#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_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_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_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_match_norm_validation_allele1	i_refseq_mrna_id	i_secondary_variant_classification
ABLIM1	3983	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	116201492	116201492	+	Missense_Mutation	SNP	C	C	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr10:116201492C>A	ENST00000277895.5	-	18	2084	c.1987G>T	c.(1987-1989)Ggg>Tgg	p.G663W	ABLIM1_ENST00000392952.3_Missense_Mutation_p.G340W|ABLIM1_ENST00000369253.2_Missense_Mutation_p.G286W|ABLIM1_ENST00000533213.2_Missense_Mutation_p.G603W|ABLIM1_ENST00000369266.3_Missense_Mutation_p.G340W|ABLIM1_ENST00000369252.4_Missense_Mutation_p.G603W	NM_002313.5	NP_002304.3	O14639	ABLM1_HUMAN	actin binding LIM protein 1	663					axon guidance (GO:0007411)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|visual perception (GO:0007601)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)	p.G340W(1)|p.G663W(1)|p.G603W(1)		breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	30		Colorectal(252;0.0373)|Breast(234;0.231)		Epithelial(162;0.0132)|all cancers(201;0.0383)		CGGTGAAGCCCATTTCTTCCA	0.428																																																	3	Substitution - Missense(3)	kidney(3)											148.0	140.0	143.0					10																	116201492		2203	4300	6503	SO:0001583	missense	3983			AF005654	CCDS7590.1, CCDS31289.1	10q25	2008-07-07		2002-09-13	ENSG00000099204	ENSG00000099204			78	protein-coding gene	gene with protein product		602330		LIMAB1, ABLIM		9245787	Standard	NM_002313		Approved	abLIM, limatin	uc021pyw.1	O14639	OTTHUMG00000019088	ENST00000277895.5:c.1987G>T	10.37:g.116201492C>A	ENSP00000277895:p.Gly663Trp	Somatic		WXS	Illumina HiSeq	Phase_I	A6NI16|A6NJ06|A8MXA9|B3KVH2|Q15039|Q5JVV1|Q5JVV2|Q5T6N2|Q5T6N3|Q5T6N5|Q68CQ9|Q9BUP1	Missense_Mutation	SNP	ENST00000277895.5	37	CCDS7590.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	29.2|29.2	4.985234|4.985234	0.93044|0.93044	.|.	.|.	ENSG00000099204|ENSG00000099204	ENST00000336585;ENST00000369252;ENST00000392952;ENST00000369257;ENST00000369267;ENST00000533213;ENST00000369262;ENST00000369263;ENST00000369266;ENST00000369256;ENST00000369260;ENST00000277895;ENST00000369253|ENST00000392955	T;T;T;T|.	0.40476|.	1.03;1.03;1.03;1.03|.	5.93|5.93	5.93|5.93	0.95920|0.95920	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.79885|0.79885	0.4523|0.4523	M|M	0.82323|0.82323	2.585|2.585	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;0.999;1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D;D;D;D;D|.	0.97110|.	0.999;0.999;0.999;0.972;0.997;1.0;0.999;0.998;1.0|.	T|T	0.79960|0.79960	-0.1583|-0.1583	10|5	0.56958|.	D|.	0.05|.	.|.	18.5344|18.5344	0.91004|0.91004	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	540;265;603;631;663;340;633;587;286|.	B7Z4H1;B4DQA3;F8W8M4;A6NKJ2;O14639;O14639-5;B3KVH2;C9K0X4;O14639-4|.	.;.;.;.;ABLM1_HUMAN;.;.;.;.|.	W|I	663;603;340;286;631;603;731;587;340;587;540;731;415|536	ENSP00000358256:G603W;ENSP00000376679:G340W;ENSP00000433629:G603W;ENSP00000358270:G340W|.	ENSP00000277895:G731W|.	G|M	-|-	1|3	0|0	ABLIM1|ABLIM1	116191482|116191482	1.000000|1.000000	0.71417|0.71417	0.986000|0.986000	0.45419|0.45419	0.997000|0.997000	0.91878|0.91878	7.431000|7.431000	0.80335|0.80335	2.826000|2.826000	0.97356|0.97356	0.655000|0.655000	0.94253|0.94253	GGG|ATG		0.428	ABLIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050469.3			
AHNAK2	113146	hgsc.bcm.edu	37	14	105415541	105415541	+	Missense_Mutation	SNP	T	T	C	rs150617757	byFrequency	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr14:105415541T>C	ENST00000333244.5	-	7	6366	c.6247A>G	c.(6247-6249)Aaa>Gaa	p.K2083E	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2083						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)			AGGTCCACTTTGGGCATCTTC	0.607													.|||	307	0.0613019	0.2156	0.0245	5008	,	,		14091	0.001		0.004	False		,,,				2504	0.0																0								T	GLU/LYS	753,2871		103,547,1162	121.0	82.0	97.0		6247	3.1	0.4	14	dbSNP_134	97	46,6190		8,30,3080	no	missense	AHNAK2	NM_138420.2	56	111,577,4242	CC,CT,TT		0.7377,20.7781,8.1034	probably-damaging	2083/5796	105415541	799,9061	1812	3118	4930	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.6247A>G	14.37:g.105415541T>C	ENSP00000353114:p.Lys2083Glu	Somatic		WXS	Illumina HiSeq	Phase_I	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	153	0.07005494505494506	138	0.2804878048780488	14	0.03867403314917127	0	0.0	1	0.0013192612137203166	-	15.14	2.745792	0.49151	0.207781	0.007377	ENSG00000185567	ENST00000333244	T	0.01838	4.61	4.37	3.13	0.36017	.	.	.	.	.	T	0.00012	0.0000	M	0.74389	2.26	0.47341	P	6.019999999999914E-4	D	0.71674	0.998	D	0.87578	0.998	T	0.33777	-0.9855	8	0.06625	T	0.88	-16.9137	12.0851	0.53691	0.0:0.0:0.1544:0.8456	.	2083	Q8IVF2	AHNK2_HUMAN	E	2083	ENSP00000353114:K2083E	ENSP00000353114:K2083E	K	-	1	0	AHNAK2	104486586	0.002000	0.14202	0.425000	0.26659	0.020000	0.10135	0.128000	0.15810	1.623000	0.50342	0.397000	0.26171	AAA		0.607	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1		NM_138420	
AIRE	326	hgsc.bcm.edu	37	21	45711063	45711075	+	Frame_Shift_Del	DEL	GCCTGTCCCCTCC	GCCTGTCCCCTCC	-	rs386833675|rs179363885		TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	GCCTGTCCCCTCC	GCCTGTCCCCTCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr21:45711063_45711075delGCCTGTCCCCTCC	ENST00000291582.5	+	8	1092_1104	c.965_977delGCCTGTCCCCTCC	c.(964-978)tgcctgtcccctccgfs	p.CLSPP322fs	AIRE_ENST00000355347.4_Frame_Shift_Del_p.CLSPP115fs|AIRE_ENST00000329347.4_Frame_Shift_Del_p.CLSPP115fs	NM_000383.3	NP_000374.1	O43918	AIRE_HUMAN	autoimmune regulator	322					humoral immune response (GO:0006959)|immune response (GO:0006955)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|transcription regulatory region DNA binding (GO:0044212)|translation regulator activity (GO:0045182)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|skin(2)|urinary_tract(1)	14				Colorectal(79;0.0806)		CACCTGGCCTGCCTGTCCCCTCCGCTCCGGGAG	0.681									Autoimmune PolyEndocrinopathy Candidiasis Ectodermal Dystrophy																																								0			GRCh37	CD971970|CI972523|CM001056|CM014030	AIRE	D|I|M	rs179363885		,	0,4264		0,0,2132					,	3.6	1.0			40	12,8236		0,12,4112	no	frameshift,frameshift	AIRE	NM_000658.2,NM_000383.2	,	0,12,6244	A1A1,A1R,RR		0.1455,0.0,0.0959	,	,		12,12500				SO:0001589	frameshift_variant	326	Familial Cancer Database	APECED	AB006684	CCDS13706.1	21q22.3	2014-09-17	2007-06-20		ENSG00000160224	ENSG00000160224		"""Zinc fingers, PHD-type"""	360	protein-coding gene	gene with protein product	"""autoimmune polyendocrinopathy candidiasis ectodermal dystrophy"""	607358	"""autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy)"""	APECED		9398840	Standard	NM_000383		Approved	PGA1, APS1	uc002zei.3	O43918	OTTHUMG00000086921	ENST00000291582.5:c.965_977delGCCTGTCCCCTCC	21.37:g.45711063_45711075delGCCTGTCCCCTCC	ENSP00000291582:p.Cys322fs	Somatic		WXS	Illumina HiSeq	Phase_I	B2RP50|O43922|O43932|O75745	Frame_Shift_Del	DEL	ENST00000291582.5	37	CCDS13706.1																																																																																				0.681	AIRE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195842.2			
SLC35G3	146861	broad.mit.edu;hgsc.bcm.edu	37	17	33520557	33520557	+	Missense_Mutation	SNP	C	C	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr17:33520557C>T	ENST00000297307.5	-	1	855	c.770G>A	c.(769-771)gGg>gAg	p.G257E	RP11-799D4.2_ENST00000590144.1_RNA	NM_152462.2	NP_689675.1	Q8N808	S35G3_HUMAN	solute carrier family 35, member G3	257						integral component of membrane (GO:0016021)		p.G257E(1)									CCCCACTGCCCCCACACAACT	0.627																																																	1	Substitution - Missense(1)	kidney(1)											105.0	98.0	100.0					17																	33520557		2203	4297	6500	SO:0001583	missense	0			AK097473	CCDS11293.1	17q21.1	2013-05-22	2011-08-03	2011-08-03	ENSG00000164729	ENSG00000164729		"""Solute carriers"""	26848	protein-coding gene	gene with protein product			"""transmembrane protein 21A"", ""acyl-malonyl condensing enzyme 1"""	TMEM21A, AMAC1			Standard	NM_152462		Approved	FLJ40154	uc002hjd.2	Q8N808	OTTHUMG00000132929	ENST00000297307.5:c.770G>A	17.37:g.33520557C>T	ENSP00000297307:p.Gly257Glu	Somatic		WXS	Illumina HiSeq	Phase_I	B9EGE9	Missense_Mutation	SNP	ENST00000297307.5	37	CCDS11293.1	.	.	.	.	.	.	.	.	.	.	C	7.208	0.594862	0.13875	.	.	ENSG00000164729	ENST00000297307	T	0.52295	0.67	.	.	.	.	0.628981	0.13032	N	0.419232	T	0.34193	0.0889	L	0.36672	1.1	0.27336	N	0.956641	B	0.27910	0.193	B	0.30029	0.11	T	0.29212	-1.0019	9	0.54805	T	0.06	-0.3551	5.844	0.18652	0.0:0.9991:0.0:9.0E-4	.	257	Q8N808	S35G3_HUMAN	E	257	ENSP00000297307:G257E	ENSP00000297307:G257E	G	-	2	0	SLC35G3	30544670	0.000000	0.05858	0.307000	0.25127	0.308000	0.27856	0.174000	0.16743	0.064000	0.16427	0.064000	0.15345	GGG		0.627	SLC35G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256445.2		NM_152462	
ANO6	196527	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	45810629	45810629	+	Missense_Mutation	SNP	A	A	G			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr12:45810629A>G	ENST00000320560.8	+	17	2361	c.2159A>G	c.(2158-2160)gAc>gGc	p.D720G	ANO6_ENST00000435642.1_Missense_Mutation_p.D720G|ANO6_ENST00000426898.2_3'UTR|ANO6_ENST00000441606.2_Missense_Mutation_p.D702G|ANO6_ENST00000423947.3_Missense_Mutation_p.D741G|ANO6_ENST00000425752.2_Missense_Mutation_p.D720G	NM_001025356.2	NP_001020527.2	Q4KMQ2	ANO6_HUMAN	anoctamin 6	720					activation of blood coagulation via clotting cascade (GO:0002543)|blood coagulation (GO:0007596)|bone mineralization involved in bone maturation (GO:0035630)|calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|dendritic cell chemotaxis (GO:0002407)|ion transmembrane transport (GO:0034220)|phosphatidylserine exposure on blood platelet (GO:0097045)|phospholipid scrambling (GO:0017121)|positive regulation of endothelial cell apoptotic process (GO:2000353)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)|voltage-gated chloride channel activity (GO:0005247)|voltage-gated ion channel activity (GO:0005244)	p.D720G(2)		central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						AAAGCCCAAGACATTGGAGCA	0.478																																																	2	Substitution - Missense(2)	kidney(2)											91.0	80.0	84.0					12																	45810629		2203	4300	6503	SO:0001583	missense	196527			AL832340	CCDS31782.1, CCDS44865.1, CCDS44866.1, CCDS55819.1	12q12-q13.11	2014-09-17	2008-08-28	2008-08-28				"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	25240	protein-coding gene	gene with protein product		608663	"""transmembrane protein 16F"""	TMEM16F		15067359, 24692353	Standard	NM_001025356		Approved	DKFZp313M0720	uc010slf.2	Q4KMQ2	OTTHUMG00000169564	ENST00000320560.8:c.2159A>G	12.37:g.45810629A>G	ENSP00000320087:p.Asp720Gly	Somatic		WXS	Illumina HiSeq	Phase_I	A6NNM6|B9EGG0|E7ENK4|E9PB30|E9PCT2|Q8N3Q2	Missense_Mutation	SNP	ENST00000320560.8	37	CCDS31782.1	.	.	.	.	.	.	.	.	.	.	A	15.17	2.753325	0.49362	.	.	ENSG00000177119	ENST00000425752;ENST00000423947;ENST00000435642;ENST00000320560;ENST00000441606	T;T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14;-0.14	5.72	4.56	0.56223	.	0.000000	0.85682	D	0.000000	T	0.60971	0.2310	M	0.69248	2.105	0.58432	D	0.999994	B;B;B;P	0.35155	0.009;0.02;0.033;0.487	B;B;B;B	0.38985	0.02;0.06;0.033;0.287	T	0.61831	-0.6982	10	0.38643	T	0.18	.	10.6319	0.45541	0.8748:0.0:0.1252:0.0	.	702;741;720;720	E9PB30;B9EGG0;E9PCT2;Q4KMQ2	.;.;.;ANO6_HUMAN	G	720;741;720;720;702	ENSP00000391417:D720G;ENSP00000409126:D741G;ENSP00000413840:D720G;ENSP00000320087:D720G;ENSP00000413137:D702G	ENSP00000320087:D720G	D	+	2	0	ANO6	44096896	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	4.539000	0.60657	2.320000	0.78422	0.528000	0.53228	GAC		0.478	ANO6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404822.1		XM_113743	
