#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Confidence	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_NTotCov	i_NVarCov	i_NVarRat	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_TVarRat	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	i_dbSNP_AF	i_dbSNP_PopFreq	i_dbSNP_Strength	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
CROCC	9696	hgsc.bcm.edu	37	1	17297201	17297201	+	Missense_Mutation	SNP	G	G	A	rs150054438		TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr1:17297201G>A	ENST00000375541.5	+	35	5792	c.5723G>A	c.(5722-5724)cGc>cAc	p.R1908H		NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		CGCCTGGACCGCACCCTCACG	0.657																																					p.R1908H		Atlas-SNP	.											.	CROCC	185	.	0			c.G5723A						PASS	.						25.0	27.0	26.0					1																	17297201		2202	4299	6501	SO:0001583	missense	9696	exon35			TGGACCGCACCCT	AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"""rootletin, ciliary rootlet protein"""	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.5723G>A	chr1.hg19:g.17297201G>A	ENSP00000364691:p.Arg1908His	197.0	0.0	.		121.0	5.0	.	NM_014675		Missense_Mutation	SNP	ENST00000375541.5	hg19	CCDS30616.1	.	.	.	.	.	.	.	.	.	.	G	19.19	3.779247	0.70107	.	.	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.10668	2.85	4.6	2.7	0.31948	.	.	.	.	.	T	0.16342	0.0393	L	0.47716	1.5	0.47065	D	0.9993	D;P;P	0.59357	0.985;0.937;0.929	P;P;P	0.54460	0.753;0.483;0.651	T	0.01460	-1.1349	9	0.37606	T	0.19	.	9.1203	0.36784	0.1828:0.0:0.8172:0.0	.	1789;1211;1908	B1AKD8;Q5TZA2-2;Q5TZA2	.;.;CROCC_HUMAN	H	1908;1789	ENSP00000364691:R1908H	ENSP00000364691:R1908H	R	+	2	0	CROCC	17169788	1.000000	0.71417	0.998000	0.56505	0.844000	0.47949	3.350000	0.52224	0.487000	0.27698	0.655000	0.94253	CGC	.	G|1.000;T|0.000	.	alt		0.657	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
TAS1R2	80834	hgsc.bcm.edu	37	1	19181460	19181460	+	Silent	SNP	G	G	A	rs373438774		TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr1:19181460G>A	ENST00000375371.3	-	3	525	c.504C>T	c.(502-504)agC>agT	p.S168S	RP13-279N23.2_ENST00000494072.3_3'UTR	NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	168					detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|sensory perception of sweet taste (GO:0050916)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(10)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(3)|stomach(1)	45		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;3.56e-05)|Kidney(64;0.000177)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Aspartame(DB00168)	GCAGCTCATCGCTGATGGCGC	0.637																																					p.S168S		Atlas-SNP	.											.	TAS1R2	134	.	0			c.C504T						PASS	.	G		1,4403	2.1+/-5.4	0,1,2201	42.0	42.0	42.0		504	-3.7	0.0	1		42	0,8598		0,0,4299	no	coding-synonymous	TAS1R2	NM_152232.2		0,1,6500	AA,AG,GG		0.0,0.0227,0.0077		168/840	19181460	1,13001	2202	4299	6501	SO:0001819	synonymous_variant	80834	exon3			CTCATCGCTGATG		CCDS187.1	1p36.13	2012-08-22	2003-03-07		ENSG00000179002	ENSG00000179002		"""Taste receptors / Type 1"", ""GPCR / Unclassified : Taste receptors"""	14905	protein-coding gene	gene with protein product		606226	"""G protein-coupled receptor 71"""	GPR71			Standard	NM_152232		Approved	T1R2, TR2	uc001bba.1	Q8TE23	OTTHUMG00000002442	ENST00000375371.3:c.504C>T	chr1.hg19:g.19181460G>A		59.0	0.0	.		33.0	8.0	.	NM_152232	Q5TZ19	Silent	SNP	ENST00000375371.3	hg19	CCDS187.1																																																																																			.	.	.	none		0.637	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1		
CD1A	909	hgsc.bcm.edu	37	1	158226807	158226807	+	Missense_Mutation	SNP	G	G	A			TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr1:158226807G>A	ENST00000289429.5	+	4	1369	c.836G>A	c.(835-837)cGg>cAg	p.R279Q		NM_001763.2	NP_001754.2	P06126	CD1A_HUMAN	CD1a molecule	279	Ig-like.				antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)		p.R279Q(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(14)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(1)	32	all_hematologic(112;0.0378)				Antithymocyte globulin(DB00098)	CTGTCCTGTCGGGTGAAGCAC	0.612																																					p.R279Q		Atlas-SNP	.											CD1A,bladder,carcinoma,0,2	CD1A	88	.	1	Substitution - Missense(1)	urinary_tract(1)	c.G836A						PASS	.						83.0	77.0	79.0					1																	158226807		2203	4300	6503	SO:0001583	missense	909	exon4			CCTGTCGGGTGAA	M28825	CCDS1174.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158477	ENSG00000158477		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	1634	protein-coding gene	gene with protein product		188370	"""CD1A antigen, a polypeptide"", ""CD1a antigen"""	CD1		2447586, 2784820	Standard	NM_001763		Approved		uc001frt.3	P06126	OTTHUMG00000017512	ENST00000289429.5:c.836G>A	chr1.hg19:g.158226807G>A	ENSP00000289429:p.Arg279Gln	105.0	0.0	.		83.0	9.0	.	NM_001763	D3DVD7|Q13962|Q5TDJ8|Q9UMM4|Q9Y5M5	Missense_Mutation	SNP	ENST00000289429.5	hg19	CCDS1174.1	.	.	.	.	.	.	.	.	.	.	G	13.72	2.320750	0.41096	.	.	ENSG00000158477	ENST00000289429	T	0.02812	4.15	3.84	1.94	0.25998	Immunoglobulin-like (1);MHC class I-like antigen recognition (1);Immunoglobulin C1-set (2);	0.221369	0.23003	N	0.053047	T	0.02304	0.0071	L	0.45137	1.4	0.09310	N	1	D	0.76494	0.999	P	0.59221	0.854	T	0.44065	-0.9352	10	0.54805	T	0.06	-15.6093	6.0141	0.19592	0.2415:0.0:0.7585:0.0	.	279	P06126	CD1A_HUMAN	Q	279	ENSP00000289429:R279Q	ENSP00000289429:R279Q	R	+	2	0	CD1A	156493431	0.000000	0.05858	0.008000	0.14137	0.385000	0.30292	-0.203000	0.09438	0.406000	0.25560	0.491000	0.48974	CGG	.	.	.	none		0.612	CD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046349.2	NM_001763	
