B4DQI4;Q96IU4	.;ABHEB_HUMAN	G	101;99;101;101;101;101;101	ENSP00000420065:E101G;ENSP00000318248:E99G;ENSP00000378455:E101G;ENSP00000354841:E101G;ENSP00000417564:E101G;ENSP00000433388:E101G	ENSP00000318248:E99G	E	-	2	0	ABHD14B	51979150	0.000000	0.05858	0.837000	0.33122	0.998000	0.95712	0.473000	0.22132	0.361000	0.24292	0.533000	0.62120	GAG		0.662	ABHD14B-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349673.1	NM_032750	
ACY1	95	hgsc.bcm.edu	37	3	52023006	52023006	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:52023006A>G	ENST00000404366.2	+	15	1288	c.1142A>G	c.(1141-1143)gAg>gGg	p.E381G	ACY1_ENST00000458031.2_Missense_Mutation_p.E471G|ACY1_ENST00000476854.1_Missense_Mutation_p.E316G|ACY1_ENST00000494103.1_Missense_Mutation_p.E309G|ACY1_ENST00000476351.1_Missense_Mutation_p.E346G|ABHD14A-ACY1_ENST00000463937.1_Missense_Mutation_p.E482G	NM_000666.2|NM_001198895.1	NP_000657.1|NP_001185824.1	Q03154	ACY1_HUMAN	aminoacylase 1	381			E -> D (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cellular amino acid metabolic process (GO:0006520)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aminoacylase activity (GO:0004046)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	11				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000534)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Acetylcysteine(DB06151)|L-Aspartic Acid(DB00128)	CGGCTGCATGAGGCTGTGTTC	0.622																																																	0			3											127.0	114.0	119.0					3																	52023006		2203	4300	6503	51998046	SO:0001583	missense	95			L07548	CCDS2844.1, CCDS56261.1, CCDS56262.1, CCDS56263.1	3p21.2	2006-02-02			ENSG00000243989	ENSG00000243989	3.5.1.14		177	protein-coding gene	gene with protein product		104620				1707030, 6948533	Standard	NM_000666		Approved		uc003dcq.3	Q03154	OTTHUMG00000157815	ENST00000404366.2:c.1142A>G	3.37:g.52023006A>G	ENSP00000384296:p.Glu381Gly		51998046	C9J6I6|C9J9D8|C9JWD4	Missense_Mutation	SNP	ENST00000404366.2	37	CCDS2844.1	.	.	.	.	.	.	.	.	.	.	A	28.3	4.908681	0.92107	.	.	ENSG00000114786;ENSG00000114786;ENSG00000114786;ENSG00000243989;ENSG00000243989;ENSG00000243989;ENSG00000243989	ENST00000458031;ENST00000463937;ENST00000232907;ENST00000476854;ENST00000476351;ENST00000494103;ENST00000404366	T;T;T;T;T;T	0.54866	0.55;0.55;0.55;0.55;3.14;0.55	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.76849	0.4045	M	0.89904	3.07	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.79572	-0.1748	10	0.38643	T	0.18	-0.6713	15.3398	0.74287	1.0:0.0:0.0:0.0	.	471;381	B4DNW0;Q03154	.;ACY1_HUMAN	G	471;482;381;316;346;309;381	ENSP00000390557:E471G;ENSP00000420487:E482G;ENSP00000419262:E316G;ENSP00000417056:E346G;ENSP00000417618:E309G;ENSP00000384296:E381G	ENSP00000384296:E381G	E	+	2	0	ACY1;RP11-155D18.11	51998046	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	8.187000	0.89708	2.145000	0.66743	0.533000	0.62120	GAG		0.622	ACY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349657.1	NM_000666	
FLNB	2317	hgsc.bcm.edu	37	3	58135604	58135604	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:58135604A>G	ENST00000295956.4	+	37	6284	c.6119A>G	c.(6118-6120)gAa>gGa	p.E2040G	FLNB_ENST00000429972.2_Missense_Mutation_p.E2029G|FLNB_ENST00000348383.5_Missense_Mutation_p.E2040G|FLNB_ENST00000490882.1_Missense_Mutation_p.E2071G|FLNB_ENST00000419752.2_Missense_Mutation_p.E1860G|FLNB_ENST00000493452.1_Missense_Mutation_p.E1847G|FLNB_ENST00000357272.4_Missense_Mutation_p.E2040G|FLNB_ENST00000358537.3_Missense_Mutation_p.E2016G	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	2040	Interaction with the cytoplasmic tail of GP1BA.				actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		TTGGCGGTGGAAGGCCCCAGC	0.567																																																	0			3											121.0	109.0	113.0					3																	58135604		2203	4300	6503	58110644	SO:0001583	missense	2317			AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"""actin binding protein 278"""	603381	"""filamin B, beta (actin binding protein 278)"", ""Larsen syndrome 1 (autosomal dominant)"""	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.6119A>G	3.37:g.58135604A>G	ENSP00000295956:p.Glu2040Gly		58110644	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Missense_Mutation	SNP	ENST00000295956.4	37	CCDS2885.1	.	.	.	.	.	.	.	.	.	.	A	33	5.204497	0.95033	.	.	ENSG00000136068	ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000348383;ENST00000357272;ENST00000493452;ENST00000419752	D;D;D;D;D;D;D;D	0.84223	-1.82;-1.82;-1.82;-1.82;-1.82;-1.82;-1.82;-1.82	6.08	6.08	0.98989	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.95245	0.8458	H	0.96662	3.86	0.80722	D	1	D;D;D;P;D;D	0.89917	0.997;0.957;1.0;0.78;1.0;1.0	D;P;D;P;D;D	0.87578	0.973;0.788;0.998;0.464;0.998;0.998	D	0.96689	0.9509	10	0.87932	D	0	.	16.6438	0.85155	1.0:0.0:0.0:0.0	.	2016;2071;1847;1860;2029;2040	O75369-2;B2ZZ83;E7EN95;O75369-7;Q60FE7;O75369	.;.;.;.;.;FLNB_HUMAN	G	2040;2071;2016;2029;2040;2040;1847;1860	ENSP00000295956:E2040G;ENSP00000420213:E2071G;ENSP00000351339:E2016G;ENSP00000415599:E2029G;ENSP00000232447:E2040G;ENSP00000349819:E2040G;ENSP00000418510:E1847G;ENSP00000414532:E1860G	ENSP00000295956:E2040G	E	+	2	0	FLNB	58110644	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.233000	0.95337	2.333000	0.79357	0.533000	0.62120	GAA		0.567	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457	
PTPRG	5793	hgsc.bcm.edu	37	3	62153747	62153747	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:62153747A>G	ENST00000474889.1	+	8	1320	c.943A>G	c.(943-945)Agg>Ggg	p.R315G	PTPRG_ENST00000295874.10_Missense_Mutation_p.R315G	NM_002841.3	NP_002832.3	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	315	Alpha-carbonic anhydrase.				brain development (GO:0007420)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of neuron projection development (GO:0010977)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|liver(2)|lung(15)|ovary(7)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	62				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)		TCTGCATGACAGGGTGGTGTC	0.502																																																	0			3											82.0	79.0	80.0					3																	62153747		2203	4300	6503	62128787	SO:0001583	missense	5793			L09247	CCDS2895.1	3p21-p14	2013-02-11			ENSG00000144724	ENSG00000144724		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9671	protein-coding gene	gene with protein product		176886		PTPG		1711217	Standard	NM_002841		Approved	RPTPG	uc003dlb.3	P23470	OTTHUMG00000158660	ENST00000474889.1:c.943A>G	3.37:g.62153747A>G	ENSP00000418112:p.Arg315Gly		62128787	B2RU12|B7ZLX5|Q15623|Q59EE0|Q68DU5	Missense_Mutation	SNP	ENST00000474889.1	37	CCDS2895.1	.	.	.	.	.	.	.	.	.	.	A	13.43	2.235482	0.39498	.	.	ENSG00000144724	ENST00000474889;ENST00000295874	T;T	0.79749	-1.3;-1.3	5.2	4.01	0.46588	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.044132	0.85682	D	0.000000	D	0.90116	0.6912	M	0.89534	3.04	0.58432	D	0.99999	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	D	0.89080	0.3475	10	0.30854	T	0.27	.	12.3494	0.55141	0.8587:0.1413:0.0:0.0	.	315;315	P23470-2;P23470	.;PTPRG_HUMAN	G	315	ENSP00000418112:R315G;ENSP00000295874:R315G	ENSP00000295874:R315G	R	+	1	2	PTPRG	62128787	1.000000	0.71417	0.974000	0.42286	0.166000	0.22503	2.711000	0.47177	0.882000	0.36016	0.533000	0.62120	AGG		0.502	PTPRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351674.1	NM_002841	
FRMD4B	23150	hgsc.bcm.edu	37	3	69244257	69244257	+	Silent	SNP	C	C	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:69244257C>G	ENST00000398540.3	-	16	1487	c.1404G>C	c.(1402-1404)ctG>ctC	p.L468L	FRMD4B_ENST00000478263.1_Silent_p.L120L|FRMD4B_ENST00000542259.1_Silent_p.L414L	NM_015123.1	NP_055938	Q9Y2L6	FRM4B_HUMAN	FERM domain containing 4B	468					establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|ruffle (GO:0001726)				NS(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(2)	19		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)		CGCCTATGTTCAGGGGATACT	0.468																																																	0			3											114.0	109.0	110.0					3																	69244257		1922	4127	6049	69326947	SO:0001819	synonymous_variant	23150			AL832231	CCDS46863.1	3p14.2	2006-04-12			ENSG00000114541	ENSG00000114541			24886	protein-coding gene	gene with protein product						10231032, 11445584	Standard	XM_005264720		Approved	KIAA1013, GRSP1	uc003dnv.2	Q9Y2L6	OTTHUMG00000158772	ENST00000398540.3:c.1404G>C	3.37:g.69244257C>G			69326947	Q8TAI3	Silent	SNP	ENST00000398540.3	37	CCDS46863.1																																																																																				0.468	FRMD4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352111.1		
EPHA3	2042	hgsc.bcm.edu	37	3	89480460	89480460	+	Missense_Mutation	SNP	G	G	T			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:89480460G>T	ENST00000336596.2	+	13	2522	c.2297G>T	c.(2296-2298)gGa>gTa	p.G766V	EPHA3_ENST00000494014.1_Missense_Mutation_p.G766V	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	766	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		G -> E (in a lung adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)	p.G766E(1)		NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		TCTGATTTCGGACTTTCGCGT	0.438										TSP Lung(6;0.00050)																																							1	Substitution - Missense(1)	lung(1)	3											142.0	133.0	136.0					3																	89480460		2203	4300	6503	89563150	SO:0001583	missense	2042			M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3387	protein-coding gene	gene with protein product		179611	"""EphA3"""	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.2297G>T	3.37:g.89480460G>T	ENSP00000337451:p.Gly766Val		89563150	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	37	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	G	18.56	3.650500	0.67472	.	.	ENSG00000044524	ENST00000336596;ENST00000494014	D;D	0.92858	-3.12;-3.12	5.33	5.33	0.75918	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.98397	0.9467	H	0.99894	4.905	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99605	1.0979	9	.	.	.	.	19.3726	0.94495	0.0:0.0:1.0:0.0	.	766	P29320	EPHA3_HUMAN	V	766	ENSP00000337451:G766V;ENSP00000419190:G766V	.	G	+	2	0	EPHA3	89563150	1.000000	0.71417	1.000000	0.80357	0.245000	0.25701	9.813000	0.99286	2.648000	0.89879	0.585000	0.79938	GGA		0.438	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233	
DZIP3	9666	hgsc.bcm.edu	37	3	108391419	108391419	+	Silent	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:108391419A>G	ENST00000361582.3	+	23	2735	c.2505A>G	c.(2503-2505)gaA>gaG	p.E835E	DZIP3_ENST00000463306.1_Silent_p.E835E	NM_014648.3	NP_055463.1	Q86Y13	DZIP3_HUMAN	DAZ interacting zinc finger protein 3	835					protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|phosphatase binding (GO:0019902)|poly(A) RNA binding (GO:0044822)|polyubiquitin binding (GO:0031593)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(21)|ovary(1)|pancreas(1)|prostate(5)|skin(1)	45						CTCAGTGGGAAATGGAAAAAC	0.373																																																	0			3											100.0	96.0	97.0					3																	108391419		2203	4299	6502	109874109	SO:0001819	synonymous_variant	9666			AF279370	CCDS2952.1	3q13.13	2013-05-22	2013-05-22		ENSG00000198919	ENSG00000198919		"""RING-type (C3HC4) zinc fingers"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	30938	protein-coding gene	gene with protein product	"""human RNA-binding ubiquitin ligase of 138 kDa"", ""protein phosphatase 1, regulatory subunit 66"""	608672	"""DAZ interacting protein 3, zinc finger"""			9734811, 12538761	Standard	NM_014648		Approved	hRUL138, PPP1R66	uc003dxd.3	Q86Y13	OTTHUMG00000159232	ENST00000361582.3:c.2505A>G	3.37:g.108391419A>G			109874109	B3KN01|O75162|Q6P3R9|Q6PH82|Q86Y14|Q86Y15|Q86Y16|Q8IWI0|Q96RS9	Silent	SNP	ENST00000361582.3	37	CCDS2952.1																																																																																				0.373	DZIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353968.1	NM_014648	
MYLK	4638	hgsc.bcm.edu	37	3	123333149	123333149	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:123333149T>C	ENST00000475616.1	-	31	5547	c.5548A>G	c.(5548-5550)Agg>Ggg	p.R1850G	MYLK_ENST00000418370.2_Missense_Mutation_p.R90G|MYLK_ENST00000360304.3_Missense_Mutation_p.R1850G|MYLK_ENST00000578202.1_Missense_Mutation_p.R89G|MYLK_ENST00000359169.1_Missense_Mutation_p.R1799G|MYLK-AS1_ENST00000463408.1_RNA|MYLK-AS1_ENST00000485162.1_RNA|MYLK_ENST00000583087.1_Missense_Mutation_p.R90G|MYLK-AS1_ENST00000470449.1_RNA|MYLK_ENST00000354792.5_Missense_Mutation_p.R650G|MYLK_ENST00000346322.5_Missense_Mutation_p.R1781G|MYLK_ENST00000360772.3_Missense_Mutation_p.R1799G			Q15746	MYLK_HUMAN	myosin light chain kinase	1850	Ig-like C2-type 9.				actin filament organization (GO:0007015)|aorta smooth muscle tissue morphogenesis (GO:0060414)|bleb assembly (GO:0032060)|cellular hypotonic response (GO:0071476)|muscle contraction (GO:0006936)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell migration (GO:0030335)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|smooth muscle contraction (GO:0006939)|tonic smooth muscle contraction (GO:0014820)	cell-cell junction (GO:0005911)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|metal ion binding (GO:0046872)|myosin light chain kinase activity (GO:0004687)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(37)|ovary(7)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	113		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		CGGGACTCCCTGATTGACTGG	0.473																																																	0			3											104.0	103.0	103.0					3																	123333149		2203	4300	6503	124815839	SO:0001583	missense	4638			X85337	CCDS3023.1, CCDS43141.1, CCDS46896.1, CCDS46897.1, CCDS58849.1	3q21	2013-02-11	2008-01-23		ENSG00000065534	ENSG00000065534	2.7.11.18	"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7590	protein-coding gene	gene with protein product	"""smooth muscle myosin light chain kinase"""	600922	"""myosin, light polypeptide kinase"""			8575746	Standard	NM_053026		Approved	MLCK, smMLCK, MYLK1, MLCK1	uc003ego.3	Q15746	OTTHUMG00000141304	ENST00000475616.1:c.5548A>G	3.37:g.123333149T>C	ENSP00000418335:p.Arg1850Gly		124815839	B4DUE3|D3DN97|O95796|O95797|O95798|O95799|Q14844|Q16794|Q17S15|Q3ZCP9|Q5MY99|Q5MYA0|Q6P2N0|Q7Z4J0|Q9C0L5|Q9UBG5|Q9UBY6|Q9UIT9	Missense_Mutation	SNP	ENST00000475616.1	37	CCDS46896.1	.	.	.	.	.	.	.	.	.	.	T	14.79	2.640826	0.47153	.	.	ENSG00000065534	ENST00000360772;ENST00000360304;ENST00000359169;ENST00000418370;ENST00000346322;ENST00000354792;ENST00000475616	T;T;T;T;T;T;T	0.68331	-0.32;-0.32;-0.32;-0.32;-0.32;-0.32;-0.32	5.27	1.38	0.22167	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.67126	0.2860	L	0.31664	0.95	0.35488	D	0.798739	P;D;P;P;P;B	0.54601	0.837;0.967;0.837;0.935;0.866;0.05	P;P;P;P;P;B	0.59115	0.637;0.852;0.637;0.755;0.752;0.008	T	0.72786	-0.4188	9	0.72032	D	0.01	.	12.0458	0.53479	0.0:0.0:0.4248:0.5752	.	1849;1730;1799;1781;1850;162	Q15746-6;Q15746-4;Q15746-3;Q15746-2;Q15746;Q05D81	.;.;.;.;MYLK_HUMAN;.	G	1799;1850;1799;90;1781;650;1850	ENSP00000354004:R1799G;ENSP00000353452:R1850G;ENSP00000352088:R1799G;ENSP00000428967:R90G;ENSP00000320622:R1781G;ENSP00000346846:R650G;ENSP00000418335:R1850G	ENSP00000320622:R1781G	R	-	1	2	MYLK	124815839	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.710000	0.37920	0.079000	0.16929	0.528000	0.53228	AGG		0.473	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025	
ZNF148	7707	hgsc.bcm.edu	37	3	125032365	125032365	+	Silent	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:125032365T>C	ENST00000360647.4	-	4	605	c.120A>G	c.(118-120)ggA>ggG	p.G40G	ZNF148_ENST00000485866.1_Silent_p.G40G|ZNF148_ENST00000484491.1_Silent_p.G40G|ZNF148_ENST00000544464.1_Intron|ZNF148_ENST00000468369.1_Intron|ZNF148_ENST00000492394.1_Silent_p.G40G	NM_021964.2	NP_068799.2	Q9UQR1	ZN148_HUMAN	zinc finger protein 148	40					cellular defense response (GO:0006968)|gamete generation (GO:0007276)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein complex assembly (GO:0006461)|substantia nigra development (GO:0021762)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|liver(1)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(3)	28						CCTGTAGCTCTCCAGACACAG	0.453																																																	0			3											193.0	173.0	179.0					3																	125032365		2203	4300	6503	126515055	SO:0001819	synonymous_variant	7707			U09851	CCDS3031.1	3q21.2	2013-01-08	2006-06-13		ENSG00000163848	ENSG00000163848		"""Zinc fingers, C2H2-type"""	12933	protein-coding gene	gene with protein product		601897	"""zinc finger protein 148 (pHZ-52)"""			7557990, 9925940	Standard	NM_021964		Approved	BERF-1, ZBP-89, BFCOL1, HT-BETA, ZFP148, pHZ-52	uc003ehx.4	Q9UQR1	OTTHUMG00000159448	ENST00000360647.4:c.120A>G	3.37:g.125032365T>C			126515055	D3DN27|O00389|O43591|Q58EY5|Q6PJ98	Silent	SNP	ENST00000360647.4	37	CCDS3031.1																																																																																				0.453	ZNF148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355452.4	NM_021964	
PLXNA1	5361	hgsc.bcm.edu	37	3	126732873	126732873	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:126732873A>G	ENST00000393409.2	+	10	2324	c.2324A>G	c.(2323-2325)gAg>gGg	p.E775G	PLXNA1_ENST00000251772.4_Missense_Mutation_p.E752G	NM_032242.3	NP_115618.3	Q9UIW2	PLXA1_HUMAN	plexin A1	775					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)			breast(3)|central_nervous_system(5)|endometrium(10)|kidney(5)|large_intestine(4)|lung(32)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	67				GBM - Glioblastoma multiforme(114;0.155)		TACTCCTACGAGGGGAACGAT	0.607																																																	0			3											143.0	143.0	143.0					3																	126732873		2203	4300	6503	128215563	SO:0001583	missense	5361			X87832	CCDS33847.1, CCDS33847.2	3q21.2	2006-12-19				ENSG00000114554		"""Plexins"""	9099	protein-coding gene	gene with protein product		601055		PLXN1		8570614	Standard	NM_032242		Approved	NOV	uc003ejg.3	Q9UIW2		ENST00000393409.2:c.2324A>G	3.37:g.126732873A>G	ENSP00000377061:p.Glu775Gly		128215563		Missense_Mutation	SNP	ENST00000393409.2	37	CCDS33847.2	.	.	.	.	.	.	.	.	.	.	A	13.66	2.302485	0.40795	.	.	ENSG00000114554	ENST00000393409;ENST00000251772	T;T	0.55760	0.5;0.5	2.87	2.87	0.33458	.	2.623400	0.01687	N	0.026449	T	0.64316	0.2587	M	0.82823	2.61	0.44098	D	0.996867	B	0.27932	0.194	B	0.32677	0.15	T	0.57820	-0.7745	10	0.72032	D	0.01	.	11.6038	0.51020	1.0:0.0:0.0:0.0	.	775	Q9UIW2	PLXA1_HUMAN	G	775;752	ENSP00000377061:E775G;ENSP00000251772:E752G	ENSP00000251772:E752G	E	+	2	0	PLXNA1	128215563	1.000000	0.71417	0.997000	0.53966	0.350000	0.29205	7.252000	0.78309	1.558000	0.49541	0.402000	0.26972	GAG		0.607	PLXNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356451.1	NM_032242	
PLXNA1	5361	hgsc.bcm.edu	37	3	126752816	126752816	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:126752816A>G	ENST00000393409.2	+	31	5647	c.5647A>G	c.(5647-5649)Agc>Ggc	p.S1883G	PLXNA1_ENST00000251772.4_Missense_Mutation_p.S1860G|PLXNA1_ENST00000505278.1_3'UTR	NM_032242.3	NP_115618.3	Q9UIW2	PLXA1_HUMAN	plexin A1	1883					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)			breast(3)|central_nervous_system(5)|endometrium(10)|kidney(5)|large_intestine(4)|lung(32)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	67				GBM - Glioblastoma multiforme(114;0.155)		GCGGCTGCGGAGCAAGCTGGA	0.662																																																	0			3											27.0	27.0	27.0					3																	126752816		2200	4296	6496	128235506	SO:0001583	missense	5361			X87832	CCDS33847.1, CCDS33847.2	3q21.2	2006-12-19				ENSG00000114554		"""Plexins"""	9099	protein-coding gene	gene with protein product		601055		PLXN1		8570614	Standard	NM_032242		Approved	NOV	uc003ejg.3	Q9UIW2		ENST00000393409.2:c.5647A>G	3.37:g.126752816A>G	ENSP00000377061:p.Ser1883Gly		128235506		Missense_Mutation	SNP	ENST00000393409.2	37	CCDS33847.2	.	.	.	.	.	.	.	.	.	.	A	11.77	1.738510	0.30774	.	.	ENSG00000114554	ENST00000393409;ENST00000251772	T;T	0.09911	2.93;2.93	4.02	1.48	0.22813	.	0.085846	0.47852	N	0.000210	T	0.05823	0.0152	N	0.16903	0.455	0.28092	N	0.931742	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.24048	-1.0171	10	0.54805	T	0.06	.	5.4193	0.16392	0.7575:0.0:0.0884:0.1541	.	497;1883	Q6ZTY7;Q9UIW2	.;PLXA1_HUMAN	G	1883;1860	ENSP00000377061:S1883G;ENSP00000251772:S1860G	ENSP00000251772:S1860G	S	+	1	0	PLXNA1	128235506	0.918000	0.31147	0.775000	0.31657	0.947000	0.59692	1.211000	0.32382	0.114000	0.18032	0.260000	0.18958	AGC		0.662	PLXNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356451.1	NM_032242	
ISY1	57461	hgsc.bcm.edu	37	3	128852986	128852986	+	Silent	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:128852986T>C	ENST00000393295.3	-	9	911	c.594A>G	c.(592-594)gcA>gcG	p.A198A	ISY1_ENST00000471497.1_Intron|ISY1-RAB43_ENST00000418265.1_Silent_p.A198A|ISY1_ENST00000273541.8_Silent_p.A220A|ISY1_ENST00000393292.3_Missense_Mutation_p.K200E	NM_001199469.1|NM_020701.3	NP_001186398.1|NP_065752.1	Q9ULR0	ISY1_HUMAN	ISY1 splicing factor homolog (S. cerevisiae)	198					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(1)|lung(10)|prostate(1)|skin(1)	15						TTTCTCCTCTTGCCAGCCGAG	0.507																																																	0			3											102.0	106.0	105.0					3																	128852986		1971	4171	6142	130335676	SO:0001819	synonymous_variant	339122				CCDS43149.1, CCDS56277.1	3q21.3	2008-11-25			ENSG00000240682	ENSG00000240682			29201	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 33"""	612764				16103217	Standard	NM_020701		Approved	KIAA1160, fSAP33		Q9ULR0	OTTHUMG00000137365	ENST00000393295.3:c.594A>G	3.37:g.128852986T>C			130335676	Q96IL2|Q9BT05	Silent	SNP	ENST00000393295.3	37	CCDS43149.1	.	.	.	.	.	.	.	.	.	.	T	11.79	1.742324	0.30865	.	.	ENSG00000240682	ENST00000393292	.	.	.	5.64	0.267	0.15622	.	.	.	.	.	T	0.09862	0.0242	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.30966	-0.9960	5	0.07325	T	0.83	.	1.203	0.01889	0.1478:0.1656:0.1537:0.5329	.	.	.	.	E	200	.	ENSP00000376970:K200E	K	-	1	0	ISY1	130335676	0.469000	0.25846	0.994000	0.49952	0.983000	0.72400	-0.404000	0.07205	-0.174000	0.10743	-0.449000	0.05564	AAG		0.507	ISY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000267856.1	NM_020701	
NCK1	4690	hgsc.bcm.edu	37	3	136646963	136646963	+	Silent	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:136646963A>G	ENST00000481752.1	+	2	284	c.120A>G	c.(118-120)cgA>cgG	p.R40R	NCK1_ENST00000288986.2_Silent_p.R40R|NCK1_ENST00000469404.1_5'Flank			P16333	NCK1_HUMAN	NCK adaptor protein 1	40	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.				actin filament organization (GO:0007015)|axon guidance (GO:0007411)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|negative regulation of cell death (GO:0060548)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of translation (GO:0006417)|response to other organism (GO:0051707)|signal complex assembly (GO:0007172)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	cytoskeletal adaptor activity (GO:0008093)|protein kinase inhibitor activity (GO:0004860)|receptor binding (GO:0005102)|receptor signaling complex scaffold activity (GO:0030159)|receptor tyrosine kinase binding (GO:0030971)			cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	13						CCTGGTGGCGAGTTCGAAATT	0.388																																																	0			3											113.0	105.0	108.0					3																	136646963		2203	4300	6503	138129653	SO:0001819	synonymous_variant	4690			X17576	CCDS3092.1, CCDS54644.1	3q21	2013-02-14			ENSG00000158092	ENSG00000158092		"""SH2 domain containing"""	7664	protein-coding gene	gene with protein product		600508		NCK		7806213, 9737977	Standard	XM_005247498		Approved	NCKalpha	uc003erh.3	P16333	OTTHUMG00000159781	ENST00000481752.1:c.120A>G	3.37:g.136646963A>G			138129653	B7Z751|D3DNE3	Silent	SNP	ENST00000481752.1	37	CCDS3092.1	.	.	.	.	.	.	.	.	.	.	A	9.799	1.179994	0.21787	.	.	ENSG00000158092	ENST00000496489	.	.	.	5.98	3.64	0.41730	.	.	.	.	.	T	0.52565	0.1742	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48103	-0.9064	4	.	.	.	-6.6777	4.7045	0.12842	0.6758:0.162:0.1622:0.0	.	.	.	.	G	28	.	.	E	+	2	0	NCK1	138129653	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	2.129000	0.42055	1.082000	0.41137	-0.263000	0.10527	GAG		0.388	NCK1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357307.1	NM_006153	
CLSTN2	64084	hgsc.bcm.edu	37	3	140281734	140281734	+	Missense_Mutation	SNP	G	G	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:140281734G>A	ENST00000458420.3	+	14	2484	c.2294G>A	c.(2293-2295)cGg>cAg	p.R765Q		NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	765			R -> Q (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)	p.R765Q(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						CTTGAGGCCCGGCGTTTCCGG	0.572										HNSCC(16;0.037)																											GBM(45;858 913 3709 36904 37282)												1	Substitution - Missense(1)	large_intestine(1)	3											54.0	52.0	53.0					3																	140281734		2203	4300	6503	141764424	SO:0001583	missense	64084			AJ278018	CCDS3112.1	3q23	2011-07-01			ENSG00000158258	ENSG00000158258		"""Cadherins / Cadherin-related"""	17448	protein-coding gene	gene with protein product	"""cadherin-related family member 13"""	611323				12498782	Standard	NM_022131		Approved	CSTN2, CS2, FLJ39113, CDHR13	uc003etn.3	Q9H4D0	OTTHUMG00000160139	ENST00000458420.3:c.2294G>A	3.37:g.140281734G>A	ENSP00000402460:p.Arg765Gln		141764424	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Missense_Mutation	SNP	ENST00000458420.3	37	CCDS3112.1	.	.	.	.	.	.	.	.	.	.	G	33	5.226507	0.95173	.	.	ENSG00000158258	ENST00000458420	T	0.35236	1.32	4.83	4.83	0.62350	.	0.000000	0.85682	D	0.000000	T	0.63931	0.2553	M	0.85630	2.765	0.58432	D	0.999997	D	0.89917	1.0	D	0.79108	0.992	T	0.69194	-0.5209	9	.	.	.	-25.2099	15.766	0.78126	0.0:0.0:1.0:0.0	.	765	Q9H4D0	CSTN2_HUMAN	Q	765	ENSP00000402460:R765Q	.	R	+	2	0	CLSTN2	141764424	1.000000	0.71417	0.727000	0.30756	0.871000	0.50021	9.813000	0.99286	2.377000	0.81083	0.563000	0.77884	CGG		0.572	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131	
ATR	545	hgsc.bcm.edu	37	3	142176491	142176491	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:142176491T>C	ENST00000350721.4	-	45	7731	c.7610A>G	c.(7609-7611)gAa>gGa	p.E2537G	ATR_ENST00000383101.3_Missense_Mutation_p.E2473G	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	2537	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		E -> Q (in a breast infiltrating ductal carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		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						CATTGTAACTTCACATGCTCT	0.388								Other conserved DNA damage response genes																																									0			3											105.0	99.0	101.0					3																	142176491		2203	4300	6503	143659181	SO:0001583	missense	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.7610A>G	3.37:g.142176491T>C	ENSP00000343741:p.Glu2537Gly		143659181	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	37	CCDS3124.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	27.6|27.6	4.846962|4.846962	0.91277|0.91277	.|.	.|.	ENSG00000175054|ENSG00000175054	ENST00000350721;ENST00000383101|ENST00000513291	T;T|.	0.78003|.	-1.14;-1.14|.	5.2|5.2	5.2|5.2	0.72013|0.72013	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|.	0.87759|.	0.6258|.	H|H	0.96833|0.96833	3.89|3.89	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	D|.	0.91921|.	0.5547|.	10|.	0.87932|.	D|.	0|.	-20.4584|-20.4584	15.3539|15.3539	0.74412|0.74412	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	2537|.	Q13535|.	ATR_HUMAN|.	G|W	2537;2473|383	ENSP00000343741:E2537G;ENSP00000372581:E2473G|.	ENSP00000343741:E2537G|.	E|X	-|-	2|3	0|0	ATR|ATR	143659181|143659181	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.946000|0.946000	0.59487|0.59487	7.997000|7.997000	0.88414|0.88414	2.102000|2.102000	0.63906|0.63906	0.397000|0.397000	0.26171|0.26171	GAA|TGA		0.388	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184	
ATR	545	hgsc.bcm.edu	37	3	142204012	142204012	+	Missense_Mutation	SNP	A	A	T			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:142204012A>T	ENST00000350721.4	-	36	6312	c.6191T>A	c.(6190-6192)cTc>cAc	p.L2064H	ATR_ENST00000383101.3_Missense_Mutation_p.L2000H	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	2064	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				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						ATACCGGATGAGATCACCTTG	0.388								Other conserved DNA damage response genes																																									0			3											212.0	198.0	203.0					3																	142204012		2203	4300	6503	143686702	SO:0001583	missense	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.6191T>A	3.37:g.142204012A>T	ENSP00000343741:p.Leu2064His		143686702	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	37	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	A	18.01	3.527922	0.64860	.	.	ENSG00000175054	ENST00000350721;ENST00000383101	T;T	0.68479	-0.33;-0.33	5.2	5.2	0.72013	PIK-related kinase (1);PIK-related kinase, FAT (1);	0.133808	0.51477	D	0.000097	T	0.70771	0.3262	L	0.56199	1.76	0.80722	D	1	P	0.49961	0.93	P	0.52159	0.691	T	0.68640	-0.5355	10	0.28530	T	0.3	-7.7811	15.343	0.74311	1.0:0.0:0.0:0.0	.	2064	Q13535	ATR_HUMAN	H	2064;2000	ENSP00000343741:L2064H;ENSP00000372581:L2000H	ENSP00000343741:L2064H	L	-	2	0	ATR	143686702	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	9.128000	0.94424	2.088000	0.63022	0.377000	0.23210	CTC		0.388	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184	
MED12L	116931	hgsc.bcm.edu	37	3	150883639	150883639	+	Missense_Mutation	SNP	C	C	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:150883639C>A	ENST00000474524.1	+	10	1402	c.1364C>A	c.(1363-1365)aCt>aAt	p.T455N	MED12L_ENST00000273432.4_Missense_Mutation_p.T315N|MED12L_ENST00000422248.2_Missense_Mutation_p.T455N|MED12L_ENST00000309237.4_Missense_Mutation_p.T455N	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	455						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			ATAGGGGTGACTATTAGTCGG	0.378																																																	0			3											157.0	150.0	152.0					3																	150883639		2203	4300	6503	152366329	SO:0001583	missense	116931			AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"""			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.1364C>A	3.37:g.150883639C>A	ENSP00000417235:p.Thr455Asn		152366329	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Missense_Mutation	SNP	ENST00000474524.1	37	CCDS33876.1	.	.	.	.	.	.	.	.	.	.	C	31	5.089802	0.94149	.	.	ENSG00000144893	ENST00000422248;ENST00000309237;ENST00000474524;ENST00000273432	T;T;T;T	0.32753	1.44;1.44;1.44;1.44	5.69	5.69	0.88448	Mediator complex, subunit Med12, LCEWAV-domain (1);	0.000000	0.85682	D	0.000000	T	0.55226	0.1907	M	0.64170	1.965	0.52501	D	0.999954	P;D;D;P	0.76494	0.936;0.999;0.997;0.873	P;D;P;P	0.69824	0.756;0.966;0.9;0.461	T	0.55464	-0.8137	10	0.87932	D	0	-22.2358	19.3996	0.94623	0.0:1.0:0.0:0.0	.	315;455;455;455	F8WAE6;Q86YW9;Q86YW9-2;Q86YW9-3	.;MD12L_HUMAN;.;.	N	455;455;455;315	ENSP00000403308:T455N;ENSP00000310760:T455N;ENSP00000417235:T455N;ENSP00000273432:T315N	ENSP00000273432:T315N	T	+	2	0	MED12L	152366329	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	6.831000	0.75324	2.676000	0.91093	0.655000	0.94253	ACT		0.378	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002	
SHOX2	6474	hgsc.bcm.edu	37	3	157823550	157823550	+	Silent	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:157823550T>C	ENST00000425436.3	-	1	289	c.264A>G	c.(262-264)ggA>ggG	p.G88G	SHOX2_ENST00000554685.1_5'UTR|SHOX2_ENST00000389589.4_Silent_p.G88G|SHOX2_ENST00000441443.2_5'UTR|RSRC1_ENST00000480820.1_5'Flank|SHOX2_ENST00000490689.2_5'Flank|SHOX2_ENST00000483851.2_Silent_p.G88G	NM_001163678.1|NM_006884.3	NP_001157150.1|NP_006875.2	O60902	SHOX2_HUMAN	short stature homeobox 2	88					cardiac atrium morphogenesis (GO:0003209)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte development (GO:0002063)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic skeletal joint morphogenesis (GO:0060272)|heart development (GO:0007507)|heart valve development (GO:0003170)|muscle tissue morphogenesis (GO:0060415)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|osteoblast differentiation (GO:0001649)|positive regulation of axonogenesis (GO:0050772)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of skeletal muscle fiber development (GO:0048743)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of chondrocyte differentiation (GO:0032330)|skeletal system development (GO:0001501)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|endometrium(1)|large_intestine(1)|liver(2)|lung(10)|skin(3)|upper_aerodigestive_tract(1)	20			Lung(72;0.00318)|LUSC - Lung squamous cell carcinoma(72;0.0043)			AGCGCcctcctccagctcctc	0.751																																																	0			3											5.0	8.0	7.0					3																	157823550		1797	3830	5627	159306244	SO:0001819	synonymous_variant	6474			AJ002368	CCDS33884.1, CCDS43164.1, CCDS33884.2, CCDS54664.1	3q25.32	2011-06-20			ENSG00000168779	ENSG00000168779		"""Homeoboxes / PRD class"""	10854	protein-coding gene	gene with protein product		602504				9482898, 9466998	Standard	NM_006884		Approved	SHOT, OG12X, OG12	uc003fbs.3	O60902	OTTHUMG00000158755	ENST00000425436.3:c.264A>G	3.37:g.157823550T>C			159306244	O60465|O60467|O60903	Silent	SNP	ENST00000425436.3	37	CCDS43164.1																																																																																				0.751	SHOX2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352057.2		
PIK3CA	5290	hgsc.bcm.edu	37	3	178937020	178937020	+	Silent	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:178937020A>G	ENST00000263967.3	+	11	1858	c.1701A>G	c.(1699-1701)aaA>aaG	p.K567K		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	567	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TTCTACCCAAATTGCTTCTGT	0.353		57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)			Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	0			3											121.0	110.0	113.0					3																	178937020		1835	4079	5914	180419714	SO:0001819	synonymous_variant	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1701A>G	3.37:g.178937020A>G			180419714	Q14CW1|Q99762	Silent	SNP	ENST00000263967.3	37	CCDS43171.1																																																																																				0.353	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2		
PIK3CA	5290	hgsc.bcm.edu	37	3	178941879	178941879	+	Missense_Mutation	SNP	A	A	G	rs181194055	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:178941879A>G	ENST00000263967.3	+	15	2355	c.2198A>G	c.(2197-2199)aAg>aGg	p.K733R		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	733					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.K733R(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	GTACAGATGAAGTTTTTAGTT	0.383		57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)			A|||	4	0.000798722	0.0	0.0	5008	,	,		17323	0.004		0.0	False		,,,				2504	0.0				Colon(199;1504 1750 3362 26421 31210 32040)			Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	1	Substitution - Missense(1)	large_intestine(1)	3											131.0	117.0	121.0					3																	178941879		1817	4083	5900	180424573	SO:0001583	missense	5290				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.2198A>G	3.37:g.178941879A>G	ENSP00000263967:p.Lys733Arg		180424573	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	A	17.47	3.397526	0.62177	.	.	ENSG00000121879	ENST00000263967	T	0.81330	-1.48	6.02	6.02	0.97574	Protein kinase-like domain (1);	0.111337	0.64402	D	0.000005	T	0.78091	0.4229	L	0.60455	1.87	0.80722	D	1	B	0.09022	0.002	B	0.08055	0.003	T	0.72239	-0.4351	10	0.27082	T	0.32	-18.203	16.542	0.84395	1.0:0.0:0.0:0.0	.	733	P42336	PK3CA_HUMAN	R	733	ENSP00000263967:K733R	ENSP00000263967:K733R	K	+	2	0	PIK3CA	180424573	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.890000	0.63178	2.304000	0.77564	0.528000	0.53228	AAG		0.383	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2		