ASH1L	55870	broad.mit.edu;hgsc.bcm.edu	37	1	155491017	155491017	+	Silent	SNP	T	T	C			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr1:155491017T>C	ENST00000368346.3	-	2	933	c.294A>G	c.(292-294)aaA>aaG	p.K98K	ASH1L_ENST00000548830.1_Silent_p.K98K|ASH1L_ENST00000392403.3_Silent_p.K98K			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	98					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)	p.K98K(1)		autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			TCTTTGGAGGTTTTTTAGTTC	0.373																																																	1	Substitution - coding silent(1)	kidney(1)											166.0	170.0	168.0					1																	155491017		2202	4300	6502	SO:0001819	synonymous_variant	55870			AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.294A>G	1.37:g.155491017T>C		Somatic		WXS	Illumina HiSeq	Phase_I	Q59GP1|Q5T714|Q5T715|Q9P2C7	Silent	SNP	ENST00000368346.3	37																																																																																					0.373	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1		NM_018489	
ATP12A	479	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	25272913	25272913	+	Missense_Mutation	SNP	C	C	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr13:25272913C>T	ENST00000381946.3	+	12	1797	c.1630C>T	c.(1630-1632)Cca>Tca	p.P544S	ATP12A_ENST00000218548.6_Missense_Mutation_p.P550S			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	544					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)	p.P544S(1)		breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		CGAGGAGCACCCACTGGACAA	0.637																																					Pancreas(156;1582 1935 18898 22665 26498)												1	Substitution - Missense(1)	kidney(1)											131.0	121.0	124.0					13																	25272913		2203	4300	6503	SO:0001583	missense	479			L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"""ATPases / P-type"""	13816	protein-coding gene	gene with protein product	"""ATPase, Na+K+ transporting, alpha-1 polypeptide-like"", ""potassium-transporting ATPase alpha chain 2"", ""proton pump"", ""non-gastric H(+)/K(+) ATPase alpha subunit"", ""sodium/potassium ATPase, alpha polypeptide-like"""	182360	"""ATPase, Na+/K+ transporting, alpha polypeptide-like 1"""	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.1630C>T	13.37:g.25272913C>T	ENSP00000371372:p.Pro544Ser	Somatic		WXS	Illumina HiSeq	Phase_I	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Missense_Mutation	SNP	ENST00000381946.3	37	CCDS31948.1	.	.	.	.	.	.	.	.	.	.	C	14.48	2.548984	0.45383	.	.	ENSG00000075673	ENST00000218548;ENST00000381946	T;T	0.81163	-1.46;-1.46	6.08	3.44	0.39384	ATPase, cation-transporting, domain N (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.070980	0.64402	D	0.000014	T	0.80675	0.4668	L	0.47190	1.495	0.49299	D	0.999773	P;D	0.53462	0.855;0.96	P;P	0.55112	0.596;0.769	T	0.78147	-0.2317	10	0.56958	D	0.05	.	7.8642	0.29528	0.0:0.7194:0.1339:0.1466	.	550;544	P54707-2;P54707	.;AT12A_HUMAN	S	550;544	ENSP00000218548:P550S;ENSP00000371372:P544S	ENSP00000218548:P550S	P	+	1	0	ATP12A	24170913	1.000000	0.71417	0.978000	0.43139	0.016000	0.09150	4.892000	0.63193	0.458000	0.26988	0.655000	0.94253	CCA		0.637	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1		NM_001676	
BCL3	602	hgsc.bcm.edu;ucsc.edu	37	19	45262806	45262807	+	Frame_Shift_Del	DEL	CT	CT	-			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr19:45262806_45262807delCT	ENST00000164227.5	+	9	1543_1544	c.1299_1300delCT	c.(1297-1302)ccctttfs	p.F434fs		NM_005178.4	NP_005169.2	P20749	BCL3_HUMAN	B-cell CLL/lymphoma 3	434	Pro/Ser-rich.				antimicrobial humoral response (GO:0019730)|cellular response to DNA damage stimulus (GO:0006974)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|extracellular matrix organization (GO:0030198)|follicular dendritic cell differentiation (GO:0002268)|germinal center formation (GO:0002467)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|marginal zone B cell differentiation (GO:0002315)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-8 biosynthetic process (GO:0045415)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 biosynthetic process (GO:0045082)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|protein import into nucleus, translocation (GO:0000060)|regulation of apoptotic process (GO:0042981)|regulation of DNA binding (GO:0051101)|regulation of NF-kappaB import into nucleus (GO:0042345)|response to UV-C (GO:0010225)|response to virus (GO:0009615)|spleen development (GO:0048536)|T-helper 1 type immune response (GO:0042088)|T-helper 2 cell differentiation (GO:0045064)|transcription, DNA-templated (GO:0006351)	Bcl3-Bcl10 complex (GO:0032996)|Bcl3/NF-kappaB2 complex (GO:0033257)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			kidney(1)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10	Lung NSC(12;0.000698)|all_lung(12;0.002)	Ovarian(192;0.0728)				CCTTCCTGCCCTTTGCTGGGGT	0.678			T	IGH@	CLL																																			Dom	yes		19	19q13	602	B-cell CLL/lymphoma 3		L	0																																										SO:0001589	frameshift_variant	602			M31732	CCDS12642.2	19q13.1-q13.2	2013-01-10			ENSG00000069399	ENSG00000069399		"""Ankyrin repeat domain containing"""	998	protein-coding gene	gene with protein product	"""B-cell lymphoma 3-encoded protein"", ""B-cell leukemia/lymphoma 3"", ""chronic lymphatic leukemia protein"""	109560		D19S37, BCL4		1501714, 2180580	Standard	NM_005178		Approved		uc010xxe.2	P20749	OTTHUMG00000151517	ENST00000164227.5:c.1299_1300delCT	19.37:g.45262806_45262807delCT	ENSP00000164227:p.Phe434fs	Somatic		WXS	Illumina HiSeq	Phase_I		Frame_Shift_Del	DEL	ENST00000164227.5	37	CCDS12642.2																																																																																				0.678	BCL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322976.1		NM_005178	
BECN1	8678	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	40970428	40970428	+	Missense_Mutation	SNP	C	C	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr17:40970428C>A	ENST00000361523.4	-	7	626	c.494G>T	c.(493-495)tGt>tTt	p.C165F	BECN1_ENST00000438274.3_Missense_Mutation_p.C89F|BECN1_ENST00000590099.1_Missense_Mutation_p.C165F	NM_003766.3	NP_003757.1	Q14457	BECN1_HUMAN	beclin 1, autophagy related	165					autophagic vacuole assembly (GO:0000045)|beta-amyloid metabolic process (GO:0050435)|cellular defense response (GO:0006968)|cellular response to aluminum ion (GO:0071275)|cellular response to epidermal growth factor stimulus (GO:0071364)|cytokinesis (GO:0000910)|defense response to virus (GO:0051607)|lysosome organization (GO:0007040)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|neuron development (GO:0048666)|positive regulation of macroautophagy (GO:0016239)|regulation of catalytic activity (GO:0050790)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to vitamin E (GO:0033197)|viral process (GO:0016032)	dendrite (GO:0030425)|membrane (GO:0016020)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|protein complex (GO:0043234)|trans-Golgi network (GO:0005802)		p.C165F(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	13		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0745)		GATCTCCAAACAGCGTCTGCC	0.502																																																	1	Substitution - Missense(1)	kidney(1)											154.0	147.0	150.0					17																	40970428		2203	4300	6503	SO:0001583	missense	8678			AF077301	CCDS11441.1	17q21	2014-02-12	2008-01-14		ENSG00000126581	ENSG00000126581			1034	protein-coding gene	gene with protein product	"""ATG6 autophagy related 6 homolog (S. cerevisiae)"""	604378	"""beclin 1 (coiled-coil, moesin-like BCL2 interacting protein)"""			9765397	Standard	NM_003766		Approved	ATG6, VPS30	uc002ibn.2	Q14457		ENST00000361523.4:c.494G>T	17.37:g.40970428C>A	ENSP00000355231:p.Cys165Phe	Somatic		WXS	Illumina HiSeq	Phase_I	B2R6N7|O75595|Q9UNA8	Missense_Mutation	SNP	ENST00000361523.4	37	CCDS11441.1	.	.	.	.	.	.	.	.	.	.	C	2.719	-0.267029	0.05754	.	.	ENSG00000126581	ENST00000361523;ENST00000438274;ENST00000543382	T;T	0.36340	1.26;1.26	5.93	3.92	0.45320	.	0.000000	0.85682	D	0.000000	T	0.23688	0.0573	N	0.03115	-0.41	0.42070	D	0.991203	P;B	0.48162	0.906;0.002	P;B	0.52554	0.702;0.004	T	0.04165	-1.0972	10	0.07325	T	0.83	.	13.2549	0.60073	0.1277:0.7499:0.1224:0.0	.	89;165	E7EV84;Q14457	.;BECN1_HUMAN	F	165;89;78	ENSP00000355231:C165F;ENSP00000416173:C89F	ENSP00000355231:C165F	C	-	2	0	BECN1	38223954	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	7.263000	0.78421	0.816000	0.34421	0.655000	0.94253	TGT		0.502	BECN1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452405.1		NM_003766	
BMPR2	659	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	203421005	203421005	+	Nonsense_Mutation	SNP	C	C	T	rs137852748		TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr2:203421005C>T	ENST00000374580.4	+	12	3156	c.2617C>T	c.(2617-2619)Cga>Tga	p.R873*	BMPR2_ENST00000374574.2_Intron	NM_001204.6	NP_001195.2	Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor, type II (serine/threonine kinase)	873					activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|brain development (GO:0007420)|cellular response to starvation (GO:0009267)|chondrocyte development (GO:0002063)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm formation (GO:0001707)|negative regulation of cell growth (GO:0030308)|negative regulation of chondrocyte proliferation (GO:1902731)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of vasoconstriction (GO:0045906)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of bone mineralization (GO:0030501)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|regulation of cell proliferation (GO:0042127)|regulation of lung blood pressure (GO:0014916)|retina vasculature development in camera-type eye (GO:0061298)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|venous blood vessel development (GO:0060841)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|fully spanning plasma membrane (GO:0044214)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	activin receptor activity, type II (GO:0016362)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)	p.R873*(1)		autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(11)|lung(7)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	42						TTTACTGAGACGAGAGCAACA	0.478																																																	1	Substitution - Nonsense(1)	kidney(1)	GRCh37	CM002242	BMPR2	M	rs137852748						131.0	126.0	128.0					2																	203421005		2203	4300	6503	SO:0001587	stop_gained	659			Z48923	CCDS33361.1	2q33-q34	2014-09-17			ENSG00000204217	ENSG00000204217			1078	protein-coding gene	gene with protein product		600799	"""primary pulmonary hypertension 1"""	PPH1		7791754	Standard	NM_001204		Approved	BRK-3, T-ALK, BMPR3, BMPR-II	uc002uzf.4	Q13873	OTTHUMG00000133617	ENST00000374580.4:c.2617C>T	2.37:g.203421005C>T	ENSP00000363708:p.Arg873*	Somatic		WXS	Illumina HiSeq	Phase_I	Q13161|Q16569|Q4ZG08|Q53SA5|Q585T8	Nonsense_Mutation	SNP	ENST00000374580.4	37	CCDS33361.1	.	.	.	.	.	.	.	.	.	.	C	44	10.588075	0.99433	.	.	ENSG00000204217	ENST00000374580	.	.	.	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.581	0.76439	0.1377:0.8623:0.0:0.0	.	.	.	.	X	873	.	ENSP00000363708:R873X	R	+	1	2	BMPR2	203129250	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.268000	0.58883	2.941000	0.99782	0.655000	0.94253	CGA		0.478	BMPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257743.1		NM_001204	