ITPKB	3707	hgsc.bcm.edu	37	1	226924884	226924884	+	Silent	SNP	G	G	A	rs147889095	byFrequency	TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr1:226924884G>A	ENST00000272117.3	-	1	275	c.276C>T	c.(274-276)agC>agT	p.S92S	ITPKB_ENST00000429204.1_Silent_p.S92S|ITPKB_ENST00000366784.1_Silent_p.S92S			P27987	IP3KB_HUMAN	inositol-trisphosphate 3-kinase B	92					cell surface receptor signaling pathway (GO:0007166)|inositol phosphate metabolic process (GO:0043647)|MAPK cascade (GO:0000165)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of Ras protein signal transduction (GO:0046579)|positive thymic T cell selection (GO:0045059)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(1)	30		Prostate(94;0.0773)				tactgccgctgctgccgctgc	0.751																																					p.S92S	Colon(84;110 1851 5306 33547)	Atlas-SNP	.											.,1	ITPKB	158	.	0			c.C276T						PASS	.						4.0	5.0	5.0					1																	226924884		1803	3692	5495	SO:0001819	synonymous_variant	3707	exon2			GCCGCTGCTGCCG	AJ242780	CCDS1555.1	1q42.12	2011-04-28	2011-04-28		ENSG00000143772	ENSG00000143772	2.7.1.127		6179	protein-coding gene	gene with protein product		147522	"""inositol 1,4,5-trisphosphate 3-kinase B"""			1654894, 1330886	Standard	NM_002221		Approved	IP3KB, IP3-3KB	uc010pvo.2	P27987	OTTHUMG00000037582	ENST00000272117.3:c.276C>T	chr1.hg19:g.226924884G>A		6.0	0.0	.		8.0	4.0	.	NM_002221	Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47	Silent	SNP	ENST00000272117.3	hg19	CCDS1555.1																																																																																			.	.	.	none		0.751	ITPKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091632.1	NM_002221	
TMIE	259236	hgsc.bcm.edu	37	3	46751076	46751076	+	Missense_Mutation	SNP	G	G	T	rs552239745|rs397817178|rs10578999|rs544504092|rs538183178|rs71619660|rs75020261	byFrequency	TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr3:46751076G>T	ENST00000326431.3	+	4	524	c.369G>T	c.(367-369)aaG>aaT	p.K123N		NM_147196.2	NP_671729.2	Q8NEW7	TMIE_HUMAN	transmembrane inner ear	123	Lys-rich.				inner ear morphogenesis (GO:0042472)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)				endometrium(1)|lung(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000688)|KIRC - Kidney renal clear cell carcinoma(197;0.0177)|Kidney(197;0.0208)		CAGAGGATaagaagaagaaga	0.502																																					p.K123N		Atlas-SNP	.											.	TMIE	16	.	0			c.G369T						PASS	.						56.0	61.0	60.0					3																	46751076		1899	4121	6020	SO:0001583	missense	259236	exon4			GGATAAGAAGAAG	AY081842	CCDS43081.1	3p21	2010-01-06	2004-05-19		ENSG00000181585	ENSG00000181585			30800	protein-coding gene	gene with protein product		607237	"""deafness, autosomal recessive 6"""	DFNB6		12140191, 12145746	Standard	NM_147196		Approved		uc010hjk.1	Q8NEW7	OTTHUMG00000149909	ENST00000326431.3:c.369G>T	chr3.hg19:g.46751076G>T	ENSP00000324775:p.Lys123Asn	119.0	0.0	.		68.0	14.0	.	NM_147196	A0AV93|A8K0R0	Missense_Mutation	SNP	ENST00000326431.3	hg19	CCDS43081.1	.	.	.	.	.	.	.	.	.	.	G	4.335	0.061563	0.08339	.	.	ENSG00000181585	ENST00000326431	D	0.86230	-2.09	.	.	.	.	0.415784	0.26349	N	0.024899	T	0.76821	0.4041	L	0.40543	1.245	0.09310	N	1	B	0.25441	0.126	B	0.06405	0.002	T	0.64765	-0.6330	8	0.48119	T	0.1	-5.4402	.	.	.	.	123	Q8NEW7	TMIE_HUMAN	N	123	ENSP00000324775:K123N	ENSP00000324775:K123N	K	+	3	2	TMIE	46726080	0.976000	0.34144	0.425000	0.26659	0.475000	0.33008	1.894000	0.39768	0.121000	0.18284	0.123000	0.15791	AAG	.	.	.	weak		0.502	TMIE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313853.1	NM_147196	
FAM157A	728262	hgsc.bcm.edu	37	3	197880167	197880167	+	lincRNA	SNP	G	G	A			TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr3:197880167G>A	ENST00000437428.2	+	0	47							C9JC47	F157A_HUMAN	family with sequence similarity 157, member A											NS(1)|skin(1)	2						agcagcagcagcagcaACTGG	0.527																																					p.Q82Q		Atlas-SNP	.											.	FAM157A	4	.	0			c.G246A						PASS	.						2.0	6.0	5.0					3																	197880167		369	1057	1426			728262	exon2			GCAGCAGCAGCAA			3q29	2013-01-30			ENSG00000236438	ENSG00000236438			34079	other	unknown							Standard	NM_001145248		Approved		uc011bup.1	C9JC47			chr3.hg19:g.197880167G>A		461.0	0.0	.		347.0	20.0	.	NM_001145248		Silent	SNP	ENST00000437428.2	hg19																																																																																				.	.	.	none		0.527	FAM157A-001	KNOWN	not_best_in_genome_evidence|mRNA_end_NF|basic	lincRNA	lincRNA	OTTHUMT00000340078.2	NM_001145248	
SEC24A	10802	hgsc.bcm.edu	37	5	134010440	134010440	+	Missense_Mutation	SNP	C	C	G			TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr5:134010440C>G	ENST00000398844.2	+	5	1241	c.953C>G	c.(952-954)cCa>cGa	p.P318R	SEC24A_ENST00000322887.4_Missense_Mutation_p.P318R	NM_021982.2	NP_068817.1	O95486	SC24A_HUMAN	SEC24 family member A	318					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of protein secretion (GO:0050714)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045714)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	36			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TTGAATTACCCAAGTGGGCCA	0.418																																					p.P318R		Atlas-SNP	.											.	SEC24A	77	.	0			c.C953G						PASS	.						71.0	65.0	66.0					5																	134010440		1848	4097	5945	SO:0001583	missense	10802	exon5			ATTACCCAAGTGG	AJ131244	CCDS43363.1, CCDS58967.1	5q31.1	2013-10-21	2013-10-21		ENSG00000113615	ENSG00000113615			10703	protein-coding gene	gene with protein product		607183	"""SEC24 (S. cerevisiae) related gene family, member A"", ""SEC24 family, member A (S. cerevisiae)"""			10075675, 10329445	Standard	NM_021982		Approved		uc003kzs.3	O95486	OTTHUMG00000163064	ENST00000398844.2:c.953C>G	chr5.hg19:g.134010440C>G	ENSP00000381823:p.Pro318Arg	320.0	0.0	.		268.0	36.0	.	NM_001252231	A8MVW3|Q8WUV2|Q96GP7	Missense_Mutation	SNP	ENST00000398844.2	hg19	CCDS43363.1	.	.	.	.	.	.	.	.	.	.	C	14.70	2.612974	0.46631	.	.	ENSG00000113615	ENST00000398844;ENST00000322887	T;T	0.23147	1.92;1.92	5.03	5.03	0.67393	.	0.438354	0.27185	N	0.020535	T	0.29061	0.0722	L	0.54323	1.7	0.54753	D	0.999988	B;B	0.27068	0.167;0.042	B;B	0.26202	0.067;0.036	T	0.04495	-1.0947	10	0.34782	T	0.22	-7.6797	18.7188	0.91686	0.0:1.0:0.0:0.0	.	82;318	B4E205;O95486	.;SC24A_HUMAN	R	318	ENSP00000381823:P318R;ENSP00000321749:P318R	ENSP00000321749:P318R	P	+	2	0	SEC24A	134038339	0.996000	0.38824	1.000000	0.80357	0.820000	0.46376	1.544000	0.36158	2.478000	0.83669	0.563000	0.77884	CCA	.	.	.	none		0.418	SEC24A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371563.1		