MUC4	4585	hgsc.bcm.edu	37	3	195512262	195512262	+	Silent	SNP	C	C	G	rs199610666	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:195512262C>G	ENST00000463781.3	-	2	6648	c.6189G>C	c.(6187-6189)acG>acC	p.T2063T	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Silent_p.T2063T	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)		CAGGAAGAGGCGTGGTGTCAC	0.577																																																	0			3																																								196996657	SO:0001819	synonymous_variant	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.6189G>C	3.37:g.195512262C>G			196996657	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																				0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MUC4	4585	hgsc.bcm.edu	37	3	195512497	195512497	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:195512497A>G	ENST00000463781.3	-	2	6413	c.5954T>C	c.(5953-5955)cTt>cCt	p.L1985P	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.L1985P	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)		GGTGACAGGAAGAGGGGTGGC	0.602																																																	0			3											50.0	41.0	44.0					3																	195512497		691	1590	2281	196996892	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.5954T>C	3.37:g.195512497A>G	ENSP00000417498:p.Leu1985Pro		196996892	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	A	4.493	0.091372	0.08632	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.51325	0.86;0.71	.	.	.	.	.	.	.	.	T	0.24275	0.0588	N	0.19112	0.55	0.09310	N	1	B	0.31077	0.307	B	0.27796	0.083	T	0.13980	-1.0489	7	.	.	.	.	4.0602	0.09834	0.6463:0.3536:1.0E-4:0.0	.	1985	E7ESK3	.	P	1985	ENSP00000417498:L1985P;ENSP00000420243:L1985P	.	L	-	2	0	MUC4	196996892	0.019000	0.18553	0.001000	0.08648	0.194000	0.23727	-0.233000	0.09041	-0.848000	0.04163	0.055000	0.15244	CTT		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
UBXN7	26043	hgsc.bcm.edu	37	3	196088743	196088743	+	Missense_Mutation	SNP	A	A	T			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:196088743A>T	ENST00000296328.4	-	10	1354	c.1280T>A	c.(1279-1281)aTc>aAc	p.I427N	UBXN7_ENST00000535858.1_Missense_Mutation_p.I279N|UBXN7_ENST00000428095.1_Missense_Mutation_p.I265N	NM_015562.1	NP_056377.1	O94888	UBXN7_HUMAN	UBX domain protein 7	427	UBX. {ECO:0000255|PROSITE- ProRule:PRU00215}.					Cdc48p-Npl4p-Ufd1p AAA ATPase complex (GO:0034098)|nucleus (GO:0005634)	transcription factor binding (GO:0008134)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)			NS(1)|endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	18						TGGAAGAGTGATCTGTTCCCT	0.418																																																	0			3											135.0	124.0	128.0					3																	196088743		1881	4109	5990	197573140	SO:0001583	missense	26043			AB018337	CCDS43191.1	3q29	2012-07-06	2008-07-25	2008-07-25	ENSG00000163960	ENSG00000163960		"""UBX domain containing"""	29119	protein-coding gene	gene with protein product			"""UBX domain containing 7"""	UBXD7		9872452, 22537386	Standard	NM_015562		Approved	KIAA0794	uc003fwm.4	O94888	OTTHUMG00000155639	ENST00000296328.4:c.1280T>A	3.37:g.196088743A>T	ENSP00000296328:p.Ile427Asn		197573140	D3DXB3|Q6ZP77|Q86X20|Q8N327	Missense_Mutation	SNP	ENST00000296328.4	37	CCDS43191.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.460848	0.84317	.	.	ENSG00000163960	ENST00000296328;ENST00000428095;ENST00000535858	.	.	.	5.19	5.19	0.71726	UBX (3);	0.000000	0.85682	D	0.000000	T	0.61726	0.2370	L	0.40543	1.245	0.80722	D	1	P	0.49559	0.925	P	0.53401	0.725	T	0.64525	-0.6387	9	0.56958	D	0.05	-9.1729	15.3445	0.74324	1.0:0.0:0.0:0.0	.	427	O94888	UBXN7_HUMAN	N	427;265;279	.	ENSP00000296328:I427N	I	-	2	0	UBXN7	197573140	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.561000	0.90715	2.096000	0.63516	0.533000	0.62120	ATC		0.418	UBXN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340938.2	XM_087353	
MLF2	8079	hgsc.bcm.edu	37	12	6859909	6859909	+	Silent	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr12:6859909A>G	ENST00000203630.5	-	5	884	c.240T>C	c.(238-240)ttT>ttC	p.F80F	MLF2_ENST00000435120.1_Silent_p.F80F|MLF2_ENST00000542154.1_Silent_p.F80F|MLF2_ENST00000564181.1_5'UTR|MLF2_ENST00000539187.1_Silent_p.F80F			Q15773	MLF2_HUMAN	myeloid leukemia factor 2	80			F -> C (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		defense response (GO:0006952)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				kidney(2)|large_intestine(3)|lung(4)	9						TCATCATCCCAAACATGTCCA	0.478																																																	0			12											159.0	128.0	139.0					12																	6859909		2203	4300	6503	6730170	SO:0001819	synonymous_variant	8079			U57342	CCDS8559.1	12p13.31	2014-09-11			ENSG00000089693	ENSG00000089693			7126	protein-coding gene	gene with protein product		601401				8661158	Standard	NM_005439		Approved	NTN4	uc010sfi.2	Q15773	OTTHUMG00000168717	ENST00000203630.5:c.240T>C	12.37:g.6859909A>G			6730170		Silent	SNP	ENST00000203630.5	37	CCDS8559.1																																																																																				0.478	MLF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400733.2		
LRP6	4040	hgsc.bcm.edu	37	12	12397443	12397443	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr12:12397443T>C	ENST00000261349.4	-	2	278	c.202A>G	c.(202-204)Agt>Ggt	p.S68G	LRP6_ENST00000543091.1_Missense_Mutation_p.S68G	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	68	Beta-propeller 1.				anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				CTGACATCACTCCAGTATATC	0.448																																																	0			12											121.0	101.0	108.0					12																	12397443		2203	4300	6503	12288710	SO:0001583	missense	4040			AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"""Low density lipoprotein receptors"""	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.202A>G	12.37:g.12397443T>C	ENSP00000261349:p.Ser68Gly		12288710	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	37	CCDS8647.1	.	.	.	.	.	.	.	.	.	.	T	25.4	4.631983	0.87660	.	.	ENSG00000070018	ENST00000261349;ENST00000543091	D;D	0.91996	-2.95;-2.95	5.04	5.04	0.67666	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	U	0.000007	D	0.93035	0.7783	M	0.82630	2.6	0.80722	D	1	P;P	0.50943	0.94;0.893	B;P	0.44897	0.21;0.463	D	0.94160	0.7413	10	0.87932	D	0	.	14.9552	0.71107	0.0:0.0:0.0:1.0	.	68;68	F5H7J9;O75581	.;LRP6_HUMAN	G	68	ENSP00000261349:S68G;ENSP00000442472:S68G	ENSP00000261349:S68G	S	-	1	0	LRP6	12288710	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.868000	0.87116	2.123000	0.65237	0.377000	0.23210	AGT		0.448	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1		
KRAS	3845	hgsc.bcm.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	rs121913529		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr12:25398284C>A	ENST00000256078.4	-	2	98	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000311936.3_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000556131.1_Missense_Mutation_p.G12V	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.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|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)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	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"""	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	12											91.0	81.0	85.0					12																	25398284		2203	4300	6503	25289551	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.35G>T	12.37:g.25398284C>A	ENSP00000256078:p.Gly12Val		25289551	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808637	0.90707	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90373	0.6987	M	0.90650	3.135	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72625	0.969;0.978	D	0.91773	0.5429	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	V	12	ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V	ENSP00000256078:G12V	G	-	2	0	KRAS	25289551	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		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360	
BICD1	636	hgsc.bcm.edu	37	12	32481358	32481358	+	Missense_Mutation	SNP	C	C	T			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr12:32481358C>T	ENST00000281474.5	+	5	2072	c.1969C>T	c.(1969-1971)Cgg>Tgg	p.R657W	BICD1_ENST00000548411.1_Missense_Mutation_p.R657W	NM_001714.2	NP_001705.2	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 (Drosophila)	657					anatomical structure morphogenesis (GO:0009653)|intracellular mRNA localization (GO:0008298)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900737)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein localization to organelle (GO:0033365)|regulation of proteinase activated receptor activity (GO:1900276)|RNA processing (GO:0006396)|stress granule assembly (GO:0034063)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|host cell viral assembly compartment (GO:0072517)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	cytoskeletal adaptor activity (GO:0008093)|dynactin binding (GO:0034452)|dynein binding (GO:0045502)|proteinase activated receptor binding (GO:0031871)|Rab GTPase binding (GO:0017137)|structural constituent of cytoskeleton (GO:0005200)	p.R657W(1)		NS(1)|breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)			AGCAGCGGCTCGGGAGCTAGC	0.507																																																	1	Substitution - Missense(1)	ovary(1)	12											73.0	78.0	76.0					12																	32481358		2203	4300	6503	32372625	SO:0001583	missense	636			U90028	CCDS8726.1, CCDS44859.1	12p11.2-p11.1	2005-01-13	2001-11-28			ENSG00000151746			1049	protein-coding gene	gene with protein product		602204	"""Bicaudal D (Drosophila) homolog 1"""			9367685	Standard	NM_001714		Approved		uc001rku.3	Q96G01	OTTHUMG00000169307	ENST00000281474.5:c.1969C>T	12.37:g.32481358C>T	ENSP00000281474:p.Arg657Trp		32372625	A8K2C3|F8W113|O43892|O43893	Missense_Mutation	SNP	ENST00000281474.5	37	CCDS8726.1	.	.	.	.	.	.	.	.	.	.	C	16.65	3.183320	0.57800	.	.	ENSG00000151746	ENST00000548411;ENST00000281474	T;T	0.47869	0.83;0.83	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	T	0.64516	0.2605	M	0.64997	1.995	0.80722	D	1	D;D	0.89917	1.0;1.0	P;D	0.74348	0.897;0.983	T	0.67428	-0.5673	10	0.72032	D	0.01	.	13.3962	0.60853	0.1573:0.8427:0.0:0.0	.	657;657	F8W113;Q96G01	.;BICD1_HUMAN	W	657	ENSP00000446793:R657W;ENSP00000281474:R657W	ENSP00000281474:R657W	R	+	1	2	BICD1	32372625	0.959000	0.32827	0.991000	0.47740	0.883000	0.51084	2.247000	0.43151	2.333000	0.79357	0.655000	0.94253	CGG		0.507	BICD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403380.1	NM_001714	
PRICKLE1	144165	hgsc.bcm.edu	37	12	42854287	42854287	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr12:42854287A>G	ENST00000455697.1	-	8	2105	c.1820T>C	c.(1819-1821)aTc>aCc	p.I607T	PRICKLE1_ENST00000548696.1_Missense_Mutation_p.I607T|PRICKLE1_ENST00000552240.1_Missense_Mutation_p.I607T|RP11-328C8.4_ENST00000547824.1_RNA|PRICKLE1_ENST00000445766.2_Missense_Mutation_p.I607T|PRICKLE1_ENST00000345127.3_Missense_Mutation_p.I607T	NM_001144882.1|NM_001144883.1	NP_001138354.1|NP_001138355.1	Q96MT3	PRIC1_HUMAN	prickle homolog 1 (Drosophila)	607					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)		TTCAGGCAGGATTTTCTCTGG	0.458																																																	0			12											124.0	119.0	120.0					12																	42854287		2203	4300	6503	41140554	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.1820T>C	12.37:g.42854287A>G	ENSP00000401060:p.Ile607Thr		41140554	Q14C83|Q71QF8|Q96N00	Missense_Mutation	SNP	ENST00000455697.1	37	CCDS8742.1	.	.	.	.	.	.	.	.	.	.	A	11.14	1.552347	0.27739	.	.	ENSG00000139174	ENST00000455697;ENST00000445766;ENST00000548696;ENST00000345127;ENST00000552240	T;T;T;T;T	0.61040	0.14;0.14;0.14;0.14;0.14	5.53	3.17	0.36434	.	0.369538	0.30159	N	0.010264	T	0.35770	0.0943	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.16394	-1.0404	10	0.24483	T	0.36	0.001	8.9118	0.35557	0.6587:0.0:0.3413:0.0	.	607	Q96MT3	PRIC1_HUMAN	T	607	ENSP00000401060:I607T;ENSP00000398947:I607T;ENSP00000448359:I607T;ENSP00000345064:I607T;ENSP00000449819:I607T	ENSP00000345064:I607T	I	-	2	0	PRICKLE1	41140554	0.103000	0.21917	0.413000	0.26509	0.988000	0.76386	2.644000	0.46613	0.476000	0.27440	0.528000	0.53228	ATC		0.458	PRICKLE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404069.1		
TWF1	5756	hgsc.bcm.edu	37	12	44191532	44191532	+	Silent	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr12:44191532T>C	ENST00000395510.2	-	6	717	c.588A>G	c.(586-588)agA>agG	p.R196R	TWF1_ENST00000552521.1_Silent_p.R98R|TWF1_ENST00000325127.4_Silent_p.R230R|TWF1_ENST00000548315.1_Silent_p.R203R	NM_001242397.1|NM_002822.4	NP_001229326.1|NP_002813.3	Q12792	TWF1_HUMAN	twinfilin actin-binding protein 1	196	ADF-H 2. {ECO:0000255|PROSITE- ProRule:PRU00599}.				barbed-end actin filament capping (GO:0051016)|negative regulation of actin filament polymerization (GO:0030837)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of actin phosphorylation (GO:0043538)|sequestering of actin monomers (GO:0042989)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|myofibril (GO:0030016)|perinuclear region of cytoplasm (GO:0048471)|ruffle membrane (GO:0032587)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(2)|large_intestine(6)|lung(4)|prostate(1)|stomach(1)	14	all_cancers(12;0.00125)	Lung NSC(34;0.0804)|all_lung(34;0.181)		GBM - Glioblastoma multiforme(48;0.0474)		AGTTGAGCTGTCTATTATTCA	0.373																																																	0			12											92.0	95.0	94.0					12																	44191532		2203	4300	6503	42477799	SO:0001819	synonymous_variant	5756			U02680	CCDS31780.1, CCDS31780.2, CCDS55818.1	12q12	2013-04-25	2013-04-25	2006-11-13					9620	protein-coding gene	gene with protein product		610932	"""protein tyrosine kinase 9"", ""PTK9 protein tyrosine kinase 9"", ""twinfilin, actin-binding protein, homolog 1 (Drosophila)"""	PTK9		7507208	Standard	NM_002822		Approved	A6	uc001rob.3	Q12792		ENST00000395510.2:c.588A>G	12.37:g.44191532T>C			42477799	A8K5A8|B3KXS6|B4DLX9|Q59G07|Q5U0B1|Q6FHJ1|Q6FHL6|Q6NUK9|Q86XL6|Q8TCD3	Silent	SNP	ENST00000395510.2	37	CCDS31780.2																																																																																				0.373	TWF1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403956.1	NM_002822	
OR6C4	341418	hgsc.bcm.edu	37	12	55945194	55945194	+	Missense_Mutation	SNP	C	C	T	rs139634367		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr12:55945194C>T	ENST00000394256.2	+	1	212	c.184C>T	c.(184-186)Cgg>Tgg	p.R62W	RP11-110A12.2_ENST00000556750.1_RNA|RP11-110A12.2_ENST00000555138.1_RNA	NM_001005494.1	NP_001005494.1	Q8NGE1	OR6C4_HUMAN	olfactory receptor, family 6, subfamily C, member 4	62						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R62W(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|skin(1)	11						TTTCTTCCTCCGGAATTTCTC	0.428																																																	1	Substitution - Missense(1)	endometrium(1)	12											141.0	146.0	144.0					12																	55945194		2202	4300	6502	54231461	SO:0001583	missense	341418			BK004261	CCDS31827.1	12q14.2	2012-08-09				ENSG00000179626		"""GPCR / Class A : Olfactory receptors"""	19632	protein-coding gene	gene with protein product							Standard	NM_001005494		Approved		uc010spp.2	Q8NGE1	OTTHUMG00000169959	ENST00000394256.2:c.184C>T	12.37:g.55945194C>T	ENSP00000377799:p.Arg62Trp		54231461	A8MZG7|B2RNN2|Q6IFK1	Missense_Mutation	SNP	ENST00000394256.2	37	CCDS31827.1	.	.	.	.	.	.	.	.	.	.	C	11.73	1.726383	0.30593	.	.	ENSG00000179626	ENST00000394256	T	0.01092	5.35	4.77	2.88	0.33553	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44097	D	0.000492	T	0.02418	0.0074	M	0.84326	2.69	0.09310	N	0.999999	B	0.22683	0.073	B	0.17098	0.017	T	0.25187	-1.0139	10	0.66056	D	0.02	.	10.1441	0.42753	0.2718:0.5967:0.1315:0.0	.	62	Q8NGE1	OR6C4_HUMAN	W	62	ENSP00000377799:R62W	ENSP00000377799:R62W	R	+	1	2	OR6C4	54231461	0.000000	0.05858	0.998000	0.56505	0.982000	0.71751	-2.251000	0.01186	0.685000	0.31468	-0.153000	0.13522	CGG		0.428	OR6C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406678.1		
NACA	4666	hgsc.bcm.edu	37	12	57111608	57111608	+	Missense_Mutation	SNP	A	A	G	rs12822307		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr12:57111608A>G	ENST00000454682.1	-	3	3987	c.3706T>C	c.(3706-3708)Tcc>Ccc	p.S1236P	NACA_ENST00000393891.4_Intron|NACA_ENST00000551793.1_Intron|NACA_ENST00000548563.1_Intron|NACA_ENST00000550952.1_Intron|NACA_ENST00000546392.1_Intron|NACA_ENST00000552540.1_Intron|NACA_ENST00000356769.3_Intron	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	1236	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						CCTTTGGGGGATGGGGTAGCC	0.667			T	BCL6	NHL																																			Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	0			12											58.0	78.0	72.0					12																	57111608		1230	2824	4054	55397875	SO:0001583	missense	4666			X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"""nascent-polypeptide-associated complex alpha polypeptide"""			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.3706T>C	12.37:g.57111608A>G	ENSP00000403817:p.Ser1236Pro		55397875		Missense_Mutation	SNP	ENST00000454682.1	37		.	.	.	.	.	.	.	.	.	.	A	6.444	0.450025	0.12223	.	.	ENSG00000196531	ENST00000454682	T	0.43688	0.94	3.89	-4.59	0.03400	.	.	.	.	.	T	0.19805	0.0476	.	.	.	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.19910	-1.0291	7	.	.	.	.	3.5713	0.07918	0.364:0.0:0.2606:0.3754	rs12822307	1236	E9PAV3	.	P	1236	ENSP00000403817:S1236P	.	S	-	1	0	NACA	55397875	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-5.237000	0.00138	-1.100000	0.03030	-1.185000	0.01705	TCC		0.667	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594	
NACA	4666	hgsc.bcm.edu	37	12	57111932	57111932	+	Missense_Mutation	SNP	T	T	G	rs558038375	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr12:57111932T>G	ENST00000454682.1	-	3	3663	c.3382A>C	c.(3382-3384)Acc>Ccc	p.T1128P	NACA_ENST00000393891.4_Intron|NACA_ENST00000551793.1_Intron|NACA_ENST00000548563.1_Intron|NACA_ENST00000550952.1_Intron|NACA_ENST00000546392.1_Intron|NACA_ENST00000552540.1_Intron|NACA_ENST00000356769.3_Intron	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	1128	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.T1127fs*215(1)		breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						GCAGCTGGGGTTGTGGGTGCC	0.637			T	BCL6	NHL								-|||	294	0.0587061	0.0159	0.0519	5008	,	,		4348	0.0377		0.0408	False		,,,				2504	0.1616							Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	1	Deletion - Frameshift(1)	prostate(1)	12																																								55398199	SO:0001583	missense	4666			X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"""nascent-polypeptide-associated complex alpha polypeptide"""			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.3382A>C	12.37:g.57111932T>G	ENSP00000403817:p.Thr1128Pro		55398199		Missense_Mutation	SNP	ENST00000454682.1	37		.	.	.	.	.	.	.	.	.	.	N	1.204	-0.631660	0.03584	.	.	ENSG00000196531	ENST00000454682	T	0.48522	0.81	2.51	-5.02	0.02982	.	.	.	.	.	T	0.23054	0.0557	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.08186	-1.0734	7	.	.	.	.	0.4619	0.00518	0.334:0.1221:0.1737:0.3702	.	1128	E9PAV3	.	P	1128	ENSP00000403817:T1128P	.	T	-	1	0	NACA	55398199	0.031000	0.19500	0.000000	0.03702	0.012000	0.07955	-0.022000	0.12480	-3.442000	0.00162	-1.928000	0.00512	ACC		0.637	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594	
NACA	4666	hgsc.bcm.edu	37	12	57112022	57112022	+	Missense_Mutation	SNP	A	A	G	rs560117011	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr12:57112022A>G	ENST00000454682.1	-	3	3573	c.3292T>C	c.(3292-3294)Tcc>Ccc	p.S1098P	NACA_ENST00000393891.4_Intron|NACA_ENST00000551793.1_Intron|NACA_ENST00000548563.1_Intron|NACA_ENST00000550952.1_Intron|NACA_ENST00000546392.1_Intron|NACA_ENST00000552540.1_Intron|NACA_ENST00000356769.3_Intron	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	1098	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						CCTTTGGGGGATGGGGTAGCT	0.667			T	BCL6	NHL								-|||	4	0.000798722	0.0008	0.0	5008	,	,		6986	0.0		0.003	False		,,,				2504	0.0							Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	0			12											46.0	56.0	53.0					12																	57112022		1330	2920	4250	55398289	SO:0001583	missense	4666			X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"""nascent-polypeptide-associated complex alpha polypeptide"""			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.3292T>C	12.37:g.57112022A>G	ENSP00000403817:p.Ser1098Pro		55398289		Missense_Mutation	SNP	ENST00000454682.1	37		.	.	.	.	.	.	.	.	.	.	a	6.029	0.373746	0.11409	.	.	ENSG00000196531	ENST00000454682	T	0.50813	0.73	3.67	-4.92	0.03075	.	.	.	.	.	T	0.25568	0.0622	.	.	.	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.20405	-1.0276	7	.	.	.	.	7.5955	0.28046	0.2853:0.2822:0.4325:0.0	.	1098	E9PAV3	.	P	1098	ENSP00000403817:S1098P	.	S	-	1	0	NACA	55398289	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	-9.909000	0.00008	-1.295000	0.02357	-0.923000	0.02734	TCC		0.667	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594	
NR1H4	9971	hgsc.bcm.edu	37	12	100904822	100904822	+	Missense_Mutation	SNP	G	G	A	rs375599105	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr12:100904822G>A	ENST00000551379.1	+	2	404	c.376G>A	c.(376-378)Gcg>Acg	p.A126T	NR1H4_ENST00000548884.1_Missense_Mutation_p.A116T|NR1H4_ENST00000549996.1_Missense_Mutation_p.A116T|NR1H4_ENST00000188403.7_Missense_Mutation_p.A126T|NR1H4_ENST00000392986.3_Missense_Mutation_p.A116T			Q96RI1	NR1H4_HUMAN	nuclear receptor subfamily 1, group H, member 4	126					bile acid metabolic process (GO:0008206)|cellular response to acid chemical (GO:0071229)|cellular response to organonitrogen compound (GO:0071417)|digestive tract development (GO:0048565)|gene expression (GO:0010467)|intracellular bile acid receptor signaling pathway (GO:0038185)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of bile acid biosynthetic process (GO:0070858)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nitrogen catabolite activation of transcription from RNA polymerase II promoter (GO:0001080)|positive regulation of ammonia assimilation cycle (GO:2001250)|positive regulation of glutamate metabolic process (GO:2000213)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of carbohydrate metabolic process (GO:0006109)|regulation of cholesterol metabolic process (GO:0090181)|regulation of urea metabolic process (GO:0034255)|response to glucose (GO:0009749)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)	bile acid binding (GO:0032052)|bile acid receptor activity (GO:0038181)|chenodeoxycholic acid binding (GO:1902122)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|ligand-dependent nuclear receptor binding (GO:0016922)|peptide binding (GO:0042277)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|thyroid hormone receptor activity (GO:0004887)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	44					Chenodeoxycholic acid(DB06777)	CCGCATGGGCGCGTCAGCAGG	0.522													G|||	2	0.000399361	0.0015	0.0	5008	,	,		17385	0.0		0.0	False		,,,				2504	0.0																0			12						G	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	0,4406		0,0,2203	97.0	102.0	100.0		346,346,346,376,376,346	-8.7	0.0	12		100	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense,missense	NR1H4	NM_001206977.1,NM_001206978.1,NM_001206979.1,NM_001206992.1,NM_001206993.1,NM_005123.3	58,58,58,58,58,58	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign,benign,benign,benign	116/477,116/426,116/477,126/483,126/487,116/473	100904822	1,13005	2203	4300	6503	99428953	SO:0001583	missense	9971			U68233	CCDS9078.1, CCDS55873.1, CCDS55874.1, CCDS55875.1, CCDS55876.1	12q23.1	2013-01-16				ENSG00000012504		"""Nuclear hormone receptors"""	7967	protein-coding gene	gene with protein product		603826				7774010, 9223286	Standard	NM_001206977		Approved	FXR, RIP14, HRR1, HRR-1	uc001tht.2	Q96RI1	OTTHUMG00000170359	ENST00000551379.1:c.376G>A	12.37:g.100904822G>A	ENSP00000447149:p.Ala126Thr		99428953	A1L4K5|B7Z412|B7ZM06|F8VYG8|Q8NFP5|Q8NFP6|Q92943	Missense_Mutation	SNP	ENST00000551379.1	37	CCDS55876.1	.	.	.	.	.	.	.	.	.	.	G	5.280	0.237135	0.10023	0.0	1.16E-4	ENSG00000012504	ENST00000548884;ENST00000392986;ENST00000549996;ENST00000551379;ENST00000188403	D;D;D;D;D	0.93133	-2.95;-3.0;-3.17;-3.01;-2.95	5.9	-8.68	0.00859	.	1.496650	0.03088	N	0.159433	D	0.83908	0.5356	N	0.20685	0.6	0.09310	N	1	B;B;B;B;B	0.09022	0.002;0.0;0.002;0.001;0.0	B;B;B;B;B	0.06405	0.002;0.001;0.002;0.001;0.001	T	0.72197	-0.4363	10	0.30078	T	0.28	.	5.5969	0.17331	0.5244:0.1889:0.2149:0.0717	.	116;126;126;116;116	F8VYG8;Q96RI1;Q96RI1-4;F1DAL1;B6ZGS9	.;NR1H4_HUMAN;.;.;.	T	116;116;116;126;126	ENSP00000448506:A116T;ENSP00000376712:A116T;ENSP00000448978:A116T;ENSP00000447149:A126T;ENSP00000188403:A126T	ENSP00000188403:A126T	A	+	1	0	NR1H4	99428953	0.000000	0.05858	0.000000	0.03702	0.213000	0.24496	-1.660000	0.01974	-1.431000	0.01982	-0.312000	0.09012	GCG		0.522	NR1H4-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409140.1	NM_005123	
RIC8B	55188	hgsc.bcm.edu	37	12	107254119	107254119	+	Silent	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr12:107254119A>G	ENST00000392839.2	+	8	1486	c.1380A>G	c.(1378-1380)ggA>ggG	p.G460G	RIC8B_ENST00000549643.1_5'UTR|RIC8B_ENST00000392837.4_Silent_p.G460G|RIC8B_ENST00000355478.2_Silent_p.G420G	NM_018157.2	NP_060627.2	Q9NVN3	RIC8B_HUMAN	RIC8 guanine nucleotide exchange factor B	460					regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	G-protein alpha-subunit binding (GO:0001965)|guanyl-nucleotide exchange factor activity (GO:0005085)			kidney(2)|large_intestine(5)|lung(10)|ovary(1)|urinary_tract(1)	19						TCTTGGCTGGAGGAAGAGGAG	0.433																																																	0			12											84.0	82.0	83.0					12																	107254119		2203	4300	6503	105778249	SO:0001819	synonymous_variant	55188			AK128102	CCDS9109.2	12q23.3	2013-08-05	2013-08-05		ENSG00000111785	ENSG00000111785			25555	protein-coding gene	gene with protein product		609147	"""resistance to inhibitors of cholinesterase 8 homolog B (C. elegans)"""				Standard	XM_005268998		Approved	FLJ10620, hSyn, RIC8	uc001tlx.3	Q9NVN3	OTTHUMG00000144188	ENST00000392839.2:c.1380A>G	12.37:g.107254119A>G			105778249	A2RTZ0|Q4G103|Q6ZRN4|Q86WD3	Silent	SNP	ENST00000392839.2	37	CCDS9109.2																																																																																				0.433	RIC8B-006	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000291398.2	NM_018157	
SELPLG	6404	hgsc.bcm.edu	37	12	109017442	109017442	+	Silent	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr12:109017442A>G	ENST00000550948.1	-	2	866	c.642T>C	c.(640-642)acT>acC	p.T214T	SELPLG_ENST00000388962.3_Silent_p.T204T|SELPLG_ENST00000228463.6_Silent_p.T230T			Q14242	SELPL_HUMAN	selectin P ligand	214	12 X 10 AA tandem repeats.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to interleukin-6 (GO:0071354)|leukocyte adhesive activation (GO:0050902)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|prostate(3)|skin(1)	12						CTGCTGGTGGAGTGGTCTGTG	0.612																																																	0			12											169.0	150.0	157.0					12																	109017442		2201	4300	6501	107541571	SO:0001819	synonymous_variant	6404				CCDS31895.1, CCDS31895.2, CCDS55881.1	12q24	2014-01-30						"""CD molecules"", ""Endogenous ligands"""	10722	protein-coding gene	gene with protein product		600738				7505206	Standard	NM_003006		Approved	PSGL-1, CD162	uc010sxe.2	Q14242		ENST00000550948.1:c.642T>C	12.37:g.109017442A>G			107541571	A8K2Y0|B4DQC3|B7Z5C7|J3KMX6|Q12775|Q6GTW7|Q8N7J7	Silent	SNP	ENST00000550948.1	37	CCDS31895.2																																																																																				0.612	SELPLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403904.1		
TCHP	84260	hgsc.bcm.edu	37	12	110340935	110340935	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr12:110340935A>G	ENST00000312777.5	+	2	318	c.104A>G	c.(103-105)gAg>gGg	p.E35G	TCHP_ENST00000405876.4_Missense_Mutation_p.E35G	NM_032300.4	NP_115676.1			trichoplein, keratin filament binding											NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|skin(2)	22						CAGCAGTGGGAGCAGAACAGC	0.597																																																	0			12											76.0	72.0	73.0					12																	110340935		2203	4300	6503	108825318	SO:0001583	missense	84260			AK092736	CCDS9137.1	12q24.11	2011-08-25	2006-01-27			ENSG00000139437			28135	protein-coding gene	gene with protein product	"""mitostatin"""	612654				15731013, 20930847	Standard	NM_032300		Approved	MGC10854, TpMs	uc001tpn.3	Q9BT92		ENST00000312777.5:c.104A>G	12.37:g.110340935A>G	ENSP00000324404:p.Glu35Gly		108825318		Missense_Mutation	SNP	ENST00000312777.5	37	CCDS9137.1	.	.	.	.	.	.	.	.	.	.	A	17.68	3.448888	0.63178	.	.	ENSG00000139437	ENST00000405876;ENST00000536868;ENST00000312777;ENST00000536408	T;T;T	0.51574	1.35;1.35;0.7	4.7	4.7	0.59300	.	0.237506	0.40728	N	0.001035	T	0.39759	0.1090	L	0.47716	1.5	0.80722	D	1	P	0.34522	0.455	B	0.31016	0.123	T	0.38067	-0.9678	10	0.51188	T	0.08	-3.4974	12.1862	0.54241	1.0:0.0:0.0:0.0	.	35	Q9BT92	TCHP_HUMAN	G	35	ENSP00000384520:E35G;ENSP00000324404:E35G;ENSP00000441835:E35G	ENSP00000324404:E35G	E	+	2	0	TCHP	108825318	1.000000	0.71417	0.924000	0.36721	0.979000	0.70002	5.789000	0.69029	1.775000	0.52247	0.369000	0.22263	GAG		0.597	TCHP-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403289.1	NM_032300	
TMEM132B	114795	hgsc.bcm.edu	37	12	126137096	126137096	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr12:126137096T>C	ENST00000299308.3	+	8	2017	c.2009T>C	c.(2008-2010)cTc>cCc	p.L670P	TMEM132B_ENST00000535886.1_Missense_Mutation_p.L182P	NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	670						integral component of membrane (GO:0016021)				NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		GGCATGTCTCTCTCCCTGCAG	0.607																																																	0			12											54.0	58.0	57.0					12																	126137096		2137	4257	6394	124703049	SO:0001583	missense	114795			AB067493	CCDS41859.1, CCDS66501.1	12q24.31	2006-03-02							29397	protein-coding gene	gene with protein product						11572484	Standard	NM_001286219		Approved	KIAA1906, KIAA1786	uc001uhe.1	Q14DG7		ENST00000299308.3:c.2009T>C	12.37:g.126137096T>C	ENSP00000299308:p.Leu670Pro		124703049	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Missense_Mutation	SNP	ENST00000299308.3	37	CCDS41859.1	.	.	.	.	.	.	.	.	.	.	T	19.66	3.869499	0.72065	.	.	ENSG00000139364	ENST00000299308;ENST00000535886	T;T	0.59906	0.23;0.23	5.53	5.53	0.82687	.	0.000000	0.56097	D	0.000021	T	0.76335	0.3973	M	0.78637	2.42	0.80722	D	1	D	0.89917	1.0	D	0.74348	0.983	T	0.79974	-0.1577	10	0.87932	D	0	.	15.6483	0.77070	0.0:0.0:0.0:1.0	.	670	Q14DG7	T132B_HUMAN	P	670;182	ENSP00000299308:L670P;ENSP00000440436:L182P	ENSP00000299308:L670P	L	+	2	0	TMEM132B	124703049	1.000000	0.71417	0.160000	0.22671	0.526000	0.34562	7.700000	0.84556	2.081000	0.62600	0.533000	0.62120	CTC		0.607	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907	
CASC5	57082	hgsc.bcm.edu	37	15	40920343	40920343	+	Missense_Mutation	SNP	C	C	T			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr15:40920343C>T	ENST00000346991.5	+	12	5920	c.5530C>T	c.(5530-5532)Cca>Tca	p.P1844S	CASC5_ENST00000399668.2_Missense_Mutation_p.P1818S			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	1844	Necessary for kinetochore localization and for interaction with NSL1 and DSN1.				acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		GAGCAGGACCCCATCTAGTTG	0.403																																																	0			15											84.0	86.0	85.0					15																	40920343		1847	4090	5937	38707635	SO:0001583	missense	57082			AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	24054	protein-coding gene	gene with protein product	"""cancer/testis antigen 29"", ""kinetochore null 1 homolog (C. elegans)"", ""blinkin, bub-linking kinetochore protein"", ""protein phosphatase 1, regulatory subunit 55"""	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.5530C>T	15.37:g.40920343C>T	ENSP00000335463:p.Pro1844Ser		38707635	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Missense_Mutation	SNP	ENST00000346991.5	37	CCDS42023.1	.	.	.	.	.	.	.	.	.	.	C	19.95	3.921669	0.73213	.	.	ENSG00000137812	ENST00000346991;ENST00000399668	T;T	0.05649	3.41;3.41	5.59	4.68	0.58851	.	0.132262	0.34986	N	0.003521	T	0.10637	0.0260	L	0.60455	1.87	0.49389	D	0.999788	P;P	0.46142	0.873;0.873	P;P	0.45310	0.476;0.476	T	0.09818	-1.0657	10	0.33940	T	0.23	.	12.2836	0.54779	0.0:0.9209:0.0:0.0791	.	1818;1844	Q8NG31-2;Q8NG31	.;CASC5_HUMAN	S	1844;1818	ENSP00000335463:P1844S;ENSP00000382576:P1818S	ENSP00000335463:P1844S	P	+	1	0	CASC5	38707635	0.290000	0.24343	0.998000	0.56505	0.985000	0.73830	2.091000	0.41691	1.367000	0.46095	0.650000	0.86243	CCA		0.403	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508	
SPTBN5	51332	hgsc.bcm.edu	37	15	42167130	42167130	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr15:42167130A>G	ENST00000320955.6	-	23	4639	c.4412T>C	c.(4411-4413)cTg>cCg	p.L1471P		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	1471					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		CTTGGCAGCCAGGGTCCGGCT	0.667																																																	0			15											36.0	42.0	40.0					15																	42167130		2004	4158	6162	39954422	SO:0001583	missense	51332			AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"""beta V spectrin"""	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.4412T>C	15.37:g.42167130A>G	ENSP00000317790:p.Leu1471Pro		39954422		Missense_Mutation	SNP	ENST00000320955.6	37		.	.	.	.	.	.	.	.	.	.	.	14.09	2.431409	0.43122	.	.	ENSG00000137877	ENST00000320955	T	0.75367	-0.93	4.77	4.77	0.60923	.	0.000000	0.53938	D	0.000047	D	0.84365	0.5456	M	0.74258	2.255	0.46678	D	0.999155	D	0.89917	1.0	D	0.87578	0.998	D	0.84835	0.0804	10	0.46703	T	0.11	.	12.2624	0.54658	1.0:0.0:0.0:0.0	.	1471	Q9NRC6	SPTN5_HUMAN	P	1471	ENSP00000317790:L1471P	ENSP00000317790:L1471P	L	-	2	0	SPTBN5	39954422	1.000000	0.71417	0.717000	0.30585	0.011000	0.07611	6.288000	0.72679	1.771000	0.52183	0.454000	0.30748	CTG		0.667	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
TGM5	9333	hgsc.bcm.edu	37	15	43527820	43527820	+	Missense_Mutation	SNP	G	G	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr15:43527820G>C	ENST00000220420.5	-	10	1568	c.1561C>G	c.(1561-1563)Cag>Gag	p.Q521E	TGM5_ENST00000349114.4_Missense_Mutation_p.Q439E	NM_201631.3	NP_963925.2	O43548	TGM5_HUMAN	transglutaminase 5	521			Q -> R (in dbSNP:rs35985214).		cellular protein modification process (GO:0006464)|epidermis development (GO:0008544)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(11)|lung(15)|skin(6)|urinary_tract(1)	44		all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;4e-07)	L-Glutamine(DB00130)	CATATATCCTGGCCCATGTTG	0.577																																																	0			15											100.0	81.0	88.0					15																	43527820		2203	4299	6502	41315112	SO:0001583	missense	9333			AF035960	CCDS32211.1, CCDS32212.1	15q15	2004-07-07				ENSG00000104055		"""Transglutaminases"""	11781	protein-coding gene	gene with protein product		603805				9452468, 11390390	Standard	NM_201631		Approved	TGX	uc001zrd.2	O43548		ENST00000220420.5:c.1561C>G	15.37:g.43527820G>C	ENSP00000220420:p.Gln521Glu		41315112	O43549|Q0VF40|Q9UEZ4	Missense_Mutation	SNP	ENST00000220420.5	37	CCDS32212.1	.	.	.	.	.	.	.	.	.	.	G	6.964	0.547755	0.13312	.	.	ENSG00000104055	ENST00000220420;ENST00000349114;ENST00000396996	T;T	0.69926	-0.44;-0.44	5.58	4.67	0.58626	Transglutaminase, C-terminal (2);Immunoglobulin-like fold (1);	0.134279	0.47852	D	0.000201	T	0.54549	0.1865	L	0.37800	1.135	0.28500	N	0.914064	B;B	0.18013	0.002;0.025	B;B	0.23150	0.011;0.044	T	0.52525	-0.8564	10	0.49607	T	0.09	-8.616	8.215	0.31505	0.0839:0.1569:0.7592:0.0	.	439;521	O43548-2;O43548	.;TGM5_HUMAN	E	521;439;520	ENSP00000220420:Q521E;ENSP00000220419:Q439E	ENSP00000220420:Q521E	Q	-	1	0	TGM5	41315112	1.000000	0.71417	1.000000	0.80357	0.049000	0.14656	1.827000	0.39102	1.368000	0.46115	-0.137000	0.14449	CAG		0.577	TGM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432257.1	NM_004245	