BTBD7	55727	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	93761005	93761005	+	Missense_Mutation	SNP	C	C	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr14:93761005C>A	ENST00000334746.5	-	3	668	c.361G>T	c.(361-363)Gct>Tct	p.A121S	BTBD7_ENST00000298896.3_Missense_Mutation_p.A121S|BTBD7_ENST00000554565.1_Intron|BTBD7_ENST00000393170.2_5'Flank|BTBD7_ENST00000555525.1_Missense_Mutation_p.A121S	NM_001002860.2	NP_001002860.2	Q9P203	BTBD7_HUMAN	BTB (POZ) domain containing 7	121					multicellular organismal development (GO:0007275)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)	nucleus (GO:0005634)		p.A121S(2)		breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|skin(8)|upper_aerodigestive_tract(1)	35		all_cancers(154;0.08)		Epithelial(152;0.196)|COAD - Colon adenocarcinoma(157;0.212)|all cancers(159;0.223)		TCTGGTCTAGCCAAACTGGCT	0.408																																																	2	Substitution - Missense(2)	kidney(2)											72.0	64.0	67.0					14																	93761005		2203	4300	6503	SO:0001583	missense	55727			AB040958	CCDS32146.1, CCDS32147.1, CCDS73684.1	14q32.13	2013-01-08			ENSG00000011114	ENSG00000011114		"""BTB/POZ domain containing"""	18269	protein-coding gene	gene with protein product		610386				10819331, 11527404	Standard	NM_001289133		Approved	FLJ10648, FUP1	uc001ybo.3	Q9P203	OTTHUMG00000171269	ENST00000334746.5:c.361G>T	14.37:g.93761005C>A	ENSP00000335615:p.Ala121Ser	Somatic		WXS	Illumina HiSeq	Phase_I	A8K5V7|Q69Z05|Q7Z308|Q86TS0|Q9HAA4|Q9NVM0	Missense_Mutation	SNP	ENST00000334746.5	37	CCDS32146.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.153031	0.78001	.	.	ENSG00000011114	ENST00000334746;ENST00000298896;ENST00000555525	T	0.41400	1.0	5.38	5.38	0.77491	BTB/POZ fold (1);	0.000000	0.85682	D	0.000000	T	0.63850	0.2546	M	0.64170	1.965	0.80722	D	1	D;D;D	0.69078	0.996;0.996;0.997	D;D;D	0.77557	0.99;0.986;0.985	T	0.62473	-0.6847	10	0.49607	T	0.09	.	19.487	0.95033	0.0:1.0:0.0:0.0	.	121;121;121	Q9P203-3;G3V3T2;Q9P203	.;.;BTBD7_HUMAN	S	121	ENSP00000335615:A121S	ENSP00000298896:A121S	A	-	1	0	BTBD7	92830758	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.776000	0.85560	2.687000	0.91594	0.655000	0.94253	GCT		0.408	BTBD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412701.1		NM_001002860	
BTN1A1	696	hgsc.bcm.edu	37	6	26509395	26509395	+	Missense_Mutation	SNP	C	C	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr6:26509395C>T	ENST00000244513.6	+	7	1640	c.1574C>T	c.(1573-1575)gCa>gTa	p.A525V		NM_001732.2	NP_001723.2	Q13410	BT1A1_HUMAN	butyrophilin, subfamily 1, member A1	525						extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)	p.A525V(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(1)	26						AGCCAAGGGGCACCTTAAGGA	0.522																																																	1	Substitution - Missense(1)	kidney(1)											78.0	83.0	81.0					6																	26509395		2200	4294	6494	SO:0001583	missense	696			U39576	CCDS4614.1	6p22.1	2014-01-14			ENSG00000124557	ENSG00000124557		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1135	protein-coding gene	gene with protein product		601610		BTN		8114113, 9382921	Standard	NM_001732		Approved	BT, BTN1	uc003nif.4	Q13410	OTTHUMG00000016358	ENST00000244513.6:c.1574C>T	6.37:g.26509395C>T	ENSP00000244513:p.Ala525Val	Somatic		WXS	Illumina HiSeq	Phase_I	Q4VAN3|Q4VAN4|Q9H458	Missense_Mutation	SNP	ENST00000244513.6	37	CCDS4614.1	.	.	.	.	.	.	.	.	.	.	C	7.304	0.613652	0.14066	.	.	ENSG00000124557	ENST00000244513;ENST00000377586	T	0.35789	1.29	5.41	3.61	0.41365	.	0.509492	0.18356	N	0.143728	T	0.07954	0.0199	N	0.14661	0.345	0.09310	N	0.999999	B	0.06786	0.001	B	0.04013	0.001	T	0.27905	-1.0060	10	0.33940	T	0.23	.	8.8719	0.35320	0.0:0.8137:0.0:0.1863	.	525	Q13410	BT1A1_HUMAN	V	525;493	ENSP00000244513:A525V	ENSP00000244513:A525V	A	+	2	0	BTN1A1	26617374	0.000000	0.05858	0.035000	0.18076	0.307000	0.27823	-0.100000	0.10990	0.807000	0.34208	0.655000	0.94253	GCA		0.522	BTN1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043776.1		NM_001732	
KIAA1211L	343990	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	99448880	99448880	+	Silent	SNP	G	G	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr2:99448880G>A	ENST00000397899.2	-	5	802	c.471C>T	c.(469-471)gaC>gaT	p.D157D	KIAA1211L_ENST00000462314.1_5'UTR	NM_207362.2	NP_997245.2	Q6NV74	K121L_HUMAN	KIAA1211-like	157								p.D157D(2)									GCAGCCCGTCGTCCTCAGAGC	0.587																																																	2	Substitution - coding silent(2)	endometrium(1)|kidney(1)											60.0	68.0	66.0					2																	99448880		1943	4143	6086	SO:0001819	synonymous_variant	0			BC068277	CCDS42720.1	2q11.2	2012-08-03	2012-08-03	2012-08-03	ENSG00000196872	ENSG00000196872			33454	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 55"""	C2orf55			Standard	NM_207362		Approved	MGC42367	uc002szf.1	Q6NV74	OTTHUMG00000153171	ENST00000397899.2:c.471C>T	2.37:g.99448880G>A		Somatic		WXS	Illumina HiSeq	Phase_I		Silent	SNP	ENST00000397899.2	37	CCDS42720.1																																																																																				0.587	KIAA1211L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329933.1		NM_207362	
STPG2	285555	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	99049685	99049685	+	Missense_Mutation	SNP	C	C	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr4:99049685C>A	ENST00000295268.3	-	3	370	c.281G>T	c.(280-282)tGt>tTt	p.C94F		NM_174952.2	NP_777612.1	Q8N412	STPG2_HUMAN	sperm-tail PG-rich repeat containing 2	94								p.C94F(1)									TGACTTTCCACAAGAAGGAAT	0.348																																																	1	Substitution - Missense(1)	kidney(1)											63.0	60.0	61.0					4																	99049685		2203	4298	6501	SO:0001583	missense	0			BC036870	CCDS3645.1	4q22.3-q23	2013-10-11	2012-07-30	2012-07-30	ENSG00000163116	ENSG00000163116			28712	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 37"""	C4orf37		23031811	Standard	NM_174952		Approved	MGC46496	uc003htt.2	Q8N412	OTTHUMG00000131009	ENST00000295268.3:c.281G>T	4.37:g.99049685C>A	ENSP00000295268:p.Cys94Phe	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000295268.3	37	CCDS3645.1	.	.	.	.	.	.	.	.	.	.	C	1.631	-0.518958	0.04171	.	.	ENSG00000163116	ENST00000295268	T	0.10960	2.82	5.14	-1.64	0.08318	.	0.396254	0.26086	N	0.026432	T	0.03783	0.0107	N	0.14661	0.345	0.09310	N	0.999997	B	0.10296	0.003	B	0.11329	0.006	T	0.39603	-0.9606	10	0.10111	T	0.7	-23.1369	2.2579	0.04060	0.0989:0.318:0.2595:0.3236	.	94	Q8N412	CD037_HUMAN	F	94	ENSP00000295268:C94F	ENSP00000295268:C94F	C	-	2	0	C4orf37	99268708	0.763000	0.28462	0.061000	0.19648	0.219000	0.24729	-0.310000	0.08135	-0.653000	0.05401	-0.797000	0.03246	TGT		0.348	STPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253642.1		NM_174952	
CCNL1	57018	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	156867954	156867954	+	Frame_Shift_Del	DEL	G	G	-			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr3:156867954delG	ENST00000295926.3	-	7	897	c.779delC	c.(778-780)ccgfs	p.P260fs	CCNL1_ENST00000479052.1_5'UTR|CCNL1_ENST00000461804.1_Frame_Shift_Del_p.P260fs	NM_020307.2	NP_064703.1	Q9UK58	CCNL1_HUMAN	cyclin L1	260	Cyclin-like 2.				regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	nuclear speck (GO:0016607)|nucleus (GO:0005634)				NS(1)|breast(1)|cervix(2)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|stomach(1)	18			LUSC - Lung squamous cell carcinoma(72;0.0295)|Lung(72;0.0308)			AGTTGGCAACGGAATCTAAAC	0.343																																																	0													49.0	50.0	50.0					3																	156867954		2203	4299	6502	SO:0001589	frameshift_variant	57018			AF180920	CCDS3178.1	3q25.31	2008-02-05			ENSG00000163660	ENSG00000163660			20569	protein-coding gene	gene with protein product		613384				11980906	Standard	NM_020307		Approved	ania-6a	uc003fbf.3	Q9UK58	OTTHUMG00000158713	ENST00000295926.3:c.779delC	3.37:g.156867954delG	ENSP00000295926:p.Pro260fs	Somatic		WXS	Illumina HiSeq	Phase_I	B3KMY3|Q6NVY9|Q6UWS7|Q8NI48|Q96QT0|Q9NZF3	Frame_Shift_Del	DEL	ENST00000295926.3	37	CCDS3178.1																																																																																				0.343	CCNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351859.1		NM_020307	
CHIT1	1118	hgsc.bcm.edu	37	1	203188855	203188856	+	Frame_Shift_Ins	INS	-	-	G	rs546717884		TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr1:203188855_203188856insG	ENST00000367229.1	-	8	885_886	c.851_852insC	c.(850-852)ccafs	p.P284fs	CHIT1_ENST00000255427.3_Frame_Shift_Ins_p.P265fs|CHIT1_ENST00000535569.1_Frame_Shift_Ins_p.P275fs|CHIT1_ENST00000484834.1_5'UTR	NM_001270509.1|NM_003465.2	NP_001257438.1|NP_003456.1	Q13231	CHIT1_HUMAN	chitinase 1 (chitotriosidase)	284					chitin catabolic process (GO:0006032)|immune response (GO:0006955)|polysaccharide catabolic process (GO:0000272)|response to bacterium (GO:0009617)	extracellular space (GO:0005615)|lysosome (GO:0005764)	chitin binding (GO:0008061)|chitinase activity (GO:0004568)|endochitinase activity (GO:0008843)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(1)|stomach(2)	27						ACCCTGTGGCTGGGGCCCCCAC	0.599																																																	0																																										SO:0001589	frameshift_variant	1118			U29615	CCDS1436.1, CCDS58057.1	1q32.1	2013-06-06			ENSG00000133063	ENSG00000133063			1936	protein-coding gene	gene with protein product		600031				9748235, 9492324	Standard	NM_003465		Approved	CHIT, CHI3	uc001gzn.2	Q13231	OTTHUMG00000042126	ENST00000367229.1:c.852dupC	1.37:g.203188859_203188859dupG	ENSP00000356198:p.Pro284fs	Somatic		WXS	Illumina HiSeq	Phase_I	B3KNW6|J3KN09|Q0VGG5|Q0VGG6|Q3ZAR1|Q6ISC2|Q9H3V8|Q9UDJ8	Frame_Shift_Ins	INS	ENST00000367229.1	37	CCDS1436.1																																																																																				0.599	CHIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100275.2		NM_003465	
CMYA5	202333	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	79031741	79031741	+	Missense_Mutation	SNP	C	C	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr5:79031741C>T	ENST00000446378.2	+	2	7184	c.7153C>T	c.(7153-7155)Cca>Tca	p.P2385S		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2385					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)		p.P2385S(2)		NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		AGATAAGGTGCCACAACAGCC	0.353																																																	2	Substitution - Missense(2)	kidney(2)											36.0	37.0	37.0					5																	79031741		1891	4124	6015	SO:0001583	missense	202333			AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"""Tripartite motif containing / Tripartite motif containing"", ""A-kinase anchor proteins"", ""Fibronectin type III domain containing"""	14305	protein-coding gene	gene with protein product	"""genethonin-3"", ""tripartite motif-containing 76"""	612193	"""chromosome 5 open reading frame 10"""	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.7153C>T	5.37:g.79031741C>T	ENSP00000394770:p.Pro2385Ser	Somatic		WXS	Illumina HiSeq	Phase_I	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	C	11.15	1.552819	0.27739	.	.	ENSG00000164309	ENST00000446378	T	0.21031	2.03	5.51	1.75	0.24633	.	1.028080	0.07727	N	0.944615	T	0.17365	0.0417	L	0.55103	1.725	0.09310	N	0.999999	B	0.27498	0.18	B	0.24541	0.054	T	0.37478	-0.9704	10	0.15952	T	0.53	.	4.2178	0.10544	0.1606:0.5844:0.0:0.255	.	2385	Q8N3K9	CMYA5_HUMAN	S	2385	ENSP00000394770:P2385S	ENSP00000394770:P2385S	P	+	1	0	CMYA5	79067497	0.000000	0.05858	0.631000	0.29282	0.835000	0.47333	-0.440000	0.06888	0.094000	0.17404	0.655000	0.94253	CCA		0.353	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1		NM_153610	
COL6A1	1291	hgsc.bcm.edu;ucsc.edu	37	21	47402547	47402549	+	Splice_Site	DEL	GAC	GAC	-			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	GAC	GAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr21:47402547_47402549delGAC	ENST00000361866.3	+	2	211_213	c.97_99delGAC	c.(97-99)gacdel	p.D33del		NM_001848.2	NP_001839.2	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1	33	N-terminal globular domain.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|osteoblast differentiation (GO:0001649)|protein heterotrimerization (GO:0070208)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)	platelet-derived growth factor binding (GO:0048407)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33	all_hematologic(128;0.24)			Colorectal(79;0.0265)|READ - Rectum adenocarcinoma(84;0.0649)		TCTTCGGCCAGACTGCCCCGTGG	0.65																																																	0																																										SO:0001630	splice_region_variant	1291			M20776	CCDS13727.1	21q22.3	2014-09-17			ENSG00000142156	ENSG00000142156		"""Collagens"""	2211	protein-coding gene	gene with protein product		120220					Standard	XM_006723964		Approved		uc002zhu.1	P12109	OTTHUMG00000090440	ENST00000361866.3:c.98-1GAC>-	21.37:g.47402547_47402549delGAC		Somatic		WXS	Illumina HiSeq	Phase_I	O00117|O00118|Q14040|Q14041|Q16258|Q7Z645|Q9BSA8	Frame_Shift_Del	DEL	ENST00000361866.3	37	CCDS13727.1																																																																																				0.650	COL6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206877.1		NM_001848	In_Frame_Del