DNAH8	1769	hgsc.bcm.edu	37	6	38818151	38818151	+	Missense_Mutation	SNP	T	T	C			TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr6:38818151T>C	ENST00000359357.3	+	36	4927	c.4673T>C	c.(4672-4674)tTa>tCa	p.L1558S	DNAH8_ENST00000449981.2_Missense_Mutation_p.L1775S|DNAH8_ENST00000441566.1_Missense_Mutation_p.L1558S			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	1558					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						TTACCTCATTTACATGAGCAG	0.363																																					p.L1775S		Atlas-SNP	.											.	DNAH8	1239	.	0			c.T5324C						PASS	.						135.0	127.0	130.0					6																	38818151		2203	4300	6503	SO:0001583	missense	1769	exon38			CTCATTTACATGA	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.4673T>C	chr6.hg19:g.38818151T>C	ENSP00000352312:p.Leu1558Ser	46.0	0.0	.		51.0	16.0	.	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	hg19		.	.	.	.	.	.	.	.	.	.	T	24.1	4.493327	0.84962	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.64085	-0.08;-0.08;-0.08	5.66	5.66	0.87406	Dynein heavy chain, domain-2 (1);	0.000000	0.64402	D	0.000004	T	0.75939	0.3918	M	0.81112	2.525	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.79017	-0.1975	10	0.54805	T	0.06	.	15.9012	0.79377	0.0:0.0:0.0:1.0	.	1558	Q96JB1	DYH8_HUMAN	S	1763;1763;1558;1558	ENSP00000333363:L1763S;ENSP00000352312:L1558S;ENSP00000402294:L1558S	ENSP00000333363:L1763S	L	+	2	0	DNAH8	38926129	1.000000	0.71417	0.893000	0.35052	0.962000	0.63368	7.886000	0.87288	2.167000	0.68274	0.528000	0.53228	TTA	.	.	.	none		0.363	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
DLK2	65989	hgsc.bcm.edu	37	6	43422491	43422491	+	Nonsense_Mutation	SNP	G	G	A			TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr6:43422491G>A	ENST00000357338.3	-	2	773	c.73C>T	c.(73-75)Cga>Tga	p.R25*	DLK2_ENST00000372488.3_Nonsense_Mutation_p.R25*|DLK2_ENST00000372485.1_Nonsense_Mutation_p.R25*|DLK2_ENST00000414245.1_Nonsense_Mutation_p.R25*	NM_206539.1	NP_996262.1	Q6UY11	DLK2_HUMAN	delta-like 2 homolog (Drosophila)	25					negative regulation of Notch signaling pathway (GO:0045746)|regulation of fat cell differentiation (GO:0045598)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	7	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			CGCTCACCTCGGACAGGCTGA	0.721											OREG0017451	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R25X		Atlas-SNP	.											.	DLK2	22	.	0			c.C73T						PASS	.						9.0	12.0	11.0					6																	43422491		2139	4177	6316	SO:0001587	stop_gained	65989	exon2			CACCTCGGACAGG	AK055380	CCDS4897.1, CCDS75461.1	6p21.1	2008-02-05	2007-07-05	2007-07-05	ENSG00000171462	ENSG00000171462			21113	protein-coding gene	gene with protein product			"""EGF-like-domain, multiple 9"""	EGFL9			Standard	NM_001286656		Approved	MGC2487	uc003ovb.3	Q6UY11	OTTHUMG00000014735	ENST00000357338.3:c.73C>T	chr6.hg19:g.43422491G>A	ENSP00000349893:p.Arg25*	112.0	0.0	.	916	54.0	5.0	.	NM_023932	B3KNZ7|Q5T3T8|Q9BQ54	Nonsense_Mutation	SNP	ENST00000357338.3	hg19	CCDS4897.1	.	.	.	.	.	.	.	.	.	.	G	37	6.367189	0.97511	.	.	ENSG00000171462	ENST00000372485;ENST00000372488;ENST00000372496;ENST00000357338;ENST00000414245	.	.	.	4.34	-3.28	0.05033	.	0.857967	0.09956	N	0.734079	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11182	T	0.66	.	8.7775	0.34771	0.0:0.2362:0.2638:0.5	.	.	.	.	X	25	.	ENSP00000349893:R25X	R	-	1	2	DLK2	43530469	1.000000	0.71417	0.943000	0.38184	0.992000	0.81027	0.597000	0.24059	-0.832000	0.04251	0.555000	0.69702	CGA	.	.	.	none		0.721	DLK2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040618.1	NM_023932	
ACTB	60	hgsc.bcm.edu	37	7	5569022	5569022	+	Missense_Mutation	SNP	C	C	T			TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr7:5569022C>T	ENST00000331789.5	-	3	324	c.133G>A	c.(133-135)Gtg>Atg	p.V45M	AC006483.1_ENST00000579427.1_RNA|ACTB_ENST00000464611.1_5'Flank	NM_001101.3	NP_001092.1	P63261	ACTG_HUMAN	actin, beta	45					adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|platelet aggregation (GO:0070527)|retina homeostasis (GO:0001895)|sarcomere organization (GO:0045214)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|membrane (GO:0016020)|myofibril (GO:0030016)|nucleus (GO:0005634)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(2)|prostate(2)	8		Ovarian(82;0.0606)		UCEC - Uterine corpus endometrioid carcinoma (126;0.175)|OV - Ovarian serous cystadenocarcinoma(56;4.24e-37)		CCCATGCCCACCATCACGCCC	0.627																																					p.V45M		Atlas-SNP	.											.	ACTB	45	.	0			c.G133A						PASS	.						63.0	68.0	66.0					7																	5569022		2203	4300	6503	SO:0001583	missense	60	exon3			TGCCCACCATCAC	M28424	CCDS5341.1	7p22	2014-09-17			ENSG00000075624	ENSG00000075624			132	protein-coding gene	gene with protein product		102630				1505215	Standard	NM_001101		Approved		uc003sot.4	P60709	OTTHUMG00000023268	ENST00000331789.5:c.133G>A	chr7.hg19:g.5569022C>T	ENSP00000349960:p.Val45Met	204.0	0.0	.		113.0	17.0	.	NM_001101	A8K7C2|P02571|P14104|P99022|Q5U032|Q96E67	Missense_Mutation	SNP	ENST00000331789.5	hg19	CCDS5341.1	.	.	.	.	.	.	.	.	.	.	C	11.02	1.516604	0.27123	.	.	ENSG00000075624	ENST00000331789;ENST00000445914;ENST00000400179;ENST00000432588;ENST00000443528;ENST00000417101;ENST00000414620	D;D;D;D;D	0.92099	-2.97;-2.97;-2.97;-2.97;-2.97	4.9	3.1	0.35709	.	0.000000	0.53938	D	0.000044	D	0.93733	0.7997	M	0.74546	2.27	0.38415	D	0.94602	B	0.20988	0.05	P	0.44990	0.466	D	0.91871	0.5507	10	0.87932	D	0	.	9.1398	0.36897	0.0:0.8199:0.0:0.1801	.	45	P60709	ACTB_HUMAN	M	45;45;45;45;45;48;45	ENSP00000349960:V45M;ENSP00000407473:V45M;ENSP00000393951:V45M;ENSP00000399487:V48M;ENSP00000401032:V45M	ENSP00000349960:V45M	V	-	1	0	ACTB	5535548	1.000000	0.71417	0.998000	0.56505	0.979000	0.70002	5.882000	0.69714	0.490000	0.27771	0.557000	0.71058	GTG	.	.	.	none		0.627	ACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059589.4	NM_001101	
ABCA13	154664	hgsc.bcm.edu	37	7	48278921	48278921	+	Silent	SNP	C	C	T			TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr7:48278921C>T	ENST00000435803.1	+	9	1005	c.981C>T	c.(979-981)caC>caT	p.H327H		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	327					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						AATGGGGCCACGTTGGAGGCT	0.498																																					p.H327H		Atlas-SNP	.											.	ABCA13	1192	.	0			c.C981T						PASS	.						69.0	72.0	71.0					7																	48278921		2015	4179	6194	SO:0001819	synonymous_variant	154664	exon9			GGGCCACGTTGGA	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"""ATP binding cassette transporters / subfamily A"""	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.981C>T	chr7.hg19:g.48278921C>T		58.0	0.0	.		48.0	4.0	.	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	hg19	CCDS47584.1																																																																																			.	.	.	none		0.498	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