EFTUD1	79631	hgsc.bcm.edu	37	15	82533623	82533623	+	Silent	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr15:82533623T>C	ENST00000268206.7	-	5	534	c.366A>G	c.(364-366)ggA>ggG	p.G122G	EFTUD1_ENST00000359445.3_Silent_p.G71G	NM_024580.5	NP_078856.4	Q7Z2Z2	ETUD1_HUMAN	elongation factor Tu GTP binding domain containing 1	122	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				GTP catabolic process (GO:0006184)|mature ribosome assembly (GO:0042256)		GTP binding (GO:0005525)|GTPase activity (GO:0003924)|ribosome binding (GO:0043022)|translation elongation factor activity (GO:0003746)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(14)|ovary(1)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32						GTGGACAGACTCCTTCCACAG	0.443																																																	0			15											79.0	74.0	75.0					15																	82533623		1911	4119	6030	80320678	SO:0001819	synonymous_variant	79631			AK056656	CCDS42070.1, CCDS42071.1	15q25.2	2012-07-04			ENSG00000140598	ENSG00000140598			25789	protein-coding gene	gene with protein product	"""ribosome assembly 1 homolog (yeast)"""					14702039	Standard	NM_024580		Approved	FLJ13119, FAM42A, HsT19294, RIA1	uc002bgt.1	Q7Z2Z2	OTTHUMG00000172573	ENST00000268206.7:c.366A>G	15.37:g.82533623T>C			80320678	A6NKY5|B7Z6I0|Q9H8Z6	Silent	SNP	ENST00000268206.7	37	CCDS42071.1																																																																																				0.443	EFTUD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419252.1	NM_024580	
NTRK3	4916	hgsc.bcm.edu	37	15	88678529	88678529	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr15:88678529A>G	ENST00000360948.2	-	9	1168	c.1007T>C	c.(1006-1008)cTg>cCg	p.L336P	NTRK3_ENST00000394480.2_Missense_Mutation_p.L336P|NTRK3_ENST00000558676.1_Missense_Mutation_p.L336P|NTRK3_ENST00000317501.3_Missense_Mutation_p.L336P|NTRK3_ENST00000540489.2_Missense_Mutation_p.L336P|NTRK3_ENST00000557856.1_Missense_Mutation_p.L336P|NTRK3_ENST00000542733.2_Missense_Mutation_p.L238P|NTRK3_ENST00000355254.2_Missense_Mutation_p.L336P|NTRK3_ENST00000357724.2_Missense_Mutation_p.L336P	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	336	Ig-like C2-type 2.		L -> Q (in a lung adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|cochlea development (GO:0090102)|lens fiber cell differentiation (GO:0070306)|mechanoreceptor differentiation (GO:0042490)|modulation by virus of host transcription (GO:0019056)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell death (GO:0060548)|negative regulation of protein phosphorylation (GO:0001933)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|neurotrophin signaling pathway (GO:0038179)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of axon extension involved in regeneration (GO:0048691)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of positive chemotaxis (GO:0050927)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|neurotrophin binding (GO:0043121)|neurotrophin receptor activity (GO:0005030)|p53 binding (GO:0002039)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.L336Q(2)	ETV6/NTRK3(238)	breast(3)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(22)|lung(63)|ovary(6)|pancreas(3)|prostate(1)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)	119			BRCA - Breast invasive adenocarcinoma(143;0.211)			CCCATTGTGCAGCCAGTGCAG	0.607			T	ETV6	"""congenital fibrosarcoma, Secretory breast """					TSP Lung(13;0.10)																														Dom	yes		15	15q25	4916	"""neurotrophic tyrosine kinase, receptor, type 3"""		"""E, M"""	2	Substitution - Missense(2)	lung(2)	15											82.0	84.0	83.0					15																	88678529		2201	4299	6500	86479533	SO:0001583	missense	4916			U05012	CCDS10340.1, CCDS32322.1, CCDS32323.1, CCDS58399.1	15q24-q25	2013-01-11			ENSG00000140538	ENSG00000140538	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"""	8033	protein-coding gene	gene with protein product		191316				7806211	Standard	NM_001012338		Approved	TRKC	uc002bme.2	Q16288	OTTHUMG00000148677	ENST00000360948.2:c.1007T>C	15.37:g.88678529A>G	ENSP00000354207:p.Leu336Pro		86479533	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Missense_Mutation	SNP	ENST00000360948.2	37	CCDS32322.1	.	.	.	.	.	.	.	.	.	.	A	19.60	3.858573	0.71834	.	.	ENSG00000140538	ENST00000394480;ENST00000360948;ENST00000357724;ENST00000355254;ENST00000542733;ENST00000540489;ENST00000317501	T;T;T;T;T;T;T	0.74315	-0.83;-0.83;-0.83;-0.83;-0.83;-0.83;-0.83	5.28	5.28	0.74379	Immunoglobulin I-set (1);Immunoglobulin-like fold (1);	0.223524	0.40222	N	0.001151	D	0.89767	0.6810	H	0.95816	3.725	0.80722	D	1	D;D;P;D;D;P	0.89917	0.997;0.966;0.956;1.0;0.967;0.956	D;P;D;D;P;D	0.72338	0.93;0.77;0.936;0.977;0.73;0.936	D	0.92618	0.6105	10	0.72032	D	0.01	.	14.4172	0.67158	1.0:0.0:0.0:0.0	.	238;336;336;336;336;336	B7Z7U4;E9PG56;B7Z4C5;Q96CY4;Q16288-3;Q16288	.;.;.;.;.;NTRK3_HUMAN	P	336;336;336;336;238;336;336	ENSP00000377990:L336P;ENSP00000354207:L336P;ENSP00000350356:L336P;ENSP00000347397:L336P;ENSP00000437773:L238P;ENSP00000444673:L336P;ENSP00000318328:L336P	ENSP00000318328:L336P	L	-	2	0	NTRK3	86479533	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	6.874000	0.75546	1.988000	0.58038	0.460000	0.39030	CTG		0.607	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding			
MCTP2	55784	hgsc.bcm.edu	37	15	94910857	94910857	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr15:94910857T>C	ENST00000357742.4	+	10	1325	c.1325T>C	c.(1324-1326)cTc>cCc	p.L442P	MCTP2_ENST00000451018.3_Missense_Mutation_p.L442P|MCTP2_ENST00000331706.4_Missense_Mutation_p.L30P|MCTP2_ENST00000557742.1_Missense_Mutation_p.L30P	NM_018349.3	NP_060819.3	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2	442					calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|liver(1)|lung(12)|ovary(1)|pancreas(1)|skin(9)|stomach(2)	49	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)			ATCTCGGCACTCCCTCTGAAG	0.522																																																	0			15											102.0	104.0	103.0					15																	94910857		2197	4298	6495	92711861	SO:0001583	missense	55784			AK002037	CCDS32338.1, CCDS53975.1, CCDS53976.1	15q26.2	2006-02-08				ENSG00000140563			25636	protein-coding gene	gene with protein product						15528213	Standard	NM_018349		Approved	FLJ11175, FLJ33303	uc002btj.3	Q6DN12		ENST00000357742.4:c.1325T>C	15.37:g.94910857T>C	ENSP00000350377:p.Leu442Pro		92711861	A2RRC2|C6G483|C6G484|Q49AB0|Q8TAX2|Q9NUS2|Q9NUW7	Missense_Mutation	SNP	ENST00000357742.4	37	CCDS32338.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.943464	0.73672	.	.	ENSG00000140563	ENST00000451018;ENST00000331706;ENST00000357742	T;T;T	0.75154	2.61;-0.91;2.61	5.33	5.33	0.75918	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.137404	0.48767	D	0.000169	D	0.86130	0.5859	M	0.77313	2.365	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.988;0.987	D	0.88097	0.2817	10	0.87932	D	0	.	15.3122	0.74042	0.0:0.0:0.0:1.0	.	442;30;442	Q6DN12-2;Q6DN12-4;Q6DN12	.;.;MCTP2_HUMAN	P	442;30;442	ENSP00000395109:L442P;ENSP00000329646:L30P;ENSP00000350377:L442P	ENSP00000329646:L30P	L	+	2	0	MCTP2	92711861	1.000000	0.71417	0.846000	0.33378	0.996000	0.88848	6.664000	0.74437	2.016000	0.59253	0.528000	0.53228	CTC		0.522	MCTP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415060.3	NM_018349	
SYNM	23336	hgsc.bcm.edu	37	15	99672941	99672941	+	Missense_Mutation	SNP	C	C	T			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr15:99672941C>T	ENST00000336292.6	+	5	4493	c.4373C>T	c.(4372-4374)tCg>tTg	p.S1458L	SYNM_ENST00000560674.1_Intron|SYNM_ENST00000561323.1_3'UTR|RP11-6O2.4_ENST00000566974.1_RNA|SYNM_ENST00000328642.7_Intron	NM_145728.2	NP_663780.2	O15061	SYNEM_HUMAN	synemin, intermediate filament protein	1459	Interaction with DMD and UTRN.|Interaction with TLN1 and VCL.|Tail.				intermediate filament cytoskeleton organization (GO:0045104)	adherens junction (GO:0005912)|costamere (GO:0043034)|intermediate filament (GO:0005882)|membrane (GO:0016020)|neurofilament cytoskeleton (GO:0060053)	intermediate filament binding (GO:0019215)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(6)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	29						AAAGAAACTTCGTTTACCTTT	0.552																																					Pancreas(125;1071 1762 21750 40003 40381)												0			15											177.0	182.0	181.0					15																	99672941		2075	4208	6283	97490464	SO:0001583	missense	23336			AK026420	CCDS73786.1, CCDS73787.1	15q26.3	2014-09-17	2008-09-19	2008-09-19	ENSG00000182253	ENSG00000182253		"""A-kinase anchor proteins"", ""Intermediate filaments type IV"""	24466	protein-coding gene	gene with protein product	"""synemin alpha"", ""synemin beta"""	606087	"""desmuslin"""	DMN		11737198, 11454237	Standard	NM_145728		Approved	KIAA0353, SYN	uc002bup.3	O15061		ENST00000336292.6:c.4373C>T	15.37:g.99672941C>T	ENSP00000336775:p.Ser1458Leu		97490464	A7E2Y2|Q2TBJ4|Q5NJJ9|Q8TE61|Q8TE62	Missense_Mutation	SNP	ENST00000336292.6	37		.	.	.	.	.	.	.	.	.	.	C	16.17	3.046579	0.55110	.	.	ENSG00000182253	ENST00000336292	T	0.15834	2.39	5.55	2.67	0.31697	.	.	.	.	.	T	0.12092	0.0294	.	.	.	0.80722	D	1	P	0.34412	0.453	B	0.17722	0.019	T	0.06625	-1.0816	8	0.87932	D	0	.	9.9826	0.41821	0.0:0.7838:0.0:0.2162	.	1459	O15061	SYNEM_HUMAN	L	1458	ENSP00000336775:S1458L	ENSP00000336775:S1458L	S	+	2	0	SYNM	97490464	0.779000	0.28652	0.261000	0.24466	0.981000	0.71138	1.588000	0.36633	0.311000	0.23014	0.655000	0.94253	TCG		0.552	SYNM-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_145728	
PHKA2	5256	hgsc.bcm.edu	37	X	18954250	18954250	+	Missense_Mutation	SNP	C	C	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chrX:18954250C>A	ENST00000379942.4	-	11	1725	c.1060G>T	c.(1060-1062)Gcc>Tcc	p.A354S		NM_000292.2	NP_000283.1	P46019	KPB2_HUMAN	phosphorylase kinase, alpha 2 (liver)	354					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			NS(1)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61	Hepatocellular(33;0.183)					CCCTCCAGGGCCTCTCGGTAT	0.542																																																	0			X											82.0	58.0	67.0					X																	18954250		2203	4300	6503	18864171	SO:0001583	missense	5256				CCDS14190.1	Xp22.2-p22.1	2009-07-10			ENSG00000044446	ENSG00000044446	2.7.11.19		8926	protein-coding gene	gene with protein product		300798		PHK, PYK		2387090	Standard	NM_000292		Approved		uc004cyv.4	P46019	OTTHUMG00000021222	ENST00000379942.4:c.1060G>T	X.37:g.18954250C>A	ENSP00000369274:p.Ala354Ser		18864171	A8K1T1|Q6LAJ5|Q7Z6W0|Q96CR3|Q9UDA1	Missense_Mutation	SNP	ENST00000379942.4	37	CCDS14190.1	.	.	.	.	.	.	.	.	.	.	C	33	5.210827	0.95069	.	.	ENSG00000044446	ENST00000379942	D	0.92965	-3.14	5.41	5.41	0.78517	Six-hairpin glycosidase-like (1);Glycoside hydrolase 15-related (1);	0.000000	0.85682	D	0.000000	D	0.96002	0.8698	M	0.87456	2.885	0.80722	D	1	D	0.55385	0.971	P	0.59357	0.856	D	0.95571	0.8638	10	0.41790	T	0.15	-18.9081	18.5226	0.90959	0.0:1.0:0.0:0.0	.	354	P46019	KPB2_HUMAN	S	354	ENSP00000369274:A354S	ENSP00000369274:A354S	A	-	1	0	PHKA2	18864171	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	7.731000	0.84895	2.402000	0.81655	0.600000	0.82982	GCC		0.542	PHKA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055960.1	NM_000292	
RPS6KA3	6197	hgsc.bcm.edu	37	X	20213211	20213211	+	Silent	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chrX:20213211A>G	ENST00000379565.3	-	5	585	c.378T>C	c.(376-378)aaT>aaC	p.N126N	RPS6KA3_ENST00000540702.1_Silent_p.N98N|RPS6KA3_ENST00000544447.1_Silent_p.N98N|RPS6KA3_ENST00000379548.4_Silent_p.N97N	NM_004586.2	NP_004577.1	P51812	KS6A3_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 3	126	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell cycle (GO:0007049)|central nervous system development (GO:0007417)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|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)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(14)|lung(7)|ovary(1)|stomach(1)	41					Acetylsalicylic acid(DB00945)	TAAAAGGATGATTAACCTCTA	0.378																																																	0			X	GRCh37	CD060659	RPS6KA3	D							182.0	141.0	155.0					X																	20213211		2203	4300	6503	20123132	SO:0001819	synonymous_variant	6197			U08316	CCDS14197.1	Xp22.2-p22.1	2013-06-03	2002-08-29		ENSG00000177189	ENSG00000177189			10432	protein-coding gene	gene with protein product		300075	"""ribosomal protein S6 kinase, 90kD, polypeptide 3"", ""mental retardation, X-linked 19"", ""Coffin-Lowry syndrome"""	MRX19, CLS		8141249, 11896450, 16879200	Standard	XM_005274573		Approved	RSK, RSK2, HU-3	uc004czu.3	P51812	OTTHUMG00000021231	ENST00000379565.3:c.378T>C	X.37:g.20213211A>G			20123132	B2R9V4|Q4VAP3|Q59H26|Q5JPK8|Q7Z3Z7	Silent	SNP	ENST00000379565.3	37	CCDS14197.1																																																																																				0.378	RPS6KA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056011.3	NM_004586	
CNGA2	1260	hgsc.bcm.edu	37	X	150908071	150908071	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chrX:150908071A>G	ENST00000329903.4	+	3	274	c.241A>G	c.(241-243)Aac>Gac	p.N81D		NM_005140.1	NP_005131.1	Q16280	CNGA2_HUMAN	cyclic nucleotide gated channel alpha 2	81					phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sensory perception of smell (GO:0007608)	integral component of plasma membrane (GO:0005887)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			breast(4)|endometrium(4)|large_intestine(5)|lung(34)|prostate(2)	49	Acute lymphoblastic leukemia(192;6.56e-05)					AGAATGGGCCAACAAGAATTT	0.527																																																	0			X											112.0	88.0	96.0					X																	150908071		2203	4300	6503	150658727	SO:0001583	missense	1260			S76067	CCDS14701.1	Xq27	2011-07-05			ENSG00000183862	ENSG00000183862		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2149	protein-coding gene	gene with protein product		300338		CNCA1, CNCA		7532814, 16382102	Standard	NM_005140		Approved	CNG2, OCNC1, OCNCa, OCNCALPHA, OCNCalpha, FLJ46312	uc004fey.1	Q16280	OTTHUMG00000024173	ENST00000329903.4:c.241A>G	X.37:g.150908071A>G	ENSP00000328478:p.Asn81Asp		150658727	A0AVD0	Missense_Mutation	SNP	ENST00000329903.4	37	CCDS14701.1	.	.	.	.	.	.	.	.	.	.	A	14.25	2.480601	0.44044	.	.	ENSG00000183862	ENST00000329903	T	0.41758	0.99	5.25	2.82	0.32997	.	0.225320	0.47455	D	0.000234	T	0.29850	0.0746	L	0.47190	1.495	0.27562	N	0.950163	B	0.14805	0.011	B	0.14023	0.01	T	0.30149	-0.9988	10	0.54805	T	0.06	.	1.8247	0.03118	0.5705:0.1699:0.0928:0.1669	.	81	Q16280	CNGA2_HUMAN	D	81	ENSP00000328478:N81D	ENSP00000328478:N81D	N	+	1	0	CNGA2	150658727	1.000000	0.71417	0.995000	0.50966	0.918000	0.54935	5.244000	0.65400	0.251000	0.21505	0.430000	0.28490	AAC		0.527	CNGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060888.1	NM_005140	
KIT	3815	hgsc.bcm.edu	37	4	55593601	55593601	+	Missense_Mutation	SNP	A	A	G	rs121913234		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr4:55593601A>G	ENST00000288135.5	+	11	1764	c.1667A>G	c.(1666-1668)cAg>cGg	p.Q556R		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	556			Missing (in GIST; somatic mutation). {ECO:0000269|PubMed:15824741, ECO:0000269|PubMed:9438854}.		actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.Y553_K558>(8)|p.E554_K558del(8)|p.W557_K558del(8)|p.M552_W557del(8)|p.K550_K558del(7)|p.Q556_V560del(6)|p.Y553_Q556del(4)|p.Y553_K558del(4)|p.V555_K558del(3)|p.Y553_W557del(3)|p.Y553_T574>S(3)|p.P551_Q556del(3)|p.V555_I571del(3)|p.V555_V560del(3)|p.V555_P573del(3)|p.V555_V559del(3)|p.V555_Q556del(2)|p.W557_E561del(2)|p.Q556_L576del(2)|p.K550_V559del(2)|p.K550fs*6(2)|p.Q556_K558del(2)|p.V555_E562del(2)|p.Q556_V559del(2)|p.M552_Q556del(2)|p.V555_G565del(1)|p.M552_W557>R(1)|p.P551_K558del(1)|p.M552_E561>K(1)|p.E554_I571del(1)|p.Q556_V560>F(1)|p.V555_Y570del(1)|p.Q556_N566>SNNLQLY(1)|p.M552_T574>TESA(1)|p.Q556_D572>PS(1)|p.Q556_D572del(1)|p.Q556R(1)|p.V555_N566>D(1)|p.M552_Q556>(1)|p.V555_V560>V(1)|p.Q556_W557del(1)|p.M552_K558del(1)|p.Q556_E561del(1)|p.Q556_E561>HH(1)|p.Q556_K558>R(1)|p.K550_Q556del(1)|p.Q556_W557>R(1)|p.E554_E562del(1)|p.E554_N564del(1)|p.Q556_V560>TTF(1)|p.K550_W557del(1)|p.V555_I563del(1)|p.M552_D572del(1)|p.Y553_V559>E(1)|p.Q556_T574del(1)|p.P551_V559del>L(1)|p.K550_Q556>II(1)|p.Q556_P573del(1)|p.E554_D572del(1)|p.Y553_V559del(1)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TATGAAGTACAGTGGAAGGTT	0.383		1	"""Mis, O"""		"""GIST, AML, TGCT, mastocytosis, mucosal melanoma"""	"""GIST, epithelioma"""	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																														yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"""L, M, O, E"""	130	Deletion - In frame(101)|Complex - deletion inframe(26)|Deletion - Frameshift(2)|Substitution - Missense(1)	soft_tissue(127)|skin(2)|testis(1)	4											80.0	82.0	82.0					4																	55593601		2203	4300	6503	55288358	SO:0001583	missense	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6342	protein-coding gene	gene with protein product		164920	"""piebald trait"""	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.1667A>G	4.37:g.55593601A>G	ENSP00000288135:p.Gln556Arg		55288358	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	37	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	A	16.03	3.006138	0.54361	.	.	ENSG00000157404	ENST00000288135;ENST00000412167	D;D	0.92965	-3.14;-3.14	6.06	6.06	0.98353	Protein kinase-like domain (1);	0.000000	0.64402	D	0.000015	D	0.91905	0.7437	L	0.31752	0.955	0.80722	D	1	P;D;D	0.60575	0.928;0.988;0.963	B;D;P	0.67103	0.411;0.949;0.861	D	0.88088	0.2811	10	0.06099	T	0.92	.	16.6003	0.84812	1.0:0.0:0.0:0.0	.	63;552;556	D5MAV8;P10721-2;P10721	.;.;KIT_HUMAN	R	556;552	ENSP00000288135:Q556R;ENSP00000390987:Q552R	ENSP00000288135:Q556R	Q	+	2	0	KIT	55288358	1.000000	0.71417	0.999000	0.59377	0.884000	0.51177	6.200000	0.72118	2.319000	0.78375	0.533000	0.62120	CAG		0.383	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1		
KIT	3815	hgsc.bcm.edu	37	4	55593632	55593632	+	Silent	SNP	C	C	T			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr4:55593632C>T	ENST00000288135.5	+	11	1795	c.1698C>T	c.(1696-1698)aaC>aaT	p.N566N		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	566					actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.V560_L576del(4)|p.N566N(4)|p.Y553_T574>S(3)|p.V555_I571del(3)|p.V555_P573del(3)|p.I563_L576del(2)|p.Q556_L576del(2)|p.W557_P573>S(2)|p.N564_Y578del(2)|p.W557_Q575del(2)|p.N564_L576del(2)|p.I563_D572del(1)|p.E562_V569>D(1)|p.E562_P573del(1)|p.N564_T574del(1)|p.E554_I571del(1)|p.K558_Q575del(1)|p.V555_Y570del(1)|p.M552_T574>TESA(1)|p.Q556_T574del(1)|p.Q556_D572>PS(1)|p.E561_P577del(1)|p.Q556_D572del(1)|p.N564_P573>T(1)|p.K558_L576>NV(1)|p.V559_P573>A(1)|p.V560_I571del(1)|p.W557_I571del(1)|p.N564_P577del(1)|p.V559_L576del(1)|p.K558_D572del(1)|p.Q556_D572>H(1)|p.K558_Y570>N(1)|p.N567_L576>E(1)|p.M552_D572del(1)|p.V559_I571del(1)|p.Q556_P573del(1)|p.E554_D572del(1)|p.N564_P573>TS(1)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TAAATGGAAACAATTATGTTT	0.388		1	"""Mis, O"""		"""GIST, AML, TGCT, mastocytosis, mucosal melanoma"""	"""GIST, epithelioma"""	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																														yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"""L, M, O, E"""	57	Deletion - In frame(38)|Complex - deletion inframe(15)|Substitution - coding silent(4)	soft_tissue(52)|haematopoietic_and_lymphoid_tissue(4)|testis(1)	4											80.0	81.0	81.0					4																	55593632		2203	4300	6503	55288389	SO:0001819	synonymous_variant	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6342	protein-coding gene	gene with protein product		164920	"""piebald trait"""	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.1698C>T	4.37:g.55593632C>T			55288389	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Silent	SNP	ENST00000288135.5	37	CCDS3496.1																																																																																				0.388	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1		
KIT	3815	hgsc.bcm.edu	37	4	55593665	55593665	+	Silent	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr4:55593665T>C	ENST00000288135.5	+	11	1828	c.1731T>C	c.(1729-1731)ccT>ccC	p.P577P		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	577					actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.N564_Y578del(2)|p.P577_D579del(1)|p.P577_Y578del(1)|p.E561_P577del(1)|p.Q575_P577>T(1)|p.N564_P577del(1)|p.I571_N587del(1)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CACAACTTCCTTATGATCACA	0.418		1	"""Mis, O"""		"""GIST, AML, TGCT, mastocytosis, mucosal melanoma"""	"""GIST, epithelioma"""	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																														yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"""L, M, O, E"""	8	Deletion - In frame(7)|Complex - deletion inframe(1)	soft_tissue(6)|thymus(1)|skin(1)	4											73.0	72.0	73.0					4																	55593665		2203	4300	6503	55288422	SO:0001819	synonymous_variant	3815	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6342	protein-coding gene	gene with protein product		164920	"""piebald trait"""	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.1731T>C	4.37:g.55593665T>C			55288422	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Silent	SNP	ENST00000288135.5	37	CCDS3496.1																																																																																				0.418	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1		
IGFBP7	3490	hgsc.bcm.edu	37	4	57898691	57898691	+	Missense_Mutation	SNP	C	C	T			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr4:57898691C>T	ENST00000295666.4	-	4	763	c.730G>A	c.(730-732)Gga>Aga	p.G244R	IGFBP7_ENST00000537922.1_Missense_Mutation_p.G244R|IGFBP7_ENST00000512512.1_5'UTR	NM_001553.2	NP_001544.1	Q16270	IBP7_HUMAN	insulin-like growth factor binding protein 7	244	Ig-like C2-type.				cell adhesion (GO:0007155)|cellular response to hormone stimulus (GO:0032870)|embryo implantation (GO:0007566)|inner ear development (GO:0048839)|negative regulation of cell proliferation (GO:0008285)|regulation of cell growth (GO:0001558)|regulation of steroid biosynthetic process (GO:0050810)|response to cortisol (GO:0051414)|response to heat (GO:0009408)|response to retinoic acid (GO:0032526)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(1)|lung(3)	5	Glioma(25;0.08)|all_neural(26;0.181)				"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	TCATATTCTCCAGCATCTTCC	0.418																																																	0			4											121.0	111.0	115.0					4																	57898691		2203	4300	6503	57593448	SO:0001583	missense	3490			S75725	CCDS3512.1	4q12	2013-01-11			ENSG00000163453	ENSG00000163453		"""Immunoglobulin superfamily / I-set domain containing"""	5476	protein-coding gene	gene with protein product		602867				7694637, 7980422	Standard	NM_001553		Approved	MAC25, IGFBP-7, PSF, FSTL2	uc003hcn.3	Q16270	OTTHUMG00000128772	ENST00000295666.4:c.730G>A	4.37:g.57898691C>T	ENSP00000295666:p.Gly244Arg		57593448	B4E1N2|B7Z9W7|Q07822|Q53YE6|Q9UCA8	Missense_Mutation	SNP	ENST00000295666.4	37	CCDS3512.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.400640	0.83120	.	.	ENSG00000163453	ENST00000295666;ENST00000537922	T;T	0.81247	-1.47;-1.47	5.71	5.71	0.89125	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.94391	0.8196	H	0.98996	4.395	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96390	0.9288	10	0.87932	D	0	-8.058	18.043	0.89324	0.0:1.0:0.0:0.0	.	244;244	B4E1N2;Q16270	.;IBP7_HUMAN	R	244	ENSP00000295666:G244R;ENSP00000444146:G244R	ENSP00000295666:G244R	G	-	1	0	IGFBP7	57593448	1.000000	0.71417	0.998000	0.56505	0.766000	0.43426	6.968000	0.76086	2.689000	0.91719	0.655000	0.94253	GGA		0.418	IGFBP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250693.1		
EPHA5	2044	hgsc.bcm.edu	37	4	66286178	66286178	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr4:66286178T>C	ENST00000273854.3	-	6	2108	c.1508A>G	c.(1507-1509)gAa>gGa	p.E503G	EPHA5_ENST00000432638.2_Missense_Mutation_p.E339G|EPHA5_ENST00000511294.1_Missense_Mutation_p.E503G|EPHA5_ENST00000354839.4_Missense_Mutation_p.E503G	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	503	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.		E -> K (in a lung large cell carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		axon guidance (GO:0007411)|cAMP-mediated signaling (GO:0019933)|ephrin receptor signaling pathway (GO:0048013)|hippocampus development (GO:0021766)|negative regulation of synapse assembly (GO:0051964)|neuron development (GO:0048666)|positive regulation of CREB transcription factor activity (GO:0032793)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of Rac GTPase activity (GO:0032314)	dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|GPI-linked ephrin receptor activity (GO:0005004)|transmembrane-ephrin receptor activity (GO:0005005)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(25)|liver(1)|lung(76)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	142						ATACTTGATTTCATACTCTAG	0.338										TSP Lung(17;0.13)																																							0			4											148.0	142.0	144.0					4																	66286178		2203	4300	6503	65968773	SO:0001583	missense	2044			L36644	CCDS3513.1, CCDS3514.1, CCDS75131.1, CCDS75132.1, CCDS75133.1	4q13.1	2013-02-11	2004-10-28		ENSG00000145242	ENSG00000145242		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3389	protein-coding gene	gene with protein product		600004	"""EphA5"""			9267020, 7528718	Standard	NM_004439		Approved	Hek7, TYRO4, CEK7, EHK1	uc003hcy.3	P54756	OTTHUMG00000129273	ENST00000273854.3:c.1508A>G	4.37:g.66286178T>C	ENSP00000273854:p.Glu503Gly		65968773	Q7Z3F2	Missense_Mutation	SNP	ENST00000273854.3	37	CCDS3513.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.348405	0.82132	.	.	ENSG00000145242	ENST00000273854;ENST00000432638;ENST00000354839;ENST00000511294	T;T;T;T	0.59906	0.23;0.23;0.23;0.23	5.17	5.17	0.71159	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.56097	D	0.000024	D	0.85186	0.5639	H	0.98407	4.225	0.58432	D	0.999997	D;D;D;D	0.89917	1.0;0.998;0.999;1.0	D;D;D;D	0.91635	0.999;0.986;0.999;0.999	D	0.91065	0.4888	10	0.87932	D	0	.	15.0155	0.71581	0.0:0.0:0.0:1.0	.	503;503;503;503	B7ZKW7;B7ZKJ3;P54756-2;P54756	.;.;.;EPHA5_HUMAN	G	503;339;503;503	ENSP00000273854:E503G;ENSP00000389208:E339G;ENSP00000346899:E503G;ENSP00000427638:E503G	ENSP00000273854:E503G	E	-	2	0	EPHA5	65968773	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.005000	0.88553	1.957000	0.56846	0.383000	0.25322	GAA		0.338	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439	
DSPP	1834	hgsc.bcm.edu	37	4	88535013	88535013	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr4:88535013A>G	ENST00000282478.7	+	4	1232	c.1199A>G	c.(1198-1200)gAg>gGg	p.E400G	DSPP_ENST00000399271.1_Missense_Mutation_p.E400G|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	400					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)		GAAGGTAAAGAGGATAAAGGA	0.438																																																	0			4											131.0	121.0	124.0					4																	88535013		1942	4139	6081	88754037	SO:0001583	missense	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.1199A>G	4.37:g.88535013A>G	ENSP00000282478:p.Glu400Gly		88754037	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	A	10.68	1.419733	0.25552	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.90069	-2.61;-2.61	4.2	1.67	0.24075	.	0.811716	0.10029	N	0.725009	D	0.82318	0.5011	L	0.42245	1.32	0.09310	N	1	B	0.20052	0.041	B	0.16289	0.015	T	0.68116	-0.5494	10	0.33141	T	0.24	-3.9603	5.8433	0.18645	0.7724:0.0:0.2276:0.0	.	400	Q9NZW4	DSPP_HUMAN	G	400	ENSP00000382213:E400G;ENSP00000282478:E400G	ENSP00000282478:E400G	E	+	2	0	DSPP	88754037	0.000000	0.05858	0.004000	0.12327	0.019000	0.09904	0.055000	0.14229	0.652000	0.30806	-0.490000	0.04691	GAG		0.438	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
ANK2	287	hgsc.bcm.edu	37	4	114275325	114275325	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr4:114275325A>G	ENST00000357077.4	+	38	5604	c.5551A>G	c.(5551-5553)Act>Gct	p.T1851A	ANK2_ENST00000394537.3_Intron|ANK2_ENST00000510275.2_Intron|ANK2_ENST00000506722.1_Intron|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000264366.6_Missense_Mutation_p.T1818A	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	1851	Repeat-rich region.				atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		ATCAAGTAAAACTGAGAAACA	0.473																																																	0			4											171.0	170.0	171.0					4																	114275325		2203	4300	6503	114494774	SO:0001583	missense	287			M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"""Ankyrin repeat domain containing"""	493	protein-coding gene	gene with protein product		106410	"""long (electrocardiographic) QT syndrome 4"""	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.5551A>G	4.37:g.114275325A>G	ENSP00000349588:p.Thr1851Ala		114494774	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	37	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	A	11.50	1.658739	0.29515	.	.	ENSG00000145362	ENST00000357077;ENST00000264366	T;T	0.68331	-0.31;-0.32	5.62	5.62	0.85841	.	0.147317	0.31859	N	0.006948	T	0.56529	0.1991	L	0.38175	1.15	0.80722	D	1	B;B	0.23185	0.022;0.081	B;B	0.24541	0.024;0.054	T	0.52335	-0.8589	9	.	.	.	.	13.7834	0.63094	1.0:0.0:0.0:0.0	.	1818;1851	Q01484;Q01484-4	ANK2_HUMAN;.	A	1851;1818	ENSP00000349588:T1851A;ENSP00000264366:T1818A	.	T	+	1	0	ANK2	114494774	0.857000	0.29778	0.407000	0.26434	0.907000	0.53573	1.721000	0.38032	2.144000	0.66660	0.533000	0.62120	ACT		0.473	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148	
NDST3	9348	hgsc.bcm.edu	37	4	118975856	118975856	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr4:118975856A>G	ENST00000296499.5	+	2	1194	c.791A>G	c.(790-792)cAt>cGt	p.H264R	NDST3_ENST00000433996.2_Missense_Mutation_p.H264R	NM_004784.2	NP_004775.1	O95803	NDST3_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3	264	Heparan sulfate N-deacetylase 3.		H -> Q (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			NS(1)|breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	54						CTGGGGCTTCATGATGGAATT	0.418																																																	0			4											142.0	135.0	137.0					4																	118975856		2203	4299	6502	119195304	SO:0001583	missense	9348			AF074924	CCDS3708.1	4q26	2008-08-04			ENSG00000164100	ENSG00000164100		"""Sulfotransferases, membrane-bound"""	7682	protein-coding gene	gene with protein product		603950				9915799	Standard	NM_004784		Approved	HSST3	uc003ibx.3	O95803	OTTHUMG00000132959	ENST00000296499.5:c.791A>G	4.37:g.118975856A>G	ENSP00000296499:p.His264Arg		119195304	B4DI67|Q4W5C1|Q4W5D0|Q6UWC5|Q9UP21	Missense_Mutation	SNP	ENST00000296499.5	37	CCDS3708.1	.	.	.	.	.	.	.	.	.	.	A	14.81	2.646527	0.47258	.	.	ENSG00000164100	ENST00000296499;ENST00000433996	T;T	0.44482	1.26;0.92	5.23	5.23	0.72850	.	0.217832	0.48286	D	0.000183	T	0.57975	0.2090	M	0.66939	2.045	0.50813	D	0.999897	B;P;P	0.40230	0.085;0.708;0.617	B;P;B	0.53518	0.091;0.728;0.23	T	0.58983	-0.7539	10	0.49607	T	0.09	.	15.1164	0.72407	1.0:0.0:0.0:0.0	.	264;264;264	B4DI67;O95803;O95803-2	.;NDST3_HUMAN;.	R	264	ENSP00000296499:H264R;ENSP00000396625:H264R	ENSP00000296499:H264R	H	+	2	0	NDST3	119195304	0.999000	0.42202	0.998000	0.56505	0.953000	0.61014	6.152000	0.71812	1.963000	0.57068	0.533000	0.62120	CAT		0.418	NDST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256517.4	NM_004784	
ANKRD50	57182	hgsc.bcm.edu	37	4	125592728	125592728	+	Silent	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr4:125592728T>C	ENST00000504087.1	-	4	2741	c.1704A>G	c.(1702-1704)ggA>ggG	p.G568G	ANKRD50_ENST00000515641.1_Silent_p.G389G	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	568										NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(14)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	55						CTAAATCTGCTCCCCTAGAGA	0.428																																																	0			4											105.0	95.0	99.0					4																	125592728		2203	4300	6503	125812178	SO:0001819	synonymous_variant	57182			AB033049	CCDS34060.1, CCDS54802.1	4q28.1	2013-01-10			ENSG00000151458	ENSG00000151458		"""Ankyrin repeat domain containing"""	29223	protein-coding gene	gene with protein product							Standard	NM_020337		Approved	KIAA1223	uc010inw.3	Q9ULJ7	OTTHUMG00000161398	ENST00000504087.1:c.1704A>G	4.37:g.125592728T>C			125812178	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	Silent	SNP	ENST00000504087.1	37	CCDS34060.1																																																																																				0.428	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337	
FBXW7	55294	hgsc.bcm.edu	37	4	153249384	153249384	+	Missense_Mutation	SNP	C	C	T			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr4:153249384C>T	ENST00000281708.4	-	9	2623	c.1394G>A	c.(1393-1395)cGt>cAt	p.R465H	FBXW7_ENST00000393956.3_Missense_Mutation_p.R289H|FBXW7_ENST00000263981.5_Missense_Mutation_p.R385H|FBXW7_ENST00000603841.1_Missense_Mutation_p.R465H|FBXW7_ENST00000296555.5_Missense_Mutation_p.R347H|FBXW7_ENST00000603548.1_Missense_Mutation_p.R465H	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	465			R -> C (in a acute lymphoblastic leukemia cell line). {ECO:0000269|PubMed:11565033}.|R -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.R465H(69)|p.R385H(16)|p.R226H(16)|p.R465L(4)|p.R347H(4)|p.R465Y(2)|p.?(1)|p.R385L(1)|p.R226L(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				ATGCATACAACGCACAGTGGA	0.408			"""Mis, N, D, F"""		"""colorectal, endometrial, T-ALL"""																																			Rec	yes		4	4q31.3	55294	"""F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"""		"""E, L"""	114	Substitution - Missense(113)|Unknown(1)	haematopoietic_and_lymphoid_tissue(40)|large_intestine(39)|endometrium(24)|lung(5)|ovary(4)|cervix(1)|biliary_tract(1)	4											253.0	218.0	230.0					4																	153249384		2203	4300	6503	153468834	SO:0001583	missense	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	16712	protein-coding gene	gene with protein product	"""archipelago homolog (Drosophila)"""	606278	"""F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"", ""F-box and WD repeat domain containing 7"""			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1394G>A	4.37:g.153249384C>T	ENSP00000281708:p.Arg465His		153468834	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	C	32	5.178201	0.94846	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	6.05	6.05	0.98169	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.63827	0.2544	L	0.56124	1.755	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;1.0;1.0	T	0.62469	-0.6848	10	0.87932	D	0	-17.2313	20.6013	0.99457	0.0:1.0:0.0:0.0	.	289;465;347;385	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	H	465;347;385;289	ENSP00000281708:R465H;ENSP00000296555:R347H;ENSP00000263981:R385H;ENSP00000377528:R289H	ENSP00000263981:R385H	R	-	2	0	FBXW7	153468834	1.000000	0.71417	0.960000	0.40013	0.996000	0.88848	7.818000	0.86416	2.878000	0.98634	0.650000	0.86243	CGT		0.408	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1		