COL7A1	1294	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	48607732	48607732	+	Silent	SNP	G	G	A	rs142651194		TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr3:48607732G>A	ENST00000328333.8	-	97	7523	c.7416C>T	c.(7414-7416)ggC>ggT	p.G2472G	COL7A1_ENST00000454817.1_Silent_p.G2440G	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	2472	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.G2472G(1)		NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CCCCACGCTCGCCTCGGGGCC	0.617													G|||	1	0.000199681	0.0	0.0	5008	,	,		17413	0.0		0.0	False		,,,				2504	0.001																1	Substitution - coding silent(1)	kidney(1)						G		0,4406		0,0,2203	74.0	82.0	79.0		7416	-1.7	1.0	3	dbSNP_134	79	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	COL7A1	NM_000094.3		0,5,6498	AA,AG,GG		0.0581,0.0,0.0384		2472/2945	48607732	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	1294			L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"""Collagens"", ""Fibronectin type III domain containing"""	2214	protein-coding gene	gene with protein product	"""collagen VII, alpha-1 polypeptide"", ""LC collagen"""	120120	"""epidermolysis bullosa, dystrophic, dominant and recessive"""	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.7416C>T	3.37:g.48607732G>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q14054|Q16507	Silent	SNP	ENST00000328333.8	37	CCDS2773.1																																																																																				0.617	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1		NM_000094	
CPNE7	27132	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	89657453	89657453	+	Missense_Mutation	SNP	C	C	A	rs376054672		TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr16:89657453C>A	ENST00000268720.5	+	14	1510	c.1380C>A	c.(1378-1380)gaC>gaA	p.D460E	CPNE7_ENST00000319518.8_Missense_Mutation_p.D385E	NM_014427.4	NP_055242.1	Q9UBL6	CPNE7_HUMAN	copine VII	460	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				lipid metabolic process (GO:0006629)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)	transporter activity (GO:0005215)	p.D460E(1)		breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(2)	17		all_hematologic(23;0.0748)		all cancers(4;3.63e-08)|OV - Ovarian serous cystadenocarcinoma(4;1.7e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0147)		ACCCTGAGGACGATGAGTGTG	0.637																																																	1	Substitution - Missense(1)	kidney(1)											76.0	71.0	73.0					16																	89657453		2198	4299	6497	SO:0001583	missense	27132			AJ133798	CCDS10980.1, CCDS10981.1	16q24.3	2008-07-03			ENSG00000178773	ENSG00000178773			2320	protein-coding gene	gene with protein product		605689					Standard	NM_014427		Approved		uc002fnq.3	Q9UBL6	OTTHUMG00000138051	ENST00000268720.5:c.1380C>A	16.37:g.89657453C>A	ENSP00000268720:p.Asp460Glu	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000268720.5	37	CCDS10980.1	.	.	.	.	.	.	.	.	.	.	C	6.456	0.452228	0.12283	.	.	ENSG00000178773	ENST00000319518;ENST00000268720;ENST00000529800	T;T;T	0.21543	2.0;2.0;2.0	3.77	-2.35	0.06684	von Willebrand factor, type A (2);Copine (1);	0.116551	0.56097	D	0.000029	T	0.21631	0.0521	L	0.39514	1.22	0.28976	N	0.888921	P;P	0.51057	0.62;0.941	B;P	0.50405	0.313;0.64	T	0.16305	-1.0407	10	0.87932	D	0	-11.0324	10.8467	0.46746	0.0:0.5019:0.0:0.4981	.	385;460	Q9UBL6-2;Q9UBL6	.;CPNE7_HUMAN	E	385;460;105	ENSP00000317374:D385E;ENSP00000268720:D460E;ENSP00000435876:D105E	ENSP00000268720:D460E	D	+	3	2	CPNE7	88184954	0.079000	0.21365	0.213000	0.23690	0.105000	0.19272	-0.741000	0.04855	-0.814000	0.04352	-1.634000	0.00779	GAC		0.637	CPNE7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269929.2			
CYP8B1	1582	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	42915969	42915969	+	Missense_Mutation	SNP	A	A	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr3:42915969A>T	ENST00000316161.4	-	1	1664	c.1340T>A	c.(1339-1341)cTc>cAc	p.L447H	KRBOX1_ENST00000426937.1_Intron|CYP8B1_ENST00000437102.1_Missense_Mutation_p.L447H|RP11-141M3.5_ENST00000471537.1_RNA	NM_004391.2	NP_004382.2	Q9UNU6	CP8B1_HUMAN	cytochrome P450, family 8, subfamily B, polypeptide 1	447					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	7alpha-hydroxycholest-4-en-3-one 12alpha-hydroxylase activity (GO:0033778)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|sterol 12-alpha-hydroxylase activity (GO:0008397)	p.L447H(1)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(2)|prostate(2)|skin(5)	23				KIRC - Kidney renal clear cell carcinoma(284;0.213)|Kidney(284;0.249)		CACCTCACTGAGTGCAAAGAA	0.542																																																	1	Substitution - Missense(1)	kidney(1)											107.0	96.0	100.0					3																	42915969		2203	4300	6503	SO:0001583	missense	1582			AF090318	CCDS2707.1	3p22.1	2004-02-27	2003-01-14		ENSG00000180432	ENSG00000180432		"""Cytochrome P450s"""	2653	protein-coding gene	gene with protein product		602172	"""cytochrome P450, subfamily VIIIB (sterol 12-alpha-hydroxylase), polypeptide 1"""			10051404	Standard	NM_004391		Approved	CYP12	uc003cmh.3	Q9UNU6	OTTHUMG00000133047	ENST00000316161.4:c.1340T>A	3.37:g.42915969A>T	ENSP00000318867:p.Leu447His	Somatic		WXS	Illumina HiSeq	Phase_I	B2RCY3|O75958|Q6NWT2|Q6NWT3	Missense_Mutation	SNP	ENST00000316161.4	37	CCDS2707.1	.	.	.	.	.	.	.	.	.	.	A	16.52	3.145876	0.57044	.	.	ENSG00000180432	ENST00000437102;ENST00000316161	T;T	0.68765	-0.35;-0.35	5.39	3.04	0.35103	.	0.524360	0.18292	N	0.145696	T	0.77123	0.4084	M	0.77406	2.37	0.30650	N	0.755556	D;D	0.67145	0.996;0.992	D;P	0.64506	0.926;0.895	T	0.74589	-0.3615	10	0.87932	D	0	-9.4179	7.1046	0.25356	0.7479:0.0:0.2521:0.0	.	447;447	C9JFR9;Q9UNU6	.;CP8B1_HUMAN	H	447	ENSP00000404499:L447H;ENSP00000318867:L447H	ENSP00000318867:L447H	L	-	2	0	CYP8B1	42890973	1.000000	0.71417	0.775000	0.31657	0.782000	0.44232	3.207000	0.51106	0.892000	0.36259	0.379000	0.24179	CTC		0.542	CYP8B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256653.1		NM_004391	
DCHS2	54798	hgsc.bcm.edu	37	4	155312411	155312411	+	Silent	SNP	G	G	A	rs62331900	byFrequency	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr4:155312411G>A	ENST00000357232.4	-	1	38	c.39C>T	c.(37-39)gaC>gaT	p.D13D	DCHS2_ENST00000339452.1_Intron	NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	13					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		tcttttctccgtcttcattct	0.373													G|||	1610	0.321486	0.4607	0.1311	5008	,	,		19449	0.3403		0.1948	False		,,,				2504	0.3793																0								G	,	1711,2693	508.3+/-366.9	348,1015,839	181.0	154.0	163.0		,39	-6.3	0.0	4	dbSNP_129	163	1529,7069	287.3+/-298.2	135,1259,2905	yes	intron,coding-synonymous	DCHS2	NM_001142552.1,NM_017639.3	,	483,2274,3744	AA,AG,GG		17.7832,38.851,24.9192	,	,13/2917	155312411	3240,9762	2202	4299	6501	SO:0001819	synonymous_variant	54798			BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.39C>T	4.37:g.155312411G>A		Somatic		WXS	Illumina HiSeq	Phase_I	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000357232.4	37	CCDS3785.1																																																																																				0.373	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2		NM_001142552	
DNAH9	1770	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	11650990	11650990	+	Missense_Mutation	SNP	C	C	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr17:11650990C>T	ENST00000262442.4	+	32	6585	c.6517C>T	c.(6517-6519)Cgg>Tgg	p.R2173W	DNAH9_ENST00000454412.2_Missense_Mutation_p.R2173W	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2173	AAA 2. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.R2173W(1)		NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		GATCATGAAACGGCGCCCCGT	0.542																																																	1	Substitution - Missense(1)	kidney(1)											91.0	84.0	86.0					17																	11650990		2203	4300	6503	SO:0001583	missense	1770			U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.6517C>T	17.37:g.11650990C>T	ENSP00000262442:p.Arg2173Trp	Somatic		WXS	Illumina HiSeq	Phase_I	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.987431	0.74589	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.56103	0.48;0.48	4.5	3.52	0.40303	ATPase, AAA+ type, core (1);ATPase, dynein-related, AAA domain (1);	0.385584	0.26638	N	0.023273	T	0.72447	0.3461	M	0.90542	3.125	0.80722	D	1	D	0.76494	0.999	D	0.66716	0.946	T	0.75221	-0.3394	10	0.87932	D	0	.	8.0598	0.30627	0.1561:0.7625:0.0:0.0814	.	2173	Q9NYC9	DYH9_HUMAN	W	2173;2173;755	ENSP00000262442:R2173W;ENSP00000414874:R2173W	ENSP00000262442:R2173W	R	+	1	2	DNAH9	11591715	1.000000	0.71417	0.881000	0.34555	0.987000	0.75469	2.893000	0.48633	1.096000	0.41439	0.557000	0.71058	CGG		0.542	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2		NM_001372	
DTNA	1837	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	18	32405233	32405233	+	Missense_Mutation	SNP	A	A	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr18:32405233A>T	ENST00000399113.3	+	9	1004	c.1004A>T	c.(1003-1005)gAt>gTt	p.D335V	DTNA_ENST00000269191.6_Missense_Mutation_p.D335V|DTNA_ENST00000444659.1_Missense_Mutation_p.D335V|DTNA_ENST00000598774.1_Missense_Mutation_p.D335V|DTNA_ENST00000556414.3_Intron|DTNA_ENST00000348997.5_Intron|DTNA_ENST00000598334.1_Intron|DTNA_ENST00000595022.1_Intron|DTNA_ENST00000399121.5_Intron|DTNA_ENST00000283365.9_Missense_Mutation_p.D335V|DTNA_ENST00000315456.6_Missense_Mutation_p.D335V|DTNA_ENST00000599844.1_Intron|DTNA_ENST00000597674.1_Intron|DTNA_ENST00000399097.3_Intron|DTNA_ENST00000591182.1_Intron|DTNA_ENST00000597599.1_Intron|DTNA_ENST00000601125.1_Intron|DTNA_ENST00000598142.1_Missense_Mutation_p.D335V|DTNA_ENST00000269190.7_Intron|DTNA_ENST00000554864.3_Intron|DTNA_ENST00000596745.1_Intron|DTNA_ENST00000269192.7_Intron			Q9Y4J8	DTNA_HUMAN	dystrobrevin, alpha	335					neuromuscular synaptic transmission (GO:0007274)|signal transduction (GO:0007165)|striated muscle contraction (GO:0006941)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)	p.D335V(2)		endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(2)|lung(19)|prostate(1)|upper_aerodigestive_tract(1)	29						GCCAAAAGTGATACTTGGTAA	0.348																																																	2	Substitution - Missense(2)	kidney(2)											226.0	205.0	212.0					18																	32405233		1863	4110	5973	SO:0001583	missense	1837			U84540	CCDS11908.1, CCDS11909.1, CCDS42426.1, CCDS45848.1, CCDS56060.1, CCDS56061.1, CCDS56062.1, CCDS56063.1, CCDS59309.1, CCDS59310.1, CCDS59311.1, CCDS59312.1, CCDS59313.1, CCDS59314.1	18q12	2014-09-17			ENSG00000134769	ENSG00000134769			3057	protein-coding gene	gene with protein product	"""dystrophin-related protein 3"""	601239				8081380, 15834686	Standard	NM_001390		Approved	D18S892E, DTN, DTN-1, DTN-2, DTN-3, DRP3	uc010dmn.1	Q9Y4J8	OTTHUMG00000132309	ENST00000399113.3:c.1004A>T	18.37:g.32405233A>T	ENSP00000382064:p.Asp335Val	Somatic		WXS	Illumina HiSeq	Phase_I	A8K541|A8MSZ0|A8MUY4|B4DGS6|B4DIR0|B4DIU8|M0QYX6|M0R397|O15332|O15333|O75697|Q13197|Q13198|Q13199|Q13498|Q13499|Q13500|Q59GK7|Q9BS59	Missense_Mutation	SNP	ENST00000399113.3	37	CCDS59311.1	.	.	.	.	.	.	.	.	.	.	A	12.65	2.001447	0.35320	.	.	ENSG00000134769	ENST00000283365;ENST00000315456;ENST00000444659;ENST00000269191;ENST00000399113	T;T;T;T;T	0.18657	2.25;2.27;2.25;2.2;2.25	5.52	5.52	0.82312	.	.	.	.	.	T	0.12561	0.0305	N	0.22421	0.69	0.80722	D	1	B;B;B;P;P	0.40302	0.019;0.078;0.038;0.712;0.463	B;B;B;B;B	0.28232	0.015;0.087;0.025;0.047;0.034	T	0.05666	-1.0871	9	0.56958	D	0.05	.	12.3128	0.54938	1.0:0.0:0.0:0.0	.	335;335;335;335;335	Q9Y4J8;Q9Y4J8-3;Q9Y4J8-2;Q9Y4J8-5;Q9Y4J8-7	DTNA_HUMAN;.;.;.;.	V	335	ENSP00000283365:D335V;ENSP00000322519:D335V;ENSP00000405819:D335V;ENSP00000269191:D335V;ENSP00000382064:D335V	ENSP00000269191:D335V	D	+	2	0	DTNA	30659231	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.899000	0.63245	2.216000	0.71823	0.528000	0.53228	GAT		0.348	DTNA-005	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255422.2		NM_001390	