FLNC	2318	hgsc.bcm.edu	37	7	128492929	128492929	+	Missense_Mutation	SNP	C	C	T			TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr7:128492929C>T	ENST00000325888.8	+	37	6313	c.6052C>T	c.(6052-6054)Cgc>Tgc	p.R2018C	RP11-309L24.2_ENST00000469965.1_RNA|FLNC_ENST00000346177.6_Missense_Mutation_p.R1985C	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	2018					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						GGTGAGCGTGCGCAAGAGTGG	0.637																																					p.R2018C		Atlas-SNP	.											.	FLNC	339	.	0			c.C6052T						PASS	.						60.0	68.0	66.0					7																	128492929		2078	4199	6277	SO:0001583	missense	2318	exon37			AGCGTGCGCAAGA	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"""actin binding protein 280"""	102565	"""filamin C, gamma (actin binding protein 280)"""	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.6052C>T	chr7.hg19:g.128492929C>T	ENSP00000327145:p.Arg2018Cys	249.0	0.0	.		125.0	16.0	.	NM_001458	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Missense_Mutation	SNP	ENST00000325888.8	hg19	CCDS43644.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.590842	0.86851	.	.	ENSG00000128591	ENST00000325888;ENST00000346177	T;T	0.44881	0.91;0.91	5.73	5.73	0.89815	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.135360	0.48767	D	0.000161	T	0.49881	0.1583	L	0.40543	1.245	0.53005	D	0.999969	D;D	0.76494	0.999;0.995	P;P	0.57846	0.828;0.696	T	0.49881	-0.8892	10	0.87932	D	0	.	12.9057	0.58152	0.2697:0.7303:0.0:0.0	.	1985;2018	Q14315-2;Q14315	.;FLNC_HUMAN	C	2018;1985	ENSP00000327145:R2018C;ENSP00000344002:R1985C	ENSP00000327145:R2018C	R	+	1	0	FLNC	128280165	0.102000	0.21896	1.000000	0.80357	0.986000	0.74619	1.868000	0.39509	2.722000	0.93159	0.655000	0.94253	CGC	.	.	.	none		0.637	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3		
PPP1R3B	79660	hgsc.bcm.edu	37	8	8998922	8998922	+	Silent	SNP	C	C	T			TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr8:8998922C>T	ENST00000310455.3	-	2	390	c.240G>A	c.(238-240)tcG>tcA	p.S80S	PPP1R3B_ENST00000519699.1_Silent_p.S80S|RP11-10A14.3_ENST00000520017.1_RNA|RP11-10A14.3_ENST00000522057.1_RNA	NM_001201329.1|NM_024607.3	NP_001188258.1|NP_078883.2	Q86XI6	PPR3B_HUMAN	protein phosphatase 1, regulatory subunit 3B	80					glycogen metabolic process (GO:0005977)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of glycogen catabolic process (GO:0005981)	glycogen granule (GO:0042587)|intracellular membrane-bounded organelle (GO:0043231)|protein phosphatase type 1 complex (GO:0000164)	protein phosphatase regulator activity (GO:0019888)			endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	12				COAD - Colon adenocarcinoma(149;0.0717)|READ - Rectum adenocarcinoma(644;0.241)		CATCGAATTCCGAGAACACTT	0.532																																					p.S80S		Atlas-SNP	.											.	PPP1R3B	30	.	0			c.G240A						PASS	.						117.0	110.0	113.0					8																	8998922		2203	4300	6503	SO:0001819	synonymous_variant	79660	exon2			GAATTCCGAGAAC	AK024067	CCDS5973.1	8p23.1	2012-04-17	2011-10-04		ENSG00000173281	ENSG00000173281		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14942	protein-coding gene	gene with protein product	"""PP1 subunit R4"", ""hepatic glycogen-targeting subunit, G(L)"""	610541	"""protein phosphatase 1, regulatory (inhibitor) subunit 3B"""			11948623, 17555403	Standard	NM_024607		Approved	GL, FLJ14005, PPP1R4	uc003wsn.4	Q86XI6	OTTHUMG00000129329	ENST00000310455.3:c.240G>A	chr8.hg19:g.8998922C>T		68.0	0.0	.		53.0	5.0	.	NM_001201329	B3KTV3|Q9H812	Silent	SNP	ENST00000310455.3	hg19	CCDS5973.1																																																																																			.	.	.	none		0.532	PPP1R3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251472.1	NM_024607	
FAM73B	84895	hgsc.bcm.edu	37	9	131832229	131832229	+	Silent	SNP	C	C	G	rs371991039		TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr9:131832229C>G	ENST00000358369.4	+	15	1786	c.1560C>G	c.(1558-1560)gtC>gtG	p.V520V	FAM73B_ENST00000277475.5_3'UTR|FAM73B_ENST00000406926.2_3'UTR	NM_032809.2	NP_116198.2	Q7L4E1	FA73B_HUMAN	family with sequence similarity 73, member B	520					bone development (GO:0060348)	integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(1)	13						TTGCTGAAGTCTGTGCTTTCT	0.562																																					p.V520V		Atlas-SNP	.											.	FAM73B	37	.	0			c.C1560G						PASS	.						213.0	204.0	207.0					9																	131832229		2203	4300	6503	SO:0001819	synonymous_variant	84895	exon15			TGAAGTCTGTGCT	AK074127	CCDS6917.1	9q34.13	2008-02-05	2005-08-11	2005-08-11	ENSG00000148343	ENSG00000148343			23621	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 54"""	C9orf54			Standard	NM_032809		Approved	FLJ14596, FLJ00199	uc004bxa.3	Q7L4E1	OTTHUMG00000020770	ENST00000358369.4:c.1560C>G	chr9.hg19:g.131832229C>G		74.0	0.0	.		49.0	9.0	.	NM_032809	Q8NBM3|Q8TEJ6|Q969E6	Silent	SNP	ENST00000358369.4	hg19	CCDS6917.1																																																																																			.	.	.	alt		0.562	FAM73B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054542.7	NM_032809	
ARRDC1	92714	hgsc.bcm.edu	37	9	140508149	140508149	+	Silent	SNP	C	C	G			TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr9:140508149C>G	ENST00000371421.4	+	4	427	c.363C>G	c.(361-363)tcC>tcG	p.S121S	C9orf37_ENST00000496793.1_5'Flank|ARRDC1_ENST00000491911.1_3'UTR	NM_152285.2	NP_689498.1	Q8N5I2	ARRD1_HUMAN	arrestin domain containing 1	121						cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(2)|lung(4)|prostate(1)|urinary_tract(1)	13	all_cancers(76;0.106)			OV - Ovarian serous cystadenocarcinoma(145;0.000273)|Epithelial(140;0.000464)		CACGGTTTTCCAAGGATCACA	0.572																																					p.S121S		Atlas-SNP	.											.	ARRDC1	24	.	0			c.C363G						PASS	.						189.0	162.0	171.0					9																	140508149		2203	4300	6503	SO:0001819	synonymous_variant	92714	exon4			GTTTTCCAAGGAT	AJ420420	CCDS7049.1	9q34.3	2013-10-11			ENSG00000197070	ENSG00000197070			28633	protein-coding gene	gene with protein product	"""alpha-arrestin 1"""					23886940	Standard	XM_005266119		Approved	MGC40555	uc004cns.3	Q8N5I2	OTTHUMG00000020993	ENST00000371421.4:c.363C>G	chr9.hg19:g.140508149C>G		103.0	0.0	.		76.0	25.0	.	NM_152285		Silent	SNP	ENST00000371421.4	hg19	CCDS7049.1																																																																																			.	.	.	none		0.572	ARRDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055358.1	NM_152285	