FBXW7	55294	hgsc.bcm.edu	37	4	153249456	153249456	+	Missense_Mutation	SNP	C	C	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr4:153249456C>A	ENST00000281708.4	-	9	2551	c.1322G>T	c.(1321-1323)cGg>cTg	p.R441L	FBXW7_ENST00000393956.3_Missense_Mutation_p.R265L|FBXW7_ENST00000263981.5_Missense_Mutation_p.R361L|FBXW7_ENST00000603841.1_Missense_Mutation_p.R441L|FBXW7_ENST00000296555.5_Missense_Mutation_p.R323L|FBXW7_ENST00000603548.1_Missense_Mutation_p.R441L	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	441					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.R441L(2)|p.R441Q(2)|p.R202L(1)|p.?(1)|p.R361Q(1)|p.R323Q(1)|p.R361L(1)|p.R202Q(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				TTTGAGTGTCCGATCTGTAGA	0.408			"""Mis, N, D, F"""		"""colorectal, endometrial, T-ALL"""																																			Rec	yes		4	4q31.3	55294	"""F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"""		"""E, L"""	10	Substitution - Missense(9)|Unknown(1)	endometrium(5)|breast(4)|haematopoietic_and_lymphoid_tissue(1)	4											306.0	258.0	275.0					4																	153249456		2203	4300	6503	153468906	SO:0001583	missense	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	16712	protein-coding gene	gene with protein product	"""archipelago homolog (Drosophila)"""	606278	"""F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"", ""F-box and WD repeat domain containing 7"""			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1322G>T	4.37:g.153249456C>A	ENSP00000281708:p.Arg441Leu		153468906	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	C	32	5.157370	0.94686	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	T;T;T;T	0.41065	1.01;1.01;1.01;1.01	5.9	5.9	0.94986	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.65709	0.2717	M	0.67517	2.055	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.72982	0.972;0.979;0.974;0.974	T	0.65977	-0.6037	10	0.87932	D	0	-19.4947	20.2787	0.98501	0.0:1.0:0.0:0.0	.	265;441;323;361	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	L	441;323;361;265	ENSP00000281708:R441L;ENSP00000296555:R323L;ENSP00000263981:R361L;ENSP00000377528:R265L	ENSP00000263981:R361L	R	-	2	0	FBXW7	153468906	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.818000	0.86416	2.798000	0.96311	0.650000	0.86243	CGG		0.408	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1		
RXFP1	59350	hgsc.bcm.edu	37	4	159568118	159568118	+	Silent	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr4:159568118A>G	ENST00000307765.5	+	16	1772	c.1521A>G	c.(1519-1521)acA>acG	p.T507T	RXFP1_ENST00000470033.1_Silent_p.T474T|RXFP1_ENST00000460056.2_Silent_p.T426T|RXFP1_ENST00000343542.5_Silent_p.T459T|RXFP1_ENST00000448688.2_Silent_p.T402T	NM_001253727.1|NM_001253728.1|NM_001253730.1|NM_001253732.1|NM_001253733.1|NM_021634.3	NP_001240656.1|NP_001240657.1|NP_001240659.1|NP_001240661.1|NP_001240662.1|NP_067647.2	Q9HBX9	RXFP1_HUMAN	relaxin/insulin-like family peptide receptor 1	507					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|lung connective tissue development (GO:0060427)|nipple morphogenesis (GO:0060658)|parturition (GO:0007567)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|hormone binding (GO:0042562)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|liver(2)|lung(22)|prostate(1)|skin(10)	49	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0219)		CATTTCTGACATTGGAAAAAT	0.388																																																	0			4											127.0	117.0	120.0					4																	159568118		1881	4116	5997	159787568	SO:0001819	synonymous_variant	59350			AF190500	CCDS43276.1, CCDS58929.1, CCDS58930.1, CCDS75204.1, CCDS75205.1, CCDS75206.1	4q31.3	2012-08-08	2006-05-09	2006-05-09	ENSG00000171509	ENSG00000171509		"""GPCR / Class A : Relaxin family peptide receptors"""	19718	protein-coding gene	gene with protein product		606654	"""leucine-rich repeat-containing G protein-coupled receptor 7"""	LGR7		15956688, 16507880	Standard	NM_021634		Approved	RXFPR1	uc003ipz.3	Q9HBX9	OTTHUMG00000149973	ENST00000307765.5:c.1521A>G	4.37:g.159568118A>G			159787568	B4DHD1|B4DTV2|Q2M215|Q3KU24|Q3KU25|Q3KU26	Silent	SNP	ENST00000307765.5	37	CCDS43276.1																																																																																				0.388	RXFP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314865.1	NM_021634	
APOB	338	hgsc.bcm.edu	37	2	21233813	21233813	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:21233813T>C	ENST00000233242.1	-	26	6054	c.5927A>G	c.(5926-5928)gAg>gGg	p.E1976G		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	1976					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCCTGTCTGCTCAGCTGGAGT	0.448																																																	0			2											147.0	137.0	140.0					2																	21233813		2203	4300	6503	21087318	SO:0001583	missense	338			M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.5927A>G	2.37:g.21233813T>C	ENSP00000233242:p.Glu1976Gly		21087318	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	T	15.92	2.976297	0.53720	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.01279	5.06	5.46	5.46	0.80206	.	0.000000	0.56097	D	0.000023	T	0.08846	0.0219	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	T	0.00800	-1.1561	10	0.72032	D	0.01	.	15.5233	0.75881	0.0:0.0:0.0:1.0	.	1976	P04114	APOB_HUMAN	G	1976	ENSP00000233242:E1976G	ENSP00000233242:E1976G	E	-	2	0	APOB	21087318	0.996000	0.38824	1.000000	0.80357	0.914000	0.54420	4.726000	0.61986	2.065000	0.61736	0.454000	0.30748	GAG		0.448	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
MAPRE3	22924	hgsc.bcm.edu	37	2	27248575	27248575	+	Silent	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:27248575T>C	ENST00000233121.2	+	5	792	c.594T>C	c.(592-594)acT>acC	p.T198T	MAPRE3_ENST00000405074.3_Silent_p.T183T|MAPRE3_ENST00000402218.1_Silent_p.T183T			Q9UPY8	MARE3_HUMAN	microtubule-associated protein, RP/EB family, member 3	198	EB1 C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00576}.				mitotic nuclear division (GO:0007067)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of microtubule plus-end binding (GO:1903033)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)	microtubule binding (GO:0008017)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(3)|upper_aerodigestive_tract(1)	13	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCCATGAGACTGATGCCCAAA	0.572																																																	0			2											53.0	51.0	52.0					2																	27248575		2203	4300	6503	27102079	SO:0001819	synonymous_variant	22924			Y11174	CCDS1731.1	2p23.3-p23.1	2008-06-04			ENSG00000084764	ENSG00000084764			6892	protein-coding gene	gene with protein product		605788				9233623	Standard	NM_012326		Approved	RP3, EB3	uc002rhw.3	Q9UPY8	OTTHUMG00000097067	ENST00000233121.2:c.594T>C	2.37:g.27248575T>C			27102079	B7WPK5|O00265|Q6FHB0|Q6FI15|Q9BZP7|Q9BZP8	Silent	SNP	ENST00000233121.2	37	CCDS1731.1																																																																																				0.572	MAPRE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214183.1	NM_012326	
C2orf71	388939	hgsc.bcm.edu	37	2	29294302	29294302	+	Silent	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:29294302A>G	ENST00000331664.5	-	1	2825	c.2826T>C	c.(2824-2826)agT>agC	p.S942S		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	942					response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						TCTCTGCCTGACTCCAAGTCC	0.657																																																	0			2											28.0	32.0	30.0					2																	29294302		2049	4199	6248	29147806	SO:0001819	synonymous_variant	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.2826T>C	2.37:g.29294302A>G			29147806		Silent	SNP	ENST00000331664.5	37	CCDS42669.1																																																																																				0.657	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883	
SULT6B1	391365	hgsc.bcm.edu	37	2	37398687	37398687	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:37398687A>G	ENST00000535679.1	-	6	670	c.671T>C	c.(670-672)tTt>tCt	p.F224S	SULT6B1_ENST00000407963.1_Missense_Mutation_p.F186S|SULT6B1_ENST00000260637.3_Missense_Mutation_p.F186S|SULT6B1_ENST00000379149.2_Missense_Mutation_p.F120S			Q6IMI4	ST6B1_HUMAN	sulfotransferase family, cytosolic, 6B, member 1	224						cytoplasm (GO:0005737)	sulfotransferase activity (GO:0008146)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(3)|lung(5)|ovary(1)	12		all_hematologic(82;0.248)				CCCAGTTAGAAAGAATCCCAA	0.423																																																	0			2											112.0	110.0	111.0					2																	37398687		2203	4300	6503	37252191	SO:0001583	missense	391365			AY289770, AY289774	CCDS33182.1	2p22.2	2007-07-26			ENSG00000138068	ENSG00000138068		"""Sulfotransferases, cytosolic"""	33433	protein-coding gene	gene with protein product						14676822	Standard	XM_005264307		Approved		uc002rpu.3	Q6IMI4	OTTHUMG00000152160	ENST00000535679.1:c.671T>C	2.37:g.37398687A>G	ENSP00000444081:p.Phe224Ser		37252191	B2RTS7	Missense_Mutation	SNP	ENST00000535679.1	37		.	.	.	.	.	.	.	.	.	.	A	0.011	-1.727283	0.00694	.	.	ENSG00000138068	ENST00000535679;ENST00000379149;ENST00000260637;ENST00000407963	T;T;T;T	0.09255	3.0;3.0;3.0;3.0	4.87	3.0	0.34707	Sulfotransferase domain (1);	0.462043	0.24518	N	0.037832	T	0.01189	0.0039	N	0.00010	-3.02	0.24009	N	0.996182	B	0.02656	0.0	B	0.01281	0.0	T	0.42682	-0.9437	10	0.02654	T	1	.	8.5685	0.33554	0.0883:0.1543:0.7573:0.0	.	224	Q6IMI4	ST6B1_HUMAN	S	224;120;186;186	ENSP00000444081:F224S;ENSP00000368444:F120S;ENSP00000260637:F186S;ENSP00000384950:F186S	ENSP00000260637:F186S	F	-	2	0	SULT6B1	37252191	1.000000	0.71417	0.768000	0.31515	0.197000	0.23852	1.251000	0.32862	0.600000	0.29862	-0.462000	0.05337	TTT		0.423	SULT6B1-203	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001032377	
MSH2	4436	hgsc.bcm.edu	37	2	47707837	47707837	+	Missense_Mutation	SNP	G	G	T			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:47707837G>T	ENST00000233146.2	+	15	2684	c.2461G>T	c.(2461-2463)Gtc>Ttc	p.V821F	MSH2_ENST00000406134.1_Missense_Mutation_p.V821F|MSH2_ENST00000543555.1_Missense_Mutation_p.V755F	NM_000251.2	NP_000242.1	P43246	MSH2_HUMAN	mutS homolog 2	821					ATP catabolic process (GO:0006200)|B cell differentiation (GO:0030183)|B cell mediated immunity (GO:0019724)|cell cycle arrest (GO:0007050)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|intra-S DNA damage checkpoint (GO:0031573)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|isotype switching (GO:0045190)|maintenance of DNA repeat elements (GO:0043570)|male gonad development (GO:0008584)|meiotic gene conversion (GO:0006311)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reciprocal meiotic recombination (GO:0045128)|oxidative phosphorylation (GO:0006119)|positive regulation of helicase activity (GO:0051096)|postreplication repair (GO:0006301)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSalpha complex (GO:0032301)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|guanine/thymine mispair binding (GO:0032137)|heteroduplex DNA loop binding (GO:0000404)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|Y-form DNA binding (GO:0000403)	p.0?(2)|p.?(2)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(5)|large_intestine(50)|lung(18)|ovary(5)|prostate(2)|skin(3)|small_intestine(1)|stomach(2)|urinary_tract(1)	112		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TCTTATAGGTGTCTGTGATCA	0.398			"""D, Mis, N, F, S"""		"""colorectal, endometrial, ovarian"""	"""colorectal, endometrial, ovarian"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																														yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p22-p21	4436	mutS homolog 2 (E. coli)		E	4	Whole gene deletion(2)|Unknown(2)	haematopoietic_and_lymphoid_tissue(3)|prostate(1)	2											77.0	74.0	75.0					2																	47707837		2203	4300	6503	47561341	SO:0001583	missense	4436	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	U03911	CCDS1834.1, CCDS58709.1	2p21	2014-09-17	2013-09-12		ENSG00000095002	ENSG00000095002			7325	protein-coding gene	gene with protein product		609309	"""mutS (E. coli) homolog 2 (colon cancer, nonpolyposis type 1)"", ""mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)"""	COCA1		8484120, 9843200	Standard	NM_000251		Approved	HNPCC, HNPCC1	uc002rvy.2	P43246	OTTHUMG00000128861	ENST00000233146.2:c.2461G>T	2.37:g.47707837G>T	ENSP00000233146:p.Val821Phe		47561341	B4E2Z2|O75488	Missense_Mutation	SNP	ENST00000233146.2	37	CCDS1834.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.062062	0.76187	.	.	ENSG00000095002	ENST00000233146;ENST00000543555;ENST00000406134;ENST00000413880	D;D;D	0.86230	-2.09;-2.09;-2.09	5.62	4.75	0.60458	DNA mismatch repair protein MutS, C-terminal (2);	0.107611	0.64402	D	0.000006	D	0.92440	0.7600	M	0.71296	2.17	0.80722	D	1	D;D;D	0.89917	1.0;0.98;0.997	D;D;D	0.87578	0.998;0.929;0.985	D	0.92435	0.5957	10	0.49607	T	0.09	-4.0305	14.5562	0.68101	0.07:0.0:0.93:0.0	.	755;821;821	B4E2Z2;E9PHA6;P43246	.;.;MSH2_HUMAN	F	821;755;821;607	ENSP00000233146:V821F;ENSP00000442697:V755F;ENSP00000384199:V821F	ENSP00000233146:V821F	V	+	1	0	MSH2	47561341	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	6.075000	0.71261	1.394000	0.46624	0.563000	0.77884	GTC		0.398	MSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250805.3		
LOXL3	84695	hgsc.bcm.edu	37	2	74776631	74776631	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:74776631T>C	ENST00000264094.3	-	4	628	c.557A>G	c.(556-558)gAg>gGg	p.E186G	LOXL3_ENST00000484369.1_5'UTR|LOXL3_ENST00000393937.2_Intron|LOXL3_ENST00000409549.1_Missense_Mutation_p.E186G|LOXL3_ENST00000409249.1_Missense_Mutation_p.E186G|DOK1_ENST00000409429.1_Intron|LOXL3_ENST00000409986.1_Intron	NM_032603.2	NP_115992.1	P58215	LOXL3_HUMAN	lysyl oxidase-like 3	186	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.				epithelial to mesenchymal transition (GO:0001837)|negative regulation of transcription, DNA-templated (GO:0045892)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|nucleus (GO:0005634)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)			endometrium(7)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30						CACCAGCCCCTCCGTCACGGG	0.662																																																	0			2											34.0	30.0	31.0					2																	74776631		2203	4299	6502	74630139	SO:0001583	missense	84695			AF282619	CCDS1953.1, CCDS74527.1	2p13	2008-05-23			ENSG00000115318	ENSG00000115318			13869	protein-coding gene	gene with protein product		607163				11386757	Standard	NM_032603		Approved		uc002smp.1	P58215	OTTHUMG00000129953	ENST00000264094.3:c.557A>G	2.37:g.74776631T>C	ENSP00000264094:p.Glu186Gly		74630139	D6W5J1|Q2EHP2|Q6IPL7|Q96RS1	Missense_Mutation	SNP	ENST00000264094.3	37	CCDS1953.1	.	.	.	.	.	.	.	.	.	.	T	29.6	5.016823	0.93404	.	.	ENSG00000115318	ENST00000264094;ENST00000409249;ENST00000409549;ENST00000413469	T;T;T;T	0.40476	1.03;1.03;1.03;1.03	5.26	5.26	0.73747	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.000000	0.85682	D	0.000000	T	0.72153	0.3425	M	0.93283	3.4	0.80722	D	1	D;D	0.76494	0.973;0.999	P;D	0.87578	0.795;0.998	T	0.79928	-0.1596	10	0.87932	D	0	.	13.1704	0.59595	0.0:0.0:0.0:1.0	.	186;186	E7END4;P58215	.;LOXL3_HUMAN	G	186	ENSP00000264094:E186G;ENSP00000387103:E186G;ENSP00000386696:E186G;ENSP00000398260:E186G	ENSP00000264094:E186G	E	-	2	0	LOXL3	74630139	1.000000	0.71417	0.999000	0.59377	0.737000	0.42083	7.834000	0.86773	2.201000	0.70794	0.460000	0.39030	GAG		0.662	LOXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252215.1	NM_032603	
TEKT4	150483	hgsc.bcm.edu	37	2	95540621	95540621	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:95540621T>C	ENST00000295201.4	+	4	951	c.814T>C	c.(814-816)Tgc>Cgc	p.C272R	AC097374.2_ENST00000568768.1_RNA	NM_144705.2	NP_653306.1	Q8WW24	TEKT4_HUMAN	tektin 4	272			C -> S (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cell projection organization (GO:0030030)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)|nucleus (GO:0005634)		p.C272S(1)		NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	28						GCTGGTGGACTGCATCCTTCG	0.701																																																	1	Substitution - Missense(1)	breast(1)	2											26.0	31.0	29.0					2																	95540621		2198	4297	6495	94904348	SO:0001583	missense	150483			AK097438	CCDS2005.1	2q11.2	2008-02-05			ENSG00000163060	ENSG00000163060			31012	protein-coding gene	gene with protein product							Standard	XM_005263876		Approved	MGC27019	uc002stw.1	Q8WW24	OTTHUMG00000130396	ENST00000295201.4:c.814T>C	2.37:g.95540621T>C	ENSP00000295201:p.Cys272Arg		94904348		Missense_Mutation	SNP	ENST00000295201.4	37	CCDS2005.1	.	.	.	.	.	.	.	.	.	.	.	4.426	0.078825	0.08533	.	.	ENSG00000163060	ENST00000295201	T	0.02236	4.38	2.18	-1.28	0.09318	.	0.853589	0.10277	N	0.694098	T	0.01222	0.0040	N	0.16201	0.385	0.44685	D	0.997676	B	0.16166	0.016	B	0.10450	0.005	T	0.49254	-0.8959	10	0.15499	T	0.54	-1.76	2.6206	0.04915	0.4084:0.0:0.2215:0.3701	.	272	Q8WW24	TEKT4_HUMAN	R	272	ENSP00000295201:C272R	ENSP00000295201:C272R	C	+	1	0	TEKT4	94904348	0.065000	0.20965	0.931000	0.37212	0.541000	0.35023	0.814000	0.27239	0.087000	0.17167	0.382000	0.24955	TGC		0.701	TEKT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252777.1	NM_144705	
CNOT11	55571	hgsc.bcm.edu	37	2	101874388	101874388	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:101874388A>G	ENST00000289382.3	+	2	813	c.650A>G	c.(649-651)gAc>gGc	p.D217G		NM_017546.4	NP_060016.3	Q9UKZ1	CNO11_HUMAN	CCR4-NOT transcription complex, subunit 11	217					cell proliferation (GO:0008283)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytosol (GO:0005829)|nucleus (GO:0005634)											CAGTCTGTGGACATTAGTGGG	0.502																																																	0			2											113.0	89.0	97.0					2																	101874388		2203	4300	6503	101240820	SO:0001583	missense	55571			AF103798	CCDS2050.1	2q12.1	2013-01-24	2013-01-24	2013-01-24	ENSG00000158435	ENSG00000158435			25217	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 29"""	C2orf29		10497265, 23232451, 23303381	Standard	NM_017546		Approved	C40	uc002taw.4	Q9UKZ1	OTTHUMG00000130686	ENST00000289382.3:c.650A>G	2.37:g.101874388A>G	ENSP00000289382:p.Asp217Gly		101240820	Q6P2M9|Q8N681	Missense_Mutation	SNP	ENST00000289382.3	37	CCDS2050.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.357882	0.82243	.	.	ENSG00000158435	ENST00000289382	T	0.38560	1.13	6.14	6.14	0.99180	.	0.156059	0.56097	D	0.000026	T	0.65112	0.2660	M	0.69823	2.125	0.80722	D	1	D	0.69078	0.997	D	0.77004	0.989	T	0.66878	-0.5812	10	0.62326	D	0.03	-21.637	16.806	0.85666	1.0:0.0:0.0:0.0	.	217	Q9UKZ1	CB029_HUMAN	G	217	ENSP00000289382:D217G	ENSP00000289382:D217G	D	+	2	0	C2orf29	101240820	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.030000	0.93725	2.367000	0.80283	0.529000	0.55759	GAC		0.502	CNOT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253181.1	NM_017546	
C2orf40	84417	hgsc.bcm.edu	37	2	106690440	106690440	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:106690440A>G	ENST00000238044.3	+	3	335	c.226A>G	c.(226-228)Act>Gct	p.T76A	C2orf40_ENST00000409944.1_Missense_Mutation_p.T40A|C2orf40_ENST00000489174.1_3'UTR	NM_032411.2	NP_115787.1	Q9H1Z8	AUGN_HUMAN	chromosome 2 open reading frame 40	76					cellular senescence (GO:0090398)|cyclin catabolic process (GO:0008054)|G1 to G0 transition (GO:0070314)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)				lung(7)|urinary_tract(1)	8						GTGGGACCGGACTCGGCCCGA	0.572																																																	0			2											79.0	88.0	85.0					2																	106690440		2203	4300	6503	106056872	SO:0001583	missense	84417			BC021742	CCDS2072.1	2q12.2	2014-01-28			ENSG00000119147	ENSG00000119147			24642	protein-coding gene	gene with protein product	"""esophageal cancer related gene 4 protein"""	611752				12800218	Standard	NM_032411		Approved	ECRG4, augurin	uc010fjf.3	Q9H1Z8	OTTHUMG00000130921	ENST00000238044.3:c.226A>G	2.37:g.106690440A>G	ENSP00000238044:p.Thr76Ala		106056872	D3DVK2	Missense_Mutation	SNP	ENST00000238044.3	37	CCDS2072.1	.	.	.	.	.	.	.	.	.	.	A	14.90	2.673505	0.47781	.	.	ENSG00000119147	ENST00000409944;ENST00000238044;ENST00000437659	T;T;T	0.44083	0.93;0.93;0.93	5.62	3.1	0.35709	.	0.317197	0.36519	N	0.002560	T	0.36853	0.0982	L	0.51422	1.61	0.09310	N	1	B	0.26195	0.144	B	0.26094	0.066	T	0.36841	-0.9731	10	0.62326	D	0.03	-15.1452	10.974	0.47454	0.7515:0.0:0.0:0.2485	.	76	Q9H1Z8	AUGN_HUMAN	A	40;76;78	ENSP00000386421:T40A;ENSP00000238044:T76A;ENSP00000388664:T78A	ENSP00000238044:T76A	T	+	1	0	C2orf40	106056872	0.002000	0.14202	0.414000	0.26521	0.879000	0.50718	1.356000	0.34079	0.932000	0.37266	0.533000	0.62120	ACT		0.572	C2orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253515.2	NM_032411	
CHCHD5	84269	hgsc.bcm.edu	37	2	113343592	113343592	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:113343592A>G	ENST00000324913.5	+	2	251	c.44A>G	c.(43-45)gAg>gGg	p.E15G	CHCHD5_ENST00000409719.1_Missense_Mutation_p.E15G|CHCHD5_ENST00000489052.1_3'UTR	NM_032309.2	NP_115685.1	Q9BSY4	CHCH5_HUMAN	coiled-coil-helix-coiled-coil-helix domain containing 5	15						mitochondrion (GO:0005739)				NS(1)|endometrium(1)|large_intestine(4)|urinary_tract(1)	7						TGTGGCCGGGAGCTGGAGCAG	0.602																																																	0			2											50.0	54.0	53.0					2																	113343592		2203	4300	6503	113060063	SO:0001583	missense	84269			BC004498	CCDS2098.1	2q14.1	2012-10-15	2004-01-19	2004-01-21	ENSG00000125611	ENSG00000125611		"""Coiled-coil-helix-coiled-coil-helix domain containing"""	17840	protein-coding gene	gene with protein product	"""mitochondrial intermembrane space cysteine motif protein of 14 kDa homolog (S. cerevisiae)"""		"""chromosome 2 open reading frame 9"""	C2orf9		22842048	Standard	NM_032309		Approved	MGC11104, MIC14	uc002thz.1	Q9BSY4	OTTHUMG00000131312	ENST00000324913.5:c.44A>G	2.37:g.113343592A>G	ENSP00000325655:p.Glu15Gly		113060063	Q585T4|Q8N8C4	Missense_Mutation	SNP	ENST00000324913.5	37	CCDS2098.1	.	.	.	.	.	.	.	.	.	.	A	28.3	4.911595	0.92178	.	.	ENSG00000125611	ENST00000324913;ENST00000409719	T;T	0.16897	2.31;2.31	5.64	5.64	0.86602	.	0.000000	0.64402	D	0.000003	T	0.31606	0.0802	L	0.36672	1.1	0.53005	D	0.999969	D;D	0.89917	1.0;0.997	D;D	0.71184	0.972;0.916	T	0.02610	-1.1134	10	0.87932	D	0	-23.6804	14.1064	0.65093	1.0:0.0:0.0:0.0	.	15;15	Q8N8C4;Q9BSY4	.;CHCH5_HUMAN	G	15	ENSP00000325655:E15G;ENSP00000386994:E15G	ENSP00000325655:E15G	E	+	2	0	CHCHD5	113060063	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	7.360000	0.79487	2.285000	0.76669	0.528000	0.53228	GAG		0.602	CHCHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254081.2	NM_032309	
FOXD4L1	200350	hgsc.bcm.edu	37	2	114257866	114257866	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:114257866T>C	ENST00000306507.5	+	1	1206	c.1033T>C	c.(1033-1035)Tcc>Ccc	p.S345P		NM_012184.4	NP_036316.1	Q9NU39	FX4L1_HUMAN	forkhead box D4-like 1	345					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(2)	26						GCAGAGTTTGTCCCCGACCGC	0.627																																																	0			2											12.0	16.0	15.0					2																	114257866		2052	3973	6025	113974336	SO:0001583	missense	200350			AF452723	CCDS2117.1	2q14.1	2008-02-05			ENSG00000184492	ENSG00000184492			18521	protein-coding gene	gene with protein product		611084				12421752, 15233989	Standard	NM_012184		Approved	FOXD5	uc002tjw.4	Q9NU39	OTTHUMG00000131359	ENST00000306507.5:c.1033T>C	2.37:g.114257866T>C	ENSP00000302756:p.Ser345Pro		113974336	B3KWN1|B9EGF3	Missense_Mutation	SNP	ENST00000306507.5	37	CCDS2117.1	.	.	.	.	.	.	.	.	.	.	.	2.545	-0.305358	0.05495	.	.	ENSG00000184492	ENST00000306507	D	0.94687	-3.49	1.64	-0.538	0.11868	.	0.891937	0.09041	N	0.857344	D	0.84835	0.5560	N	0.11560	0.145	0.24829	N	0.992535	B	0.02656	0.0	B	0.04013	0.001	T	0.72465	-0.4285	10	0.33141	T	0.24	.	4.3512	0.11157	0.0:0.5798:0.0:0.4202	.	345	Q9NU39	FX4L1_HUMAN	P	345	ENSP00000302756:S345P	ENSP00000302756:S345P	S	+	1	0	FOXD4L1	113974336	0.000000	0.05858	0.038000	0.18304	0.355000	0.29361	-0.168000	0.09925	-0.158000	0.11040	0.155000	0.16302	TCC		0.627	FOXD4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254148.1	NM_012184	
POTEF	728378	hgsc.bcm.edu	37	2	130869607	130869607	+	Missense_Mutation	SNP	T	T	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:130869607T>A	ENST00000409914.2	-	6	1277	c.878A>T	c.(877-879)aAg>aTg	p.K293M	POTEF_ENST00000360967.5_Missense_Mutation_p.K293M|POTEF_ENST00000357462.5_Missense_Mutation_p.K293M|AC018804.3_ENST00000433507.1_RNA|POTEF_ENST00000361163.4_Missense_Mutation_p.K303M|RNU6-1049P_ENST00000516414.1_RNA	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	293					retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						CGCTTTTTTCTTAATTAAAAA	0.338																																																	0			2											38.0	48.0	45.0					2																	130869607		1508	3580	5088	130586077	SO:0001583	missense	728378			EF523384	CCDS46409.1	2q21.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000196604	ENSG00000196604		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33905	protein-coding gene	gene with protein product			"""ANKRD26-like family C, member 1B"""	A26C1B		17101985	Standard	NM_001099771		Approved	POTEACTIN, POTE2alpha	uc010fmh.2	A5A3E0	OTTHUMG00000153628	ENST00000409914.2:c.878A>T	2.37:g.130869607T>A	ENSP00000386786:p.Lys293Met		130586077	A6NC34	Missense_Mutation	SNP	ENST00000409914.2	37	CCDS46409.1	.	.	.	.	.	.	.	.	.	.	.	9.788	1.177175	0.21787	.	.	ENSG00000196604	ENST00000357462;ENST00000409914;ENST00000360967;ENST00000361163	T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.2	1.16	-0.0886	0.13672	Ankyrin repeat-containing domain (4);	0.193103	0.24547	N	0.037595	T	0.68742	0.3034	M	0.70903	2.155	0.09310	N	1	D	0.71674	0.998	P	0.56612	0.802	T	0.60301	-0.7290	10	0.87932	D	0	.	3.0851	0.06275	0.0:0.2815:0.0:0.7185	.	293	A5A3E0	POTEF_HUMAN	M	293;293;293;303	ENSP00000350052:K293M;ENSP00000386786:K293M;ENSP00000354232:K293M;ENSP00000355012:K303M	ENSP00000350052:K293M	K	-	2	0	POTEF	130586077	0.005000	0.15991	0.001000	0.08648	0.033000	0.12548	0.863000	0.27913	-0.027000	0.13873	0.136000	0.15936	AAG		0.338	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771	
AMER3	205147	hgsc.bcm.edu	37	2	131519679	131519679	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:131519679T>C	ENST00000423981.1	+	2	144	c.34T>C	c.(34-36)Tcc>Ccc	p.S12P	AMER3_ENST00000321420.4_Missense_Mutation_p.S12P	NM_001105193.1|NM_001105194.1|NM_001105195.1|NM_152698.2	NP_001098663.1|NP_001098664.1|NP_001098665.1|NP_689911.2	Q8N944	AMER3_HUMAN	APC membrane recruitment protein 3	12					Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	lipid binding (GO:0008289)										CTTCATCAAGTCCAGCCTGCA	0.617																																																	0			2											18.0	21.0	20.0					2																	131519679		2198	4295	6493	131236149	SO:0001583	missense	205147			AK095696	CCDS2164.1	2q21.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000178171	ENSG00000178171		"""-"""	26771	protein-coding gene	gene with protein product			"""family with sequence similarity 123C"""	FAM123C		20843316	Standard	NM_001105195		Approved	FLJ38377	uc002trw.2	Q8N944	OTTHUMG00000131637	ENST00000423981.1:c.34T>C	2.37:g.131519679T>C	ENSP00000392700:p.Ser12Pro		131236149	B7ZLH6	Missense_Mutation	SNP	ENST00000423981.1	37	CCDS2164.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.255113	0.80135	.	.	ENSG00000178171	ENST00000321420;ENST00000431758;ENST00000458606;ENST00000423981	T;T	0.61510	0.1;0.1	5.28	5.28	0.74379	.	0.000000	0.53938	D	0.000059	T	0.65312	0.2679	L	0.34521	1.04	0.35748	D	0.819234	D	0.89917	1.0	D	0.83275	0.996	T	0.74503	-0.3644	10	0.87932	D	0	.	11.8905	0.52626	0.0:0.0:0.0:1.0	.	12	Q8N944	F123C_HUMAN	P	12	ENSP00000314914:S12P;ENSP00000392700:S12P	ENSP00000314914:S12P	S	+	1	0	FAM123C	131236149	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	3.219000	0.51200	2.133000	0.65898	0.459000	0.35465	TCC		0.617	AMER3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254531.3	NM_152698	
LCT	3938	hgsc.bcm.edu	37	2	136581530	136581530	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:136581530A>G	ENST00000264162.2	-	4	858	c.848T>C	c.(847-849)cTc>cCc	p.L283P	AC011893.3_ENST00000437007.1_RNA	NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	283	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	GCAGTCTGGGAGTTTTAGGTT	0.468																																																	0			2											120.0	113.0	115.0					2																	136581530		2203	4300	6503	136298000	SO:0001583	missense	3938			X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.848T>C	2.37:g.136581530A>G	ENSP00000264162:p.Leu283Pro		136298000	Q4ZG58	Missense_Mutation	SNP	ENST00000264162.2	37	CCDS2178.1	.	.	.	.	.	.	.	.	.	.	A	8.022	0.759852	0.15846	.	.	ENSG00000115850	ENST00000264162	T	0.32023	1.47	5.35	4.16	0.48862	.	0.368126	0.25558	N	0.029856	T	0.27798	0.0684	L	0.59436	1.845	0.50813	D	0.999894	B	0.02656	0.0	B	0.06405	0.002	T	0.06110	-1.0845	10	0.34782	T	0.22	-12.4698	8.1891	0.31357	0.9098:0.0:0.0902:0.0	.	283	P09848	LPH_HUMAN	P	283	ENSP00000264162:L283P	ENSP00000264162:L283P	L	-	2	0	LCT	136298000	0.995000	0.38212	0.978000	0.43139	0.044000	0.14063	3.432000	0.52824	1.007000	0.39238	0.454000	0.30748	CTC		0.468	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299	
ITGB6	3694	hgsc.bcm.edu	37	2	161051922	161051922	+	Missense_Mutation	SNP	G	G	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:161051922G>A	ENST00000283249.2	-	4	788	c.551C>T	c.(550-552)cCt>cTt	p.P184L	ITGB6_ENST00000485635.1_5'UTR|ITGB6_ENST00000409872.1_Missense_Mutation_p.P184L|ITGB6_ENST00000409967.2_Missense_Mutation_p.P184L|ITGB6_ENST00000428609.2_Missense_Mutation_p.P142L	NM_001282353.1|NM_001282354.1|NM_001282388.1	NP_001269282.1|NP_001269283.1|NP_001269317.1	P18564	ITB6_HUMAN	integrin, beta 6	184	VWFA.				cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|multicellular organismal development (GO:0007275)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	virus receptor activity (GO:0001618)			breast(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	23						TTTCACAAAAGGGGATACAGG	0.438																																																	0			2											102.0	107.0	106.0					2																	161051922		2203	4300	6503	160760168	SO:0001583	missense	3694				CCDS2212.1, CCDS63040.1, CCDS74596.1, CCDS74597.1	2q24.2	2010-03-23			ENSG00000115221	ENSG00000115221		"""Integrins"""	6161	protein-coding gene	gene with protein product		147558				1729173, 8120056	Standard	NM_001282353		Approved		uc002ubh.2	P18564	OTTHUMG00000132026	ENST00000283249.2:c.551C>T	2.37:g.161051922G>A	ENSP00000283249:p.Pro184Leu		160760168	B2R9W5|C9JA97|Q0VA95|Q16500|Q53RG5|Q53RR6	Missense_Mutation	SNP	ENST00000283249.2	37	CCDS2212.1	.	.	.	.	.	.	.	.	.	.	G	16.29	3.080368	0.55753	.	.	ENSG00000115221	ENST00000283249;ENST00000428609;ENST00000409967;ENST00000409872	D;D;D;D	0.96200	-3.94;-3.94;-3.94;-3.94	6.05	5.17	0.71159	Integrin beta subunit, N-terminal (2);von Willebrand factor, type A (1);	0.051908	0.85682	N	0.000000	D	0.98409	0.9471	H	0.95679	3.705	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99517	1.0957	10	0.87932	D	0	.	15.3846	0.74687	0.0665:0.0:0.9335:0.0	.	142;184	E9PEE8;P18564	.;ITB6_HUMAN	L	184;142;184;184	ENSP00000283249:P184L;ENSP00000408024:P142L;ENSP00000386828:P184L;ENSP00000386367:P184L	ENSP00000283249:P184L	P	-	2	0	ITGB6	160760168	1.000000	0.71417	1.000000	0.80357	0.171000	0.22731	7.908000	0.87438	1.577000	0.49804	-0.145000	0.13849	CCT		0.438	ITGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255036.1	NM_000888	
SCN2A	6326	hgsc.bcm.edu	37	2	166172175	166172175	+	Silent	SNP	G	G	A	rs141269163		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:166172175G>A	ENST00000375437.2	+	11	1868	c.1578G>A	c.(1576-1578)tcG>tcA	p.S526S	SCN2A_ENST00000357398.3_Silent_p.S526S|SCN2A_ENST00000283256.6_Silent_p.S526S|SCN2A_ENST00000375427.2_Silent_p.S526S	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	526					intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TCCGAAAATCGGAATCTGAAG	0.373																																																	0			2						G	,,	1,4405	2.1+/-5.4	0,1,2202	59.0	61.0	60.0		1578,1578,1578	-8.2	0.2	2	dbSNP_134	60	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	SCN2A	NM_001040142.1,NM_001040143.1,NM_021007.2	,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,	526/2006,526/2006,526/2006	166172175	1,13005	2203	4300	6503	165880421	SO:0001819	synonymous_variant	6326			AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10588	protein-coding gene	gene with protein product		182390	"""sodium channel, voltage-gated, type II, alpha 2 polypeptide"", ""sodium channel, voltage-gated, type II, alpha 1 polypeptide"""	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.1578G>A	2.37:g.166172175G>A			165880421	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Silent	SNP	ENST00000375437.2	37	CCDS33314.1																																																																																				0.373	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007	
PPIG	9360	hgsc.bcm.edu	37	2	170489711	170489711	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:170489711T>C	ENST00000260970.3	+	12	1191	c.971T>C	c.(970-972)cTt>cCt	p.L324P	PPIG_ENST00000448752.2_Missense_Mutation_p.L324P|PPIG_ENST00000409714.3_Missense_Mutation_p.L309P|PPIG_ENST00000462903.1_Missense_Mutation_p.L324P|PPIG_ENST00000482772.1_3'UTR	NM_004792.2	NP_004783.2	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G (cyclophilin G)	324					protein folding (GO:0006457)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(17)|ovary(2)|stomach(1)|urinary_tract(1)	43					L-Proline(DB00172)	CAGAGACGACTTTTAGTTACT	0.388																																																	0			2											70.0	69.0	69.0					2																	170489711		2203	4300	6503	170197957	SO:0001583	missense	9360			X99717	CCDS2235.1	2q31.1	2010-07-23	2006-01-12		ENSG00000138398	ENSG00000138398	6.1.1.16		14650	protein-coding gene	gene with protein product	"""SR-related CTD-associated factor 10"""	606093	"""peptidyl-prolyl isomerase G (cyclophilin G)"""			8973360, 9153302	Standard	NM_004792		Approved	CARS-Cyp, SRCyp, SCAF10	uc002uez.3	Q13427	OTTHUMG00000132206	ENST00000260970.3:c.971T>C	2.37:g.170489711T>C	ENSP00000260970:p.Leu324Pro		170197957	D3DPC5|D3DPC6|O00706|Q53R40|Q53SN4|Q96DG9	Missense_Mutation	SNP	ENST00000260970.3	37	CCDS2235.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.128964	0.77549	.	.	ENSG00000138398	ENST00000260970;ENST00000530133;ENST00000433207;ENST00000409714;ENST00000462903;ENST00000448752	T;T;T;T;T	0.21031	2.46;2.03;2.46;2.15;2.46	5.38	5.38	0.77491	.	0.068748	0.64402	D	0.000015	T	0.30135	0.0755	N	0.17564	0.495	0.80722	D	1	P;P;D;D;P	0.76494	0.952;0.844;0.996;0.999;0.844	P;P;P;D;P	0.85130	0.641;0.543;0.853;0.997;0.543	T	0.11155	-1.0599	10	0.49607	T	0.09	-4.2688	13.6124	0.62088	0.0:0.0:0.0:1.0	.	317;309;309;324;324	C9JM79;E9PG73;Q2NKQ6;Q13427-2;Q13427	.;.;.;.;PPIG_HUMAN	P	324;324;317;309;324;324	ENSP00000260970:L324P;ENSP00000408683:L317P;ENSP00000386245:L309P;ENSP00000435987:L324P;ENSP00000407083:L324P	ENSP00000260970:L324P	L	+	2	0	PPIG	170197957	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.042000	0.76565	2.013000	0.59113	0.460000	0.39030	CTT		0.388	PPIG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255264.2		