EDA	1896	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	69255287	69255287	+	Missense_Mutation	SNP	G	G	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chrX:69255287G>T	ENST00000374552.4	+	8	1246	c.1004G>T	c.(1003-1005)aGc>aTc	p.S335I	EDA_ENST00000524573.1_Missense_Mutation_p.S330I|EDA_ENST00000374553.2_Missense_Mutation_p.S333I	NM_001399.4	NP_001390.1	Q92838	EDA_HUMAN	ectodysplasin A	335					cell differentiation (GO:0030154)|cell-matrix adhesion (GO:0007160)|ectoderm development (GO:0007398)|gene expression (GO:0010467)|hair follicle placode formation (GO:0060789)|immune response (GO:0006955)|odontogenesis of dentin-containing tooth (GO:0042475)|pigmentation (GO:0043473)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|salivary gland cavitation (GO:0060662)|signal transduction (GO:0007165)|trachea gland development (GO:0061153)	apical part of cell (GO:0045177)|collagen trimer (GO:0005581)|cytoskeleton (GO:0005856)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)	p.S335I(2)		breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(2)|urinary_tract(1)	14						TGCACACGCAGCATCGAGACG	0.547																																																	2	Substitution - Missense(2)	kidney(2)											109.0	69.0	82.0					X																	69255287		2203	4300	6503	SO:0001583	missense	1896			U59227	CCDS14394.1, CCDS35318.1, CCDS35319.1, CCDS43966.1, CCDS35318.2, CCDS35319.2, CCDS55436.1	Xq12-q13.1	2013-05-22	2004-08-09	2004-08-12	ENSG00000158813	ENSG00000158813		"""Tumor necrosis factor (ligand) superfamily"""	3157	protein-coding gene	gene with protein product		300451	"""ectodermal dysplasia 1, anhidrotic"", ""oligodontia 1"""	ED1, EDA2, ODT1		8696334, 18657636, 16583127	Standard	NM_001005612		Approved	EDA1, XLHED, HED, XHED, ED1-A1, ED1-A2, EDA-A1, EDA-A2	uc004dxs.3	Q92838	OTTHUMG00000021764	ENST00000374552.4:c.1004G>T	X.37:g.69255287G>T	ENSP00000363680:p.Ser335Ile	Somatic		WXS	Illumina HiSeq	Phase_I	A0AUZ2|A2A337|B7ZLU2|B7ZLU4|O75910|Q5JS00|Q5JUM7|Q9UP77|Q9Y6L0|Q9Y6L1|Q9Y6L2|Q9Y6L3|Q9Y6L4	Missense_Mutation	SNP	ENST00000374552.4	37	CCDS14394.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.843514	0.91197	.	.	ENSG00000158813	ENST00000374552;ENST00000374553;ENST00000524573	D;D;D	0.99532	-3.44;-6.1;-6.1	5.42	5.42	0.78866	Tumour necrosis factor (3);Tumour necrosis factor-like (2);	0.000000	0.85682	D	0.000000	D	0.99573	0.9846	M	0.78456	2.415	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	D	0.98186	1.0460	10	0.87932	D	0	-15.2628	17.1546	0.86787	0.0:0.0:1.0:0.0	.	330;335;333	Q92838-9;Q92838;Q92838-3	.;EDA_HUMAN;.	I	335;333;330	ENSP00000363680:S335I;ENSP00000363681:S333I;ENSP00000432585:S330I	ENSP00000363680:S335I	S	+	2	0	EDA	69172012	1.000000	0.71417	0.999000	0.59377	0.982000	0.71751	9.125000	0.94402	2.261000	0.74972	0.529000	0.55759	AGC		0.547	EDA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057048.2		NM_001399	
ENAM	10117	hgsc.bcm.edu;ucsc.edu	37	4	71500242	71500242	+	Frame_Shift_Del	DEL	C	C	-			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr4:71500242delC	ENST00000396073.3	+	6	709	c.428delC	c.(427-429)tcafs	p.S143fs		NM_031889.2	NP_114095.2	Q9NRM1	ENAM_HUMAN	enamelin	143					amelogenesis (GO:0097186)|biomineral tissue development (GO:0031214)	proteinaceous extracellular matrix (GO:0005578)				haematopoietic_and_lymphoid_tissue(1)|ovary(3)|upper_aerodigestive_tract(2)	6			Lung(101;0.235)			AAGCAGCCATCACATAATCAA	0.483																																																	0													97.0	101.0	100.0					4																	71500242		2203	4296	6499	SO:0001589	frameshift_variant	10117			AF125373	CCDS3544.2	4q13.3	2008-02-05			ENSG00000132464	ENSG00000132464			3344	protein-coding gene	gene with protein product		606585	"""amelogenesis imperfecta 2, hypocalcification (autosomal dominant)"""	AIH2		11978766	Standard	NM_031889		Approved		uc011caw.1	Q9NRM1	OTTHUMG00000129914	ENST00000396073.3:c.428delC	4.37:g.71500242delC	ENSP00000379383:p.Ser143fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q17RI5|Q9H3D1	Frame_Shift_Del	DEL	ENST00000396073.3	37	CCDS3544.2																																																																																				0.483	ENAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252166.3		NM_031889	
FAM120AOS	158293	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	96209937	96209937	+	Missense_Mutation	SNP	T	T	G			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr9:96209937T>G	ENST00000375412.5	-	3	1609	c.727A>C	c.(727-729)Acc>Ccc	p.T243P	FAM120AOS_ENST00000423591.1_Missense_Mutation_p.T61P|FAM120AOS_ENST00000479094.1_5'UTR	NM_198841.2	NP_942138.2	Q5T036	F120S_HUMAN	family with sequence similarity 120A opposite strand	243								p.T243P(1)		kidney(1)|large_intestine(1)|lung(3)|skin(1)	6						GGTTTTGTGGTTTTCTTTGAG	0.333																																																	1	Substitution - Missense(1)	kidney(1)											230.0	213.0	218.0					9																	96209937		2203	4300	6503	SO:0001583	missense	158293			AK056096	CCDS6705.1	9q22.32	2008-02-05	2006-07-04	2006-07-04	ENSG00000188938	ENSG00000188938			23389	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 10 opposite strand"""	C9orf10OS		14585507	Standard	NM_198841		Approved		uc004atu.4	Q5T036	OTTHUMG00000020251	ENST00000375412.5:c.727A>C	9.37:g.96209937T>G	ENSP00000364561:p.Thr243Pro	Somatic		WXS	Illumina HiSeq	Phase_I	A6NN20	Missense_Mutation	SNP	ENST00000375412.5	37	CCDS6705.1	.	.	.	.	.	.	.	.	.	.	T	6.120	0.390364	0.11581	.	.	ENSG00000188938	ENST00000423591;ENST00000375412;ENST00000375409;ENST00000428378	T;T;T	0.57107	0.48;0.46;0.42	1.92	0.719	0.18208	.	.	.	.	.	T	0.26195	0.0639	N	0.08118	0	0.09310	N	1	B	0.30361	0.277	B	0.17979	0.02	T	0.14896	-1.0456	9	0.87932	D	0	.	4.9211	0.13871	0.0:0.0:0.3826:0.6174	.	243	Q5T036	F120S_HUMAN	P	61;243;60;60	ENSP00000414298:T61P;ENSP00000364561:T243P;ENSP00000416978:T60P	ENSP00000364558:T60P	T	-	1	0	FAM120AOS	95249758	0.004000	0.15560	0.001000	0.08648	0.009000	0.06853	0.588000	0.23924	0.180000	0.19960	-0.482000	0.04802	ACC		0.333	FAM120AOS-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053154.1			
FASTKD1	79675	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	170416921	170416921	+	Missense_Mutation	SNP	A	A	G			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr2:170416921A>G	ENST00000453153.2	-	5	1293	c.947T>C	c.(946-948)aTt>aCt	p.I316T	FASTKD1_ENST00000453929.2_Missense_Mutation_p.I316T	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	316					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)	p.I316T(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(5)|large_intestine(10)|lung(9)|ovary(4)|prostate(3)	37						AGGTCCTGCAATGGGTCCCAA	0.358																																																	1	Substitution - Missense(1)	kidney(1)											96.0	108.0	104.0					2																	170416921		2187	4294	6481	SO:0001583	missense	79675			AL832058	CCDS33318.1, CCDS63051.1	2q31.1	2008-02-05			ENSG00000138399	ENSG00000138399			26150	protein-coding gene	gene with protein product						11347906	Standard	NM_024622		Approved	FLJ21901	uc002uev.4	Q53R41	OTTHUMG00000154953	ENST00000453153.2:c.947T>C	2.37:g.170416921A>G	ENSP00000400513:p.Ile316Thr	Somatic		WXS	Illumina HiSeq	Phase_I	Q8N583|Q8TEA9|Q96JM5|Q96N71|Q9H6T4	Missense_Mutation	SNP	ENST00000453153.2	37	CCDS33318.1	.	.	.	.	.	.	.	.	.	.	A	11.34	1.608424	0.28623	.	.	ENSG00000138399	ENST00000453153;ENST00000453929	T;T	0.18502	2.21;2.21	5.44	4.25	0.50352	.	1.885840	0.02208	N	0.062915	T	0.18173	0.0436	L	0.43152	1.355	0.29257	N	0.871577	P;P;P	0.43094	0.698;0.799;0.698	B;B;B	0.36092	0.108;0.217;0.108	T	0.34204	-0.9838	10	0.22706	T	0.39	-12.5173	11.6581	0.51330	0.8513:0.1487:0.0:0.0	.	293;316;316	D3DPC4;Q53R41-2;Q53R41	.;.;FAKD1_HUMAN	T	316	ENSP00000400513:I316T;ENSP00000403229:I316T	ENSP00000400513:I316T	I	-	2	0	FASTKD1	170125167	1.000000	0.71417	0.263000	0.24496	0.933000	0.57130	7.232000	0.78116	0.862000	0.35528	0.528000	0.53228	ATT		0.358	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2		NM_024622	
FUT6	2528	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	5832203	5832203	+	Missense_Mutation	SNP	G	G	A	rs111589452	byFrequency	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr19:5832203G>A	ENST00000318336.4	-	3	1570	c.376C>T	c.(376-378)Cgg>Tgg	p.R126W	FUT6_ENST00000286955.5_Missense_Mutation_p.R126W|FUT6_ENST00000592563.1_Missense_Mutation_p.R126W|FUT6_ENST00000527106.1_Missense_Mutation_p.R126W|FUT6_ENST00000524754.1_Missense_Mutation_p.R126W	NM_000150.2	NP_000141.1	P51993	FUT6_HUMAN	fucosyltransferase 6 (alpha (1,3) fucosyltransferase)	126					fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity (GO:0017060)|alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)	p.R126W(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(2)	6						TGCCCCTGCCGCCTCGGGGAG	0.617																																																	1	Substitution - Missense(1)	kidney(1)											70.0	58.0	62.0					19																	5832203		2203	4300	6503	SO:0001583	missense	2528				CCDS12152.1	19p13.3	2013-02-26			ENSG00000156413	ENSG00000156413	2.4.1.65	"""Fucosyltransferases"""	4017	protein-coding gene	gene with protein product	"""alpha-(1,3)-fucosyltransferase"", ""galactoside 3-L-fucosyltransferase"""	136836				1520296, 7782074	Standard	NM_001040701		Approved	FT1A, FCT3A, FucT-VI, FLJ40754	uc002mdh.1	P51993	OTTHUMG00000167335	ENST00000318336.4:c.376C>T	19.37:g.5832203G>A	ENSP00000313398:p.Arg126Trp	Somatic		WXS	Illumina HiSeq	Phase_I	A6NEX0|D6W637|Q9UND8	Missense_Mutation	SNP	ENST00000318336.4	37	CCDS12152.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.937106	0.73557	.	.	ENSG00000156413	ENST00000524754;ENST00000527106;ENST00000318336;ENST00000286955;ENST00000341530;ENST00000529165	T;T;T;T;T	0.24350	1.86;1.86;1.86;1.86;1.86	3.09	3.09	0.35607	.	0.333138	0.24740	N	0.035984	T	0.25865	0.0630	L	0.42245	1.32	0.30040	N	0.812724	P;P	0.50272	0.933;0.844	P;P	0.45167	0.472;0.472	T	0.20371	-1.0277	10	0.87932	D	0	.	12.3817	0.55311	0.0:0.0:1.0:0.0	.	126;126	C9J8A2;P51993	.;FUT6_HUMAN	W	126	ENSP00000431708:R126W;ENSP00000432954:R126W;ENSP00000313398:R126W;ENSP00000286955:R126W;ENSP00000436547:R126W	ENSP00000286955:R126W	R	-	1	2	FUT6	5783203	1.000000	0.71417	0.029000	0.17559	0.001000	0.01503	6.454000	0.73493	1.666000	0.50821	0.436000	0.28706	CGG		0.617	FUT6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394218.2		NM_000150	