SNX19	399979	hgsc.bcm.edu	37	11	130781599	130781599	+	Missense_Mutation	SNP	C	C	T			TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr11:130781599C>T	ENST00000265909.4	-	2	2311	c.1742G>A	c.(1741-1743)cGt>cAt	p.R581H	SNX19_ENST00000528555.1_5'UTR|SNX19_ENST00000530356.1_5'UTR|SNX19_ENST00000545537.1_5'Flank|SNX19_ENST00000533214.1_Missense_Mutation_p.R581H|SNX19_ENST00000533318.1_5'UTR|SNX19_ENST00000539184.1_Missense_Mutation_p.R24H	NM_014758.2	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19	581	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(8)|ovary(3)|prostate(1)|skin(6)|urinary_tract(1)	35	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)		CCGATAGCGACGATTCACAGT	0.512																																					p.R581H		Atlas-SNP	.											.	SNX19	84	.	0			c.G1742A						PASS	.						111.0	107.0	108.0					11																	130781599		2201	4297	6498	SO:0001583	missense	399979	exon2			TAGCGACGATTCA	D87443	CCDS31721.1, CCDS73416.1	11q25	2010-04-20			ENSG00000120451	ENSG00000120451		"""Sorting nexins"""	21532	protein-coding gene	gene with protein product							Standard	NM_014758		Approved	KIAA0254, CHET8	uc001qgk.4	Q92543	OTTHUMG00000165663	ENST00000265909.4:c.1742G>A	chr11.hg19:g.130781599C>T	ENSP00000265909:p.Arg581His	35.0	0.0	.		46.0	14.0	.	NM_014758	E9PKB9|Q8IV55	Missense_Mutation	SNP	ENST00000265909.4	hg19	CCDS31721.1	.	.	.	.	.	.	.	.	.	.	C	35	5.437081	0.96168	.	.	ENSG00000120451	ENST00000265909;ENST00000539184;ENST00000533214	T;T;T	0.62364	0.03;0.03;0.03	5.53	5.53	0.82687	Phox homologous domain (5);	0.050680	0.85682	D	0.000000	D	0.82440	0.5037	M	0.85710	2.77	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;0.999;1.0	D	0.84878	0.0829	10	0.87932	D	0	-16.4214	19.466	0.94939	0.0:1.0:0.0:0.0	.	24;581;581	F5H5D1;E9PKB9;Q92543	.;.;SNX19_HUMAN	H	581;24;581	ENSP00000265909:R581H;ENSP00000443480:R24H;ENSP00000435390:R581H	ENSP00000265909:R581H	R	-	2	0	SNX19	130286809	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	7.372000	0.79612	2.607000	0.88179	0.655000	0.94253	CGT	.	.	.	none		0.512	SNX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385649.1	NM_014758	
KRAS	3845	hgsc.bcm.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	rs121913529		TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr12:25398284C>A	ENST00000256078.4	-	2	98	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000311936.3_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_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)																											p.G12V	Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	Atlas-SNP	.		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"""L, E, M, O"""	KRAS_ENST00000256078,NS,adenocarcinoma,0,66	KRAS	30930	.	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)	c.G35T						PASS	.						91.0	81.0	85.0					12																	25398284		2203	4300	6503	SO:0001583	missense	3845	exon2	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	ACGCCACCAGCTC	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	chr12.hg19:g.25398284C>A	ENSP00000256078:p.Gly12Val	142.0	0.0	.		128.0	46.0	.	NM_004985	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	hg19	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	.	.	.	weak		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360	
PKP2	5318	hgsc.bcm.edu	37	12	32949084	32949084	+	Silent	SNP	G	G	T	rs369837002		TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr12:32949084G>T	ENST00000070846.6	-	12	2472	c.2448C>A	c.(2446-2448)acC>acA	p.T816T	PKP2_ENST00000340811.4_Silent_p.T772T	NM_004572.3	NP_004563.2	Q99959	PKP2_HUMAN	plakophilin 2	816					adherens junction maintenance (GO:0034334)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential (GO:0086001)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cell-cell signaling involved in cardiac conduction (GO:0086019)|desmosome assembly (GO:0002159)|gap junction assembly (GO:0016264)|heart development (GO:0007507)|intermediate filament bundle assembly (GO:0045110)|lipid homeostasis (GO:0055088)|maintenance of organ identity (GO:0048496)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of tight junction assembly (GO:2000810)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	adherens junction (GO:0005912)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|protein kinase C binding (GO:0005080)|sodium channel regulator activity (GO:0017080)			NS(1)|breast(2)|endometrium(1)|kidney(9)|large_intestine(8)|lung(21)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	50	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					GGATGCCCCCGGTGTTTAGAA	0.498																																					p.T816T		Atlas-SNP	.											.	PKP2	110	.	0			c.C2448A						PASS	.						148.0	134.0	139.0					12																	32949084		2203	4300	6503	SO:0001819	synonymous_variant	5318	exon12			GCCCCCGGTGTTT	X97675	CCDS8731.1, CCDS31771.1	12p11	2014-09-17				ENSG00000057294		"""Armadillo repeat containing"""	9024	protein-coding gene	gene with protein product		602861				8922383	Standard	NM_001005242		Approved		uc001rlj.4	Q99959	OTTHUMG00000169500	ENST00000070846.6:c.2448C>A	chr12.hg19:g.32949084G>T		110.0	0.0	.		108.0	5.0	.	NM_004572	A0AV37|B8QFA1|B8QGS6|B8QGS7|D3DUW9|Q4VC01|Q99960	Silent	SNP	ENST00000070846.6	hg19	CCDS8731.1																																																																																			.	.	.	alt		0.498	PKP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404449.1	NM_004572	
PTPRR	5801	hgsc.bcm.edu	37	12	71155255	71155255	+	Missense_Mutation	SNP	G	G	A			TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr12:71155255G>A	ENST00000283228.2	-	4	1075	c.623C>T	c.(622-624)cCt>cTt	p.P208L	PTPRR_ENST00000342084.4_Missense_Mutation_p.P96L	NM_002849.3	NP_002840.2	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R	208					ERBB2 signaling pathway (GO:0038128)|in utero embryonic development (GO:0001701)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	41			GBM - Glioblastoma multiforme(2;5.67e-07)|Lung(24;0.00283)|OV - Ovarian serous cystadenocarcinoma(12;0.00578)|LUSC - Lung squamous cell carcinoma(43;0.132)	COAD - Colon adenocarcinoma(1;0.136)		ACATACCTCAGGAGAGACTTC	0.378																																					p.P208L		Atlas-SNP	.											.	PTPRR	109	.	0			c.C623T						PASS	.						