TTN	7273	hgsc.bcm.edu	37	2	179473354	179473354	+	Missense_Mutation	SNP	G	G	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:179473354G>C	ENST00000591111.1	-	224	47685	c.47461C>G	c.(47461-47463)Ctt>Gtt	p.L15821V	TTN_ENST00000342175.6_Missense_Mutation_p.L8589V|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.L17462V|TTN_ENST00000342992.6_Missense_Mutation_p.L14894V|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.L8522V|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.L8397V|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	15821	Fibronectin type-III 14. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)			TTAGCCACAAGTGGCTTTGAA	0.368																																																	0			2											59.0	57.0	58.0					2																	179473354		1863	4102	5965	179181599	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.47461C>G	2.37:g.179473354G>C	ENSP00000465570:p.Leu15821Val		179181599	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		.	.	.	.	.	.	.	.	.	.	G	3.628	-0.076041	0.07184	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.51325	0.71;0.71;0.71;0.71	5.72	-0.16	0.13375	Fibronectin, type III (2);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.14227	0.0344	N	0.00554	-1.385	0.28813	N	0.898122	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.17899	-1.0354	9	0.87932	D	0	.	2.9286	0.05792	0.3673:0.1349:0.4039:0.0938	.	8397;8522;8589;15821	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	V	14894;8397;8589;8522;8397	ENSP00000343764:L14894V;ENSP00000434586:L8397V;ENSP00000340554:L8589V;ENSP00000352154:L8522V	ENSP00000340554:L8589V	L	-	1	0	TTN	179181599	0.340000	0.24792	0.184000	0.23157	0.950000	0.60333	-0.146000	0.10250	-0.339000	0.08401	-1.008000	0.02478	CTT		0.368	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	hgsc.bcm.edu	37	2	179635207	179635207	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:179635207A>G	ENST00000591111.1	-	35	8536	c.8312T>C	c.(8311-8313)aTc>aCc	p.I2771T	TTN_ENST00000342175.6_Missense_Mutation_p.I2725T|TTN_ENST00000589042.1_Missense_Mutation_p.I2771T|TTN_ENST00000342992.6_Missense_Mutation_p.I2771T|TTN_ENST00000359218.5_Missense_Mutation_p.I2725T|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.I2725T|TTN_ENST00000360870.5_Missense_Mutation_p.I2771T|TTN-AS1_ENST00000584485.1_RNA|TTN-AS1_ENST00000610005.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13097			I -> M (in a breast infiltrating ductal carcinoma 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)			CTCATCCACGATGGCACAGTT	0.433																																																	0			2											113.0	112.0	112.0					2																	179635207		2203	4300	6503	179343452	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.8312T>C	2.37:g.179635207A>G	ENSP00000465570:p.Ile2771Thr		179343452	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	9.934	1.215677	0.22373	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.76186	-1.0;-1.0;-1.0;-1.0;-1.0	6.06	4.9	0.64082	Immunoglobulin I-set (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.55226	0.1907	N	0.04018	-0.295	0.09310	N	1	B;B;B;B;B	0.06786	0.0;0.0;0.0;0.0;0.001	B;B;B;B;B	0.06405	0.0;0.0;0.0;0.0;0.002	T	0.52147	-0.8614	9	0.87932	D	0	.	12.3952	0.55380	0.9338:0.0:0.0662:0.0	.	2725;2725;2725;2771;2771	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	T	2771;2725;2725;2725;2725;2771	ENSP00000343764:I2771T;ENSP00000434586:I2725T;ENSP00000340554:I2725T;ENSP00000352154:I2725T;ENSP00000354117:I2771T	ENSP00000340554:I2725T	I	-	2	0	TTN	179343452	0.933000	0.31639	0.017000	0.16124	0.939000	0.58152	5.275000	0.65575	2.315000	0.78130	0.533000	0.62120	ATC		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	hgsc.bcm.edu	37	2	179636187	179636187	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:179636187A>G	ENST00000591111.1	-	34	8091	c.7867T>C	c.(7867-7869)Tcc>Ccc	p.S2623P	TTN_ENST00000342175.6_Missense_Mutation_p.S2577P|TTN_ENST00000589042.1_Missense_Mutation_p.S2623P|TTN_ENST00000342992.6_Missense_Mutation_p.S2623P|TTN_ENST00000359218.5_Missense_Mutation_p.S2577P|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.S2577P|TTN_ENST00000360870.5_Missense_Mutation_p.S2623P|TTN-AS1_ENST00000584485.1_RNA|TTN-AS1_ENST00000610005.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12948	Ig-like 15.				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)			AGTGGCTTGGAGATGGCCCCA	0.423																																																	0			2											99.0	87.0	91.0					2																	179636187		2203	4300	6503	179344432	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.7867T>C	2.37:g.179636187A>G	ENSP00000465570:p.Ser2623Pro		179344432	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	14.81	2.646855	0.47258	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.68903	-0.36;-0.36;-0.36;-0.36;-0.36	6.17	6.17	0.99709	Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.78672	0.4320	M	0.64997	1.995	0.26093	N	0.980923	D;D;D;D;D	0.76494	0.988;0.988;0.988;0.996;0.999	P;P;P;P;D	0.71656	0.856;0.856;0.856;0.898;0.974	T	0.72557	-0.4257	9	0.87932	D	0	.	11.8437	0.52371	0.8695:0.0:0.0:0.1305	.	2577;2577;2577;2623;2623	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	P	2623;2577;2577;2577;2577;2623	ENSP00000343764:S2623P;ENSP00000434586:S2577P;ENSP00000340554:S2577P;ENSP00000352154:S2577P;ENSP00000354117:S2623P	ENSP00000340554:S2577P	S	-	1	0	TTN	179344432	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.671000	0.68095	2.371000	0.80710	0.533000	0.62120	TCC		0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ANKRD44	91526	hgsc.bcm.edu	37	2	197866500	197866500	+	Silent	SNP	G	G	T			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:197866500G>T	ENST00000328737.2	-	22	2413	c.2337C>A	c.(2335-2337)ccC>ccA	p.P779P	ANKRD44_ENST00000337207.5_Silent_p.P779P|ANKRD44_ENST00000450567.1_Silent_p.P779P|ANKRD44_ENST00000282272.8_Silent_p.P796P			Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	804										NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(20)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.246)			GTGGAGTAAAGGGATTACCGA	0.338																																																	0			2											108.0	109.0	109.0					2																	197866500		2203	4300	6503	197574745	SO:0001819	synonymous_variant	91526			AK097086	CCDS33355.1, CCDS33355.2, CCDS74619.1	2q33.1	2013-01-10			ENSG00000065413	ENSG00000065413		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"", ""Ankyrin repeat domain containing"""	25259	protein-coding gene	gene with protein product	"""protein phosphatase 6 ankyrin repeat subunit B"""						Standard	NM_153697		Approved	PP6-ARS-B	uc021vuj.1	Q8N8A2	OTTHUMG00000154411	ENST00000328737.2:c.2337C>A	2.37:g.197866500G>T			197574745	Q53SL9|Q6P480|Q86VL5|Q8IZ72|Q9UFA4	Silent	SNP	ENST00000328737.2	37																																																																																					0.338	ANKRD44-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335113.1	NM_153697	
COQ10B	80219	hgsc.bcm.edu	37	2	198318329	198318329	+	Silent	SNP	G	G	A	rs375808557		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:198318329G>A	ENST00000263960.2	+	1	183	c.45G>A	c.(43-45)tcG>tcA	p.S15S	COQ10B_ENST00000545340.1_5'Flank|COQ10B_ENST00000409010.1_5'Flank|COQ10B_ENST00000409398.1_Silent_p.S15S	NM_025147.3	NP_079423.1	Q9H8M1	CQ10B_HUMAN	coenzyme Q10 homolog B (S. cerevisiae)	15						mitochondrial inner membrane (GO:0005743)				endometrium(1)|large_intestine(2)|lung(3)	6			Epithelial(96;0.231)|OV - Ovarian serous cystadenocarcinoma(117;0.246)			GGGTAGTCTCGGGATGCCGTC	0.652																																																	0			2											41.0	50.0	47.0					2																	198318329		2203	4300	6503	198026574	SO:0001819	synonymous_variant	80219			AK023510	CCDS2319.1	2q33.1	2008-02-05	2006-04-04		ENSG00000115520	ENSG00000115520			25819	protein-coding gene	gene with protein product			"""coenzyme Q10 homolog B (yeast)"""				Standard	NM_025147		Approved	FLJ13448	uc002uuh.1	Q9H8M1	OTTHUMG00000132745	ENST00000263960.2:c.45G>A	2.37:g.198318329G>A			198026574	B7Z1Y4	Silent	SNP	ENST00000263960.2	37	CCDS2319.1																																																																																				0.652	COQ10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256105.2	NM_025147	
SATB2	23314	hgsc.bcm.edu	37	2	200213525	200213525	+	Missense_Mutation	SNP	C	C	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:200213525C>A	ENST00000417098.1	-	7	1888	c.1072G>T	c.(1072-1074)Gtg>Ttg	p.V358L	SATB2_ENST00000443023.1_Missense_Mutation_p.V299L|SATB2_ENST00000260926.5_Missense_Mutation_p.V358L|SATB2_ENST00000457245.1_Missense_Mutation_p.V358L|SATB2_ENST00000428695.1_Missense_Mutation_p.V240L	NM_001172509.1	NP_001165980.1	Q9UPW6	SATB2_HUMAN	SATB homeobox 2	358					cartilage development (GO:0051216)|cellular response to organic substance (GO:0071310)|chromatin remodeling (GO:0006338)|embryonic pattern specification (GO:0009880)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|osteoblast development (GO:0002076)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)	p.V358M(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(40)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						GAGACTTCCACGGAAGAGTTG	0.547																																					Colon(30;262 767 11040 24421 36230)												1	Substitution - Missense(1)	lung(1)	2											176.0	168.0	171.0					2																	200213525		2203	4300	6503	199921770	SO:0001583	missense	23314			AB028957	CCDS2327.1	2q33.1	2011-06-20	2007-02-15		ENSG00000119042	ENSG00000119042		"""Homeoboxes / CUT class"""	21637	protein-coding gene	gene with protein product		608148	"""SATB family member 2"""				Standard	NM_015265		Approved	KIAA1034, FLJ21474	uc002uva.2	Q9UPW6	OTTHUMG00000132767	ENST00000417098.1:c.1072G>T	2.37:g.200213525C>A	ENSP00000401112:p.Val358Leu		199921770	A8K5Z8|Q3ZB87|Q4V763	Missense_Mutation	SNP	ENST00000417098.1	37	CCDS2327.1	.	.	.	.	.	.	.	.	.	.	C	18.47	3.631068	0.67015	.	.	ENSG00000119042	ENST00000417098;ENST00000443023;ENST00000260926;ENST00000428695;ENST00000457245	T;T;T;T;T	0.43294	0.95;0.96;0.95;0.95;0.95	5.72	5.72	0.89469	Homeodomain protein CUT (2);Lambda repressor-like, DNA-binding (1);	0.142736	0.46145	D	0.000313	T	0.32675	0.0837	N	0.08118	0	0.42555	D	0.993128	B;P;P	0.49447	0.301;0.924;0.802	B;P;P	0.46659	0.189;0.523;0.494	T	0.12243	-1.0555	10	0.26408	T	0.33	-13.7282	19.8861	0.96913	0.0:1.0:0.0:0.0	.	240;106;358	Q3ZB87;Q9H726;Q9UPW6	.;.;SATB2_HUMAN	L	358;299;358;240;358	ENSP00000401112:V358L;ENSP00000388764:V299L;ENSP00000260926:V358L;ENSP00000388581:V240L;ENSP00000405420:V358L	ENSP00000260926:V358L	V	-	1	0	SATB2	199921770	0.998000	0.40836	0.999000	0.59377	0.984000	0.73092	3.734000	0.55037	2.711000	0.92665	0.655000	0.94253	GTG		0.547	SATB2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256140.1	NM_015265	
KCTD18	130535	hgsc.bcm.edu	37	2	201371657	201371657	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:201371657T>C	ENST00000359878.3	-	2	593	c.83A>G	c.(82-84)gAg>gGg	p.E28G	KCTD18_ENST00000468413.1_5'UTR|KCTD18_ENST00000409157.1_Missense_Mutation_p.E28G	NM_152387.2	NP_689600.2	Q6PI47	KCD18_HUMAN	potassium channel tetramerization domain containing 18	28	BTB.				protein homooligomerization (GO:0051260)					endometrium(5)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15						GCACAAGGACTCCCGCCGGGC	0.512																																																	0			2											69.0	77.0	74.0					2																	201371657		2203	4300	6503	201079902	SO:0001583	missense	130535			AK055884	CCDS2330.1	2q33.1	2013-06-20	2013-06-20		ENSG00000155729	ENSG00000155729			26446	protein-coding gene	gene with protein product			"""potassium channel tetramerisation domain containing 18"""				Standard	NM_152387		Approved	FLJ31322, 6530404F10Rik, FLJ37818	uc002uvs.3	Q6PI47	OTTHUMG00000132781	ENST00000359878.3:c.83A>G	2.37:g.201371657T>C	ENSP00000352941:p.Glu28Gly		201079902	Q53T21|Q6NW26|Q6PCD8|Q8N9B7|Q96N73	Missense_Mutation	SNP	ENST00000359878.3	37	CCDS2330.1	.	.	.	.	.	.	.	.	.	.	T	18.02	3.529668	0.64860	.	.	ENSG00000155729	ENST00000359878;ENST00000409157	T;T	0.42513	0.97;0.97	5.46	4.3	0.51218	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.285799	0.30519	N	0.009447	T	0.34454	0.0898	N	0.20685	0.6	0.33487	D	0.588168	B;P	0.40000	0.02;0.698	B;P	0.45276	0.034;0.475	T	0.48969	-0.8987	10	0.38643	T	0.18	-15.072	12.4828	0.55854	0.0:0.0:0.1398:0.8602	.	28;28	Q6PI47-2;Q6PI47	.;KCD18_HUMAN	G	28	ENSP00000352941:E28G;ENSP00000386751:E28G	ENSP00000352941:E28G	E	-	2	0	KCTD18	201079902	0.940000	0.31905	0.960000	0.40013	0.995000	0.86356	3.182000	0.50910	1.068000	0.40764	0.533000	0.62120	GAG		0.512	KCTD18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256188.1	NM_152387	
GPBAR1	151306	hgsc.bcm.edu	37	2	219128239	219128239	+	Silent	SNP	C	C	T			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:219128239C>T	ENST00000522678.1	+	2	1660	c.792C>T	c.(790-792)tcC>tcT	p.S264S	GPBAR1_ENST00000479077.1_Silent_p.S264S|GPBAR1_ENST00000519574.1_Silent_p.S264S|GPBAR1_ENST00000521462.1_Silent_p.S264S	NM_001077191.1	NP_001070659.1	Q8TDU6	GPBAR_HUMAN	G protein-coupled bile acid receptor 1	264					cell surface bile acid receptor signaling pathway (GO:0038184)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bile acid receptor activity (GO:0038181)|G-protein coupled bile acid receptor activity (GO:0038182)			cervix(1)|kidney(1)|large_intestine(1)|ovary(1)	4		Renal(207;0.0474)		Epithelial(149;7.19e-07)|all cancers(144;0.000131)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CACTGTTGTCCCTCCTCTCCC	0.677																																																	0			2											12.0	14.0	13.0					2																	219128239		1951	4087	6038	218836483	SO:0001819	synonymous_variant	151306			AB086170	CCDS46515.1	2q35	2012-08-08			ENSG00000179921	ENSG00000179921			19680	protein-coding gene	gene with protein product		610147				12419312	Standard	NM_170699		Approved	BG37, GPCR, TGR5, M-BAR, GPCR19, GPR131, MGC40597	uc010zjw.1	Q8TDU6	OTTHUMG00000155203	ENST00000522678.1:c.792C>T	2.37:g.219128239C>T			218836483	B3KV35	Missense_Mutation	SNP	ENST00000522678.1	37	CCDS46515.1																																																																																				0.677	GPBAR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338767.3	NM_001077191	
SPEG	10290	hgsc.bcm.edu	37	2	220337720	220337720	+	Missense_Mutation	SNP	G	G	A	rs376367804		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:220337720G>A	ENST00000312358.7	+	16	4181	c.4049G>A	c.(4048-4050)cGt>cAt	p.R1350H	SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	1350	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		ACAGGGCTGCGTAAGGGGGTC	0.657																																																	0			2											41.0	49.0	46.0					2																	220337720		2083	4210	6293	220045964	SO:0001583	missense	10290			BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"""Immunoglobulin superfamily / I-set domain containing"""	16901	protein-coding gene	gene with protein product		615950	"""aortic preferentially expressed gene 1"""	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.4049G>A	2.37:g.220337720G>A	ENSP00000311684:p.Arg1350His		220045964	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	37	CCDS42824.1	.	.	.	.	.	.	.	.	.	.	G	9.020	0.984686	0.18889	.	.	ENSG00000072195	ENST00000312358;ENST00000265327	T	0.54866	0.55	5.11	4.22	0.49857	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.232949	0.22510	N	0.059116	T	0.39835	0.1093	L	0.52905	1.665	0.80722	D	1	P	0.43024	0.798	B	0.35182	0.197	T	0.28364	-1.0046	10	0.38643	T	0.18	.	5.1143	0.14825	0.1883:0.1731:0.6386:0.0	.	1350	Q15772	SPEG_HUMAN	H	1350	ENSP00000311684:R1350H	ENSP00000265327:R1350H	R	+	2	0	SPEG	220045964	0.999000	0.42202	0.933000	0.37362	0.177000	0.22998	3.420000	0.52735	1.120000	0.41904	0.561000	0.74099	CGT		0.657	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876	
NGEF	25791	hgsc.bcm.edu	37	2	233839512	233839512	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:233839512A>G	ENST00000264051.3	-	2	367	c.89T>C	c.(88-90)gTg>gCg	p.V30A		NM_019850.2	NP_062824.2	Q8N5V2	NGEF_HUMAN	neuronal guanine nucleotide exchange factor	30	Regulatory region; modulates activity toward RHOA, RAC1 and CDC42. {ECO:0000250}.				apoptotic signaling pathway (GO:0097190)|ephrin receptor signaling pathway (GO:0048013)|negative regulation of dendritic spine morphogenesis (GO:0061002)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.V30A(1)		central_nervous_system(4)|endometrium(8)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|pancreas(1)|skin(4)	35		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.00793)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;8.65e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(119;0.00984)|GBM - Glioblastoma multiforme(43;0.0604)		CTCAGGTTTCACCTTGGCTGG	0.448																																																	1	Substitution - Missense(1)	central_nervous_system(1)	2											225.0	204.0	211.0					2																	233839512		2203	4300	6503	233547756	SO:0001583	missense	25791			AJ238899	CCDS2500.1, CCDS46544.1	2q37	2012-07-24			ENSG00000066248	ENSG00000066248		"""Rho guanine nucleotide exchange factors"""	7807	protein-coding gene	gene with protein product	"""ephexin"""	605991				10777665	Standard	NM_019850		Approved	ARHGEF27	uc002vts.2	Q8N5V2	OTTHUMG00000133272	ENST00000264051.3:c.89T>C	2.37:g.233839512A>G	ENSP00000264051:p.Val30Ala		233547756	B4DMB8|B9A045|E9PC42|Q53QQ4|Q53ST7|Q6GMQ5|Q9NQD6	Missense_Mutation	SNP	ENST00000264051.3	37	CCDS2500.1	.	.	.	.	.	.	.	.	.	.	A	11.26	1.586841	0.28268	.	.	ENSG00000066248	ENST00000264051	T	0.71461	-0.57	5.05	-1.6	0.08426	.	0.993583	0.08151	N	0.990107	T	0.43853	0.1266	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.32508	-0.9904	10	0.02654	T	1	-8.203	0.8436	0.01155	0.3356:0.2229:0.2868:0.1547	.	30	Q8N5V2	NGEF_HUMAN	A	30	ENSP00000264051:V30A	ENSP00000264051:V30A	V	-	2	0	NGEF	233547756	0.000000	0.05858	0.006000	0.13384	0.087000	0.18053	0.111000	0.15458	-0.138000	0.11434	0.533000	0.62120	GTG		0.448	NGEF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257051.2	XM_044799	
ANKMY1	51281	hgsc.bcm.edu	37	2	241494338	241494338	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr2:241494338T>C	ENST00000272972.3	-	2	228	c.14A>G	c.(13-15)gAg>gGg	p.E5G	ANKMY1_ENST00000373318.2_Missense_Mutation_p.E94G|ANKMY1_ENST00000536462.1_Missense_Mutation_p.E47G|ANKMY1_ENST00000405002.1_Missense_Mutation_p.E5G|ANKMY1_ENST00000401804.1_Missense_Mutation_p.E94G|ANKMY1_ENST00000405523.3_Missense_Mutation_p.E94G|ANKMY1_ENST00000403283.1_Missense_Mutation_p.E173G|ANKMY1_ENST00000391987.1_Missense_Mutation_p.E5G|ANKMY1_ENST00000373320.4_Missense_Mutation_p.E5G|ANKMY1_ENST00000462004.1_5'UTR|ANKMY1_ENST00000361678.4_Missense_Mutation_p.E94G|ANKMY1_ENST00000406958.1_Missense_Mutation_p.E94G	NM_016552.2	NP_057636.2	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1	5							metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	30		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.03e-30)|all cancers(36;4.78e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.45e-14)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.8e-06)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.01)|Colorectal(34;0.0101)|COAD - Colon adenocarcinoma(134;0.0476)		CAACCCAAACTCCCCCTGGTA	0.592																																																	0			2											179.0	157.0	165.0					2																	241494338		2203	4300	6503	241143011	SO:0001583	missense	51281			AB034636	CCDS2535.1, CCDS2536.1, CCDS63184.1, CCDS63185.1, CCDS74681.1	2q37.3	2013-01-10			ENSG00000144504	ENSG00000144504		"""Zinc fingers, MYND-type"", ""Ankyrin repeat domain containing"""	20987	protein-coding gene	gene with protein product							Standard	XM_005247020		Approved	FLJ20499, ZMYND13	uc002vyz.1	Q9P2S6	OTTHUMG00000133355	ENST00000272972.3:c.14A>G	2.37:g.241494338T>C	ENSP00000272972:p.Glu5Gly		241143011	B2RB78|Q4ZFV3|Q8IYX5|Q8NDK5|Q9H0V8|Q9NX10	Missense_Mutation	SNP	ENST00000272972.3	37	CCDS2536.1	.	.	.	.	.	.	.	.	.	.	T	13.78	2.337889	0.41398	.	.	ENSG00000144504	ENST00000373318;ENST00000406958;ENST00000272972;ENST00000361678;ENST00000391987;ENST00000373320;ENST00000403283;ENST00000401804;ENST00000536462;ENST00000405523;ENST00000405002;ENST00000539830;ENST00000441168;ENST00000418708;ENST00000418505	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.61859	0.82;0.82;0.82;0.82;0.82;0.82;0.82;0.85;0.07;0.07;0.07;0.07;0.07;0.07	3.85	3.85	0.44370	.	0.775582	0.10788	N	0.634025	T	0.69513	0.3119	M	0.80982	2.52	0.31570	N	0.656429	B;P;P;P;P;B	0.43826	0.322;0.782;0.818;0.611;0.782;0.322	B;P;P;B;P;B	0.50314	0.156;0.503;0.637;0.422;0.503;0.156	T	0.72516	-0.4269	10	0.72032	D	0.01	-0.8773	11.2478	0.49006	0.0:0.0:0.0:1.0	.	5;5;94;94;94;5	Q4ZFV3;Q9P2S6-4;Q6GPI0;B5MBY4;Q9P2S6-2;Q9P2S6	.;.;.;.;.;ANKY1_HUMAN	G	94;94;5;94;5;5;173;94;47;94;5;5;47;5;5	ENSP00000362415:E94G;ENSP00000384555:E94G;ENSP00000272972:E5G;ENSP00000355097:E94G;ENSP00000375847:E5G;ENSP00000362417:E5G;ENSP00000383968:E173G;ENSP00000385887:E94G;ENSP00000444707:E47G;ENSP00000385635:E94G;ENSP00000385145:E5G;ENSP00000405938:E47G;ENSP00000407015:E5G;ENSP00000412094:E5G	ENSP00000272972:E5G	E	-	2	0	ANKMY1	241143011	0.862000	0.29867	0.872000	0.34217	0.064000	0.16182	4.171000	0.58236	1.971000	0.57363	0.533000	0.62120	GAG		0.592	ANKMY1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257187.2	NM_017844	
AK3	50808	hgsc.bcm.edu	37	9	4719198	4719198	+	Silent	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr9:4719198A>G	ENST00000381809.3	-	3	611	c.381T>C	c.(379-381)gcT>gcC	p.A127A	AK3_ENST00000447596.4_Silent_p.A87A|AK3_ENST00000359883.2_Silent_p.A57A	NM_016282.3	NP_057366.2	P27144	KAD4_HUMAN	adenylate kinase 3	125	LID.				ADP biosynthetic process (GO:0006172)|AMP metabolic process (GO:0046033)|ATP metabolic process (GO:0046034)|brain development (GO:0007420)|GTP metabolic process (GO:0046039)|liver development (GO:0001889)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|response to drug (GO:0042493)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|GTP binding (GO:0005525)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside triphosphate adenylate kinase activity (GO:0046899)			large_intestine(2)|lung(1)|ovary(2)	5	all_hematologic(13;0.137)	Breast(48;0.238)		GBM - Glioblastoma multiforme(50;0.0302)	Adefovir Dipivoxil(DB00718)|Tenofovir(DB00300)	GAATCCAGCGAGCAGTAAGGC	0.478																																																	0			9											98.0	84.0	88.0					9																	4719198		2203	4300	6503	4709198	SO:0001819	synonymous_variant	50808			BC013771	CCDS6455.1, CCDS56561.1, CCDS56562.1	9p24.1	2010-09-29	2004-06-11	2005-04-07	ENSG00000147853	ENSG00000147853			17376	protein-coding gene	gene with protein product		609290	"""adenylate kinase 6"", ""adenylate kinase 3 like 1"""	AK6, AK3L1		8288, 182062	Standard	NM_001199852		Approved	AKL3L1	uc003ziq.2	Q9UIJ7	OTTHUMG00000019472	ENST00000381809.3:c.381T>C	9.37:g.4719198A>G			4709198	B2R927|D3DQ62|Q6IBH4|Q6NXQ5|Q8IUU9	Silent	SNP	ENST00000381809.3	37	CCDS6455.1																																																																																				0.478	AK3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051585.1	NM_016282	
JAK2	3717	hgsc.bcm.edu	37	9	5070030	5070030	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr9:5070030T>C	ENST00000381652.3	+	12	2113	c.1619T>C	c.(1618-1620)aTc>aCc	p.I540T	JAK2_ENST00000539801.1_Missense_Mutation_p.I540T|JAK2_ENST00000544510.1_Missense_Mutation_p.I391T	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	540					actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)	p.I540T(1)|p.I540_E543>KK(1)	BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18)	breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1)	32998	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	TTTCACAAAATCAGAAATGAA	0.333		1	"""T, Mis, O"""	"""ETV6, PCM1, BCR"""	"""ALL, AML, MPD,  CML"""				Polycythemia Vera, Familial																															Dom	yes		9	9p24	3717	Janus kinase 2		L	2	Substitution - Missense(1)|Complex - deletion inframe(1)	haematopoietic_and_lymphoid_tissue(2)	9											88.0	82.0	84.0					9																	5070030		2202	4300	6502	5060030	SO:0001583	missense	3717	Familial Cancer Database			CCDS6457.1	9p24	2014-09-17	2009-04-23		ENSG00000096968	ENSG00000096968	2.7.10.1	"""SH2 domain containing"""	6192	protein-coding gene	gene with protein product		147796				1848670	Standard	NM_004972		Approved	JTK10	uc003ziw.3	O60674	OTTHUMG00000019490	ENST00000381652.3:c.1619T>C	9.37:g.5070030T>C	ENSP00000371067:p.Ile540Thr		5060030	O14636|O75297	Missense_Mutation	SNP	ENST00000381652.3	37	CCDS6457.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.234067	0.79688	.	.	ENSG00000096968	ENST00000539801;ENST00000381652;ENST00000544510	T;T;T	0.27557	1.66;1.66;1.66	5.07	5.07	0.68467	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.54631	0.1870	M	0.83953	2.67	0.80722	D	1	D	0.76494	0.999	P	0.59546	0.859	T	0.63256	-0.6678	10	0.87932	D	0	-9.0565	14.4823	0.67592	0.0:0.0:0.0:1.0	.	540	O60674	JAK2_HUMAN	T	540;540;391	ENSP00000440387:I540T;ENSP00000371067:I540T;ENSP00000443103:I391T	ENSP00000371067:I540T	I	+	2	0	JAK2	5060030	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.656000	0.83736	1.892000	0.54788	0.455000	0.32223	ATC		0.333	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1		
JAK2	3717	hgsc.bcm.edu	37	9	5070046	5070046	+	Silent	SNP	G	G	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr9:5070046G>A	ENST00000381652.3	+	12	2129	c.1635G>A	c.(1633-1635)ttG>ttA	p.L545L	JAK2_ENST00000539801.1_Silent_p.L545L|JAK2_ENST00000544510.1_Silent_p.L396L	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	545	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)		BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18)	breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1)	32998	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	ATGAAGATTTGATATTTGTAA	0.323		1	"""T, Mis, O"""	"""ETV6, PCM1, BCR"""	"""ALL, AML, MPD,  CML"""				Polycythemia Vera, Familial																															Dom	yes		9	9p24	3717	Janus kinase 2		L	0			9											83.0	78.0	79.0					9																	5070046		2202	4298	6500	5060046	SO:0001819	synonymous_variant	3717	Familial Cancer Database			CCDS6457.1	9p24	2014-09-17	2009-04-23		ENSG00000096968	ENSG00000096968	2.7.10.1	"""SH2 domain containing"""	6192	protein-coding gene	gene with protein product		147796				1848670	Standard	NM_004972		Approved	JTK10	uc003ziw.3	O60674	OTTHUMG00000019490	ENST00000381652.3:c.1635G>A	9.37:g.5070046G>A			5060046	O14636|O75297	Silent	SNP	ENST00000381652.3	37	CCDS6457.1																																																																																				0.323	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1		
CDKN2A	1029	hgsc.bcm.edu	37	9	21970944	21970944	+	Silent	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr9:21970944T>C	ENST00000304494.5	-	2	684	c.414A>G	c.(412-414)agA>agG	p.R138R	CDKN2A_ENST00000497750.1_Silent_p.R87R|CDKN2A_ENST00000498628.2_Silent_p.R87R|CDKN2A_ENST00000494262.1_Silent_p.R87R|CDKN2A_ENST00000579122.1_Intron|CDKN2A_ENST00000498124.1_Silent_p.R138R|CDKN2A_ENST00000579755.1_3'UTR|CDKN2A_ENST00000361570.3_3'UTR|CDKN2A_ENST00000578845.2_Silent_p.R87R|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000530628.2_Intron|CDKN2A_ENST00000446177.1_Silent_p.R138R|CDKN2A_ENST00000479692.2_Silent_p.R87R	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	138					cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular senescence (GO:2000774)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|Ras protein signal transduction (GO:0007265)|replicative senescence (GO:0090399)|senescence-associated heterochromatin focus assembly (GO:0035986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|senescence-associated heterochromatin focus (GO:0035985)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.0?(1315)|p.?(13)|p.R128fs*12(3)|p.A118fs*10(1)|p.0(1)		NS(28)|adrenal_gland(6)|autonomic_ganglia(11)|biliary_tract(74)|bone(84)|breast(46)|central_nervous_system(522)|cervix(23)|endometrium(14)|eye(4)|genital_tract(15)|haematopoietic_and_lymphoid_tissue(698)|kidney(39)|large_intestine(11)|liver(92)|lung(365)|meninges(18)|oesophagus(239)|ovary(98)|pancreas(263)|pleura(94)|prostate(13)|salivary_gland(10)|skin(541)|small_intestine(1)|soft_tissue(93)|stomach(48)|thymus(4)|thyroid(24)|upper_aerodigestive_tract(436)|urinary_tract(283)|vulva(2)	4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		GGTTACTGCCTCTGGTGCCCC	0.632		17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)																																							1333	Whole gene deletion(1316)|Unknown(13)|Deletion - Frameshift(4)	haematopoietic_and_lymphoid_tissue(278)|skin(168)|central_nervous_system(164)|lung(143)|urinary_tract(90)|bone(73)|soft_tissue(57)|pleura(51)|upper_aerodigestive_tract(49)|oesophagus(48)|ovary(34)|kidney(30)|breast(30)|pancreas(29)|thyroid(13)|NS(12)|biliary_tract(12)|stomach(12)|autonomic_ganglia(7)|meninges(7)|large_intestine(6)|liver(6)|salivary_gland(4)|thymus(4)|vulva(2)|endometrium(2)|prostate(2)	9											30.0	33.0	32.0					9																	21970944		2203	4300	6503	21960944	SO:0001819	synonymous_variant	1029			L27211	CCDS6510.1, CCDS6511.1, CCDS6511.2, CCDS56565.1	9p21	2014-09-17	2012-03-08		ENSG00000147889	ENSG00000147889			1787	protein-coding gene	gene with protein product		600160	"""cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)"""	CDKN2, MLM		8152487, 7606716	Standard	NM_058195		Approved	CDK4I, p16, INK4a, MTS1, CMM2, ARF, p19, p14, INK4, p16INK4a, p19Arf	uc003zpk.3	P42771	OTTHUMG00000019686	ENST00000304494.5:c.414A>G	9.37:g.21970944T>C			21960944	A5X2G7|D3DRK1|O95440|Q15191|Q5VVJ5|Q96B52|Q9NP05	Silent	SNP	ENST00000304494.5	37	CCDS6510.1																																																																																				0.632	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	NM_000077	
CLTA	1211	hgsc.bcm.edu	37	9	36191149	36191149	+	Silent	SNP	T	T	C	rs2274524	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr9:36191149T>C	ENST00000242285.6	+	1	216	c.96T>C	c.(94-96)gcT>gcC	p.A32A	CLTA_ENST00000396603.2_Silent_p.A32A|CLTA_ENST00000466396.1_Silent_p.A32A|CLTA_ENST00000538225.1_Silent_p.A32A|CLTA_ENST00000470744.1_Silent_p.A32A|CLTA_ENST00000345519.5_Silent_p.A32A|CLTA_ENST00000433436.2_Silent_p.A32A|CLTA_ENST00000540080.1_Silent_p.A32A			P09496	CLCA_HUMAN	clathrin, light chain A	32					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|post-Golgi vesicle-mediated transport (GO:0006892)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	clathrin heavy chain binding (GO:0032050)|peptide binding (GO:0042277)|structural molecule activity (GO:0005198)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(1)	6			STAD - Stomach adenocarcinoma(86;0.228)			AAGACCCGGCTGCGGCCTTCT	0.746													C|||	673	0.134385	0.1747	0.0634	5008	,	,		11673	0.1806		0.0497	False		,,,				2504	0.1697																0			9						C	,,,,,	525,3703		24,477,1613	8.0	9.0	9.0		96,96,96,96,96,96	4.5	1.0	9	dbSNP_100	9	447,7817		9,429,3694	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CLTA	NM_001076677.2,NM_001184760.1,NM_001184761.1,NM_001184762.1,NM_001833.3,NM_007096.3	,,,,,	33,906,5307	CC,CT,TT		5.409,12.4172,7.781	,,,,,	32/237,32/231,32/169,32/167,32/219,32/249	36191149	972,11520	2114	4132	6246	36181149	SO:0001819	synonymous_variant	1211				CCDS6600.1, CCDS6601.1, CCDS43802.1, CCDS55306.1, CCDS55307.1	9p13.3	2010-05-11	2010-05-11		ENSG00000122705	ENSG00000122705			2090	protein-coding gene	gene with protein product		118960	"""clathrin, light polypeptide (Lca)"""			7713494	Standard	NM_007096		Approved	Lca	uc003zzc.3	P09496	OTTHUMG00000019896	ENST00000242285.6:c.96T>C	9.37:g.36191149T>C			36181149	A8K4W3|B4DIN1|F5H6N3|Q2XPN5|Q53XZ1	Silent	SNP	ENST00000242285.6	37	CCDS6601.1																																																																																				0.746	CLTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052405.1	NM_007096	
ECM2	1842	hgsc.bcm.edu	37	9	95285114	95285114	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr9:95285114A>G	ENST00000344604.5	-	2	184	c.35T>C	c.(34-36)cTt>cCt	p.L12P	ECM2_ENST00000375540.1_Missense_Mutation_p.L12P|CENPP_ENST00000375587.3_Intron|ECM2_ENST00000444490.2_Missense_Mutation_p.L12P	NM_001197295.1|NM_001393.3	NP_001184224.1|NP_001384.1	O94769	ECM2_HUMAN	extracellular matrix protein 2, female organ and adipocyte specific	12					cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	interstitial matrix (GO:0005614)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27						AAAAATGATAAGCAGAAAAAA	0.333																																																	0			9											46.0	49.0	48.0					9																	95285114		2202	4300	6502	94324935	SO:0001583	missense	1842			AB011792	CCDS6698.1, CCDS56578.1	9q22.3	2008-07-21			ENSG00000106823	ENSG00000106823			3154	protein-coding gene	gene with protein product	"""matrix glycoprotein SC1/ECM2"""	603479				9790758	Standard	NM_001393		Approved		uc011lty.2	O94769	OTTHUMG00000020226	ENST00000344604.5:c.35T>C	9.37:g.95285114A>G	ENSP00000344758:p.Leu12Pro		94324935	B2R730|E2PU11|Q5T9F2|Q7Z3D0	Missense_Mutation	SNP	ENST00000344604.5	37	CCDS6698.1	.	.	.	.	.	.	.	.	.	.	A	18.94	3.729281	0.69074	.	.	ENSG00000106823	ENST00000444490;ENST00000344604;ENST00000375540;ENST00000395534	T;T;T;T	0.33438	1.41;1.41;1.41;1.41	4.28	4.28	0.50868	.	0.303544	0.27340	N	0.019818	T	0.42063	0.1186	L	0.34521	1.04	0.80722	D	1	D;D;D;D	0.76494	0.998;0.998;0.997;0.999	D;P;P;D	0.66351	0.909;0.831;0.831;0.943	T	0.39800	-0.9596	10	0.87932	D	0	.	13.5504	0.61728	1.0:0.0:0.0:0.0	.	12;12;12;12	Q5T9F3;O94769;B4DK93;O94769-2	.;ECM2_HUMAN;.;.	P	12	ENSP00000393971:L12P;ENSP00000344758:L12P;ENSP00000364690:L12P;ENSP00000378905:L12P	ENSP00000344758:L12P	L	-	2	0	ECM2	94324935	1.000000	0.71417	0.602000	0.28890	0.943000	0.58893	5.725000	0.68507	1.948000	0.56530	0.528000	0.53228	CTT		0.333	ECM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053091.1	NM_001393	
PTCH1	5727	hgsc.bcm.edu	37	9	98239882	98239882	+	Nonsense_Mutation	SNP	C	C	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr9:98239882C>A	ENST00000331920.6	-	10	1749	c.1450G>T	c.(1450-1452)Gga>Tga	p.G484*	PTCH1_ENST00000421141.1_Nonsense_Mutation_p.G333*|PTCH1_ENST00000429896.2_Nonsense_Mutation_p.G333*|PTCH1_ENST00000375274.2_Nonsense_Mutation_p.G483*|PTCH1_ENST00000437951.1_Nonsense_Mutation_p.G418*|PTCH1_ENST00000548379.1_5'Flank|PTCH1_ENST00000430669.2_Nonsense_Mutation_p.G418*|PTCH1_ENST00000418258.1_Nonsense_Mutation_p.G333*	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	484	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				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)	p.G484R(1)		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)				AGGCCCAGTCCTGCAGCCACT	0.572																																																	1	Substitution - Missense(1)	skin(1)	9	GRCh37	CM032341	PTCH1	M							50.0	53.0	52.0					9																	98239882		2203	4300	6503	97279703	SO:0001587	stop_gained	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.1450G>T	9.37:g.98239882C>A	ENSP00000332353:p.Gly484*		97279703	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Nonsense_Mutation	SNP	ENST00000331920.6	37	CCDS6714.1	.	.	.	.	.	.	.	.	.	.	C	42	9.412021	0.99163	.	.	ENSG00000185920	ENST00000331920;ENST00000437951;ENST00000421141;ENST00000418258;ENST00000430669;ENST00000429896;ENST00000375274	.	.	.	5.06	4.17	0.49024	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-9.8386	13.802	0.63206	0.0:0.9261:0.0:0.0739	.	.	.	.	X	484;418;333;333;418;333;483	.	ENSP00000332353:G484X	G	-	1	0	PTCH1	97279703	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.320000	0.79064	1.351000	0.45789	0.655000	0.94253	GGA		0.572	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264	
PTCH1	5727	hgsc.bcm.edu	37	9	98248086	98248086	+	Silent	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr9:98248086A>G	ENST00000331920.6	-	3	764	c.465T>C	c.(463-465)ccT>ccC	p.P155P	PTCH1_ENST00000421141.1_Silent_p.P4P|PTCH1_ENST00000429896.2_Silent_p.P4P|PTCH1_ENST00000375274.2_Silent_p.P154P|PTCH1_ENST00000468211.2_Silent_p.P89P|PTCH1_ENST00000437951.1_Silent_p.P89P|PTCH1_ENST00000548379.1_5'UTR|PTCH1_ENST00000430669.2_Silent_p.P89P|PTCH1_ENST00000418258.1_Silent_p.P4P	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	155					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)				TCATGAGTTGAGGATTAAACA	0.453																																																	0			9											218.0	229.0	225.0					9																	98248086		2203	4300	6503	97287907	SO:0001819	synonymous_variant	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.465T>C	9.37:g.98248086A>G			97287907	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Silent	SNP	ENST00000331920.6	37	CCDS6714.1																																																																																				0.453	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264	