GABBR1	2550	broad.mit.edu;hgsc.bcm.edu	37	6	29573438	29573438	+	Missense_Mutation	SNP	G	G	T	rs368201041		TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr6:29573438G>T	ENST00000377034.4	-	20	2682	c.2347C>A	c.(2347-2349)Ctg>Atg	p.L783M	GABBR1_ENST00000376977.3_3'UTR|GABBR1_ENST00000355973.3_Missense_Mutation_p.L666M|GABBR1_ENST00000377012.4_Missense_Mutation_p.L666M|GABBR1_ENST00000377016.4_Missense_Mutation_p.L721M	NM_001470.2	NP_001461.1	Q9UBS5	GABR1_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 1	783					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	G-protein coupled GABA receptor activity (GO:0004965)	p.L783M(1)		endometrium(3)|kidney(1)|large_intestine(13)|liver(1)|lung(16)|ovary(5)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47					Baclofen(DB00181)|Progabide(DB00837)|Vigabatrin(DB01080)	AAGATTCCCAGCAGCAGCAGC	0.512																																																	1	Substitution - Missense(1)	kidney(1)											136.0	111.0	120.0					6																	29573438		1511	2709	4220	SO:0001583	missense	2550			Y11044	CCDS4663.1, CCDS4664.1, CCDS4665.1	6p21.3	2012-08-29			ENSG00000204681	ENSG00000204681		"""GABA receptors"", ""GPCR / Class C : GABA(B) receptors"""	4070	protein-coding gene	gene with protein product	"""GABA-B receptor"""	603540				9753614, 9798068	Standard	NM_001470		Approved	hGB1a, GPRC3A	uc003nmt.4	Q9UBS5	OTTHUMG00000031095	ENST00000377034.4:c.2347C>A	6.37:g.29573438G>T	ENSP00000366233:p.Leu783Met	Somatic		WXS	Illumina HiSeq	Phase_I	B0UXY7|O95375|O95468|O95975|O96022|Q5STL4|Q5SUJ8|Q5SUL3|Q71SG6|Q86W60|Q9UQQ0	Missense_Mutation	SNP	ENST00000377034.4	37	CCDS4663.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.993946	0.74703	.	.	ENSG00000204681	ENST00000355973;ENST00000377016;ENST00000377012;ENST00000377034	D;D;D;D	0.89123	-2.47;-2.47;-2.47;-2.47	5.18	3.4	0.38934	GPCR, family 3, C-terminal (2);	0.073544	0.56097	D	0.000033	D	0.88463	0.6443	L	0.49126	1.545	0.80722	D	1	D;D;D	0.69078	0.997;0.997;0.995	D;D;D	0.67548	0.94;0.952;0.913	D	0.88649	0.3181	10	0.72032	D	0.01	-21.1235	9.7889	0.40692	0.1706:0.0:0.8294:0.0	.	721;783;666	Q9UBS5-3;Q9UBS5;Q5SUJ9	.;GABR1_HUMAN;.	M	666;721;666;783	ENSP00000348248:L666M;ENSP00000366215:L721M;ENSP00000366211:L666M;ENSP00000366233:L783M	ENSP00000348248:L666M	L	-	1	2	GABBR1	29681417	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	4.959000	0.63666	0.691000	0.31592	0.655000	0.94253	CTG		0.512	GABBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076141.3			
CPTP	80772	hgsc.bcm.edu;ucsc.edu	37	1	1262701	1262701	+	Frame_Shift_Del	DEL	G	G	-	rs199828648	byFrequency	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr1:1262701delG	ENST00000343938.4	+	3	614	c.203delG	c.(202-204)aggfs	p.R68fs	CPSF3L_ENST00000411962.1_5'Flank|CPSF3L_ENST00000450926.2_5'Flank|GLTPD1_ENST00000464957.1_3'UTR|CPSF3L_ENST00000545578.1_5'Flank|CPSF3L_ENST00000419704.1_5'Flank|CPSF3L_ENST00000435064.1_5'Flank|CPSF3L_ENST00000421495.2_5'Flank|CPSF3L_ENST00000540437.1_5'Flank	NM_001029885.1	NP_001025056.1	Q5TA50	CPTP_HUMAN		68					ceramide 1-phosphate transport (GO:1902389)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ceramide 1-phosphate binding (GO:1902387)|ceramide 1-phosphate transporter activity (GO:1902388)|glycolipid binding (GO:0051861)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)			lung(1)	1	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;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;4.95e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		GAGCGCCTCAGGGGCGGCCCG	0.662																																																	0													44.0	44.0	44.0					1																	1262701		2198	4299	6497	SO:0001589	frameshift_variant	80772																														ENST00000343938.4:c.203delG	1.37:g.1262701delG	ENSP00000343890:p.Arg68fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q4G0E6|Q7L5A4	Frame_Shift_Del	DEL	ENST00000343938.4	37	CCDS30555.1																																																																																				0.662	GLTPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008742.1			
GPM6A	2823	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	176622807	176622807	+	Missense_Mutation	SNP	G	G	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr4:176622807G>A	ENST00000280187.7	-	3	194	c.149C>T	c.(148-150)gCg>gTg	p.A50V	GPM6A_ENST00000393658.2_Missense_Mutation_p.A50V|GPM6A_ENST00000506894.1_Missense_Mutation_p.A39V|GPM6A_ENST00000515090.1_Missense_Mutation_p.A43V	NM_005277.4	NP_005268.1	P51674	GPM6A_HUMAN	glycoprotein M6A	50					neural retina development (GO:0003407)|neuron migration (GO:0001764)|neuron projection morphogenesis (GO:0048812)|positive regulation of filopodium assembly (GO:0051491)|stem cell differentiation (GO:0048863)|synapse assembly (GO:0007416)	axonal growth cone (GO:0044295)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	calcium channel activity (GO:0005262)	p.A50V(3)		NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(16)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	33		Breast(14;7.35e-05)|Melanoma(52;0.00909)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;9.21e-19)|Epithelial(43;3.01e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.02e-09)|STAD - Stomach adenocarcinoma(60;0.00083)|GBM - Glioblastoma multiforme(59;0.00168)|LUSC - Lung squamous cell carcinoma(193;0.0388)		TCCAGAAAGCGCTTCATGACC	0.488																																																	3	Substitution - Missense(3)	kidney(2)|prostate(1)											154.0	144.0	148.0					4																	176622807		2203	4300	6503	SO:0001583	missense	2823				CCDS3824.1, CCDS54822.1, CCDS58936.1	4q34	2008-08-29				ENSG00000150625			4460	protein-coding gene	gene with protein product		601275		GPM6		8661015, 18574501	Standard	NM_005277		Approved		uc003iug.4	P51674		ENST00000280187.7:c.149C>T	4.37:g.176622807G>A	ENSP00000280187:p.Ala50Val	Somatic		WXS	Illumina HiSeq	Phase_I	B7Z642|E9PHI5|Q92602	Missense_Mutation	SNP	ENST00000280187.7	37	CCDS3824.1	.	.	.	.	.	.	.	.	.	.	G	36	5.598683	0.96614	.	.	ENSG00000150625	ENST00000280187;ENST00000393658;ENST00000506894;ENST00000515090;ENST00000503397;ENST00000513365;ENST00000505304	D;D;D;D;D;D;D	0.99548	-6.14;-6.14;-6.14;-6.14;-6.14;-6.14;-6.14	6.01	6.01	0.97437	.	0.000000	0.85682	D	0.000000	D	0.99635	0.9866	M	0.80616	2.505	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.996;0.996	D	0.98505	1.0616	10	0.87932	D	0	-0.21	20.5211	0.99222	0.0:0.0:1.0:0.0	.	43;39;50	B7Z642;E9PHI5;P51674	.;.;GPM6A_HUMAN	V	50;50;39;43;42;50;43	ENSP00000280187:A50V;ENSP00000377268:A50V;ENSP00000421578:A39V;ENSP00000423984:A43V;ENSP00000422959:A42V;ENSP00000423122:A50V;ENSP00000425463:A43V	ENSP00000280187:A50V	A	-	2	0	GPM6A	176859801	1.000000	0.71417	0.970000	0.41538	0.897000	0.52465	9.476000	0.97823	2.861000	0.98227	0.650000	0.86243	GCG		0.488	GPM6A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362163.1			
GRIK3	2899	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	37335385	37335385	+	Missense_Mutation	SNP	C	C	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr1:37335385C>T	ENST00000373091.3	-	5	766	c.750G>A	c.(748-750)atG>atA	p.M250I	GRIK3_ENST00000373093.4_Missense_Mutation_p.M250I	NM_000831.3	NP_000822.2	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3	250					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	adenylate cyclase inhibiting G-protein coupled glutamate receptor activity (GO:0001640)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|kainate selective glutamate receptor activity (GO:0015277)	p.M250I(1)		breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(27)|lung(35)|ovary(5)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	89		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)				ACTCAGTCATCATGCCCATGG	0.557																																																	1	Substitution - Missense(1)	kidney(1)											145.0	121.0	129.0					1																	37335385		2203	4300	6503	SO:0001583	missense	2899			U16127	CCDS416.1	1p34.3	2012-08-29			ENSG00000163873	ENSG00000163873		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4581	protein-coding gene	gene with protein product		138243				8128318	Standard	NM_000831		Approved	GluK3, GLUR7	uc001caz.2	Q13003	OTTHUMG00000004189	ENST00000373091.3:c.750G>A	1.37:g.37335385C>T	ENSP00000362183:p.Met250Ile	Somatic		WXS	Illumina HiSeq	Phase_I	A9Z1Z8|B1AMS6|Q13004|Q16136	Missense_Mutation	SNP	ENST00000373091.3	37	CCDS416.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.774105	0.90108	.	.	ENSG00000163873	ENST00000373091;ENST00000373093	D;D	0.84070	-1.8;-1.8	4.71	4.71	0.59529	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.86285	0.5896	M	0.63208	1.945	0.58432	D	0.999999	P;P	0.47409	0.828;0.895	P;P	0.50162	0.527;0.633	D	0.88339	0.2973	10	0.72032	D	0.01	.	18.0477	0.89337	0.0:1.0:0.0:0.0	.	250;250	A9Z1Z8;Q13003	.;GRIK3_HUMAN	I	250	ENSP00000362183:M250I;ENSP00000362185:M250I	ENSP00000362183:M250I	M	-	3	0	GRIK3	37107972	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.453000	0.80700	2.343000	0.79666	0.655000	0.94253	ATG		0.557	GRIK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012053.1		NM_000831	
HAUS6	54801	hgsc.bcm.edu	37	9	19063108	19063108	+	Silent	SNP	T	T	C	rs13302748	byFrequency	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr9:19063108T>C	ENST00000380502.3	-	14	1994	c.1527A>G	c.(1525-1527)ttA>ttG	p.L509L	SCARNA8_ENST00000515924.1_RNA|HAUS6_ENST00000380496.1_Silent_p.L373L	NM_001270890.1|NM_017645.4	NP_001257819.1|NP_060115.3	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6	509					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)				autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						CAACATCTGATAATGGAGAAT	0.358													T|||	1763	0.352037	0.1702	0.4035	5008	,	,		19022	0.38		0.4493	False		,,,				2504	0.4325																0								T		888,3518	341.2+/-306.6	104,680,1419	105.0	96.0	99.0		1527	2.0	0.0	9	dbSNP_121	99	3911,4685	544.6+/-384.6	883,2145,1270	no	coding-synonymous	HAUS6	NM_017645.3		987,2825,2689	CC,CT,TT		45.4979,20.1543,36.9097		509/956	19063108	4799,8203	2203	4298	6501	SO:0001819	synonymous_variant	54801			AL832495	CCDS6489.1	9p22.1	2011-10-24	2009-04-20	2009-04-20	ENSG00000147874	ENSG00000147874		"""HAUS augmin-like complex subunits"""	25948	protein-coding gene	gene with protein product		613433	"""family with sequence similarity 29, member A"""	FAM29A		10997877, 19427217	Standard	NM_001270890		Approved	FLJ20060, KIAA1574, dgt6	uc003znk.4	Q7Z4H7	OTTHUMG00000019622	ENST00000380502.3:c.1527A>G	9.37:g.19063108T>C		Somatic		WXS	Illumina HiSeq	Phase_I	B3KPK4|B4DX82|Q05CG1|Q14CB6|Q14CD9|Q2TA91|Q6IQ10|Q6NZX5|Q8IZQ4|Q96FN0|Q9H950|Q9H998|Q9HCJ8|Q9NXT8	Silent	SNP	ENST00000380502.3	37	CCDS6489.1																																																																																				0.358	HAUS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051825.1		NM_017645	
HECTD1	25831	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	31576011	31576011	+	Missense_Mutation	SNP	C	C	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr14:31576011C>T	ENST00000399332.1	-	38	7555	c.7067G>A	c.(7066-7068)aGa>aAa	p.R2356K	HECTD1_ENST00000553700.1_Missense_Mutation_p.R2356K	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	2356	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)	p.R2356K(1)		breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		AAATCTGGCTCTGTGTGGGTT	0.358																																																	1	Substitution - Missense(1)	kidney(1)											77.0	71.0	72.0					14																	31576011		1799	4065	5864	SO:0001583	missense	25831			AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"""Ankyrin repeat domain containing"""	20157	protein-coding gene	gene with protein product			"""HECT domain containing 1"""			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.7067G>A	14.37:g.31576011C>T	ENSP00000382269:p.Arg2356Lys	Somatic		WXS	Illumina HiSeq	Phase_I	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Missense_Mutation	SNP	ENST00000399332.1	37	CCDS41939.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.5|22.5	4.291848|4.291848	0.80914|0.80914	.|.	.|.	ENSG00000092148|ENSG00000092148	ENST00000554882|ENST00000553700;ENST00000261312;ENST00000399332	.|T;T	.|0.57752	.|0.38;0.38	5.96|5.96	5.96|5.96	0.96718|0.96718	.|HECT (4);	.|0.000000	.|0.85682	.|U	.|0.000000	T|T	0.67618|0.67618	0.2912|0.2912	L|L	0.52364|0.52364	1.645|1.645	0.80722|0.80722	D|D	1|1	.|P	.|0.49185	.|0.92	.|D	.|0.63957	.|0.92	T|T	0.58504|0.58504	-0.7625|-0.7625	5|10	.|0.27785	.|T	.|0.31	-11.4768|-11.4768	20.4082|20.4082	0.99013|0.99013	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|2356	.|Q9ULT8	.|HECD1_HUMAN	K|K	722|2356;2358;2356	.|ENSP00000450697:R2356K;ENSP00000382269:R2356K	.|ENSP00000261312:R2358K	E|R	-|-	1|2	0|0	HECTD1|HECTD1	30645762|30645762	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	7.484000|7.484000	0.81180|0.81180	2.814000|2.814000	0.96858|0.96858	0.655000|0.655000	0.94253|0.94253	GAG|AGA		0.358	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			