126.0	129.0	128.0					12																	71155255		2203	4300	6503	SO:0001583	missense	5801	exon4			ACCTCAGGAGAGA	D64053	CCDS8998.1, CCDS44945.1, CCDS55847.1, CCDS55848.1	12q15	2011-10-07			ENSG00000153233	ENSG00000153233		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9680	protein-coding gene	gene with protein product		602853		PTPRQ		7557444, 10393441	Standard	NM_002849		Approved	PTPBR7, PTP-SL, EC-PTP, PCPTP1	uc001swi.2	Q15256	OTTHUMG00000169502	ENST00000283228.2:c.623C>T	chr12.hg19:g.71155255G>A	ENSP00000283228:p.Pro208Leu	65.0	0.0	.		68.0	25.0	.	NM_002849	B2R5Z7|B7Z3J1|F5GXR7|O00342|Q92682|Q9UE65	Missense_Mutation	SNP	ENST00000283228.2	hg19	CCDS8998.1	.	.	.	.	.	.	.	.	.	.	G	13.43	2.235084	0.39498	.	.	ENSG00000153233	ENST00000283228;ENST00000342084	T;T	0.32515	1.45;1.45	5.68	5.68	0.88126	.	0.127647	0.35466	U	0.003200	T	0.44664	0.1304	L	0.51422	1.61	0.80722	D	1	P;D	0.56521	0.617;0.976	B;P	0.52481	0.121;0.7	T	0.35351	-0.9792	10	0.87932	D	0	-6.8931	19.7965	0.96487	0.0:0.0:1.0:0.0	.	96;208	F5GXR7;Q15256	.;PTPRR_HUMAN	L	208;96	ENSP00000283228:P208L;ENSP00000339605:P96L	ENSP00000283228:P208L	P	-	2	0	PTPRR	69441522	1.000000	0.71417	1.000000	0.80357	0.144000	0.21451	7.920000	0.87521	2.686000	0.91538	0.448000	0.29417	CCT	.	.	.	none		0.378	PTPRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404485.1	NM_002849	
IGDCC3	9543	hgsc.bcm.edu	37	15	65621833	65621833	+	Silent	SNP	T	T	G	rs375413312		TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr15:65621833T>G	ENST00000327987.4	-	13	2351	c.2100A>C	c.(2098-2100)ggA>ggC	p.G700G	IGDCC3_ENST00000559231.1_5'Flank	NM_004884.3	NP_004875.2	Q8IVU1	IGDC3_HUMAN	immunoglobulin superfamily, DCC subclass, member 3	700					neuromuscular process controlling balance (GO:0050885)	integral component of plasma membrane (GO:0005887)				breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(9)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						GGCCCCGCTGTCCCCGTCTCG	0.647																																					p.G700G		Atlas-SNP	.											.	IGDCC3	82	.	0			c.A2100C						PASS	.	G		0,4394		0,0,2197	38.0	45.0	43.0		2100	-8.0	0.0	15		43	1,8579		0,1,4289	no	coding-synonymous	IGDCC3	NM_004884.3		0,1,6486	GG,GT,TT		0.0117,0.0,0.0077		700/815	65621833	1,12973	2197	4290	6487	SO:0001819	synonymous_variant	9543	exon13			CCGCTGTCCCCGT	AF063936	CCDS10205.1	15q22.3-q23	2013-02-11	2009-01-08	2009-01-08	ENSG00000174498	ENSG00000174498		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9700	protein-coding gene	gene with protein product		604184	"""putative neuronal cell adhesion molecule"""	PUNC		9922388	Standard	NM_004884		Approved	HsT18880	uc002aos.2	Q8IVU1	OTTHUMG00000133137	ENST00000327987.4:c.2100A>C	chr15.hg19:g.65621833T>G		87.0	0.0	.		48.0	18.0	.	NM_004884	O95215	Silent	SNP	ENST00000327987.4	hg19	CCDS10205.1																																																																																			.	.	.	weak		0.647	IGDCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256826.1	NM_004884	
CDH8	1006	hgsc.bcm.edu	37	16	61687964	61687964	+	Nonsense_Mutation	SNP	C	C	A			TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr16:61687964C>A	ENST00000577390.1	-	12	2902	c.1948G>T	c.(1948-1950)Gaa>Taa	p.E650*	CDH8_ENST00000299345.6_Nonsense_Mutation_p.E650*|CDH8_ENST00000577730.1_Nonsense_Mutation_p.E650*	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	650					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|response to cold (GO:0009409)|synaptic transmission, glutamatergic (GO:0035249)	axon terminus (GO:0043679)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(22)|liver(2)|lung(49)|ovary(6)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(4)	112		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		ATTAATGGTTCATTTTTATGC	0.398																																					p.E650X		Atlas-SNP	.											.	CDH8	273	.	0			c.G1948T						PASS	.						72.0	71.0	71.0					16																	61687964		2203	4300	6503	SO:0001587	stop_gained	1006	exon12			ATGGTTCATTTTT	L34060	CCDS10802.1	16q22.1	2010-01-26			ENSG00000150394	ENSG00000150394		"""Cadherins / Major cadherins"""	1767	protein-coding gene	gene with protein product		603008				9615235, 2059658	Standard	NM_001796		Approved		uc002eog.2	P55286	OTTHUMG00000137493	ENST00000577390.1:c.1948G>T	chr16.hg19:g.61687964C>A	ENSP00000462701:p.Glu650*	104.0	0.0	.		149.0	12.0	.	NM_001796	B3KWC1|Q14DC6|Q9ULB2	Nonsense_Mutation	SNP	ENST00000577390.1	hg19	CCDS10802.1	.	.	.	.	.	.	.	.	.	.	C	47	13.421152	0.99741	.	.	ENSG00000150394	ENST00000299345	.	.	.	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.8311	0.92139	0.0:1.0:0.0:0.0	.	.	.	.	X	650	.	ENSP00000299345:E650X	E	-	1	0	CDH8	60245465	1.000000	0.71417	0.851000	0.33527	0.702000	0.40608	7.770000	0.85390	2.679000	0.91253	0.655000	0.94253	GAA	.	.	.	none		0.398	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796	
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274266	39274266	+	Missense_Mutation	SNP	C	C	T			TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr17:39274266C>T	ENST00000391413.2	-	1	340	c.302G>A	c.(301-303)cGc>cAc	p.R101H		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	101	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament (GO:0045095)				endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			gcatctggggcggcagcaAGT	0.647																																					p.R101H		Atlas-SNP	.											.	KRTAP4-11	94	.	0			c.G302A						PASS	.						5.0	9.0	8.0					17																	39274266		655	1560	2215	SO:0001583	missense	653240	exon1			CTGGGGCGGCAGC	AC025904	CCDS45675.1	17q21.2	2013-06-25			ENSG00000212721	ENSG00000212721		"""Keratin associated proteins"""	18911	protein-coding gene	gene with protein product			"""keratin associated protein 4-14"""	KRTAP4-14			Standard	NM_033059		Approved	KAP4.11, KAP4.14	uc002hvz.3	Q9BYQ6	OTTHUMG00000133586	ENST00000391413.2:c.302G>A	chr17.hg19:g.39274266C>T	ENSP00000375232:p.Arg101His	40.0	0.0	.		40.0	5.0	.	NM_033059	A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	hg19	CCDS45675.1	.	.	.	.	.	.	.	.	.	.	.	10.07	1.249110	0.22880	.	.	ENSG00000212721	ENST00000391413	T	0.00638	6.04	3.99	1.96	0.26148	.	1.399950	0.05646	U	0.584357	T	0.01189	0.0039	M	0.78456	2.415	0.09310	N	1	B	0.15473	0.013	B	0.08055	0.003	T	0.50550	-0.8815	10	0.42905	T	0.14	.	3.6707	0.08273	0.1929:0.5877:0.0:0.2193	.	101	Q9BYQ6	KR411_HUMAN	H	101	ENSP00000375232:R101H	ENSP00000375232:R101H	R	-	2	0	KRTAP4-11	36527792	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.701000	0.05075	0.180000	0.19960	-0.192000	0.12808	CGC	.	.	.	none		0.647	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1		