ABCA1	19	hgsc.bcm.edu	37	9	107584854	107584854	+	Silent	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr9:107584854A>G	ENST00000374736.3	-	19	3145	c.2751T>C	c.(2749-2751)gaT>gaC	p.D917D		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	917	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.		D -> Y (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		apolipoprotein A-I-mediated signaling pathway (GO:0038027)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|endosomal transport (GO:0016197)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|interleukin-1 beta secretion (GO:0050702)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|lysosome organization (GO:0007040)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|peptide secretion (GO:0002790)|phagocytosis, engulfment (GO:0006911)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phospholipid translocation (GO:0045332)|platelet dense granule organization (GO:0060155)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cholesterol efflux (GO:0010875)|protein lipidation (GO:0006497)|regulation of Cdc42 protein signal transduction (GO:0032489)|response to drug (GO:0042493)|response to laminar fluid shear stress (GO:0034616)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)	endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein A-I receptor activity (GO:0034188)|apolipoprotein binding (GO:0034185)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase binding (GO:0051117)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|receptor binding (GO:0005102)|small GTPase binding (GO:0031267)|syntaxin binding (GO:0019905)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	115				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599)	GTGCCAGGCCATCGACAGCCA	0.552																																																	0			9											142.0	133.0	136.0					9																	107584854		2203	4300	6503	106624675	SO:0001819	synonymous_variant	19			AJ012376	CCDS6762.1	9q31	2014-03-14			ENSG00000165029	ENSG00000165029		"""ATP binding cassette transporters / subfamily A"""	29	protein-coding gene	gene with protein product	"""Tangier disease"""	600046		ABC1, HDLDT1		8088782, 10431236, 10431237, 10431238	Standard	NM_005502		Approved	TGD	uc004bcl.3	O95477	OTTHUMG00000020417	ENST00000374736.3:c.2751T>C	9.37:g.107584854A>G			106624675	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Silent	SNP	ENST00000374736.3	37	CCDS6762.1																																																																																				0.552	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502	
ABL1	25	hgsc.bcm.edu	37	9	133760130	133760130	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr9:133760130T>C	ENST00000318560.5	+	11	2834	c.2453T>C	c.(2452-2454)cTc>cCc	p.L818P		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	818	Pro-rich.				actin cytoskeleton organization (GO:0030036)|autophagy (GO:0006914)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dopamine (GO:1903351)|cellular response to oxidative stress (GO:0034599)|DNA damage induced protein phosphorylation (GO:0006975)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mismatch repair (GO:0006298)|mitochondrial depolarization (GO:0051882)|mitotic nuclear division (GO:0007067)|muscle cell differentiation (GO:0042692)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)|signal transduction in response to DNA damage (GO:0042770)	actin cytoskeleton (GO:0015629)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase binding (GO:0051019)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|SH3 domain binding (GO:0017124)|syntaxin binding (GO:0019905)			breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Bosutinib(DB06616)|Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Ponatinib(DB08901)|Regorafenib(DB08896)	CCAAAACCCCTCCGGCGGCAG	0.622			"""T, Mis"""	"""BCR, ETV6, NUP214"""	"""CML, ALL, T-ALL"""																																			Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	0			9											14.0	18.0	17.0					9																	133760130		2198	4289	6487	132749951	SO:0001583	missense	25			M14752	CCDS35165.1, CCDS35166.1	9q34.1	2014-09-17	2014-06-26		ENSG00000097007	ENSG00000097007		"""SH2 domain containing"""	76	protein-coding gene	gene with protein product		189980	"""v-abl Abelson murine leukemia viral oncogene homolog 1"", ""c-abl oncogene 1, receptor tyrosine kinase"", ""c-abl oncogene 1, non-receptor tyrosine kinase"""	ABL		1857987, 12626632	Standard	NM_007313		Approved	JTK7, c-ABL, p150	uc004bzv.3	P00519	OTTHUMG00000020813	ENST00000318560.5:c.2453T>C	9.37:g.133760130T>C	ENSP00000323315:p.Leu818Pro		132749951	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Missense_Mutation	SNP	ENST00000318560.5	37	CCDS35166.1	.	.	.	.	.	.	.	.	.	.	T	9.064	0.995133	0.19043	.	.	ENSG00000097007	ENST00000444970;ENST00000372348;ENST00000318560	T;T	0.16457	2.34;2.34	5.54	3.17	0.36434	.	0.800466	0.11693	N	0.538717	T	0.09774	0.0240	N	0.19112	0.55	0.54753	D	0.999983	B;B	0.32128	0.357;0.357	B;B	0.33620	0.167;0.167	T	0.24368	-1.0162	10	0.28530	T	0.3	.	2.7618	0.05308	0.1489:0.0819:0.1525:0.6167	.	818;855	P00519;Q59FK4	ABL1_HUMAN;.	P	633;837;818	ENSP00000361423:L837P;ENSP00000323315:L818P	ENSP00000323315:L818P	L	+	2	0	ABL1	132749951	0.751000	0.28327	0.116000	0.21606	0.642000	0.38348	1.223000	0.32527	0.894000	0.36317	0.459000	0.35465	CTC		0.622	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313	
FIBCD1	84929	hgsc.bcm.edu	37	9	133787222	133787222	+	Silent	SNP	C	C	T			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr9:133787222C>T	ENST00000372338.4	-	5	1145	c.903G>A	c.(901-903)gcG>gcA	p.A301A	FIBCD1_ENST00000253018.4_Silent_p.A143A|FIBCD1_ENST00000372337.2_Silent_p.A143A|FIBCD1_ENST00000448616.1_Silent_p.A301A	NM_032843.4	NP_116232.3	Q8N539	FBCD1_HUMAN	fibrinogen C domain containing 1	301	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.					integral component of membrane (GO:0016021)|membrane (GO:0016020)	chitin binding (GO:0008061)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(3)|lung(2)|prostate(5)|urinary_tract(1)	12	all_hematologic(7;0.0028)			OV - Ovarian serous cystadenocarcinoma(145;3.52e-05)|Epithelial(140;0.00019)		CGTCTCGGTACGCATCCCAGC	0.677																																																	0			9											46.0	39.0	42.0					9																	133787222		2198	4300	6498	132777043	SO:0001819	synonymous_variant	84929			AK027716	CCDS6937.1	9q34.2	2013-02-06			ENSG00000130720	ENSG00000130720		"""Fibrinogen C domain containing"""	25922	protein-coding gene	gene with protein product		613357				12975309	Standard	NM_001145106		Approved	FLJ14810	uc004bzz.3	Q8N539	OTTHUMG00000020814	ENST00000372338.4:c.903G>A	9.37:g.133787222C>T			132777043	A3KFK0|Q6UXK6|Q96SJ7	Silent	SNP	ENST00000372338.4	37	CCDS6937.1	.	.	.	.	.	.	.	.	.	.	C	1.277	-0.611303	0.03690	.	.	ENSG00000130720	ENST00000444139	.	.	.	5.17	-10.3	0.00346	.	.	.	.	.	T	0.55016	0.1894	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.76610	-0.2896	4	.	.	.	.	10.9936	0.47563	0.0607:0.123:0.5413:0.275	.	.	.	.	H	255	.	.	R	-	2	0	FIBCD1	132777043	0.000000	0.05858	0.001000	0.08648	0.195000	0.23768	-9.652000	0.00010	-6.722000	0.00003	-1.464000	0.01018	CGT		0.677	FIBCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054687.2	NM_032843	
C9orf171	389799	hgsc.bcm.edu	37	9	135374875	135374875	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr9:135374875A>G	ENST00000343036.2	+	4	568	c.520A>G	c.(520-522)Aac>Gac	p.N174D	C9orf171_ENST00000393215.3_Missense_Mutation_p.N138D|C9orf171_ENST00000393216.2_Missense_Mutation_p.N138D	NM_207417.1	NP_997300.1	Q6ZQR2	CI171_HUMAN	chromosome 9 open reading frame 171	174										large_intestine(7)|lung(9)|ovary(4)|prostate(3)	23						TGCCCGGGAGAACTTGCTCTA	0.597																																																	0			9											87.0	87.0	87.0					9																	135374875		2203	4300	6503	134364696	SO:0001583	missense	389799			AK128819	CCDS6949.1, CCDS65167.1	9q34.13	2012-04-03			ENSG00000188523	ENSG00000188523			33776	protein-coding gene	gene with protein product							Standard	NM_207417		Approved	FLJ46082	uc004cbn.3	Q6ZQR2	OTTHUMG00000131684	ENST00000343036.2:c.520A>G	9.37:g.135374875A>G	ENSP00000343290:p.Asn174Asp		134364696	Q147X1	Missense_Mutation	SNP	ENST00000343036.2	37	CCDS6949.1	.	.	.	.	.	.	.	.	.	.	A	18.05	3.537613	0.65085	.	.	ENSG00000188523	ENST00000393215;ENST00000343036;ENST00000393216	T;T;T	0.22743	1.94;1.94;1.94	5.26	4.07	0.47477	.	0.394558	0.24904	N	0.034664	T	0.15305	0.0369	L	0.40543	1.245	0.26124	N	0.980506	B;P	0.40515	0.413;0.719	B;B	0.38985	0.098;0.287	T	0.10660	-1.0620	10	0.35671	T	0.21	.	5.7025	0.17891	0.5359:0.3145:0.0:0.1496	.	138;174	Q6ZQR2-2;Q6ZQR2	.;CI171_HUMAN	D	138;174;138	ENSP00000376908:N138D;ENSP00000343290:N174D;ENSP00000376909:N138D	ENSP00000343290:N174D	N	+	1	0	C9orf171	134364696	0.970000	0.33590	0.991000	0.47740	0.818000	0.46254	2.327000	0.43858	2.116000	0.64780	0.459000	0.35465	AAC		0.597	C9orf171-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254589.1	NM_207417	
RALGDS	5900	hgsc.bcm.edu	37	9	135983446	135983446	+	Missense_Mutation	SNP	T	T	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr9:135983446T>G	ENST00000372050.3	-	6	1147	c.1126A>C	c.(1126-1128)Agt>Cgt	p.S376R	RALGDS_ENST00000372062.3_Missense_Mutation_p.S347R|RALGDS_ENST00000542690.1_Missense_Mutation_p.S447R|RALGDS_ENST00000393157.3_Missense_Mutation_p.S375R|RALGDS_ENST00000469972.1_5'UTR|RALGDS_ENST00000372047.3_Missense_Mutation_p.S364R|RALGDS_ENST00000393160.3_Missense_Mutation_p.S321R	NM_006266.2	NP_006257.1	Q12967	GNDS_HUMAN	ral guanine nucleotide dissociation stimulator	376					neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)|regulation of catalytic activity (GO:0050790)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|small GTPase regulator activity (GO:0005083)			endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10				OV - Ovarian serous cystadenocarcinoma(145;3.66e-06)|Epithelial(140;2.77e-05)		TTCTCCTCACTCAGCCCGTTC	0.577			T	CIITA	"""PMBL, Hodgkin Lymphona, """																																Melanoma(189;762 2088 15384 21931 52515)			Dom	yes		9	9q34.3	5900	ral guanine nucleotide dissociation stimulator		L	0			9											98.0	86.0	90.0					9																	135983446		2203	4300	6503	134973267	SO:0001583	missense	5900			AB037729	CCDS6959.1, CCDS43897.1, CCDS65172.1, CCDS65173.1, CCDS65174.1	9q34.3	2009-04-08			ENSG00000160271	ENSG00000160271			9842	protein-coding gene	gene with protein product		601619				7972015	Standard	NM_006266		Approved	RGF, RalGEF, RGDS	uc004ccr.3	Q12967	OTTHUMG00000020858	ENST00000372050.3:c.1126A>C	9.37:g.135983446T>G	ENSP00000361120:p.Ser376Arg		134973267	B7Z753|E7ER93|E7ERZ0|Q5T7V4|Q6KH11|Q6PCE1|Q6ZSD5|Q9HAX7|Q9HAY1|Q9HCT1|Q9P2N8	Missense_Mutation	SNP	ENST00000372050.3	37	CCDS6959.1	.	.	.	.	.	.	.	.	.	.	T	18.53	3.643125	0.67244	.	.	ENSG00000160271	ENST00000372050;ENST00000372047;ENST00000393160;ENST00000372051;ENST00000393157;ENST00000542690;ENST00000372062;ENST00000424572	T;T;T;T;T;T;T	0.28454	1.61;1.61;1.61;1.61;1.61;1.61;1.61	5.39	-1.73	0.08081	Ras guanine nucleotide exchange factor, domain (1);	1.108720	0.06691	N	0.769766	T	0.15132	0.0365	L	0.36672	1.1	0.09310	N	1	B;B;B;B;B;B;P;P	0.46952	0.372;0.08;0.344;0.146;0.0;0.421;0.887;0.815	B;B;B;B;B;B;B;B	0.35931	0.118;0.029;0.088;0.024;0.005;0.095;0.214;0.214	T	0.18366	-1.0339	10	0.16420	T	0.52	.	0.8645	0.01200	0.3018:0.3306:0.1541:0.2136	.	447;347;376;364;321;375;364;376	F5H6M6;E7ER93;Q12967-2;Q8TEK9;Q6KH11;E7ERZ0;Q6PCE1;Q12967	.;.;.;.;.;.;.;GNDS_HUMAN	R	376;364;321;145;375;447;347;8	ENSP00000361120:S376R;ENSP00000361117:S364R;ENSP00000376867:S321R;ENSP00000376864:S375R;ENSP00000437518:S447R;ENSP00000361132:S347R;ENSP00000391814:S8R	ENSP00000361117:S364R	S	-	1	0	RALGDS	134973267	0.000000	0.05858	0.008000	0.14137	0.936000	0.57629	-0.704000	0.05058	-0.229000	0.09854	0.533000	0.62120	AGT		0.577	RALGDS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054837.1	NM_006266	
COL5A1	1289	hgsc.bcm.edu	37	9	137623961	137623961	+	Silent	SNP	G	G	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr9:137623961G>A	ENST00000371817.3	+	9	1791	c.1377G>A	c.(1375-1377)gcG>gcA	p.A459A		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	459	Interrupted collagenous region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		GAGAACCAGCGATTATCGAGC	0.557																																																	0			9											110.0	95.0	101.0					9																	137623961		2203	4300	6503	136763782	SO:0001819	synonymous_variant	1289			D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"""Collagens"""	2209	protein-coding gene	gene with protein product	"""alpha 1 type V collagen"""	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.1377G>A	9.37:g.137623961G>A			136763782	Q15094|Q5SUX4	Silent	SNP	ENST00000371817.3	37	CCDS6982.1																																																																																				0.557	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	
MTUS2	23281	hgsc.bcm.edu	37	13	30062047	30062047	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr13:30062047T>C	ENST00000380808.2	+	4	563	c.347T>C	c.(346-348)cTc>cCc	p.L116P	MTUS2-AS1_ENST00000323380.5_RNA|MTUS2-AS1_ENST00000587588.1_RNA|MTUS2_ENST00000542829.1_Missense_Mutation_p.L26P|MTUS2_ENST00000431530.3_Missense_Mutation_p.L1147P	NM_015233.5	NP_056048.1	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	1137						cytoplasm (GO:0005737)|microtubule (GO:0005874)	microtubule binding (GO:0008017)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	20						GTGGAAGATCTCACCGCCAGC	0.512																																																	0			13											95.0	98.0	97.0					13																	30062047		2090	4219	6309	28960047	SO:0001583	missense	0			AB018317	CCDS41874.1, CCDS45022.1	13q12.3	2013-01-17	2009-10-20	2009-10-20	ENSG00000132938	ENSG00000132938			20595	protein-coding gene	gene with protein product	"""+TIP of 150 kDa"", ""cardiac zipper protein"""		"""KIAA0774"""	KIAA0774		19543227	Standard	NM_001033602		Approved	TIP150, CAZIP, ICIS	uc001usl.4	Q5JR59	OTTHUMG00000016657	ENST00000380808.2:c.347T>C	13.37:g.30062047T>C	ENSP00000370186:p.Leu116Pro		28960047	A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Missense_Mutation	SNP	ENST00000380808.2	37	CCDS41874.1	.	.	.	.	.	.	.	.	.	.	T	18.21	3.573034	0.65765	.	.	ENSG00000132938	ENST00000431530;ENST00000380808;ENST00000542829;ENST00000417109	T;T;T	0.23754	2.37;1.89;2.96	4.72	4.72	0.59763	.	0.321095	0.36815	N	0.002391	T	0.38532	0.1044	M	0.67397	2.05	0.80722	D	1	P;D	0.61080	0.942;0.989	P;P	0.53450	0.684;0.726	T	0.18366	-1.0339	9	.	.	.	.	11.6673	0.51381	0.0:0.0:0.0:1.0	.	116;1137	Q5JR59-3;Q5JR59	.;MTUS2_HUMAN	P	1147;116;26;73	ENSP00000392057:L1147P;ENSP00000370186:L116P;ENSP00000445403:L26P	.	L	+	2	0	MTUS2	28960047	1.000000	0.71417	0.908000	0.35775	0.877000	0.50540	5.668000	0.68074	1.981000	0.57761	0.533000	0.62120	CTC		0.512	MTUS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044335.2	XM_166270	
WBP4	11193	hgsc.bcm.edu	37	13	41639401	41639401	+	Silent	SNP	G	G	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr13:41639401G>A	ENST00000379487.3	+	4	640	c.240G>A	c.(238-240)ttG>ttA	p.L80L	WBP4_ENST00000542082.1_Silent_p.L59L	NM_007187.3	NP_009118.1	O75554	WBP4_HUMAN	WW domain binding protein 4	80					mRNA cis splicing, via spliceosome (GO:0045292)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spliceosomal complex (GO:0005681)	nucleic acid binding (GO:0003676)|proline-rich region binding (GO:0070064)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|prostate(1)|skin(1)	12		Lung NSC(96;3.55e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		all cancers(112;3.11e-09)|Epithelial(112;3.37e-06)|OV - Ovarian serous cystadenocarcinoma(117;8.3e-05)|GBM - Glioblastoma multiforme(144;0.00102)|BRCA - Breast invasive adenocarcinoma(63;0.07)		AAGAGGATTTGAAAAGACTTG	0.378																																																	0			13											48.0	52.0	51.0					13																	41639401		2203	4300	6503	40537401	SO:0001819	synonymous_variant	11193			AF071185	CCDS9375.1	13q13.3	2012-10-17	2012-10-17		ENSG00000120688	ENSG00000120688			12739	protein-coding gene	gene with protein product	"""formin binding protein 21"""	604981				9724750	Standard	NM_007187		Approved	FBP21, MGC117310	uc001uxt.3	O75554	OTTHUMG00000016784	ENST00000379487.3:c.240G>A	13.37:g.41639401G>A			40537401	B7Z4M2|Q32P29	Silent	SNP	ENST00000379487.3	37	CCDS9375.1																																																																																				0.378	WBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044655.2	NM_007187	
SLITRK5	26050	hgsc.bcm.edu	37	13	88328216	88328216	+	Missense_Mutation	SNP	T	T	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr13:88328216T>A	ENST00000325089.6	+	2	792	c.573T>A	c.(571-573)agT>agA	p.S191R	SLITRK5_ENST00000400028.3_Intron	NM_015567.1	NP_056382.1	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5	191					adult behavior (GO:0030534)|axonogenesis (GO:0007409)|cardiovascular system development (GO:0072358)|dendrite morphogenesis (GO:0048813)|grooming behavior (GO:0007625)|response to xenobiotic stimulus (GO:0009410)|skin development (GO:0043588)|striatum development (GO:0021756)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(14)|lung(40)|ovary(2)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(4)	81	all_neural(89;0.101)|Medulloblastoma(90;0.163)					TTTTGTCCAGTTTACCCAACA	0.483																																																	0			13											85.0	86.0	86.0					13																	88328216		2203	4300	6503	87126217	SO:0001583	missense	26050			AB020725	CCDS9465.1	13q31.1	2004-04-16	2004-01-08		ENSG00000165300	ENSG00000165300			20295	protein-coding gene	gene with protein product		609680	"""leucine rich repeat containing 11"""	LRRC11		10048485, 14557068	Standard	NM_015567		Approved	bA364G4.2, KIAA0918	uc001vln.3	O94991	OTTHUMG00000017167	ENST00000325089.6:c.573T>A	13.37:g.88328216T>A	ENSP00000366283:p.Ser191Arg		87126217	B3KNB8|B4DSH5|Q5VT81	Missense_Mutation	SNP	ENST00000325089.6	37	CCDS9465.1	.	.	.	.	.	.	.	.	.	.	T	10.83	1.461566	0.26248	.	.	ENSG00000165300	ENST00000325089	T	0.55052	0.54	5.88	5.88	0.94601	.	0.296155	0.37219	N	0.002197	T	0.43656	0.1257	L	0.46157	1.445	0.80722	D	1	P	0.36647	0.563	B	0.36378	0.223	T	0.38735	-0.9647	9	.	.	.	-1.8733	8.7309	0.34498	0.0:0.0835:0.0:0.9165	.	191	O94991	SLIK5_HUMAN	R	191	ENSP00000366283:S191R	.	S	+	3	2	SLITRK5	87126217	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.735000	0.38176	2.257000	0.74773	0.459000	0.35465	AGT		0.483	SLITRK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045416.3		
TMTC4	84899	hgsc.bcm.edu	37	13	101316492	101316492	+	Silent	SNP	G	G	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr13:101316492G>A	ENST00000376234.3	-	3	450	c.261C>T	c.(259-261)ctC>ctT	p.L87L	TMTC4_ENST00000328767.5_Intron|TMTC4_ENST00000342624.5_Silent_p.L106L	NM_001079669.1	NP_001073137.1	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat containing 4	87						integral component of membrane (GO:0016021)				breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					TCAGGACGGTGAGAGGCCGGT	0.567																																																	0			13											63.0	72.0	69.0					13																	101316492		2016	4174	6190	100114493	SO:0001819	synonymous_variant	84899				CCDS9497.2, CCDS41904.1, CCDS66575.1	13q32.3	2013-01-10	2006-01-06		ENSG00000125247	ENSG00000125247		"""Tetratricopeptide (TTC) repeat domain containing"""	25904	protein-coding gene	gene with protein product							Standard	XM_005254082		Approved	FLJ14624, FLJ22153	uc001vot.3	Q5T4D3	OTTHUMG00000017289	ENST00000376234.3:c.261C>T	13.37:g.101316492G>A			100114493	A6NLI7|B7Z666|Q5T4D4|Q5T4D5|Q5T4D6|Q8WV63|Q96SU8	Silent	SNP	ENST00000376234.3	37	CCDS41904.1																																																																																				0.567	TMTC4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045649.2	NM_032813	
ANKRD10	55608	hgsc.bcm.edu	37	13	111545496	111545496	+	Silent	SNP	G	G	A			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr13:111545496G>A	ENST00000267339.2	-	4	704	c.570C>T	c.(568-570)aaC>aaT	p.N190N	ANKRD10_ENST00000310847.4_3'UTR|ANKRD10-IT1_ENST00000426991.1_RNA|ANKRD10_ENST00000489973.2_5'UTR|ANKRD10_ENST00000375758.5_3'UTR	NM_017664.2	NP_060134.2	Q9NXR5	ANR10_HUMAN	ankyrin repeat domain 10	190										central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(3)	9	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		all cancers(43;0.0882)|BRCA - Breast invasive adenocarcinoma(86;0.188)|Lung(89;0.208)			AGATGCCATTGTTATAGAAAT	0.433																																																	0			13											127.0	127.0	127.0					13																	111545496		2203	4300	6503	110343497	SO:0001819	synonymous_variant	55608			AK000100	CCDS9520.1, CCDS66580.1	13q33.3	2013-01-10			ENSG00000088448	ENSG00000088448		"""Ankyrin repeat domain containing"""	20265	protein-coding gene	gene with protein product							Standard	NM_017664		Approved	FLJ20093	uc001vrn.3	Q9NXR5	OTTHUMG00000017349	ENST00000267339.2:c.570C>T	13.37:g.111545496G>A			110343497	Q5VW12|Q9BV12	Silent	SNP	ENST00000267339.2	37	CCDS9520.1																																																																																				0.433	ANKRD10-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045783.1		
KIAA1217	56243	hgsc.bcm.edu	37	10	24835175	24835175	+	Silent	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr10:24835175T>C	ENST00000376454.3	+	21	5784	c.5754T>C	c.(5752-5754)acT>acC	p.T1918T	KIAA1217_ENST00000376462.1_Silent_p.T1239T|KIAA1217_ENST00000396445.1_3'UTR|KIAA1217_ENST00000458595.1_Silent_p.T1324T|KIAA1217_ENST00000376451.2_3'UTR|KIAA1217_ENST00000376452.3_Silent_p.T1349T	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	1918					embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)				breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						CCATCCATACTCCCAGCCTCA	0.532																																																	0			10											76.0	71.0	72.0					10																	24835175		2203	4300	6503	24875181	SO:0001819	synonymous_variant	56243			BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"""sickle tail"""					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.5754T>C	10.37:g.24835175T>C			24875181	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Silent	SNP	ENST00000376454.3	37	CCDS31165.1																																																																																				0.532	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590	
MYPN	84665	hgsc.bcm.edu	37	10	69933946	69933946	+	Silent	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr10:69933946T>C	ENST00000358913.5	+	11	2585	c.2097T>C	c.(2095-2097)gcT>gcC	p.A699A	MYPN_ENST00000540630.1_Silent_p.A699A|MYPN_ENST00000354393.2_Silent_p.A424A	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	699					sarcomere organization (GO:0045214)	I band (GO:0031674)|nucleus (GO:0005634)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|muscle alpha-actinin binding (GO:0051371)|SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(13)|kidney(6)|large_intestine(13)|liver(1)|lung(43)|ovary(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(5)	94						ACTCCAATGCTCCCCCAGCGG	0.493																																																	0			10											138.0	126.0	130.0					10																	69933946		2203	4300	6503	69603952	SO:0001819	synonymous_variant	84665			AL834247	CCDS7275.1, CCDS73142.1	10q22.1	2014-09-17			ENSG00000138347	ENSG00000138347		"""Immunoglobulin superfamily / I-set domain containing"""	23246	protein-coding gene	gene with protein product	"""sarcomeric protein myopalladin, 145 kDa"""	608517				11309420, 12482578	Standard	NM_032578		Approved	MYOP	uc001jnm.5	Q86TC9	OTTHUMG00000018344	ENST00000358913.5:c.2097T>C	10.37:g.69933946T>C			69603952	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Silent	SNP	ENST00000358913.5	37	CCDS7275.1																																																																																				0.493	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578	
PTEN	5728	hgsc.bcm.edu	37	10	89692910	89692910	+	Missense_Mutation	SNP	G	G	T			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr10:89692910G>T	ENST00000371953.3	+	5	1751	c.394G>T	c.(394-396)Ggt>Tgt	p.G132C		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	132	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.		G -> V (in one patient with clinical findings suggesting hamartoma tumor syndrome). {ECO:0000269|PubMed:16752378}.		activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(5)|p.R55fs*1(5)|p.G132S(3)|p.Y27fs*1(2)|p.A121_F145del(1)|p.R130fs*2(1)|p.T131fs*42(1)|p.F56fs*2(1)|p.K128fs*47(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		GGGACGAACTGGTGTAATGAT	0.398		31	"""D, Mis, N, F, S"""		"""glioma,  prostate, endometrial"""	"""harmartoma, glioma,  prostate, endometrial"""			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																													yes	Rec	yes	"""Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"""	10	10q23.3	5728	phosphatase and tensin homolog gene		"""L, E, M, O"""	57	Whole gene deletion(37)|Deletion - Frameshift(11)|Unknown(5)|Substitution - Missense(3)|Deletion - In frame(1)	prostate(16)|central_nervous_system(13)|skin(6)|endometrium(5)|lung(5)|haematopoietic_and_lymphoid_tissue(4)|breast(3)|ovary(3)|soft_tissue(1)|urinary_tract(1)	10											137.0	128.0	131.0					10																	89692910		2203	4300	6503	89682890	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	9588	protein-coding gene	gene with protein product	"""mutated in multiple advanced cancers 1"""	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.394G>T	10.37:g.89692910G>T	ENSP00000361021:p.Gly132Cys		89682890	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.255594	0.80135	.	.	ENSG00000171862	ENST00000371953	D	0.99552	-6.15	5.22	4.3	0.51218	Phosphatase tensin type (1);Dual specificity phosphatase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.99816	0.9919	H	0.99026	4.405	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96700	0.9517	9	.	.	.	-10.5526	15.1176	0.72416	0.0:0.0:0.8573:0.1427	.	132	P60484	PTEN_HUMAN	C	132	ENSP00000361021:G132C	.	G	+	1	0	PTEN	89682890	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.429000	0.97481	1.157000	0.42530	-0.182000	0.12963	GGT		0.398	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314	
PTEN	5728	hgsc.bcm.edu	37	10	89692960	89692960	+	Silent	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr10:89692960A>G	ENST00000371953.3	+	5	1801	c.444A>G	c.(442-444)gcA>gcG	p.A148A		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	148	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(5)|p.R55fs*1(5)|p.Y27fs*1(2)|p.K147fs*5(1)|p.F56fs*2(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		TTTTAAAGGCACAAGAGGCCC	0.378		31	"""D, Mis, N, F, S"""		"""glioma,  prostate, endometrial"""	"""harmartoma, glioma,  prostate, endometrial"""			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																													yes	Rec	yes	"""Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"""	10	10q23.3	5728	phosphatase and tensin homolog gene		"""L, E, M, O"""	51	Whole gene deletion(37)|Deletion - Frameshift(9)|Unknown(5)	prostate(16)|central_nervous_system(11)|skin(6)|lung(5)|haematopoietic_and_lymphoid_tissue(4)|breast(3)|ovary(3)|soft_tissue(1)|endometrium(1)|urinary_tract(1)	10											69.0	70.0	70.0					10																	89692960		2203	4300	6503	89682940	SO:0001819	synonymous_variant	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	9588	protein-coding gene	gene with protein product	"""mutated in multiple advanced cancers 1"""	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.444A>G	10.37:g.89692960A>G			89682940	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Silent	SNP	ENST00000371953.3	37	CCDS31238.1																																																																																				0.378	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314	
CWF19L1	55280	hgsc.bcm.edu	37	10	101993030	101993030	+	Missense_Mutation	SNP	C	C	T	rs375717897		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr10:101993030C>T	ENST00000354105.4	-	14	1657	c.1571G>A	c.(1570-1572)cGc>cAc	p.R524H	CWF19L1_ENST00000370379.1_Missense_Mutation_p.R239H|CWF19L1_ENST00000478047.1_5'UTR|RP11-316M21.6_ENST00000444359.1_RNA	NM_018294.4	NP_060764.3	Q69YN2	C19L1_HUMAN	CWF19-like 1, cell cycle control (S. pombe)	524							catalytic activity (GO:0003824)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(4)|pancreas(1)|prostate(1)|stomach(2)	17		Colorectal(252;0.117)		Epithelial(162;3.78e-10)|all cancers(201;3.1e-08)		TTTCCGGAAGCGGCGAGCCAG	0.468																																																	0			10						C	HIS/ARG	0,4406		0,0,2203	88.0	91.0	90.0		1571	3.4	1.0	10		90	1,8599	1.2+/-3.3	0,1,4299	no	missense	CWF19L1	NM_018294.4	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	524/539	101993030	1,13005	2203	4300	6503	101983020	SO:0001583	missense	55280			AK001860	CCDS7489.1	10q24.31	2008-11-24			ENSG00000095485	ENSG00000095485			25613	protein-coding gene	gene with protein product						14702039	Standard	NM_018294		Approved	FLJ10998	uc001kqq.1	Q69YN2	OTTHUMG00000018901	ENST00000354105.4:c.1571G>A	10.37:g.101993030C>T	ENSP00000326411:p.Arg524His		101983020	B4DHX1|D3DR66|Q5W0I3|Q96HC3|Q9H865|Q9NV13	Missense_Mutation	SNP	ENST00000354105.4	37	CCDS7489.1	.	.	.	.	.	.	.	.	.	.	C	16.42	3.119088	0.56505	0.0	1.16E-4	ENSG00000095485	ENST00000354105;ENST00000370379	T;T	0.30448	1.53;1.53	5.38	3.36	0.38483	Histidine triad motif (1);Cwf19-like protein, C-terminal domain-2 (1);	0.577194	0.18770	N	0.131623	T	0.28067	0.0692	L	0.34521	1.04	0.20975	N	0.999811	D;D;P	0.58268	0.982;0.958;0.943	P;P;P	0.52710	0.707;0.467;0.586	T	0.08806	-1.0704	10	0.45353	T	0.12	-0.0378	3.0391	0.06132	0.2155:0.545:0.1426:0.0969	.	228;387;524	Q69YN2-2;Q69YN2-3;Q69YN2	.;.;C19L1_HUMAN	H	524;239	ENSP00000326411:R524H;ENSP00000359405:R239H	ENSP00000326411:R524H	R	-	2	0	CWF19L1	101983020	0.890000	0.30428	0.997000	0.53966	0.604000	0.37047	1.202000	0.32271	1.255000	0.44051	0.561000	0.74099	CGC		0.468	CWF19L1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018294	
SEMA4G	57715	hgsc.bcm.edu	37	10	102737414	102737414	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr10:102737414T>C	ENST00000370250.4	+	4	735	c.362T>C	c.(361-363)tTc>tCc	p.F121S	SEMA4G_ENST00000210633.3_Missense_Mutation_p.F121S|SEMA4G_ENST00000517724.1_Missense_Mutation_p.F121S|SEMA4G_ENST00000519756.1_3'UTR|RP11-108L7.4_ENST00000447344.1_RNA|MIR608_ENST00000384820.1_RNA	NM_017893.3	NP_060363.2	Q9NTN9	SEM4G_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4G	121	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		Colorectal(252;0.234)		Epithelial(162;3.71e-09)|all cancers(201;2.1e-07)		CATGTGCGGTTCCTGCAGCGG	0.552																																																	0			10											237.0	197.0	211.0					10																	102737414		2203	4300	6503	102727404	SO:0001583	missense	57715			AB046839	CCDS7501.1, CCDS55724.1	10q24.31	2013-01-11			ENSG00000095539	ENSG00000095539		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10735	protein-coding gene	gene with protein product							Standard	NM_017893		Approved	FLJ20590, KIAA1619	uc001krw.2	Q9NTN9	OTTHUMG00000018922	ENST00000370250.4:c.362T>C	10.37:g.102737414T>C	ENSP00000359270:p.Phe121Ser		102727404	A1A5C6|A6NJY8|Q58EY1|Q9HCF3	Missense_Mutation	SNP	ENST00000370250.4	37		.	.	.	.	.	.	.	.	.	.	T	27.7	4.859485	0.91433	.	.	ENSG00000095539	ENST00000519649;ENST00000518124;ENST00000457585;ENST00000370250;ENST00000517724;ENST00000210633	T;T;T;T;T	0.10860	2.83;2.83;2.83;2.83;2.83	5.32	5.32	0.75619	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.154036	0.64402	D	0.000015	T	0.34279	0.0892	M	0.78801	2.425	0.51482	D	0.999929	D;D;P	0.71674	0.996;0.998;0.579	D;D;B	0.76575	0.95;0.988;0.305	T	0.12218	-1.0556	10	0.87932	D	0	.	14.4545	0.67407	0.0:0.0:0.0:1.0	.	121;121;121	Q9NTN9;A1A5C6;Q9NTN9-2	SEM4G_HUMAN;.;.	S	121	ENSP00000428896:F121S;ENSP00000430103:F121S;ENSP00000359270:F121S;ENSP00000430175:F121S;ENSP00000210633:F121S	ENSP00000210633:F121S	F	+	2	0	SEMA4G	102727404	1.000000	0.71417	0.944000	0.38274	0.981000	0.71138	7.482000	0.81143	2.014000	0.59158	0.402000	0.26972	TTC		0.552	SEMA4G-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049920.2		
VWA2	340706	hgsc.bcm.edu	37	10	116038577	116038577	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr10:116038577T>C	ENST00000392982.3	+	8	1050	c.800T>C	c.(799-801)cTt>cCt	p.L267P	VWA2_ENST00000603594.1_Missense_Mutation_p.L267P			Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2	267		Cleavage.			calcium-independent cell-matrix adhesion (GO:0007161)|protein homooligomerization (GO:0051260)|regulation of insulin receptor signaling pathway (GO:0046626)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26				Epithelial(162;0.036)|all cancers(201;0.0793)		CGGCGGACCCTTGCGGTGCTG	0.667																																																	0			10											127.0	96.0	107.0					10																	116038577		2203	4300	6503	116028567	SO:0001583	missense	340706			AK127756	CCDS7589.1, CCDS7589.2	10q25.3	2009-11-06			ENSG00000165816	ENSG00000165816			24709	protein-coding gene	gene with protein product						15580307, 14506275	Standard	NM_001272046		Approved	FLJ45857, FLJ16213, CCSP-2, AMACO, NET42	uc001lbl.2	Q5GFL6	OTTHUMG00000019082	ENST00000392982.3:c.800T>C	10.37:g.116038577T>C	ENSP00000376708:p.Leu267Pro		116028567	A1A5D4|B5MDJ8|Q6ZS39|Q6ZWJ7|Q708C5|Q70UZ8	Missense_Mutation	SNP	ENST00000392982.3	37		.	.	.	.	.	.	.	.	.	.	T	0.881	-0.728643	0.03135	.	.	ENSG00000165816	ENST00000392982;ENST00000298715	T	0.67345	-0.26	5.55	-2.95	0.05564	.	1.151880	0.06035	N	0.653756	T	0.39118	0.1066	N	0.08118	0	0.21020	N	0.99981	B;B	0.10296	0.002;0.003	B;B	0.06405	0.001;0.002	T	0.06917	-1.0800	10	0.29301	T	0.29	.	2.2623	0.04070	0.3312:0.2311:0.3261:0.1117	.	267;267	Q5GFL6;Q5GFL6-2	VWA2_HUMAN;.	P	267	ENSP00000376708:L267P	ENSP00000298715:L267P	L	+	2	0	VWA2	116028567	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.710000	0.25748	-1.242000	0.02523	-4.184000	0.00009	CTT		0.667	VWA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050456.3	NM_198496	
ATRNL1	26033	hgsc.bcm.edu	37	10	117059717	117059717	+	Silent	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr10:117059717T>C	ENST00000355044.3	+	16	2715	c.2589T>C	c.(2587-2589)tgT>tgC	p.C863C	ATRNL1_ENST00000423111.2_5'Flank|ATRNL1_ENST00000303745.7_5'Flank	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	863	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(11)|liver(2)|lung(44)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		CTAATCCTTGTACATCTATGG	0.428																																																	0			10											78.0	77.0	78.0					10																	117059717		2203	4300	6503	117049707	SO:0001819	synonymous_variant	26033			AB011106	CCDS7592.1, CCDS73204.1	10q26	2004-03-04			ENSG00000107518	ENSG00000107518			29063	protein-coding gene	gene with protein product		612869				9628581	Standard	NM_001276282		Approved	KIAA0534, FLJ45344, ALP	uc001lcg.3	Q5VV63	OTTHUMG00000019096	ENST00000355044.3:c.2589T>C	10.37:g.117059717T>C			117049707	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Silent	SNP	ENST00000355044.3	37	CCDS7592.1																																																																																				0.428	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349	