IFT122	55764	hgsc.bcm.edu	37	3	129233285	129233286	+	Frame_Shift_Ins	INS	-	-	G			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr3:129233285_129233286insG	ENST00000348417.2	+	25	3118_3119	c.3041_3042insG	c.(3040-3045)ctggccfs	p.A1015fs	IFT122_ENST00000440957.2_Frame_Shift_Ins_p.A806fs|IFT122_ENST00000431818.2_Frame_Shift_Ins_p.A865fs|IFT122_ENST00000504021.1_Frame_Shift_Ins_p.A892fs|IFT122_ENST00000347300.2_Frame_Shift_Ins_p.A956fs|IFT122_ENST00000296266.3_Frame_Shift_Ins_p.A1066fs|IFT122_ENST00000349441.2_Frame_Shift_Ins_p.A905fs|IFT122_ENST00000507564.1_Frame_Shift_Ins_p.A1008fs	NM_052989.1	NP_443715.1	Q9HBG6	IF122_HUMAN	intraflagellar transport 122	1015					camera-type eye morphogenesis (GO:0048593)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic heart tube left/right pattern formation (GO:0060971)|establishment of protein localization to organelle (GO:0072594)|intraciliary anterograde transport (GO:0035720)|intraciliary retrograde transport (GO:0035721)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|protein localization to cilium (GO:0061512)|signal transduction downstream of smoothened (GO:0007227)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|intraciliary transport particle A (GO:0030991)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)				breast(3)|cervix(1)|endometrium(9)|large_intestine(10)|lung(21)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	52						GCCTACAGGCTGGCCCGGCACG	0.604																																																	0																																										SO:0001589	frameshift_variant	55764			AF244930	CCDS3059.1, CCDS3060.1, CCDS3061.1, CCDS3062.1, CCDS63770.1, CCDS63772.1, CCDS63773.1	3q21	2014-07-03	2014-07-03	2005-11-02	ENSG00000163913	ENSG00000163913		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	13556	protein-coding gene	gene with protein product		606045	"""WD repeat domain 10"", ""intraflagellar transport 122 homolog (Chlamydomonas)"""	WDR10		11242542	Standard	NM_052985		Approved	WDR140, WDR10p, SPG	uc003emm.3	Q9HBG6	OTTHUMG00000159516	ENST00000348417.2:c.3043dupG	3.37:g.129233287_129233287dupG	ENSP00000324005:p.Ala1015fs	Somatic		WXS	Illumina HiSeq	Phase_I	B3KW53|B4DEY9|B4DPW7|E7EQF4|E9PDG2|E9PDX2|G3XAB1|H7C3C0|Q53G36|Q8TC06|Q9BTB9|Q9BTY4|Q9HAT9|Q9HBG5|Q9NV68|Q9UF80	Frame_Shift_Ins	INS	ENST00000348417.2	37	CCDS3061.1																																																																																				0.604	IFT122-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355852.1		NM_018262	
ITGB1BP1	9270	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	9548243	9548243	+	Splice_Site	SNP	T	T	C			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr2:9548243T>C	ENST00000360635.3	-	6	1276	c.380A>G	c.(379-381)tAt>tGt	p.Y127C	ITGB1BP1_ENST00000456913.2_Splice_Site_p.Y127C|ITGB1BP1_ENST00000490426.1_5'UTR|ITGB1BP1_ENST00000359712.3_Splice_Site_p.Y127C|ITGB1BP1_ENST00000355346.4_Splice_Site_p.Y127C|ITGB1BP1_ENST00000238091.4_Splice_Site_p.Y127C|ITGB1BP1_ENST00000488451.1_Splice_Site_p.Y127C			O14713	ITBP1_HUMAN	integrin beta 1 binding protein 1	127	PID.				activation of protein kinase B activity (GO:0032148)|biomineral tissue development (GO:0031214)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|integrin activation (GO:0033622)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|myoblast migration (GO:0051451)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of protein binding (GO:0032091)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|Notch signaling pathway (GO:0007219)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein transport (GO:0015031)|receptor clustering (GO:0043113)|regulation of blood vessel size (GO:0050880)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of integrin-mediated signaling pathway (GO:2001044)|transcription, DNA-templated (GO:0006351)|tube formation (GO:0035148)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	GDP-dissociation inhibitor activity (GO:0005092)|integrin binding (GO:0005178)|protein complex binding (GO:0032403)|protein transporter activity (GO:0008565)	p.Y127C(1)		kidney(2)|large_intestine(2)|lung(2)|prostate(2)	8	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.23)		ATTACTTACATATTGATCTGA	0.353																																																	1	Substitution - Missense(1)	kidney(1)											30.0	34.0	32.0					2																	9548243		2200	4292	6492	SO:0001630	splice_region_variant	9270			AF012023	CCDS1662.1, CCDS1663.1	2p25.2	2008-02-05			ENSG00000119185	ENSG00000119185			23927	protein-coding gene	gene with protein product	"""integrin cytoplasmic domain-associated protein 1"", ""integrin cytoplasmic domain-associated protein 1-beta"", ""integrin cytoplasmic domain-associated protein 1-alpha"", ""bodenin"""	607153				11854171, 9281591	Standard	NM_004763		Approved	ICAP-1A, ICAP-1B, ICAP1, ICAP1A, ICAP1B, ICAP-1alpha	uc002qzj.3	O14713	OTTHUMG00000090414	ENST00000360635.3:c.381+1A>G	2.37:g.9548243T>C		Somatic		WXS	Illumina HiSeq	Phase_I	D6W4Y9|O14714|Q53RS0	Missense_Mutation	SNP	ENST00000360635.3	37	CCDS1662.1	.	.	.	.	.	.	.	.	.	.	T	13.97	2.395234	0.42512	.	.	ENSG00000119185	ENST00000360635;ENST00000238091;ENST00000355346;ENST00000359712;ENST00000488451;ENST00000456913;ENST00000492079	.	.	.	5.87	5.87	0.94306	Phosphotyrosine interaction domain (1);Pleckstrin homology-type (1);	0.094607	0.85682	D	0.000000	T	0.37865	0.1019	N	0.04508	-0.205	0.40067	D	0.975962	B;B;B;B	0.06786	0.001;0.001;0.0;0.001	B;B;B;B	0.12156	0.004;0.003;0.001;0.007	T	0.23476	-1.0187	9	0.31617	T	0.26	-17.7607	16.5764	0.84681	0.0:0.0:0.0:1.0	.	83;127;127;127	B4DQY5;A8MPU2;O14713-2;O14713	.;.;.;ITBP1_HUMAN	C	127	.	ENSP00000238091:Y127C	Y	-	2	0	ITGB1BP1	9465694	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.846000	0.62860	2.371000	0.80710	0.533000	0.62120	TAT		0.353	ITGB1BP1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314623.2		NM_004763, NM_022334	Missense_Mutation
IRS1	3667	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	227662870	227662870	+	Silent	SNP	C	C	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr2:227662870C>T	ENST00000305123.5	-	1	1605	c.585G>A	c.(583-585)gtG>gtA	p.V195V	IRS1_ENST00000498335.1_5'Flank|RP11-395N3.2_ENST00000607970.1_lincRNA	NM_005544.2	NP_005535.1	P35568	IRS1_HUMAN	insulin receptor substrate 1	195	IRS-type PTB. {ECO:0000255|PROSITE- ProRule:PRU00389}.				cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid catabolic process (GO:0016042)|mammary gland development (GO:0030879)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein kinase B signaling (GO:0043491)|protein localization to nucleus (GO:0034504)|regulation of gene expression (GO:0010468)|response to insulin (GO:0032868)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)	caveola (GO:0005901)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|insulin receptor complex (GO:0005899)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein kinase C binding (GO:0005080)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.V195V(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(10)|lung(33)|ovary(6)|pancreas(1)|prostate(1)|urinary_tract(2)	69		Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23)		Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137)		AGTTCAGCTTCACGAAGCTGA	0.567											OREG0015248	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					1	Substitution - coding silent(1)	kidney(1)											58.0	56.0	57.0					2																	227662870		2203	4300	6503	SO:0001819	synonymous_variant	3667				CCDS2463.1	2q36	2013-01-10			ENSG00000169047	ENSG00000169047		"""Pleckstrin homology (PH) domain containing"""	6125	protein-coding gene	gene with protein product		147545				1648180	Standard	NM_005544		Approved	HIRS-1	uc002voh.4	P35568	OTTHUMG00000133179	ENST00000305123.5:c.585G>A	2.37:g.227662870C>T		Somatic	2321	WXS	Illumina HiSeq	Phase_I		Silent	SNP	ENST00000305123.5	37	CCDS2463.1																																																																																				0.567	IRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256886.3		NM_005544	
KIF15	56992	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	44816791	44816791	+	Silent	SNP	T	T	C			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr3:44816791T>C	ENST00000326047.4	+	3	257	c.108T>C	c.(106-108)ccT>ccC	p.P36P		NM_020242.2	NP_064627.1	Q9NS87	KIF15_HUMAN	kinesin family member 15	36	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|plus-end kinesin complex (GO:0005873)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.P36P(1)		breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|liver(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(5)	36				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)		TTCGTCCTCCTGCAGAAAGAT	0.438																																																	1	Substitution - coding silent(1)	kidney(1)											156.0	138.0	144.0					3																	44816791		2203	4300	6503	SO:0001819	synonymous_variant	56992			AB035898	CCDS33744.1	3p21.31	2008-03-03	2005-03-15	2005-03-17	ENSG00000163808	ENSG00000163808		"""Kinesins"""	17273	protein-coding gene	gene with protein product			"""kinesin-like 7"""	KNSL7		10878014	Standard	NM_020242		Approved	HKLP2, NY-BR-62	uc003cnx.4	Q9NS87	OTTHUMG00000156307	ENST00000326047.4:c.108T>C	3.37:g.44816791T>C		Somatic		WXS	Illumina HiSeq	Phase_I	Q17RV9|Q69YL6|Q96JX7|Q9H280	Silent	SNP	ENST00000326047.4	37	CCDS33744.1																																																																																				0.438	KIF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343831.2			
KIF16B	55614	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	16509021	16509021	+	Missense_Mutation	SNP	A	A	C			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr20:16509021A>C	ENST00000354981.2	-	2	269	c.112T>G	c.(112-114)Tta>Gta	p.L38V	KIF16B_ENST00000408042.1_Missense_Mutation_p.L38V|KIF16B_ENST00000378003.2_5'UTR|KIF16B_ENST00000355755.3_Missense_Mutation_p.L38V	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	38	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|early endosome to late endosome transport (GO:0045022)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|formation of primary germ layer (GO:0001704)|Golgi to endosome transport (GO:0006895)|microtubule-based movement (GO:0007018)|receptor catabolic process (GO:0032801)|regulation of receptor recycling (GO:0001919)	early endosome (GO:0005769)|endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|plus-end-directed microtubule motor activity (GO:0008574)	p.L38V(2)		NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(24)|ovary(1)|prostate(15)|skin(3)|upper_aerodigestive_tract(2)	74						CTTGCCTTTAAGTTTGTGATT	0.408																																																	2	Substitution - Missense(2)	kidney(2)											228.0	186.0	200.0					20																	16509021		2203	4300	6503	SO:0001583	missense	55614			AK000142	CCDS13122.1, CCDS56178.1	20p11.23	2008-03-03	2008-03-03	2008-03-03	ENSG00000089177	ENSG00000089177		"""Kinesins"""	15869	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 23"""	C20orf23		16084724, 16782399	Standard	NM_024704		Approved	FLJ20135, dJ971B4.1, SNX23	uc010gci.2	Q96L93	OTTHUMG00000031927	ENST00000354981.2:c.112T>G	20.37:g.16509021A>C	ENSP00000347076:p.Leu38Val	Somatic		WXS	Illumina HiSeq	Phase_I	A6NKJ9|A7E2A8|B1AKG3|B1AKT7|C9JDN5|C9JI52|C9JSM8|C9JWJ7|Q2TBF5|Q5HYC0|Q5HYK1|Q5JWW3|Q5TFK5|Q86VL9|Q86YS5|Q8IYU0|Q9BQJ8|Q9BQM0|Q9BQM1|Q9BQM5|Q9H5U0|Q9HCI2|Q9NXN9	Missense_Mutation	SNP	ENST00000354981.2	37	CCDS13122.1	.	.	.	.	.	.	.	.	.	.	A	8.963	0.971156	0.18659	.	.	ENSG00000089177	ENST00000354981;ENST00000355755;ENST00000377997;ENST00000408042	T;T;T	0.74737	-0.87;-0.87;-0.87	5.44	3.15	0.36227	Kinesin, motor domain (4);	0.285863	0.31347	N	0.007816	T	0.37128	0.0992	N	0.01277	-0.915	0.80722	D	1	B;B;B;B	0.17667	0.005;0.023;0.005;0.007	B;B;B;B	0.16289	0.006;0.015;0.009;0.015	T	0.32771	-0.9894	10	0.05525	T	0.97	.	5.8062	0.18442	0.7446:0.1685:0.0869:0.0	.	38;38;38;38	Q96L93-4;Q96L93-2;Q96L93-6;Q96L93	.;.;.;KI16B_HUMAN	V	38	ENSP00000347076:L38V;ENSP00000347995:L38V;ENSP00000384164:L38V	ENSP00000347076:L38V	L	-	1	2	KIF16B	16457021	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.505000	0.35736	0.428000	0.26173	0.455000	0.32223	TTA		0.408	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2		NM_017683	