ZNF536	9745	hgsc.bcm.edu	37	19	30935837	30935837	+	Silent	SNP	C	C	T			TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr19:30935837C>T	ENST00000355537.3	+	2	1515	c.1368C>T	c.(1366-1368)ggC>ggT	p.G456G		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	456					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)	p.G456G(1)		NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					ATGGCAAGGGCGAGCTGCCCA	0.647																																					p.G456G		Atlas-SNP	.											ZNF536,colon,carcinoma,0,1	ZNF536	424	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1368T						PASS	.						28.0	30.0	29.0					19																	30935837		2199	4298	6497	SO:0001819	synonymous_variant	9745	exon2			CAAGGGCGAGCTG		CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"""Zinc fingers, C2H2-type"""	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.1368C>T	chr19.hg19:g.30935837C>T		158.0	0.0	.		87.0	13.0	.	NM_014717	A2RU18	Silent	SNP	ENST00000355537.3	hg19	CCDS32984.1																																																																																			.	.	.	none		0.647	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717	
MT-ND4	4538	hgsc.bcm.edu	37	M	11484	11484	+	Missense_Mutation	SNP	G	G	A			TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chrM:11484G>A	ENST00000361381.2	+	1	725	c.725G>A	c.(724-726)gGt>gAt	p.G242D	MT-TG_ENST00000387429.1_RNA|MT-TH_ENST00000387441.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-ND5_ENST00000361567.2_5'Flank			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	242					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						AGGCGGCTATGGTATAATACG	0.468																																					p.G242D		Atlas-SNP	.											.	.	.	.	0			c.G725A						PASS	.																																			SO:0001583	missense	0	exon1			GCTATGGTATAAT			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.725G>A	chrM.hg19:g.11484G>A	ENSP00000354961:p.Gly242Asp	10.0	0.0	.		277.0	275.0	.	ENST00000361381	Q6RL39|Q6RQN9|Q8HNR8	Missense_Mutation	SNP	ENST00000361381.2	hg19																																																																																				.	.	.	none		0.468	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024035	
MT-CYB	4519	hgsc.bcm.edu	37	M	15135	15135	+	Missense_Mutation	SNP	G	G	A			TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chrM:15135G>A	ENST00000361789.2	+	1	389	c.389G>A	c.(388-390)gGc>gAc	p.G130D	MT-TP_ENST00000387461.2_RNA|MT-TH_ENST00000387441.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-ND6_ENST00000361681.2_5'Flank|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA			P00156	CYB_HUMAN	mitochondrially encoded cytochrome b	130					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(6)|endometrium(25)|kidney(33)|prostate(1)	65						AGCCTTCATAGGCTATGTCCT	0.463											OREG0007583	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.G130D		Atlas-SNP	.											.	.	.	.	0			c.G389A						PASS	.																																			SO:0001583	missense	0	exon1			TCATAGGCTATGT			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198727	ENSG00000198727		"""Cytochrome b genes"", ""Mitochondrial respiratory chain complex / Complex III"""	7427	protein-coding gene	gene with protein product		516020	"""cytochrome b"""	MTCYB			Standard			Approved	COB, CYTB, UQCR3		P00156		ENST00000361789.2:c.389G>A	chrM.hg19:g.15135G>A	ENSP00000354554:p.Gly130Asp	8.0	0.0	.	585	324.0	33.0	.	ENST00000361789	Q34786|Q8HBR6|Q8HNQ0|Q8HNQ1|Q8HNQ9|Q8HNR4|Q8HNR7|Q8W7V8|Q8WCV9|Q8WCY2|Q8WCY7|Q8WCY8|Q9B1A6|Q9B1B6|Q9B1B8|Q9B1D4|Q9B1X6|Q9B2V0|Q9B2V8|Q9B2W0|Q9B2W3|Q9B2W8|Q9B2X1|Q9B2X7|Q9B2X9|Q9B2Y3|Q9B2Z0|Q9B2Z4|Q9T6H6|Q9T9Y0|Q9TEH4	Missense_Mutation	SNP	ENST00000361789.2	hg19																																																																																				.	.	.	none		0.463	MT-CYB-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024038	
HSPH1	10808	hgsc.bcm.edu	37	13	31722181	31722181	+	Frame_Shift_Del	DEL	A	A	-			TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr13:31722181delA	ENST00000320027.5	-	10	1637	c.1293delT	c.(1291-1293)gttfs	p.V431fs	HSPH1_ENST00000429785.2_Frame_Shift_Del_p.V250fs|HSPH1_ENST00000380406.5_Frame_Shift_Del_p.V390fs|HSPH1_ENST00000445273.2_Frame_Shift_Del_p.V433fs|HSPH1_ENST00000380405.4_Frame_Shift_Del_p.V431fs	NM_006644.2	NP_006635.2	Q92598	HS105_HUMAN	heat shock 105kDa/110kDa protein 1	431					chaperone mediated protein folding requiring cofactor (GO:0051085)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of NK T cell activation (GO:0051135)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	27		Lung SC(185;0.0257)		all cancers(112;0.00385)|Epithelial(112;0.0328)|OV - Ovarian serous cystadenocarcinoma(117;0.0375)|GBM - Glioblastoma multiforme(144;0.125)		GAAAGGTGAGAACTTTGGAGA	0.403																																					p.L432fs		Atlas-Indel,Pindel	.											.	HSPH1	65	.	0			c.1294delC						PASS	.						133.0	149.0	144.0					13																	31722181		2203	4300	6503	SO:0001589	frameshift_variant	10808	exon10			.	AB003333	CCDS9340.1, CCDS66525.1, CCDS73559.1	13q12.2-q13.3	2011-09-02			ENSG00000120694	ENSG00000120694		"""Heat shock proteins / HSP70"""	16969	protein-coding gene	gene with protein product		610703				9610721, 9931472	Standard	XM_005266236		Approved	HSP105B, KIAA0201, HSP105A, NY-CO-25	uc001utj.3	Q92598	OTTHUMG00000016685	ENST00000320027.5:c.1293delT	chr13.hg19:g.31722181delA	ENSP00000318687:p.Val431fs	131.0	0.0	0		164.0	27.0	0.164634	NM_006644	B4DYH1|O95739|Q5TBM6|Q5TBM7|Q5TBM8|Q9UPC4	Frame_Shift_Del	DEL	ENST00000320027.5	hg19	CCDS9340.1																																																																																			.	.	.	none		0.403	HSPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044384.1		