BAG3	9531	hgsc.bcm.edu	37	10	121432094	121432094	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr10:121432094T>C	ENST00000369085.3	+	3	1141	c.835T>C	c.(835-837)Tca>Cca	p.S279P		NM_004281.3	NP_004272.2	O95817	BAG3_HUMAN	BCL2-associated athanogene 3	279					brain development (GO:0007420)|cellular response to mechanical stimulus (GO:0071260)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|negative regulation of apoptotic process (GO:0043066)|negative regulation of striated muscle cell apoptotic process (GO:0010664)|protein folding (GO:0006457)|protein stabilization (GO:0050821)|spinal cord development (GO:0021510)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|Z disc (GO:0030018)				endometrium(3)|kidney(1)|large_intestine(3)|liver(2)|lung(5)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	20		Lung NSC(174;0.109)|all_lung(145;0.142)		all cancers(201;0.00187)|BRCA - Breast invasive adenocarcinoma(275;0.148)		CCGGGAGGGCTCACCAGCCAG	0.662																																																	0			10											43.0	50.0	48.0					10																	121432094		2203	4299	6502	121422084	SO:0001583	missense	9531			AF095193	CCDS7615.1	10q25.2-q26.2	2014-09-17			ENSG00000151929	ENSG00000151929			939	protein-coding gene	gene with protein product		603883				9873016, 18094623	Standard	XM_005270287		Approved		uc001lem.3	O95817	OTTHUMG00000019155	ENST00000369085.3:c.835T>C	10.37:g.121432094T>C	ENSP00000358081:p.Ser279Pro		121422084	A8K5L8|Q3B763|Q9NT20|Q9P120	Missense_Mutation	SNP	ENST00000369085.3	37	CCDS7615.1	.	.	.	.	.	.	.	.	.	.	T	17.04	3.287175	0.59867	.	.	ENSG00000151929	ENST00000369085;ENST00000450186	T;T	0.79247	-1.07;-1.25	5.81	4.68	0.58851	.	0.380637	0.30620	N	0.009229	T	0.78830	0.4345	L	0.34521	1.04	0.45025	D	0.998042	D;D	0.63880	0.993;0.993	P;P	0.60949	0.881;0.881	T	0.77233	-0.2663	10	0.40728	T	0.16	-14.6173	11.546	0.50694	0.0:0.0695:0.0:0.9305	.	279;279	O95817;Q53GY1	BAG3_HUMAN;.	P	279;221	ENSP00000358081:S279P;ENSP00000410036:S221P	ENSP00000358081:S279P	S	+	1	0	BAG3	121422084	1.000000	0.71417	0.827000	0.32855	0.177000	0.22998	5.852000	0.69488	1.041000	0.40125	0.383000	0.25322	TCA		0.662	BAG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050662.1	NM_004281	
TACC2	10579	hgsc.bcm.edu	37	10	123842777	123842777	+	Silent	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr10:123842777T>C	ENST00000369005.1	+	4	1102	c.762T>C	c.(760-762)gcT>gcC	p.A254A	TACC2_ENST00000515273.1_Silent_p.A254A|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000334433.3_Silent_p.A254A|TACC2_ENST00000515603.1_Silent_p.A254A|TACC2_ENST00000453444.2_Silent_p.A254A|TACC2_ENST00000513429.1_Intron	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	254					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				AGGCCCCTGCTGCAGCCCAGC	0.612																																																	0			10											39.0	46.0	44.0					10																	123842777		2203	4299	6502	123832767	SO:0001819	synonymous_variant	10579			AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.762T>C	10.37:g.123842777T>C			123832767	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Silent	SNP	ENST00000369005.1	37	CCDS7626.1																																																																																				0.612	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
BCCIP	56647	hgsc.bcm.edu	37	10	127515180	127515180	+	Silent	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr10:127515180A>G	ENST00000278100.6	+	2	198	c.186A>G	c.(184-186)gaA>gaG	p.E62E	BCCIP_ENST00000368759.5_Silent_p.E62E|BCCIP_ENST00000299130.3_Silent_p.E62E|BCCIP_ENST00000478798.1_3'UTR|BCCIP_ENST00000429863.2_Silent_p.E62E	NM_078468.2	NP_510868.1	Q9P287	BCCIP_HUMAN	BRCA2 and CDKN1A interacting protein	62	Interaction with BRCA2.				cell cycle (GO:0007049)|DNA repair (GO:0006281)|neuroendocrine cell differentiation (GO:0061101)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)	nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nucleus (GO:0005634)	kinase regulator activity (GO:0019207)|poly(A) RNA binding (GO:0044822)			breast(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(1)	8		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				TTGAATTTGAAGCTTATTCCC	0.294																																																	0			10											83.0	86.0	85.0					10																	127515180		2202	4299	6501	127505170	SO:0001819	synonymous_variant	56647			AB040451	CCDS7649.1, CCDS7650.1, CCDS7651.1	10q26.2	2008-05-14	2001-11-29		ENSG00000107949	ENSG00000107949			978	protein-coding gene	gene with protein product		611883	"""BRCA2 and CDKN1A-interacting protein"""			11313963, 10878006	Standard	NM_016567		Approved	BCCIPalpha, TOK-1	uc001ljd.4	Q9P287	OTTHUMG00000019237	ENST00000278100.6:c.186A>G	10.37:g.127515180A>G			127505170	B3KP45|Q8ND15|Q96GC4|Q9P288	Silent	SNP	ENST00000278100.6	37	CCDS7651.1																																																																																				0.294	BCCIP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050941.1		
NKD2	85409	hgsc.bcm.edu	37	5	1038205	1038205	+	Missense_Mutation	SNP	C	C	T	rs182715653	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:1038205C>T	ENST00000296849.5	+	10	1302	c.1073C>T	c.(1072-1074)cCg>cTg	p.P358L	NKD2_ENST00000382730.2_Intron|NKD2_ENST00000274150.4_3'UTR	NM_033120.3	NP_149111.1	Q969F2	NKD2_HUMAN	naked cuticle homolog 2 (Drosophila)	358	Interaction with TGFA.				exocytosis (GO:0006887)|Golgi vesicle fusion to target membrane (GO:0048210)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein processing (GO:0010954)|protein targeting to plasma membrane (GO:0072661)|Wnt signaling pathway (GO:0016055)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cytoplasmic vesicle (GO:0031410)	calcium ion binding (GO:0005509)|growth factor binding (GO:0019838)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(3)|large_intestine(1)|lung(8)|pancreas(1)	14	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09)		Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165)			TACTACCTGCCGGCCGTCCTG	0.706													C|||	6	0.00119808	0.0045	0.0	5008	,	,		11134	0.0		0.0	False		,,,				2504	0.0																0			5											7.0	8.0	8.0					5																	1038205		2062	4066	6128	1091205	SO:0001583	missense	85409			AF358137	CCDS3859.1, CCDS59486.1	5p15.3	2013-01-10			ENSG00000145506	ENSG00000145506		"""EF-hand domain containing"""	17046	protein-coding gene	gene with protein product	"""naked cuticle-2"", ""Dvl-binding protein NKD2"""	607852				11356022, 11604995	Standard	NM_033120		Approved	Naked2	uc003jbt.2	Q969F2	OTTHUMG00000090348	ENST00000296849.5:c.1073C>T	5.37:g.1038205C>T	ENSP00000296849:p.Pro358Leu		1091205	Q96EK8|Q9BSN0	Missense_Mutation	SNP	ENST00000296849.5	37	CCDS3859.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	C	6.092	0.385173	0.11524	.	.	ENSG00000145506	ENST00000296849	T	0.49720	0.77	3.84	2.92	0.33932	.	0.234568	0.35585	N	0.003111	T	0.26195	0.0639	L	0.36672	1.1	0.80722	D	1	B	0.17465	0.022	B	0.09377	0.004	T	0.06516	-1.0822	10	0.35671	T	0.21	-9.349	8.2376	0.31636	0.2503:0.7497:0.0:0.0	.	358	Q969F2	NKD2_HUMAN	L	358	ENSP00000296849:P358L	ENSP00000296849:P358L	P	+	2	0	NKD2	1091205	0.016000	0.18221	0.032000	0.17829	0.466000	0.32739	0.563000	0.23547	0.545000	0.28902	0.305000	0.20034	CCG		0.706	NKD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206720.2	NM_033120	
RXFP3	51289	hgsc.bcm.edu	37	5	33937619	33937619	+	Silent	SNP	C	C	T			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:33937619C>T	ENST00000330120.3	+	1	1129	c.774C>T	c.(772-774)cgC>cgT	p.R258R		NM_016568.3	NP_057652.1	Q9NSD7	RL3R1_HUMAN	relaxin/insulin-like family peptide receptor 3	258					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled peptide receptor activity (GO:0008528)|G-protein coupled receptor activity (GO:0004930)			endometrium(4)|large_intestine(9)|lung(24)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)	42						TGCTGGGCCGCGACAGGCAGT	0.637																																																	0			5											45.0	35.0	39.0					5																	33937619		2200	4299	6499	33973376	SO:0001819	synonymous_variant	51289			D88437	CCDS3900.1	5p15.1-p14	2012-08-08	2006-05-09	2006-03-15	ENSG00000182631	ENSG00000182631		"""GPCR / Class A : Relaxin family peptide receptors"""	24883	protein-coding gene	gene with protein product		609445	"""relaxin 3 receptor 1"", ""relaxin family peptide receptor 3"""	RLN3R1		15956688, 16507880	Standard	NM_016568		Approved	SALPR, GPCR135, RXFPR3	uc003jic.2	Q9NSD7	OTTHUMG00000090685	ENST00000330120.3:c.774C>T	5.37:g.33937619C>T			33973376	Q14DA5	Silent	SNP	ENST00000330120.3	37	CCDS3900.1																																																																																				0.637	RXFP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207369.1	NM_016568	
UGT3A1	133688	hgsc.bcm.edu	37	5	35954453	35954453	+	Missense_Mutation	SNP	C	C	T			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:35954453C>T	ENST00000274278.3	-	7	1780	c.1423G>A	c.(1423-1425)Gcc>Acc	p.A475T	UGT3A1_ENST00000513233.1_5'Flank	NM_152404.3	NP_689617.3	Q6NUS8	UD3A1_HUMAN	UDP glycosyltransferase 3 family, polypeptide A1	475				A -> V (in Ref. 1; BAB71358). {ECO:0000305}.		integral component of membrane (GO:0016021)|UDP-N-acetylglucosamine transferase complex (GO:0043541)	glucuronosyltransferase activity (GO:0015020)|UDP-glycosyltransferase activity (GO:0008194)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(2)|skin(4)	46	all_lung(31;0.000197)		Epithelial(62;0.107)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TGCTGGAAGGCATAGGGCTTG	0.602																																																	0			5											105.0	80.0	89.0					5																	35954453		2203	4300	6503	35990210	SO:0001583	missense	133688				CCDS3913.1, CCDS54841.1	5p13.2	2014-05-20			ENSG00000145626	ENSG00000145626		"""UDP glucuronosyltransferases"""	26625	protein-coding gene	gene with protein product							Standard	NM_152404		Approved	FLJ34658	uc003jjv.2	Q6NUS8	OTTHUMG00000131107	ENST00000274278.3:c.1423G>A	5.37:g.35954453C>T	ENSP00000274278:p.Ala475Thr		35990210	G5E961|Q8IYS9|Q8NAW4|Q96DM6	Missense_Mutation	SNP	ENST00000274278.3	37	CCDS3913.1	.	.	.	.	.	.	.	.	.	.	.	13.80	2.346564	0.41599	.	.	ENSG00000145626	ENST00000274278	T	0.67523	-0.27	3.6	1.77	0.24775	.	0.203527	0.30800	U	0.008845	T	0.69958	0.3169	M	0.85542	2.76	0.80722	D	1	B	0.31859	0.343	B	0.41666	0.363	T	0.67333	-0.5697	10	0.87932	D	0	.	4.6533	0.12605	0.1709:0.6287:0.0:0.2005	.	475	Q6NUS8	UD3A1_HUMAN	T	475	ENSP00000274278:A475T	ENSP00000274278:A475T	A	-	1	0	UGT3A1	35990210	0.006000	0.16342	0.882000	0.34594	0.637000	0.38172	0.853000	0.27777	0.292000	0.22492	0.411000	0.27672	GCC		0.602	UGT3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253770.2	NM_152404	
SLC1A3	6507	hgsc.bcm.edu	37	5	36680574	36680574	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:36680574T>C	ENST00000265113.4	+	8	1648	c.1172T>C	c.(1171-1173)cTc>cCc	p.L391P	SLC1A3_ENST00000381918.3_Missense_Mutation_p.L391P|CTD-2353F22.1_ENST00000510740.1_RNA	NM_004172.4	NP_004163.3	P43003	EAA1_HUMAN	solute carrier family 1 (glial high affinity glutamate transporter), member 3	391					auditory behavior (GO:0031223)|cell morphogenesis involved in neuron differentiation (GO:0048667)|cranial nerve development (GO:0021545)|D-aspartate import (GO:0070779)|gamma-aminobutyric acid biosynthetic process (GO:0009449)|glutamate biosynthetic process (GO:0006537)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|neuromuscular process controlling balance (GO:0050885)|neurotransmitter uptake (GO:0001504)|positive regulation of synaptic transmission (GO:0050806)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|response to light stimulus (GO:0009416)|response to wounding (GO:0009611)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell projection (GO:0042995)|cell surface (GO:0009986)|fibril (GO:0043205)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	glutamate binding (GO:0016595)|high-affinity glutamate transmembrane transporter activity (GO:0005314)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(23)|skin(1)	41	all_lung(31;0.000245)		Epithelial(62;0.0444)|Lung(74;0.111)|all cancers(62;0.128)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			AGATTCGTGCTCCCCGTAGGA	0.507																																																	0			5											105.0	92.0	97.0					5																	36680574		2203	4300	6503	36716331	SO:0001583	missense	6507				CCDS3919.1, CCDS54844.1	5p13	2013-05-22			ENSG00000079215	ENSG00000079215		"""Solute carriers"""	10941	protein-coding gene	gene with protein product	"""glutamate transporter variant EAAT1ex9skip"""	600111				7521911, 7698014	Standard	NM_004172		Approved	EAAT1, GLAST, EA6	uc003jkj.4	P43003	OTTHUMG00000090793	ENST00000265113.4:c.1172T>C	5.37:g.36680574T>C	ENSP00000265113:p.Leu391Pro		36716331	B2R5T3|Q4JCQ8	Missense_Mutation	SNP	ENST00000265113.4	37	CCDS3919.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.242749	0.79912	.	.	ENSG00000079215	ENST00000265113;ENST00000427100;ENST00000381918	T;T	0.64618	-0.11;-0.11	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	D	0.86268	0.5892	H	0.97240	3.965	0.80722	D	1	D;D	0.62365	0.959;0.991	P;D	0.69307	0.738;0.963	D	0.91154	0.4955	10	0.87932	D	0	-21.3719	16.1502	0.81611	0.0:0.0:0.0:1.0	.	391;391	Q4JCQ8;P43003	.;EAA1_HUMAN	P	391;339;391	ENSP00000265113:L391P;ENSP00000371343:L391P	ENSP00000265113:L391P	L	+	2	0	SLC1A3	36716331	1.000000	0.71417	1.000000	0.80357	0.477000	0.33069	8.033000	0.88852	2.224000	0.72417	0.533000	0.62120	CTC		0.507	SLC1A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207579.2	NM_004172	
NNT	23530	hgsc.bcm.edu	37	5	43649358	43649358	+	Silent	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:43649358A>G	ENST00000264663.5	+	11	1775	c.1554A>G	c.(1552-1554)ggA>ggG	p.G518G	NNT_ENST00000512996.2_Silent_p.G387G|NNT_ENST00000344920.4_Silent_p.G518G	NM_012343.3	NP_036475.3	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	518					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidation-reduction process (GO:0055114)|proton transport (GO:0015992)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	NAD binding (GO:0051287)|NAD(P)+ transhydrogenase (AB-specific) activity (GO:0008750)|NAD(P)+ transhydrogenase (B-specific) activity (GO:0003957)|NAD(P)+ transhydrogenase activity (GO:0008746)|NADP binding (GO:0050661)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(7)|large_intestine(6)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(6;2.58e-06)					CCGTCTGGGGAGTGACCCCTG	0.498																																																	0			5											296.0	279.0	284.0					5																	43649358		2203	4300	6503	43685115	SO:0001819	synonymous_variant	23530			U40490	CCDS3949.1	5p12	2008-02-05			ENSG00000112992	ENSG00000112992	1.6.1.1		7863	protein-coding gene	gene with protein product		607878				9271681, 9524818	Standard	NM_182977		Approved		uc003jof.3	Q13423	OTTHUMG00000096961	ENST00000264663.5:c.1554A>G	5.37:g.43649358A>G			43685115	Q16796|Q2TB60|Q8N3V4	Silent	SNP	ENST00000264663.5	37	CCDS3949.1																																																																																				0.498	NNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214026.1	NM_182977	
DIMT1	27292	hgsc.bcm.edu	37	5	61694695	61694695	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:61694695T>C	ENST00000199320.4	-	4	414	c.254A>G	c.(253-255)gAa>gGa	p.E85G	KIF2A_ENST00000509663.2_Intron|DIMT1_ENST00000506390.1_Missense_Mutation_p.E85G	NM_014473.2	NP_055288.1	Q9UNQ2	DIM1_HUMAN	DIM1 dimethyladenosine transferase 1 homolog (S. cerevisiae)	85						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity (GO:0052909)|poly(A) RNA binding (GO:0044822)|rRNA (adenine-N6,N6-)-dimethyltransferase activity (GO:0000179)										TGGGTCAAGTTCACAAGCAAC	0.299																																																	0			5											50.0	50.0	50.0					5																	61694695		2203	4300	6503	61730452	SO:0001583	missense	27292			AF102147	CCDS3981.1	5q12.1	2011-08-11	2011-08-11	2011-08-11	ENSG00000086189	ENSG00000086189			30217	protein-coding gene	gene with protein product		612499	"""DIM1 dimethyladenosine transferase 1-like (S. cerevisiae)"""	DIMT1L		11124703	Standard	NM_014473		Approved	HSA9761	uc003jta.3	Q9UNQ2	OTTHUMG00000131223	ENST00000199320.4:c.254A>G	5.37:g.61694695T>C	ENSP00000199320:p.Glu85Gly		61730452	O76025|Q9BU77|Q9UES1	Missense_Mutation	SNP	ENST00000199320.4	37	CCDS3981.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.011245	0.75046	.	.	ENSG00000086189	ENST00000199320;ENST00000506390	T;T	0.54479	0.57;0.57	5.5	5.5	0.81552	.	0.090319	0.85682	D	0.000000	D	0.83285	0.5221	H	0.99582	4.64	0.80722	D	1	D	0.71674	0.998	D	0.74348	0.983	D	0.89193	0.3552	10	0.87932	D	0	-20.5441	11.7321	0.51744	0.0:0.0:0.1471:0.8529	.	85	Q9UNQ2	DIM1_HUMAN	G	85	ENSP00000199320:E85G;ENSP00000421754:E85G	ENSP00000199320:E85G	E	-	2	0	DIMT1L	61730452	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.525000	0.81892	2.313000	0.78055	0.454000	0.30748	GAA		0.299	DIMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253967.1	NM_014473	
POLK	51426	hgsc.bcm.edu	37	5	74880616	74880616	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:74880616T>C	ENST00000241436.4	+	9	1263	c.1091T>C	c.(1090-1092)aTg>aCg	p.M364T	POLK_ENST00000504026.1_Missense_Mutation_p.M364T|POLK_ENST00000352007.5_Intron|POLK_ENST00000508526.1_Intron|POLK_ENST00000515295.1_Missense_Mutation_p.M364T|POLK_ENST00000506928.1_3'UTR|POLK_ENST00000380481.3_Missense_Mutation_p.M274T	NM_016218.2	NP_057302.1	Q9UBT6	POLK_HUMAN	polymerase (DNA directed) kappa	364					DNA repair (GO:0006281)|nucleotide-excision repair, DNA gap filling (GO:0006297)	nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)			endometrium(1)|kidney(4)|large_intestine(5)|lung(11)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	27		all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;2.9e-54)|all cancers(79;1.27e-42)		ACAGAGAAAATGTTAAAGGCC	0.313								DNA polymerases (catalytic subunits)																																									0			5											99.0	101.0	100.0					5																	74880616		2203	4300	6503	74916372	SO:0001583	missense	51426			AB027564	CCDS4030.1	5q13	2012-05-18			ENSG00000122008	ENSG00000122008		"""DNA polymerases"""	9183	protein-coding gene	gene with protein product	"""polymerase (DNA-directed) kappa"", ""DINB protein"", ""DNA polymerase kappa"""	605650		DINB1		10887153, 10518552	Standard	NM_016218		Approved	POLQ, DINP	uc003kdw.3	Q9UBT6	OTTHUMG00000102107	ENST00000241436.4:c.1091T>C	5.37:g.74880616T>C	ENSP00000241436:p.Met364Thr		74916372	B2RBD2|Q5Q9G5|Q5Q9G6|Q5Q9G7|Q5Q9G8|Q86VJ8|Q8IZY0|Q8IZY1|Q8NB30|Q96L01|Q96Q86|Q96Q87|Q9UHC5	Missense_Mutation	SNP	ENST00000241436.4	37	CCDS4030.1	.	.	.	.	.	.	.	.	.	.	T	14.01	2.407081	0.42715	.	.	ENSG00000122008	ENST00000241436;ENST00000515295;ENST00000504026;ENST00000380481	T;T;T;T	0.70164	-0.46;-0.46;-0.46;-0.46	5.4	5.4	0.78164	DNA polymerase type-Y, HhH motif (1);	0.035385	0.85682	D	0.000000	T	0.69691	0.3139	N	0.16656	0.425	0.80722	D	1	B;B;D	0.76494	0.037;0.036;0.999	B;B;D	0.73380	0.034;0.023;0.98	T	0.73560	-0.3944	10	0.51188	T	0.08	-17.9987	15.7002	0.77536	0.0:0.0:0.0:1.0	.	364;364;364	Q5Q9G5;Q9UBT6-2;Q9UBT6	.;.;POLK_HUMAN	T	364;364;364;274	ENSP00000241436:M364T;ENSP00000424174:M364T;ENSP00000425075:M364T;ENSP00000369848:M274T	ENSP00000241436:M364T	M	+	2	0	POLK	74916372	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.981000	0.88123	2.174000	0.68829	0.402000	0.26972	ATG		0.313	POLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219945.3	NM_016218	
AP3B1	8546	hgsc.bcm.edu	37	5	77523997	77523997	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:77523997A>G	ENST00000255194.6	-	4	521	c.346T>C	c.(346-348)Tcc>Ccc	p.S116P	AP3B1_ENST00000519295.1_Missense_Mutation_p.S67P	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	116					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein targeting to lysosome (GO:0006622)	AP-3 adaptor complex (GO:0030123)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|protein phosphatase binding (GO:0019903)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(12)|lung(12)|prostate(1)|skin(2)|urinary_tract(1)	39		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		GTGCTTATGGACAGGAGTGCA	0.383									Hermansky-Pudlak syndrome																																								0			5											102.0	97.0	98.0					5																	77523997		2203	4300	6503	77559753	SO:0001583	missense	8546	Familial Cancer Database	HPS, HPS1-8	U81504	CCDS4041.1, CCDS64186.1	5q14.1	2014-09-17			ENSG00000132842	ENSG00000132842			566	protein-coding gene	gene with protein product		603401				9182526, 9151686	Standard	NM_003664		Approved	ADTB3A, HPS2	uc003kfj.4	O00203	OTTHUMG00000106919	ENST00000255194.6:c.346T>C	5.37:g.77523997A>G	ENSP00000255194:p.Ser116Pro		77559753	E5RJ68|O00580|Q7Z393|Q9HD66	Missense_Mutation	SNP	ENST00000255194.6	37	CCDS4041.1	.	.	.	.	.	.	.	.	.	.	A	20.5	4.008176	0.75046	.	.	ENSG00000132842	ENST00000255194;ENST00000519295;ENST00000535760	T;T	0.66280	-0.2;-0.2	5.48	5.48	0.80851	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.053891	0.85682	N	0.000000	T	0.74604	0.3738	M	0.89478	3.035	0.80722	D	1	B	0.24675	0.109	B	0.37451	0.25	T	0.76664	-0.2876	10	0.87932	D	0	-2.6242	15.9032	0.79400	1.0:0.0:0.0:0.0	.	116	O00203	AP3B1_HUMAN	P	116;67;116	ENSP00000255194:S116P;ENSP00000430597:S67P	ENSP00000255194:S116P	S	-	1	0	AP3B1	77559753	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.287000	0.95975	2.211000	0.71520	0.472000	0.43445	TCC		0.383	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2		
CHD1	1105	hgsc.bcm.edu	37	5	98216997	98216997	+	Missense_Mutation	SNP	C	C	T			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:98216997C>T	ENST00000284049.3	-	20	3099	c.2950G>A	c.(2950-2952)Gaa>Aaa	p.E984K		NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	984					chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	49		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	GGCTCTTGTTCTTCTCCTTCA	0.318																																																	0			5											17.0	16.0	16.0					5																	98216997		2181	4277	6458	98244897	SO:0001583	missense	1105			AF006513	CCDS34204.1	5q15-q21	2008-07-18			ENSG00000153922	ENSG00000153922			1915	protein-coding gene	gene with protein product		602118				8460153, 9326634	Standard	XM_005271866		Approved		uc003knf.3	O14646	OTTHUMG00000162744	ENST00000284049.3:c.2950G>A	5.37:g.98216997C>T	ENSP00000284049:p.Glu984Lys		98244897	Q17RZ3	Missense_Mutation	SNP	ENST00000284049.3	37	CCDS34204.1	.	.	.	.	.	.	.	.	.	.	C	33	5.205815	0.95033	.	.	ENSG00000153922	ENST00000284049	D	0.90133	-2.62	5.23	5.23	0.72850	.	0.000000	0.34245	U	0.004127	D	0.91153	0.7214	L	0.55743	1.74	0.80722	D	1	P	0.51449	0.945	P	0.47402	0.546	D	0.92132	0.5713	10	0.72032	D	0.01	.	19.1612	0.93533	0.0:1.0:0.0:0.0	.	984	O14646	CHD1_HUMAN	K	984	ENSP00000284049:E984K	ENSP00000284049:E984K	E	-	1	0	CHD1	98244897	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	7.818000	0.86416	2.600000	0.87896	0.585000	0.79938	GAA		0.318	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270	
APC	324	hgsc.bcm.edu	37	5	112173849	112173849	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:112173849A>G	ENST00000457016.1	+	16	2938	c.2558A>G	c.(2557-2559)gAg>gGg	p.E853G	APC_ENST00000257430.4_Missense_Mutation_p.E853G|APC_ENST00000508376.2_Missense_Mutation_p.E853G|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	853	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.?(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)		AGAAGTTTGGAGAGAGAACGC	0.448		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"""	1	Unknown(1)	skin(1)	5											66.0	67.0	66.0					5																	112173849		2202	4300	6502	112201748	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.2558A>G	5.37:g.112173849A>G	ENSP00000413133:p.Glu853Gly		112201748	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	11.91	1.778440	0.31502	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	D;D;D;D;D	0.94330	-2.67;-3.4;-2.67;-2.67;-2.85	6.16	6.16	0.99307	.	0.073236	0.56097	D	0.000021	D	0.89234	0.6657	L	0.34521	1.04	0.36291	D	0.856434	B;B	0.23937	0.0;0.094	B;B	0.16722	0.001;0.016	D	0.87781	0.2612	10	0.33940	T	0.23	-17.3326	15.3771	0.74615	1.0:0.0:0.0:0.0	.	855;853	Q4LE70;P25054	.;APC_HUMAN	G	853;835;853;853;853	ENSP00000413133:E853G;ENSP00000423224:E835G;ENSP00000257430:E853G;ENSP00000427089:E853G;ENSP00000423828:E853G	ENSP00000257430:E853G	E	+	2	0	APC	112201748	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.742000	0.74843	2.367000	0.80283	0.528000	0.53228	GAG		0.448	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
APC	324	hgsc.bcm.edu	37	5	112175215	112175215	+	Silent	SNP	A	A	G	rs121913224		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:112175215A>G	ENST00000457016.1	+	16	4304	c.3924A>G	c.(3922-3924)aaA>aaG	p.K1308K	APC_ENST00000257430.4_Silent_p.K1308K|APC_ENST00000508376.2_Silent_p.K1308K|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1308	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.E1309fs*6(50)|p.E1309fs*4(37)|p.I1307fs*6(12)|p.?(1)|p.E1309fs*5(1)|p.K1192fs*3(1)|p.K1308fs*4(1)|p.I1307fs*13(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)		CAGAAATAAAAGAAAAGATTG	0.428		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"""	104	Deletion - Frameshift(53)|Insertion - Frameshift(50)|Unknown(1)	large_intestine(100)|stomach(2)|soft_tissue(1)|skin(1)	5	GRCh37	CD972006	APC	D							53.0	55.0	54.0					5																	112175215		2202	4300	6502	112203114	SO:0001819	synonymous_variant	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.3924A>G	5.37:g.112175215A>G			112203114	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				0.428	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
APC	324	hgsc.bcm.edu	37	5	112175489	112175489	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:112175489T>C	ENST00000457016.1	+	16	4578	c.4198T>C	c.(4198-4200)Tcg>Ccg	p.S1400P	APC_ENST00000257430.4_Missense_Mutation_p.S1400P|APC_ENST00000508376.2_Missense_Mutation_p.S1400P|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1400	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.S1400fs*15(2)|p.Y1376fs*41(1)|p.K1192fs*3(1)|p.?(1)|p.S1400fs*5(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)		TGAGAGTCGTTCGATTGCCAG	0.478		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"""	6	Deletion - Frameshift(5)|Unknown(1)	large_intestine(4)|soft_tissue(1)|skin(1)	5											110.0	102.0	105.0					5																	112175489		2202	4300	6502	112203388	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.4198T>C	5.37:g.112175489T>C	ENSP00000413133:p.Ser1400Pro		112203388	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	T	19.02	3.745490	0.69418	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.91945	-2.94;-2.94;-2.94	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.94997	0.8381	L	0.57536	1.79	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.994	D	0.94352	0.7580	9	.	.	.	-9.695	16.4957	0.84242	0.0:0.0:0.0:1.0	.	1402;1400	Q4LE70;P25054	.;APC_HUMAN	P	1400	ENSP00000413133:S1400P;ENSP00000257430:S1400P;ENSP00000427089:S1400P	.	S	+	1	0	APC	112203388	1.000000	0.71417	0.735000	0.30896	0.777000	0.43975	7.698000	0.84413	2.371000	0.80710	0.533000	0.62120	TCG		0.478	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
SNX2	6643	hgsc.bcm.edu	37	5	122154636	122154636	+	Missense_Mutation	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:122154636T>C	ENST00000379516.2	+	11	1238	c.1130T>C	c.(1129-1131)tTa>tCa	p.L377S	SNX2_ENST00000510372.1_3'UTR|SNX2_ENST00000514949.1_Missense_Mutation_p.L260S	NM_003100.2	NP_003091.2	O60749	SNX2_HUMAN	sorting nexin 2	377					endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|protein complex (GO:0043234)|retromer complex (GO:0030904)	epidermal growth factor receptor binding (GO:0005154)|insulin receptor binding (GO:0005158)|leptin receptor binding (GO:1990460)|phosphatidylinositol binding (GO:0035091)|transferrin receptor binding (GO:1990459)	p.L377*(1)		NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(2)|prostate(1)|skin(1)	19		all_cancers(142;1.14e-44)|all_lung(232;1.03e-13)|Lung NSC(810;2.5e-13)|Breast(839;0.000812)|Myeloproliferative disorder(839;0.0122)|Prostate(80;0.0235)|all_hematologic(541;0.0592)|all_neural(839;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	all cancers(49;2.13e-24)|Epithelial(69;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(64;5.6e-11)|BRCA - Breast invasive adenocarcinoma(61;0.00013)|GBM - Glioblastoma multiforme(465;0.000357)|COAD - Colon adenocarcinoma(49;0.000887)|Lung(113;0.0109)		ATAGACCAGTTACATCAAGAA	0.388																																																	1	Substitution - Nonsense(1)	kidney(1)	5											140.0	129.0	133.0					5																	122154636		2203	4300	6503	122182535	SO:0001583	missense	6643			AF043453	CCDS34217.1, CCDS64234.1	5q23.2	2011-05-03			ENSG00000205302	ENSG00000205302		"""Sorting nexins"""	11173	protein-coding gene	gene with protein product		605929				9819414	Standard	NM_003100		Approved		uc003kte.4	O60749	OTTHUMG00000163020	ENST00000379516.2:c.1130T>C	5.37:g.122154636T>C	ENSP00000368831:p.Leu377Ser		122182535	B3KN44|B4DEK4|B7Z408|O43650|P82862|Q53XK8|Q597H6|Q9BTS8	Missense_Mutation	SNP	ENST00000379516.2	37	CCDS34217.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.577589	0.86645	.	.	ENSG00000205302	ENST00000379516;ENST00000514949	T;T	0.32515	1.45;1.45	5.81	5.81	0.92471	Vps5 C-terminal (1);	0.076783	0.56097	D	0.000036	T	0.57359	0.2048	M	0.88377	2.95	0.80722	D	1	P	0.48764	0.915	P	0.55161	0.77	T	0.66232	-0.5975	10	0.87932	D	0	-14.176	16.1708	0.81812	0.0:0.0:0.0:1.0	.	377	O60749	SNX2_HUMAN	S	377;260	ENSP00000368831:L377S;ENSP00000421663:L260S	ENSP00000368831:L377S	L	+	2	0	SNX2	122182535	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.982000	0.88131	2.225000	0.72522	0.533000	0.62120	TTA		0.388	SNX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371392.1	NM_003100	
SMAD5	4090	hgsc.bcm.edu	37	5	135498971	135498971	+	Silent	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:135498971T>C	ENST00000545279.1	+	5	1026	c.666T>C	c.(664-666)ccT>ccC	p.P222P	SMAD5_ENST00000545620.1_Silent_p.P222P|SMAD5_ENST00000514641.2_3'UTR	NM_001001419.1|NM_005903.5	NP_001001419.1|NP_005894.3	Q99717	SMAD5_HUMAN	SMAD family member 5	222					BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|cardiac muscle contraction (GO:0060048)|cartilage development (GO:0051216)|cellular response to BMP stimulus (GO:0071773)|cellular response to organic cyclic compound (GO:0071407)|embryonic pattern specification (GO:0009880)|erythrocyte differentiation (GO:0030218)|germ cell development (GO:0007281)|intracellular signal transduction (GO:0035556)|Mullerian duct regression (GO:0001880)|osteoblast fate commitment (GO:0002051)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	metal ion binding (GO:0046872)|receptor signaling protein activity (GO:0005057)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|large_intestine(4)|lung(3)	8			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CTGATACGCCTCCTCCTGCCT	0.343																																																	0			5											106.0	101.0	102.0					5																	135498971		1937	4157	6094	135526870	SO:0001819	synonymous_variant	4090			U59913	CCDS75308.1	5q31	2008-02-05	2006-11-06	2004-05-26		ENSG00000113658		"""SMADs"""	6771	protein-coding gene	gene with protein product		603110	"""MAD, mothers against decapentaplegic homolog 5 (Drosophila)"", ""SMAD, mothers against DPP homolog 5 (Drosophila)"""	MADH5		8673135	Standard	NM_005903		Approved	Dwfc, JV5-1	uc003lbl.1	Q99717		ENST00000545279.1:c.666T>C	5.37:g.135498971T>C			135526870	O14688|Q15798|Q9UQA1	Silent	SNP	ENST00000545279.1	37		.	.	.	.	.	.	.	.	.	.	T	9.215	1.031997	0.19590	.	.	ENSG00000113658	ENST00000507637	.	.	.	6.04	4.7	0.59300	.	.	.	.	.	T	0.57154	0.2034	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55438	-0.8141	4	.	.	.	.	7.169	0.25708	0.1652:0.0804:0.0:0.7544	.	.	.	.	P	45	.	.	S	+	1	0	SMAD5	135526870	0.997000	0.39634	1.000000	0.80357	0.932000	0.56968	0.350000	0.20079	2.317000	0.78254	0.460000	0.39030	TCC		0.343	SMAD5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_005903	
EIF4EBP3	8637	hgsc.bcm.edu	37	5	139931709	139931709	+	IGR	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:139931709T>C	ENST00000310331.2	+	0	691				SRA1_ENST00000520427.1_5'UTR|SRA1_ENST00000336283.6_Missense_Mutation_p.K83R	NM_003732.2	NP_003723.1	O60516	4EBP3_HUMAN	eukaryotic translation initiation factor 4E binding protein 3						negative regulation of translational initiation (GO:0045947)	eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	translation repressor activity (GO:0030371)			endometrium(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCTGGGAGCCTTACTTGAAGG	0.582																																																	0			5											34.0	30.0	31.0					5																	139931709		2203	4300	6503	139911893	SO:0001628	intergenic_variant	58506			AF038869	CCDS4226.1	5q31.3	2007-07-18			ENSG00000243056	ENSG00000243056			3290	protein-coding gene	gene with protein product		603483				9593750	Standard	NM_003732		Approved	4E-BP3	uc003lfy.1	O60516	OTTHUMG00000129498		5.37:g.139931709T>C			139911893		Missense_Mutation	SNP	ENST00000310331.2	37	CCDS4226.1	.	.	.	.	.	.	.	.	.	.	T	12.80	2.047069	0.36085	.	.	ENSG00000213523	ENST00000336283;ENST00000520427	T	0.45668	0.89	5.75	3.18	0.36537	.	1.236330	0.05768	U	0.606128	T	0.43478	0.1249	L	0.53249	1.67	0.25508	N	0.987487	B	0.30851	0.297	B	0.35413	0.202	T	0.38023	-0.9680	9	.	.	.	.	9.5417	0.39255	0.0:0.0:0.3455:0.6545	.	83	Q9HD15	SRA1_HUMAN	R	83;9	ENSP00000337513:K83R	.	K	-	2	0	SRA1	139911893	0.835000	0.29415	0.902000	0.35471	0.994000	0.84299	0.856000	0.27818	0.979000	0.38497	0.533000	0.62120	AAG		0.582	EIF4EBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251668.2	NM_003732	
PCDHGA10	56106	hgsc.bcm.edu	37	5	140794729	140794729	+	Missense_Mutation	SNP	A	A	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:140794729A>C	ENST00000398610.2	+	1	1987	c.1987A>C	c.(1987-1989)Acg>Ccg	p.T663P	PCDHGA4_ENST00000571252.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB7_ENST00000398594.2_5'Flank|PCDHGA1_ENST00000517417.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB6_ENST00000520790.1_Intron	NM_018913.2|NM_032090.1	NP_061736.1|NP_114479.1	Q9Y5H3	PCDGA_HUMAN	protocadherin gamma subfamily A, 10	663	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGCCACTGTCACGCTCACCGT	0.657																																																	0			5											34.0	44.0	41.0					5																	140794729		2167	4229	6396	140774913	SO:0001583	missense	56106				CCDS47292.1, CCDS75343.1	5q31	2010-01-26			ENSG00000253846	ENSG00000253846		"""Cadherins / Protocadherins : Clustered"""	8697	other	protocadherin		606297				10380929	Standard	NM_018913		Approved	PCDH-GAMMA-A10		Q9Y5H3	OTTHUMG00000163688	ENST00000398610.2:c.1987A>C	5.37:g.140794729A>C	ENSP00000381611:p.Thr663Pro		140774913	Q9Y5E0	Missense_Mutation	SNP	ENST00000398610.2	37	CCDS47292.1	.	.	.	.	.	.	.	.	.	.	a	11.22	1.573219	0.28092	.	.	ENSG00000253846	ENST00000398610	T	0.55234	0.53	5.57	4.39	0.52855	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.71443	0.3340	M	0.82193	2.58	0.23893	N	0.996544	D;D	0.71674	0.976;0.998	D;D	0.76575	0.952;0.988	T	0.62115	-0.6922	9	0.87932	D	0	.	7.9393	0.29948	0.7885:0.1391:0.0724:0.0	.	663;663	Q9Y5H3-2;Q9Y5H3	.;PCDGA_HUMAN	P	663	ENSP00000381611:T663P	ENSP00000381611:T663P	T	+	1	0	PCDHGA10	140774913	0.002000	0.14202	0.905000	0.35620	0.005000	0.04900	1.895000	0.39778	0.927000	0.37143	-0.313000	0.08912	ACG		0.657	PCDHGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374747.1	NM_018913	
YIPF5	81555	hgsc.bcm.edu	37	5	143545033	143545033	+	Nonsense_Mutation	SNP	A	A	T			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:143545033A>T	ENST00000274496.5	-	3	380	c.246T>A	c.(244-246)taT>taA	p.Y82*	YIPF5_ENST00000513112.1_Nonsense_Mutation_p.Y28*|YIPF5_ENST00000448443.2_Nonsense_Mutation_p.Y82*	NM_001271732.1|NM_030799.7	NP_001258661.1|NP_110426.4	Q969M3	YIPF5_HUMAN	Yip1 domain family, member 5	82	Interaction with Sec23.				protein transport (GO:0015031)|regulation of ER to Golgi vesicle-mediated transport (GO:0060628)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum exit site (GO:0070971)|ER to Golgi transport vesicle (GO:0030134)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear outer membrane-endoplasmic reticulum membrane network (GO:0042175)				large_intestine(2)|lung(5)|ovary(1)|skin(1)	9		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)			AGTTGTTTCCATAGAAAGGCT	0.428																																																	0			5											192.0	169.0	177.0					5																	143545033		2203	4300	6503	143525226	SO:0001587	stop_gained	81555			AF318329	CCDS4279.1, CCDS64277.1	5q31.3	2009-01-12			ENSG00000145817	ENSG00000145817		"""Yip1 domain family"""	24877	protein-coding gene	gene with protein product		611483				12975309, 18718466	Standard	NM_001024947		Approved	SMAP-5, FinGER5	uc003lnl.5	Q969M3	OTTHUMG00000129679	ENST00000274496.5:c.246T>A	5.37:g.143545033A>T	ENSP00000274496:p.Tyr82*		143525226	D3DQF5|Q4VSN6|Q53EX4|Q8NHE5|Q9H338|Q9H3U4	Nonsense_Mutation	SNP	ENST00000274496.5	37	CCDS4279.1	.	.	.	.	.	.	.	.	.	.	A	36	5.704482	0.96812	.	.	ENSG00000145817	ENST00000274496;ENST00000377986;ENST00000448443;ENST00000513112;ENST00000519064;ENST00000522203;ENST00000536767	.	.	.	6.02	3.69	0.42338	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.1914	9.7802	0.40643	0.8631:0.0:0.1369:0.0	.	.	.	.	X	82;82;82;28;28;28;82	.	ENSP00000274496:Y82X	Y	-	3	2	YIPF5	143525226	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	1.988000	0.40697	1.110000	0.41699	0.528000	0.53228	TAT		0.428	YIPF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251882.1	NM_030799	