DNAJA3	9093	hgsc.bcm.edu	37	16	4498749	4498752	+	Frame_Shift_Del	DEL	CAGA	CAGA	-	rs368706161		TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	CAGA	CAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr16:4498749_4498752delCAGA	ENST00000262375.6	+	9	1218_1221	c.1141_1144delCAGA	c.(1141-1146)cagacafs	p.QT381fs	DNAJA3_ENST00000431375.2_Frame_Shift_Del_p.QT228fs|DNAJA3_ENST00000355296.4_Frame_Shift_Del_p.QT381fs	NM_005147.5	NP_005138.3	Q96EY1	DNJA3_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 3	381					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation-induced cell death of T cells (GO:0006924)|cell aging (GO:0007569)|mitochondrial DNA replication (GO:0006264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of programmed cell death (GO:0043069)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T cell proliferation (GO:0042102)|protein folding (GO:0006457)|protein stabilization (GO:0050821)|response to heat (GO:0009408)|response to interferon-gamma (GO:0034341)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|small GTPase mediated signal transduction (GO:0007264)|T cell differentiation in thymus (GO:0033077)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of plasma membrane (GO:0019897)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|interferon-gamma receptor binding (GO:0005133)|metal ion binding (GO:0046872)|NF-kappaB binding (GO:0051059)|protein kinase binding (GO:0019901)|small GTPase regulator activity (GO:0005083)|transcription factor binding (GO:0008134)			NS(1)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|upper_aerodigestive_tract(2)	15						CCCTGGGACTCAGACAGACCAGAA	0.461																																					p.380_381del		Atlas-Indel,Pindel	.											.	DNAJA3	52	.	0			c.1140_1143del						PASS	.																																			SO:0001589	frameshift_variant	9093	exon9			.	AF061749	CCDS10515.1, CCDS45400.1, CCDS66930.1	16p13.3	2011-09-02			ENSG00000103423	ENSG00000103423		"""Heat shock proteins / DNAJ (HSP40)"""	11808	protein-coding gene	gene with protein product		608382		TID1		9683573	Standard	NM_005147		Approved	hTid-1	uc002cwk.3	Q96EY1	OTTHUMG00000129470	ENST00000262375.6:c.1141_1144delCAGA	chr16.hg19:g.4498753_4498756delCAGA	ENSP00000262375:p.Gln381fs	96.0	0.0	0		72.0	13.0	0.180556	NM_001135110	B2RAJ5|B4DI33|E7ES32|O75472|Q8WUJ6|Q8WXJ3|Q96D76|Q96IV1|Q9NYH8	Frame_Shift_Del	DEL	ENST00000262375.6	hg19	CCDS10515.1																																																																																			.	.	.	none		0.461	DNAJA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251633.1		
RIMBP3B	440804	hgsc.bcm.edu	37	22	21741340	21741341	+	In_Frame_Ins	INS	-	-	TGCAGG	rs555102406	byFrequency	TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr22:21741340_21741341insTGCAGG	ENST00000434111.1	+	1	3678_3679	c.3193_3194insTGCAGG	c.(3193-3195)ctg>cTGCAGGtg	p.1067_1068insQV	SCARNA17_ENST00000516211.1_RNA|RN7SKP63_ENST00000363187.1_RNA|SCARNA18_ENST00000516505.1_RNA	NM_001128635.1	NP_001122107.1	A6NNM3	RIM3B_HUMAN	RIMS binding protein 3B	1067	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.																ATGGGACTTGCTGCAGGTGTAT	0.663																																					p.L1065delinsLQV		Pindel	.											.	RIMBP3C	6	.	0			c.3193_3194insTGCAGG						PASS	.			6,24		3,0,12						-2.0	0.0			1	7,131		3,1,65	no	coding	RIMBP3B	NM_001128635.1		6,1,77	A1A1,A1R,RR		5.0725,20.0,7.7381				13,155				SO:0001652	inframe_insertion	150221	exon1			.		CCDS46668.1	22q11.21	2008-10-23			ENSG00000196934	ENSG00000274600			33891	protein-coding gene	gene with protein product		612700				17855024	Standard	NM_001128635		Approved			A6NNM3	OTTHUMG00000150819	ENST00000434111.1:c.3194_3199dupTGCAGG	chr22.hg19:g.21741341_21741346dupTGCAGG	ENSP00000407925:p.Gln1066_Val1067dup	22.0	0.0	.		16.0	16.0	1.000	NM_001128633		In_Frame_Ins	INS	ENST00000434111.1	hg19	CCDS46668.1																																																																																			.	.	.	none		0.663	RIMBP3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320196.2	XM_036936	
CFC1	55997	hgsc.bcm.edu	37	2	131355536	131355543	+	Frame_Shift_Del	DEL	GCGCGGCC	GCGCGGCC	-			TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	GCGCGGCC	GCGCGGCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr2:131355536_131355543delGCGCGGCC	ENST00000259216.4	-	4	522_529	c.260_267delGGCCGCGC	c.(259-267)cggccgcgcfs	p.RPR87fs		NM_032545.3	NP_115934.1	P0CG37	CFC1_HUMAN	cripto, FRL-1, cryptic family 1	87	EGF-like. {ECO:0000255|PROSITE- ProRule:PRU00076}.				determination of left/right symmetry (GO:0007368)|gastrulation (GO:0007369)|nodal signaling pathway (GO:0038092)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)	nodal binding (GO:0038100)			endometrium(1)|lung(4)	5	Colorectal(110;0.1)					TCCTGCAGCAGCGCGGCCGCGCGGACGC	0.779																																					p.87_90del		Pindel	.											.	.	.	.	0			c.261_268del						PASS	.																																			SO:0001589	frameshift_variant	653275	exon4			.	AF312769	CCDS2162.1, CCDS74573.1, CCDS74574.1	2q21.2	2014-02-04			ENSG00000136698	ENSG00000136698			18292	protein-coding gene	gene with protein product		605194	"""heterotaxy 2 (autosomal dominant)"""	HTX2		11062482, 10858660	Standard	NM_032545		Approved	CRYPTIC, HTX2	uc002tro.2	P0CG37	OTTHUMG00000131628	ENST00000259216.4:c.260_267delGGCCGCGC	chr2.hg19:g.131355536_131355543delGCGCGGCC	ENSP00000259216:p.Arg87fs	389.0	0.0	.		262.0	35.0	0.134	NM_001079530	B2RCY0|B9EJD3|Q53T05|Q9GZR3	Frame_Shift_Del	DEL	ENST00000259216.4	hg19	CCDS2162.1																																																																																			.	.	.	none		0.779	CFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333367.1	NM_032545	
CFC1B	653275	hgsc.bcm.edu	37	2	131280369	131280376	+	Frame_Shift_Del	DEL	CCGCGCGG	CCGCGCGG	-			TCGA-2Z-A9JN-01A-21D-A42J-10	TCGA-2Z-A9JN-10A-01D-A42M-10	CCGCGCGG	CCGCGCGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	050ee89a-518f-41ea-942d-90fbd6889673	fb9e10b8-d6e8-48d5-a356-cd64dd61c5b4	g.chr2:131280369_131280376delCCGCGCGG	ENST00000281882.3	+	4	542_549	c.254_261delCCGCGCGG	c.(253-261)tccgcgcggfs	p.SAR85fs	AC013269.3_ENST00000450486.1_RNA	NM_001079530.1	NP_001072998.1	P0CG36	CFC1B_HUMAN	cripto, FRL-1, cryptic family 1B	85					gastrulation (GO:0007369)	extracellular region (GO:0005576)						Colorectal(110;0.1)					GCAGGTGCGTCCGCGCGGCCGCGCTGCT	0.774																																					p.85_87del		Pindel	.											.	.	.	.	0			c.253_260del						PASS	.																																			SO:0001589	frameshift_variant	653275	exon4			.		CCDS33286.1	2q21.1	2008-09-04			ENSG00000152093	ENSG00000152093			33983	protein-coding gene	gene with protein product							Standard	NM_001079530		Approved		uc002trl.2	P0CG36	OTTHUMG00000153959	ENST00000281882.3:c.254_261delCCGCGCGG	chr2.hg19:g.131280369_131280376delCCGCGCGG	ENSP00000281882:p.Ser85fs	425.0	0.0	.		219.0	57.0	0.260	NM_001079530	B2RCY0|B9EJD3|Q53T05|Q9GZR3	Frame_Shift_Del	DEL	ENST00000281882.3	hg19	CCDS33286.1																																																																																			.	.	.	none		0.774	CFC1B-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254521.1	NM_001079530	