GABRP	2568	hgsc.bcm.edu	37	5	170239185	170239185	+	Missense_Mutation	SNP	C	C	T			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:170239185C>T	ENST00000518525.1	+	11	1710	c.1246C>T	c.(1246-1248)Cac>Tac	p.H416Y	GABRP_ENST00000519385.1_3'UTR|GABRP_ENST00000265294.4_Missense_Mutation_p.H416Y			O00591	GBRP_HUMAN	gamma-aminobutyric acid (GABA) A receptor, pi	416			H -> R (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(5)|large_intestine(4)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	29	Renal(175;0.000159)|Lung NSC(126;0.0122)|all_lung(126;0.0193)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)		Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TAATGTTGATCACTATTCCAA	0.348																																																	0			5											120.0	110.0	114.0					5																	170239185		2203	4300	6503	170171763	SO:0001583	missense	2568			U95367	CCDS4375.1, CCDS75368.1	5q35.1	2012-06-22			ENSG00000094755	ENSG00000094755		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4089	protein-coding gene	gene with protein product	"""GABA(A) receptor, pi"""	602729				9182563	Standard	NM_014211		Approved		uc003mau.3	O00591	OTTHUMG00000130443	ENST00000518525.1:c.1246C>T	5.37:g.170239185C>T	ENSP00000430100:p.His416Tyr		170171763	A8KA36|D3DQL2|Q32MJ1	Missense_Mutation	SNP	ENST00000518525.1	37	CCDS4375.1	.	.	.	.	.	.	.	.	.	.	C	14.48	2.549247	0.45383	.	.	ENSG00000094755	ENST00000518525;ENST00000265294	T;T	0.81415	-1.49;-1.49	5.74	4.87	0.63330	Neurotransmitter-gated ion-channel transmembrane domain (1);	0.234387	0.41396	D	0.000893	T	0.66499	0.2795	N	0.08118	0	0.23063	N	0.998356	B	0.16166	0.016	B	0.12837	0.008	T	0.61686	-0.7012	10	0.87932	D	0	.	15.8208	0.78644	0.1372:0.8628:0.0:0.0	.	416	O00591	GBRP_HUMAN	Y	416	ENSP00000430100:H416Y;ENSP00000265294:H416Y	ENSP00000265294:H416Y	H	+	1	0	GABRP	170171763	0.179000	0.23135	0.996000	0.52242	0.874000	0.50279	1.600000	0.36762	1.402000	0.46780	0.655000	0.94253	CAC		0.348	GABRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252834.3	NM_014211	
SH3PXD2B	285590	hgsc.bcm.edu	37	5	171773255	171773255	+	Missense_Mutation	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:171773255A>G	ENST00000311601.5	-	12	1243	c.1073T>C	c.(1072-1074)cTc>cCc	p.L358P	SH3PXD2B_ENST00000519643.1_Missense_Mutation_p.L358P	NM_001017995.2	NP_001017995.1	A1X283	SPD2B_HUMAN	SH3 and PX domains 2B	358					adipose tissue development (GO:0060612)|bone development (GO:0060348)|cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|eye development (GO:0001654)|heart development (GO:0007507)|podosome assembly (GO:0071800)|positive regulation of fat cell differentiation (GO:0045600)|protein localization to membrane (GO:0072657)|skeletal system development (GO:0001501)|superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|podosome (GO:0002102)	phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)|SH2 domain binding (GO:0042169)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175)	Medulloblastoma(196;0.0207)|all_neural(177;0.0625)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CGGCAGGTTGAGGCCTCGAGG	0.592																																																	0			5											175.0	168.0	170.0					5																	171773255		2203	4300	6503	171705860	SO:0001583	missense	285590			AK095834	CCDS34291.1	5q35.2	2008-02-05	2006-02-13	2006-02-13	ENSG00000174705	ENSG00000174705			29242	protein-coding gene	gene with protein product		613293	"""KIAA1295"""	KIAA1295		10718198	Standard	NM_001017995		Approved	FLJ20831	uc003mbr.3	A1X283	OTTHUMG00000163280	ENST00000311601.5:c.1073T>C	5.37:g.171773255A>G	ENSP00000309714:p.Leu358Pro		171705860	B6F0V2|Q9P2Q1	Missense_Mutation	SNP	ENST00000311601.5	37	CCDS34291.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.32|13.32	2.201556|2.201556	0.38905|0.38905	.|.	.|.	ENSG00000174705|ENSG00000174705	ENST00000519643;ENST00000311601|ENST00000518522	T;T|.	0.62788|.	0.23;0.0|.	5.31|5.31	5.31|5.31	0.75309|0.75309	Src homology-3 domain (1);|.	0.247490|.	0.35615|.	N|.	0.003093|.	T|T	0.69691|0.69691	0.3139|0.3139	M|M	0.62723|0.62723	1.935|1.935	0.58432|0.58432	D|D	0.999999|0.999999	D|.	0.69078|.	0.997|.	D|.	0.64042|.	0.921|.	T|T	0.69217|0.69217	-0.5203|-0.5203	10|5	0.56958|.	D|.	0.05|.	-20.5633|-20.5633	13.2115|13.2115	0.59828|0.59828	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	358|.	A1X283|.	SPD2B_HUMAN|.	P|P	358|29	ENSP00000430890:L358P;ENSP00000309714:L358P|.	ENSP00000309714:L358P|.	L|S	-|-	2|1	0|0	SH3PXD2B|SH3PXD2B	171705860|171705860	1.000000|1.000000	0.71417|0.71417	0.981000|0.981000	0.43875|0.43875	0.176000|0.176000	0.22953|0.22953	6.844000|6.844000	0.75390|0.75390	2.014000|2.014000	0.59158|0.59158	0.374000|0.374000	0.22700|0.22700	CTC|TCA		0.592	SH3PXD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372449.1	NM_017963	
DBN1	1627	hgsc.bcm.edu	37	5	176884464	176884464	+	Silent	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:176884464T>C	ENST00000309007.5	-	14	2139	c.1920A>G	c.(1918-1920)gaA>gaG	p.E640E	DBN1_ENST00000393563.4_Silent_p.E372E|DBN1_ENST00000292385.5_Silent_p.E642E|DBN1_ENST00000512501.1_3'UTR|DBN1_ENST00000393565.1_Silent_p.E686E	NM_004395.3	NP_004386	Q16643	DREB_HUMAN	drebrin 1	640			E -> Q (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		actin filament organization (GO:0007015)|cell communication by chemical coupling (GO:0010643)|cell communication by electrical coupling (GO:0010644)|maintenance of protein location in cell (GO:0032507)|neural precursor cell proliferation (GO:0061351)|regulation of dendrite development (GO:0050773)|regulation of neuronal synaptic plasticity (GO:0048168)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|gap junction (GO:0005921)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|profilin binding (GO:0005522)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(12)|ovary(1)|skin(2)	25	all_cancers(89;2.17e-05)|Renal(175;0.000269)|Lung NSC(126;0.0014)|all_lung(126;0.0025)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCTCCTCCTCTTCTGGAACTG	0.622											OREG0016462	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					0			5											141.0	123.0	129.0					5																	176884464		2203	4300	6503	176817070	SO:0001819	synonymous_variant	1627				CCDS4420.1, CCDS4421.1	5q35.3	2008-02-05			ENSG00000113758	ENSG00000113758			2695	protein-coding gene	gene with protein product		126660		D0S117E		8216329	Standard	NM_004395		Approved		uc003mgy.2	Q16643	OTTHUMG00000130856	ENST00000309007.5:c.1920A>G	5.37:g.176884464T>C		1934	176817070	A8MV58|B2RBG0|Q9UFZ5	Silent	SNP	ENST00000309007.5	37	CCDS4420.1																																																																																				0.622	DBN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253429.2	NM_080881	
DOK3	79930	hgsc.bcm.edu	37	5	176930174	176930174	+	IGR	SNP	G	G	A	rs79945738|rs370427653|rs138153794	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:176930174G>A	ENST00000357198.4	-	0	1729				RP11-1334A24.6_ENST00000506025.1_RNA|DOK3_ENST00000377112.4_Missense_Mutation_p.L187F|DOK3_ENST00000312943.6_Missense_Mutation_p.L289F	NM_024872.2	NP_079148.2	Q7L591	DOK3_HUMAN	docking protein 3						Ras protein signal transduction (GO:0007265)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|lung(7)	13	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.191)			CAGGAGCAGAGGAGGGAACGC	0.632																																																	0			5											29.0	27.0	27.0					5																	176930174		688	1541	2229	176862780	SO:0001628	intergenic_variant	79930			AK026223	CCDS4426.1, CCDS47349.1, CCDS47350.1	5q35	2008-02-05			ENSG00000146094	ENSG00000146094			24583	protein-coding gene	gene with protein product		611435				10733577, 12595900	Standard	NM_024872		Approved	FLJ22570	uc003mhk.3	Q7L591	OTTHUMG00000130850		5.37:g.176930174G>A			176862780	E9PAT0|H7BXS0|Q8N864|Q9BQB3|Q9H666	Missense_Mutation	SNP	ENST00000357198.4	37	CCDS4426.1	.	.	.	.	.	.	.	.	.	.	G	14.78	2.637846	0.47049	.	.	ENSG00000146094	ENST00000312943;ENST00000377112	T;T	0.56611	0.52;0.45	2.12	0.0934	0.14477	.	.	.	.	.	T	0.23649	0.0572	N	0.08118	0	0.09310	N	1	P;P;P	0.49253	0.872;0.804;0.921	B;B;B	0.36534	0.114;0.144;0.227	T	0.11446	-1.0587	9	0.39692	T	0.17	.	4.2422	0.10654	0.4197:0.0:0.5803:0.0	.	187;289;175	E9PAT0;Q7L591-3;Q7L591-2	.;.;.	F	289;187	ENSP00000325174:L289F;ENSP00000366316:L187F	ENSP00000325174:L289F	L	-	1	0	DOK3	176862780	0.000000	0.05858	0.000000	0.03702	0.315000	0.28087	-0.417000	0.07088	0.001000	0.14605	0.297000	0.19635	CTC		0.632	DOK3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253420.4	NM_024872	
COL28A1	340267	hgsc.bcm.edu	37	7	7413179	7413179	+	Splice_Site	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr7:7413179T>C	ENST00000399429.3	-	32	2500		c.e32-2			NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1						cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		GCCCACAACCTAAAAGATGAA	0.423																																																	0			7											53.0	54.0	54.0					7																	7413179		1858	4108	5966	7379704	SO:0001630	splice_region_variant	340267			AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"""Collagens"""	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.2360-2A>G	7.37:g.7413179T>C			7379704	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Splice_Site	SNP	ENST00000399429.3	37	CCDS43553.1	.	.	.	.	.	.	.	.	.	.	T	15.48	2.846109	0.51164	.	.	ENSG00000215018	ENST00000399429	.	.	.	4.29	4.29	0.51040	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.9056	0.63834	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	COL28A1	7379704	1.000000	0.71417	0.923000	0.36655	0.503000	0.33858	7.406000	0.80017	1.925000	0.55765	0.528000	0.53228	.		0.423	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763	Intron
AHNAK2	113146	hgsc.bcm.edu	37	14	105423028	105423028	+	Splice_Site	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr14:105423028T>C	ENST00000333244.5	-	4	333		c.e4-2		AHNAK2_ENST00000557457.1_5'Flank	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2							costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GGCGTCTTCCTGCAGCCACAA	0.622																																																	0			14											59.0	64.0	63.0					14																	105423028		1976	4165	6141	104494073	SO:0001630	splice_region_variant	113146			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.214-2A>G	14.37:g.105423028T>C			104494073	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Splice_Site	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	T	13.10	2.137324	0.37728	.	.	ENSG00000185567	ENST00000333244	.	.	.	3.44	3.44	0.39384	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.5098	0.33211	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	AHNAK2	104494073	1.000000	0.71417	0.980000	0.43619	0.133000	0.20885	2.212000	0.42835	1.581000	0.49865	0.533000	0.62120	.		0.622	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	Intron
PLEKHN1	84069	hgsc.bcm.edu	37	1	908564	908564	+	Splice_Site	SNP	A	A	G			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:908564A>G	ENST00000379409.2	+	11	1338		c.e11-1		PLEKHN1_ENST00000379407.3_Intron|PLEKHN1_ENST00000379410.3_Splice_Site			Q494U1	PKHN1_HUMAN	pleckstrin homology domain containing, family N member 1											central_nervous_system(1)|endometrium(3)|kidney(1)|lung(2)|skin(1)|urinary_tract(1)	9	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.93e-23)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.00095)|Kidney(185;0.0023)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.199)		TGGTCCCCACAGGACCAGGCC	0.657																																																	0			1											6.0	8.0	7.0					1																	908564		2029	4033	6062	898427	SO:0001630	splice_region_variant	84069			AL136730	CCDS4.1, CCDS53256.1	1p36.33	2013-01-11			ENSG00000187583	ENSG00000187583		"""Pleckstrin homology (PH) domain containing"""	25284	protein-coding gene	gene with protein product						11230166	Standard	NM_032129		Approved	DKFZP434H2010	uc001acd.3	Q494U1	OTTHUMG00000040756	ENST00000379409.2:c.1309-1A>G	1.37:g.908564A>G			898427	Q494U2|Q5SV98|Q9H0M7	Splice_Site	SNP	ENST00000379409.2	37		.	.	.	.	.	.	.	.	.	.	.	7.908	0.735960	0.15574	.	.	ENSG00000187583	ENST00000379410;ENST00000379409	.	.	.	4.19	4.19	0.49359	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.5714	0.39431	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PLEKHN1	898427	0.997000	0.39634	0.846000	0.33378	0.162000	0.22319	2.152000	0.42272	1.770000	0.52166	0.386000	0.25728	.		0.657	PLEKHN1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000473256.1	NM_032129	Intron
SERINC2	347735	hgsc.bcm.edu	37	1	31905889	31905890	+	In_Frame_Ins	INS	-	-	CAG	rs33956499|rs3050461|rs5773362	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:31905889_31905890insCAG	ENST00000373709.3	+	9	1239_1240	c.1089_1090insCAG	c.(1090-1092)cag>CAGcag	p.364_364Q>QQ	SERINC2_ENST00000536384.1_In_Frame_Ins_p.368_368Q>QQ|SERINC2_ENST00000536859.1_In_Frame_Ins_p.368_368Q>QQ|SERINC2_ENST00000373710.1_In_Frame_Ins_p.373_373Q>QQ|SERINC2_ENST00000491976.1_3'UTR	NM_178865.4	NP_849196.2	Q96SA4	SERC2_HUMAN	serine incorporator 2	364					phosphatidylserine metabolic process (GO:0006658)|positive regulation of transferase activity (GO:0051347)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	L-serine transmembrane transporter activity (GO:0015194)			cervix(1)|endometrium(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2)	12		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0629)|Breast(348;0.0707)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0541)|READ - Rectum adenocarcinoma(331;0.151)		TAGACGCCACACAGCAGCAGCA	0.634														3701	0.739018	0.7617	0.7363	5008	,	,		17436	0.63		0.8598	False		,,,				2504	0.6984																0			1																																								31678477	SO:0001652	inframe_insertion	347735			AY094595	CCDS30662.1, CCDS55583.1, CCDS55584.1, CCDS55585.1	1p35.1	2008-02-05	2005-11-01	2005-11-01	ENSG00000168528	ENSG00000168528			23231	protein-coding gene	gene with protein product		614549	"""tumor differentially expressed 2-like"""	TDE2L		12949800	Standard	NM_178865		Approved	FKSG84, PRO0899, TDE2	uc010ogh.2	Q96SA4	OTTHUMG00000003796	ENST00000373709.3:c.1102_1104dupCAG	1.37:g.31905896_31905898dupCAG	ENSP00000362813:p.Gln368dup		31678476	A0AVB4|B4DJK5|B7Z567|B7ZAP2|E7EUZ9|Q86Y23	In_Frame_Ins	INS	ENST00000373709.3	37	CCDS30662.1																																																																																				0.634	SERINC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010680.1	NM_018565	
USH2A	7399	hgsc.bcm.edu	37	1	215802379	215802379	+	Splice_Site	SNP	T	T	C			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr1:215802379T>C	ENST00000307340.3	-	71	15684		c.e71-2		USH2A_ENST00000366943.2_Splice_Site|SNORD116_ENST00000365628.1_RNA	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)						hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		GGCTAACCCCTGAGAAGGAAG	0.473										HNSCC(13;0.011)																																							0			1											76.0	80.0	79.0					1																	215802379		2203	4300	6503	213869002	SO:0001630	splice_region_variant	7399			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.15298-2A>G	1.37:g.215802379T>C			213869002	Q5VVM9|Q6S362|Q9NS27	Splice_Site	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	T	16.03	3.006405	0.54361	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	.	.	.	5.67	5.67	0.87782	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9132	0.79488	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	USH2A	213869002	1.000000	0.71417	0.994000	0.49952	0.524000	0.34500	7.162000	0.77515	2.154000	0.67381	0.482000	0.46254	.		0.473	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	Intron
FANCD2	2177	hgsc.bcm.edu	37	3	10088408	10088408	+	Splice_Site	DEL	G	G	-	rs369823368|rs146316187		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:10088408delG	ENST00000419585.1	+	15	1439		c.e15+1		FANCD2_ENST00000383807.1_Splice_Site|FANCD2_ENST00000383806.1_Splice_Site|FANCD2_ENST00000287647.3_Splice_Site			Q9BXW9	FACD2_HUMAN	Fanconi anemia, complementation group D2						DNA repair (GO:0006281)|gamete generation (GO:0007276)|response to gamma radiation (GO:0010332)|synapsis (GO:0007129)	condensed chromosome (GO:0000793)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA polymerase binding (GO:0070182)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	51				OV - Ovarian serous cystadenocarcinoma(96;0.148)		TCATTACTTAGTAAGTGTCAG	0.358			"""D, Mis, N, F"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																														yes	Rec		Fanconi anaemia D2	3	3p26	2177	"""Fanconi anemia, complementation group D2"""		L	0			3							,	843,3415		0,843,1286	32.0	30.0	31.0		,	1.5	0.4	3		32	1328,6892		1,1326,2783	no	splice-5,splice-5	FANCD2	NM_033084.3,NM_001018115.1	,	1,2169,4069	A1A1,A1R,RR		16.1557,19.798,17.3986	,	,	10088408	2171,10307	2199	4279	6478	10063408	SO:0001630	splice_region_variant	2177	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AF340183	CCDS2595.1, CCDS33696.1	3p25.3	2014-09-17		2001-10-05	ENSG00000144554	ENSG00000144554		"""Fanconi anemia, complementation groups"""	3585	protein-coding gene	gene with protein product		613984		FACD, FANCD		7581463, 11239453, 18475298	Standard	XM_005264946		Approved	FAD, FA-D2	uc003buw.3	Q9BXW9	OTTHUMG00000128670	ENST00000419585.1:c.1278+1G>-	3.37:g.10088408delG			10063408	Q2LA86|Q69YP9|Q6PJN7|Q9BQ06|Q9H9T9	Frame_Shift_Del	DEL	ENST00000419585.1	37	CCDS33696.1																																																																																				0.358	FANCD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339873.1		Intron
ZNF717	100131827	hgsc.bcm.edu	37	3	75786315	75786323	+	In_Frame_Del	DEL	CTACATTCT	CTACATTCT	-	rs146447046|rs202196860		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	CTACATTCT	CTACATTCT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr3:75786315_75786323delCTACATTCT	ENST00000478296.1	-	4	2577_2585	c.2301_2309delAGAATGTAG	c.(2299-2310)aaagaatgtagg>aag	p.ECR768del	ZNF717_ENST00000491507.1_Intron|MIR4273_ENST00000582824.1_RNA|ZNF717_ENST00000422325.1_In_Frame_Del_p.ECR818del|ZNF717_ENST00000477374.1_Intron|ZNF717_ENST00000400845.3_In_Frame_Del_p.ECR811del			Q9BY31	ZN717_HUMAN	zinc finger protein 717	808					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						GAAGGTTTTCCTACATTCTTTACATTCAA	0.383																																																	0			3																																								75869013	SO:0001651	inframe_deletion	100131827			AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124		"""Zinc fingers, C2H2-type"", ""-"""	29448	protein-coding gene	gene with protein product			"""zinc finger protein 838"""	ZNF838			Standard	NM_001128223		Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.2301_2309delAGAATGTAG	3.37:g.75786315_75786323delCTACATTCT	ENSP00000419377:p.Glu768_Arg770del		75869005		In_Frame_Del	DEL	ENST00000478296.1	37																																																																																					0.383	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000352764.2	NM_001128223	
APC	324	hgsc.bcm.edu	37	5	112175148	112175148	+	Frame_Shift_Del	DEL	A	A	-			TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:112175148delA	ENST00000457016.1	+	16	4237	c.3857delA	c.(3856-3858)gaafs	p.E1286fs	APC_ENST00000257430.4_Frame_Shift_Del_p.E1286fs|APC_ENST00000508376.2_Frame_Shift_Del_p.E1286fs|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1286	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.I1287fs*1(1)|p.K1192fs*3(1)|p.?(1)|p.E1286G(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)		GCTGAAGATGAAATAGGATGT	0.348		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)	ovary(1)|large_intestine(1)|soft_tissue(1)|skin(1)	5											55.0	57.0	56.0					5																	112175148		2202	4300	6502	112203047	SO:0001589	frameshift_variant	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.3857delA	5.37:g.112175148delA	ENSP00000413133:p.Glu1286fs		112203047	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Del	DEL	ENST00000457016.1	37	CCDS4107.1																																																																																				0.348	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
GPRIN1	114787	hgsc.bcm.edu	37	5	176026120	176026143	+	In_Frame_Del	DEL	CTCAAAGACCCAGGATCCTCCTTC	CTCAAAGACCCAGGATCCTCCTTC	-	rs3797464|rs200519605|rs386695335|rs550332435|rs77245696|rs142779818|rs371149640|rs199714570|rs373697082|rs201635586	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	CTCAAAGACCCAGGATCCTCCTTC	CTCAAAGACCCAGGATCCTCCTTC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr5:176026120_176026143delCTCAAAGACCCAGGATCCTCCTTC	ENST00000303991.4	-	2	870_893	c.693_716delGAAGGAGGATCCTGGGTCTTTGAG	c.(691-717)aggaaggaggatcctgggtctttgaga>aga	p.231_239RKEDPGSLR>R		NM_052899.2	NP_443131.2	Q7Z2K8	GRIN1_HUMAN	G protein regulated inducer of neurite outgrowth 1	231				Missing (in Ref. 4; CAD38868). {ECO:0000305}.	neuron projection development (GO:0031175)	cell projection (GO:0042995)|plasma membrane (GO:0005886)		p.L238L(1)		NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ATCCACCTTTCTCAAAGACCCAGGATCCTCCTTCCTCGGTGACA	0.491																																																	1	Substitution - coding silent(1)	lung(1)	5								863,3329		131,601,1364						1.0	0.0		dbSNP_134	123	1529,6607		196,1137,2735	no	coding	GPRIN1	NM_052899.2		327,1738,4099	A1A1,A1R,RR		18.793,20.5868,19.403				2392,9936				175958749	SO:0001651	inframe_deletion	114787			AB067480	CCDS4405.1	5q35.2	2008-02-05			ENSG00000169258	ENSG00000169258			24835	protein-coding gene	gene with protein product		611239				11572484	Standard	NM_052899		Approved	GRIN1, KIAA1893	uc003meo.1	Q7Z2K8	OTTHUMG00000130659	ENST00000303991.4:c.693_716delGAAGGAGGATCCTGGGTCTTTGAG	5.37:g.176026120_176026143delCTCAAAGACCCAGGATCCTCCTTC	ENSP00000305839:p.Arg231_Leu238del		175958726	C9JM70|Q8ND74|Q96PZ4	In_Frame_Del	DEL	ENST00000303991.4	37	CCDS4405.1																																																																																				0.491	GPRIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253149.1	NM_052899	
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609239	32609241	+	In_Frame_Del	DEL	GGT	GGT	-	rs12722072|rs41556812|rs12722074|rs534654325	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	GGT	GGT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr6:32609239_32609241delGGT	ENST00000343139.5	+	2	337_339	c.235_237delGGT	c.(235-237)ggtdel	p.G79del	HLA-DQA1_ENST00000395363.1_In_Frame_Del_p.G79del|HLA-DQA1_ENST00000374949.2_In_Frame_Del_p.G79del	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	78	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						CAAATTTGGAGGTTTTGACCCGC	0.502														1751	0.349641	0.3646	0.4236	5008	,	,		12241	0.2669		0.4046	False		,,,				2504	0.3057																0			6																																								32717219	SO:0001651	inframe_deletion	3117				CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.235_237delGGT	6.37:g.32609239_32609241delGGT	ENSP00000339398:p.Gly79del		32717217	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	In_Frame_Del	DEL	ENST00000343139.5	37	CCDS4752.1																																																																																				0.502	HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
GPRC6A	222545	hgsc.bcm.edu	37	6	117113762	117113763	+	Frame_Shift_Ins	INS	-	-	A	rs386705086|rs371464745		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr6:117113762_117113763insA	ENST00000310357.3	-	6	2344_2345	c.2323_2324insT	c.(2323-2325)tatfs	p.Y775fs	GPRC6A_ENST00000368549.3_Frame_Shift_Ins_p.Y704fs|GPRC6A_ENST00000530250.1_Frame_Shift_Ins_p.Y600fs	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	775					calcium-mediated signaling (GO:0019722)|response to amino acid (GO:0043200)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|liver(1)|lung(24)|ovary(5)|pancreas(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)	65		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)		GTAATTCTCATATTTGCCTTTG	0.416																																																	0			6																																								117220456	SO:0001589	frameshift_variant	222545			AF502962	CCDS5112.1, CCDS69184.1, CCDS69185.1	6q22.31	2014-01-30	2014-01-30		ENSG00000173612	ENSG00000173612		"""GPCR / Class C : Calcium-sensing receptors"""	18510	protein-coding gene	gene with protein product			"""G protein-coupled receptor, family C, group 6, member A"""				Standard	NM_001286354		Approved	bA86F4.3	uc003pxj.1	Q5T6X5	OTTHUMG00000015447	ENST00000310357.3:c.2324dupT	6.37:g.117113763_117113763dupA	ENSP00000309493:p.Tyr775fs		117220455	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Frame_Shift_Ins	INS	ENST00000310357.3	37	CCDS5112.1																																																																																				0.416	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2		
GPRC6A	222545	hgsc.bcm.edu	37	6	117113765	117113766	+	In_Frame_Ins	INS	-	-	TCC	rs386705086|rs111974433|rs368671066	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr6:117113765_117113766insTCC	ENST00000310357.3	-	6	2341_2342	c.2320_2321insGGA	c.(2320-2322)aaa>aGGAaa	p.773_774insR	GPRC6A_ENST00000368549.3_In_Frame_Ins_p.702_703insR|GPRC6A_ENST00000530250.1_In_Frame_Ins_p.598_599insR	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	773					calcium-mediated signaling (GO:0019722)|response to amino acid (GO:0043200)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|liver(1)|lung(24)|ovary(5)|pancreas(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)	65		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)		ATTCTCATATTTGCCTTTGAAA	0.421														798	0.159345	0.4009	0.1657	5008	,	,		22554	0.006		0.0815	False		,,,				2504	0.0665																0			6																																								117220459	SO:0001652	inframe_insertion	222545			AF502962	CCDS5112.1, CCDS69184.1, CCDS69185.1	6q22.31	2014-01-30	2014-01-30		ENSG00000173612	ENSG00000173612		"""GPCR / Class C : Calcium-sensing receptors"""	18510	protein-coding gene	gene with protein product			"""G protein-coupled receptor, family C, group 6, member A"""				Standard	NM_001286354		Approved	bA86F4.3	uc003pxj.1	Q5T6X5	OTTHUMG00000015447	ENST00000310357.3:c.2320_2321insGGA	6.37:g.117113765_117113766insTCC	ENSP00000309493:p.Gly773_Lys774insArg		117220458	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	In_Frame_Ins	INS	ENST00000310357.3	37	CCDS5112.1																																																																																				0.421	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2		
GPRIN2	9721	hgsc.bcm.edu	37	10	46999591	46999592	+	In_Frame_Ins	INS	-	-	ATGAGGGAG	rs112620425	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	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		46419597	Q5SVF0	In_Frame_Ins	INS	ENST00000374317.1	37	CCDS31192.1																																																																																				0.629	GPRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047836.1	NM_014696	
MUC2	4583	hgsc.bcm.edu	37	11	1092802	1092802	+	Frame_Shift_Del	DEL	A	A	-	rs528672869|rs534872608	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr11:1092802delA	ENST00000441003.2	+	30	4648	c.4621delA	c.(4621-4623)accfs	p.T1545fs	MUC2_ENST00000359061.5_Frame_Shift_Del_p.T1546fs|MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	cactcccatcaccaccaccac	0.627													|||unknown(ALL_OTHER_Ns)	1941	0.38758	0.3911	0.3876	5008	,	,		6166	0.3403		0.3777	False		,,,				2504	0.4417																0			11											25.0	50.0	41.0					11																	1092802		1636	2920	4556	1082802	SO:0001589	frameshift_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	ENST00000441003.2:c.4621delA	11.37:g.1092802delA	ENSP00000415183:p.Thr1545fs		1082802	Q14878	Frame_Shift_Del	DEL	ENST00000441003.2	37																																																																																					0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
OR6C76	390326	hgsc.bcm.edu	37	12	55820959	55820959	+	Frame_Shift_Del	DEL	A	A	-	rs397719965|rs57387180		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	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		54107226		Frame_Shift_Del	DEL	ENST00000328314.3	37	CCDS31823.1																																																																																				0.338	OR6C76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406675.1	NM_001005183	
CD7	924	hgsc.bcm.edu	37	17	80274142	80274168	+	In_Frame_Del	DEL	CAGGGAGGGCAGAGGCTGCTGGCGGGT	CAGGGAGGGCAGAGGCTGCTGGCGGGT	-	rs201027731|rs200504177|rs555569626|rs569923406|rs569922181|rs199836102	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	CAGGGAGGGCAGAGGCTGCTGGCGGGT	CAGGGAGGGCAGAGGCTGCTGGCGGGT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr17:80274142_80274168delCAGGGAGGGCAGAGGCTGCTGGCGGGT	ENST00000312648.3	-	3	621_647	c.515_541delACCCGCCAGCAGCCTCTGCCCTCCCTG	c.(514-543)gacccgccagcagcctctgccctccctgcg>gcg	p.DPPAASALP172del	CD7_ENST00000583376.1_In_Frame_Del_p.DPPAASALP72del|CD7_ENST00000578509.1_In_Frame_Del_p.DPPAASALP72del|CD7_ENST00000584284.1_In_Frame_Del_p.DPPAASALP172del	NM_006137.6	NP_006128.1	P09564	CD7_HUMAN	CD7 molecule	172	4 X 9 AA tandem repeats, potential spacer function.				homeostasis of number of cells within a tissue (GO:0048873)|immune response (GO:0006955)|T cell activation (GO:0042110)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			endometrium(1)|large_intestine(1)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	8	Breast(20;0.000675)|all_neural(118;0.0804)|Lung NSC(278;0.128)|all_lung(278;0.145)|Ovarian(332;0.249)		OV - Ovarian serous cystadenocarcinoma(97;0.00463)|BRCA - Breast invasive adenocarcinoma(99;0.0667)			GCCAGGGCCGCAGGGAGGGCAGAGGCTGCTGGCGGGTCAGGGAGGGC	0.714																																					Pancreas(45;804 1068 19702 28207 28798)												0			17								46,4026		10,26,2000						-6.3	0.0			12	351,7627		58,235,3696	no	coding	CD7	NM_006137.6		68,261,5696	A1A1,A1R,RR		4.3996,1.1297,3.2946				397,11653				77867457	SO:0001651	inframe_deletion	924			X06180	CCDS11807.1	17q25.2-q25.3	2013-01-11	2006-03-28			ENSG00000173762		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1695	protein-coding gene	gene with protein product	"""p41 protein"", ""T-cell antigen CD7"", ""T-cell leukemia antigen"""	186820	"""CD7 antigen (p41)"""			1695199, 3501369	Standard	NM_006137		Approved	GP40, LEU-9, TP41, Tp40	uc002kel.1	P09564		ENST00000312648.3:c.515_541delACCCGCCAGCAGCCTCTGCCCTCCCTG	17.37:g.80274142_80274168delCAGGGAGGGCAGAGGCTGCTGGCGGGT	ENSP00000312027:p.Asp172_Pro180del		77867431		In_Frame_Del	DEL	ENST00000312648.3	37	CCDS11807.1																																																																																				0.714	CD7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442826.1	NM_006137	
POLI	11201	hgsc.bcm.edu	37	18	51795958	51795960	+	In_Frame_Del	DEL	CGA	CGA	-	rs78943519|rs10584411|rs3729509	byFrequency	TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	CGA	CGA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr18:51795958_51795960delCGA	ENST00000579534.1	+	1	185_187	c.42_44delCGA	c.(40-45)ggcgac>ggc	p.D17del	POLI_ENST00000217800.5_5'Flank|POLI_ENST00000406285.3_In_Frame_Del_p.D17del|POLI_ENST00000579434.1_5'UTR	NM_007195.2	NP_009126.2	Q9UNA4	POLI_HUMAN	polymerase (DNA directed) iota	17					DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)	intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)	p.D17delD(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(10)|lung(5)|ovary(3)|urinary_tract(1)	26				Colorectal(16;0.0234)|READ - Rectum adenocarcinoma(59;0.197)		AAGGCGGCGGCGACGACGACGAG	0.729								DNA polymerases (catalytic subunits)						3926	0.783946	0.9705	0.6427	5008	,	,		12312	0.7054		0.7078	False		,,,				2504	0.7914																1	Deletion - In frame(1)	large_intestine(1)	18								3523,343		1644,235,54						1.5	0.0		dbSNP_119	14	5235,2405		1985,1265,570	no	coding	POLI	NM_007195.2		3629,1500,624	A1A1,A1R,RR		31.4791,8.8722,23.8832				8758,2748				50049958	SO:0001651	inframe_deletion	11201				CCDS11954.2	18q21.1	2012-05-18			ENSG00000101751	ENSG00000101751		"""DNA polymerases"""	9182	protein-coding gene	gene with protein product		605252		RAD3OB, RAD30B		17609217	Standard	NM_007195		Approved		uc002lfj.4	Q9UNA4	OTTHUMG00000132704	ENST00000579534.1:c.42_44delCGA	18.37:g.51795967_51795969delCGA	ENSP00000462664:p.Asp17del		50049956	Q8N590|Q9H0S1|Q9NYH6	In_Frame_Del	DEL	ENST00000579534.1	37	CCDS11954.2																																																																																				0.729	POLI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256002.3	NM_007195	
LSR	51599	hgsc.bcm.edu	37	19	35758275	35758276	+	In_Frame_Ins	INS	-	-	GGA	rs397751431|rs79703261|rs35939322|rs142507475		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr19:35758275_35758276insGGA	ENST00000361790.3	+	9	1711_1712	c.1552_1553insGGA	c.(1552-1554)ggg>gGGAgg	p.519_520insR	LSR_ENST00000360798.3_In_Frame_Ins_p.451_452insR|USF2_ENST00000343550.5_5'Flank|LSR_ENST00000347609.4_In_Frame_Ins_p.461_462insR|LSR_ENST00000354900.3_In_Frame_Ins_p.500_501insR|AD000684.2_ENST00000602262.1_RNA|LSR_ENST00000602122.1_In_Frame_Ins_p.499_500insR|USF2_ENST00000222305.3_5'Flank|USF2_ENST00000594064.1_5'Flank|USF2_ENST00000595068.1_5'Flank|LSR_ENST00000427250.1_In_Frame_Ins_p.363_364insR|USF2_ENST00000379134.3_5'Flank	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		40450115	A6NDW3|B4DKL4|E9PHD4|O00112|O00426|Q6ZT80|Q8NBM0|Q9BT33|Q9UQL3	In_Frame_Ins	INS	ENST00000361790.3	37	CCDS12450.1																																																																																				0.723	LSR-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465513.2	NM_015925	
MYBL2	4605	hgsc.bcm.edu	37	20	42310481	42310482	+	Frame_Shift_Ins	INS	-	-	C	rs199623276		TCGA-EF-5830-01A-01D-1657-10	TCGA-EF-5830-10A-01D-1657-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	61fe838a-d218-407a-922a-7cb9b4fc8aa8	243fcf8d-0c9e-48cb-b0ae-08fc55a84f86	g.chr20:42310481_42310482insC	ENST00000217026.4	+	3	299_300	c.172_173insC	c.(172-174)gccfs	p.A58fs	MYBL2_ENST00000396863.4_Intron	NM_002466.2	NP_002457.1	P10244	MYBB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 2	58	HTH myb-type 1. {ECO:0000255|PROSITE- ProRule:PRU00625}.				G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle (GO:0051726)|spindle assembly involved in mitosis (GO:0090307)	Myb complex (GO:0031523)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|liver(2)|lung(18)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	46		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			GAAGTTCCTGGCCAGCCACTTC	0.609																																																	0			20																																								41743896	SO:0001589	frameshift_variant	4605				CCDS13322.1, CCDS63276.1	20q13.1	2013-07-09	2013-07-09		ENSG00000101057	ENSG00000101057			7548	protein-coding gene	gene with protein product		601415				8812502	Standard	NM_002466		Approved	BMYB, B-MYB	uc002xlb.1	P10244	OTTHUMG00000033062	ENST00000217026.4:c.174dupC	20.37:g.42310483_42310483dupC	ENSP00000217026:p.Ala58fs		41743895	B2RBS5|B7Z8D9|F8W6N6|Q53F07	Frame_Shift_Ins	INS	ENST00000217026.4	37	CCDS13322.1																																																																																				0.609	MYBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080408.1	NM_002466	