L1TD1	54596	hgsc.bcm.edu	37	1	62676248	62676251	+	Frame_Shift_Del	DEL	AACT	AACT	-	rs202029696	byFrequency	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	AACT	AACT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr1:62676248_62676251delAACT	ENST00000498273.1	+	4	2097_2100	c.1802_1805delAACT	c.(1801-1806)gaactafs	p.EL601fs	Y_RNA_ENST00000363304.1_RNA	NM_001164835.1|NM_019079.4	NP_001158307.1|NP_061952.3	Q5T7N2	LITD1_HUMAN	LINE-1 type transposase domain containing 1	601										breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	35						CACACAGAAGAACTAACATCCaaa	0.348														29	0.00579073	0.0	0.0043	5008	,	,		23431	0.0		0.0179	False		,,,				2504	0.0082																0									,	16,4250		1,14,2118					,	-0.2	0.0			38	119,8135		7,105,4015	no	frameshift,frameshift	L1TD1	NM_019079.4,NM_001164835.1	,	8,119,6133	A1A1,A1R,RR		1.4417,0.3751,1.0783	,	,		135,12385				SO:0001589	frameshift_variant	54596			BC060808	CCDS619.1	1p31.3	2009-01-12			ENSG00000240563	ENSG00000240563			25595	protein-coding gene	gene with protein product						12477932	Standard	NM_001164835		Approved	FLJ10884, ECAT11	uc001dae.4	Q5T7N2	OTTHUMG00000008914	ENST00000498273.1:c.1802_1805delAACT	1.37:g.62676248_62676251delAACT	ENSP00000419901:p.Glu601fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q8NDA1|Q9NUV8|Q9NV78	Frame_Shift_Del	DEL	ENST00000498273.1	37	CCDS619.1																																																																																				0.348	L1TD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024688.1		NM_019079	
LAMA2	3908	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	129799907	129799907	+	Silent	SNP	T	T	C			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr6:129799907T>C	ENST00000421865.2	+	54	7570	c.7521T>C	c.(7519-7521)aaT>aaC	p.N2507N	RP1-69D17.3_ENST00000442449.1_RNA	NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	2507	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)	p.N2507N(1)		NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		CTCCGTACAATATACTCAGTA	0.363																																																	1	Substitution - coding silent(1)	kidney(1)											160.0	155.0	157.0					6																	129799907		2203	4300	6503	SO:0001819	synonymous_variant	3908			Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"""Laminins"""	6482	protein-coding gene	gene with protein product	"""merosin"", ""congenital muscular dystrophy"""	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.7521T>C	6.37:g.129799907T>C		Somatic		WXS	Illumina HiSeq	Phase_I	Q14736|Q5VUM2|Q93022	Silent	SNP	ENST00000421865.2	37	CCDS5138.1																																																																																				0.363	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			
LRFN5	145581	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	42356025	42356025	+	Missense_Mutation	SNP	T	T	G			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr14:42356025T>G	ENST00000298119.4	+	3	1386	c.197T>G	c.(196-198)aTt>aGt	p.I66S	LRFN5_ENST00000554120.1_Missense_Mutation_p.I66S|LRFN5_ENST00000554171.1_Missense_Mutation_p.I66S	NM_152447.3	NP_689660.2	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III domain containing 5	66						integral component of membrane (GO:0016021)		p.I66S(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(67)|ovary(5)|pancreas(3)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(2)	120			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)		GTTACAAATATTAAAAGGAAA	0.403										HNSCC(30;0.082)																																							1	Substitution - Missense(1)	kidney(1)											50.0	48.0	49.0					14																	42356025		2203	4300	6503	SO:0001583	missense	145581			AK055365	CCDS9678.1	14q21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000165379	ENSG00000165379		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	20360	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 8"""	612811	"""chromosome 14 open reading frame 146"""	C14orf146		16828986	Standard	NM_152447		Approved	FIGLER8, SALM5	uc001wvm.3	Q96NI6	OTTHUMG00000140261	ENST00000298119.4:c.197T>G	14.37:g.42356025T>G	ENSP00000298119:p.Ile66Ser	Somatic		WXS	Illumina HiSeq	Phase_I	B3KU78|Q86XL2	Missense_Mutation	SNP	ENST00000298119.4	37	CCDS9678.1	.	.	.	.	.	.	.	.	.	.	T	16.45	3.128083	0.56721	.	.	ENSG00000165379	ENST00000298119;ENST00000554120;ENST00000554171	D;D;D	0.96011	-3.88;-3.88;-3.88	5.56	5.56	0.83823	.	0.000000	0.56097	D	0.000023	D	0.98235	0.9416	H	0.96518	3.835	0.53688	D	0.999976	P;D	0.57257	0.908;0.979	P;P	0.62740	0.791;0.906	D	0.99301	1.0901	10	0.87932	D	0	.	13.6661	0.62396	0.0:0.0:0.0:1.0	.	66;66	G3V364;Q96NI6	.;LRFN5_HUMAN	S	66	ENSP00000298119:I66S;ENSP00000451897:I66S;ENSP00000451067:I66S	ENSP00000298119:I66S	I	+	2	0	LRFN5	41425775	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.040000	0.89188	2.098000	0.63641	0.528000	0.53228	ATT		0.403	LRFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276786.1		NM_152447	
LSM7	51690	broad.mit.edu;hgsc.bcm.edu	37	19	2321719	2321719	+	Missense_Mutation	SNP	T	T	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr19:2321719T>A	ENST00000252622.10	-	4	325	c.272A>T	c.(271-273)gAg>gTg	p.E91V	LSM7_ENST00000589532.1_5'UTR	NM_016199.2	NP_057283.1	Q9UK45	LSM7_HUMAN	LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae)	91					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)	cytosol (GO:0005829)|spliceosomal complex (GO:0005681)	U6 snRNA binding (GO:0017070)	p.E91V(2)		kidney(1)|urinary_tract(1)	2				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGGGATGGCCTCCATGCCGTC	0.701																																																	2	Substitution - Missense(2)	kidney(2)											18.0	22.0	21.0					19																	2321719		2038	4158	6196	SO:0001583	missense	51690			AF182293	CCDS45907.1	19p13.3	2008-05-02			ENSG00000130332	ENSG00000130332			20470	protein-coding gene	gene with protein product		607287				10523320, 12515382	Standard	NM_016199		Approved	YNL147W	uc002lvp.4	Q9UK45		ENST00000252622.10:c.272A>T	19.37:g.2321719T>A	ENSP00000252622:p.Glu91Val	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000252622.10	37	CCDS45907.1	.	.	.	.	.	.	.	.	.	.	T	27.7	4.852506	0.91355	.	.	ENSG00000130332	ENST00000252622	T	0.54279	0.58	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.77785	0.4182	M	0.92784	3.345	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.82932	-0.0212	10	0.62326	D	0.03	-21.1389	12.9797	0.58555	0.0:0.0:0.0:1.0	.	91	Q9UK45	LSM7_HUMAN	V	91	ENSP00000252622:E91V	ENSP00000252622:E91V	E	-	2	0	LSM7	2272719	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.032000	0.76498	1.963000	0.57068	0.454000	0.30748	GAG		0.701	LSM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451375.2			
MAP1A	4130	hgsc.bcm.edu	37	15	43816122	43816123	+	Frame_Shift_Ins	INS	-	-	G			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr15:43816122_43816123insG	ENST00000300231.5	+	4	2901_2902	c.2451_2452insG	c.(2452-2454)gccfs	p.A818fs	MAP1A_ENST00000382031.1_Frame_Shift_Ins_p.A1056fs|MAP1A_ENST00000399453.1_Frame_Shift_Ins_p.A818fs			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	818					microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	ACATAGTGGCTGCCCCTTTGGC	0.52																																																	0																																										SO:0001589	frameshift_variant	4130			U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.2452dupG	15.37:g.43816123_43816123dupG	ENSP00000300231:p.Ala818fs	Somatic		WXS	Illumina HiSeq	Phase_I	O95643|Q12973|Q15882|Q9UJT4	Frame_Shift_Ins	INS	ENST00000300231.5	37	CCDS42031.1																																																																																				0.520	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5		NM_002373	
MOCS1	4337	hgsc.bcm.edu	37	6	39895285	39895285	+	Intron	SNP	G	G	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr6:39895285G>T	ENST00000340692.5	-	2	127				MOCS1_ENST00000373188.2_Intron|MOCS1_ENST00000373195.3_Intron|MOCS1_ENST00000432280.2_Silent_p.V11V|MOCS1_ENST00000425303.2_Silent_p.V11V|MOCS1_ENST00000373186.4_Silent_p.V11V|MOCS1_ENST00000308559.7_Intron|MOCS1_ENST00000373175.4_Silent_p.V11V			Q9NZB8	MOCS1_HUMAN	molybdenum cofactor synthesis 1						Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|molybdopterin synthase complex (GO:0019008)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|cyclic pyranopterin monophosphate synthase activity (GO:0061597)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)	p.V11V(1)		central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	21	Ovarian(28;0.0355)|Colorectal(47;0.196)					CCCTTACTCTGACATCTGTGC	0.582																																					NSCLC(84;861 1413 23785 24908 42279)|Melanoma(182;611 2047 9114 11847 26639)												1	Substitution - coding silent(1)	kidney(1)											63.0	59.0	60.0					6																	39895285		2203	4299	6502	SO:0001627	intron_variant	4337			AJ224328	CCDS4846.1, CCDS43460.1	6p21.2	2012-05-08			ENSG00000124615	ENSG00000124615			7190	protein-coding gene	gene with protein product		603707				9731530, 10053004	Standard	NM_001075098		Approved	MOCOD	uc003opb.3	Q9NZB8	OTTHUMG00000014656	ENST00000340692.5:c.124-91C>A	6.37:g.39895285G>T		Somatic		WXS	Illumina HiSeq	Phase_I	B3KPT7|B4DTP1|O14940|O14941|O75710|Q5J7W0|Q5TCE1|Q5TCE2|Q5TCE6|Q5TCE9|Q5TCF0|Q5TCF1|Q8N418|Q9NZB7|Q9UEM1	Silent	SNP	ENST00000340692.5	37																																																																																					0.582	MOCS1-005	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000040476.2		NM_005943	
MS4A7	58475	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	60150630	60150630	+	Missense_Mutation	SNP	C	C	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr11:60150630C>A	ENST00000300184.3	+	2	212	c.16C>A	c.(16-18)Caa>Aaa	p.Q6K	MS4A14_ENST00000531787.1_Intron|MS4A7_ENST00000534016.1_Missense_Mutation_p.Q6K|MS4A7_ENST00000530234.2_Missense_Mutation_p.Q6K|MS4A7_ENST00000358246.1_Missense_Mutation_p.Q6K	NM_021201.4|NM_206939.1	NP_067024.1|NP_996822.1	Q9GZW8	MS4A7_HUMAN	membrane-spanning 4-domains, subfamily A, member 7	6						integral component of membrane (GO:0016021)		p.Q6K(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(2)|lung(8)|ovary(1)|skin(1)	20						ATTACAATCCCAAACCATGGG	0.443																																																	1	Substitution - Missense(1)	kidney(1)											115.0	106.0	109.0					11																	60150630		2203	4300	6503	SO:0001583	missense	58475			AB026043	CCDS7985.1, CCDS7986.1	11q12	2008-03-25				ENSG00000166927			13378	protein-coding gene	gene with protein product		606502				11245982, 11401424	Standard	NM_021201		Approved	CD20L4, CFFM4, MS4A8	uc001npf.3	Q9GZW8		ENST00000300184.3:c.16C>A	11.37:g.60150630C>A	ENSP00000300184:p.Gln6Lys	Somatic		WXS	Illumina HiSeq	Phase_I	A6NP53|Q6IAG8	Missense_Mutation	SNP	ENST00000300184.3	37	CCDS7985.1	.	.	.	.	.	.	.	.	.	.	C	0.015	-1.566732	0.00895	.	.	ENSG00000166927	ENST00000300184;ENST00000358246;ENST00000534016;ENST00000530614;ENST00000530027;ENST00000530234	T;T;T;T;T;T	0.40756	3.33;2.64;2.64;2.64;2.84;1.02	3.8	-3.09	0.05331	.	2.227280	0.02170	N	0.059615	T	0.22126	0.0533	N	0.13098	0.295	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.32348	-0.9910	10	0.02654	T	1	-19.7843	8.3658	0.32385	0.2493:0.6473:0.1034:0.0	.	6;6;6	E9PIV6;Q9GZW8-2;Q9GZW8	.;.;MS4A7_HUMAN	K	6	ENSP00000300184:Q6K;ENSP00000350983:Q6K;ENSP00000434637:Q6K;ENSP00000433861:Q6K;ENSP00000434819:Q6K;ENSP00000433184:Q6K	ENSP00000300184:Q6K	Q	+	1	0	MS4A7	59907206	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.139000	0.10358	-0.619000	0.05648	-1.014000	0.02459	CAA		0.443	MS4A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394299.1			
MUC17	140453	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	100685938	100685938	+	Missense_Mutation	SNP	G	G	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr7:100685938G>T	ENST00000306151.4	+	3	11305	c.11241G>T	c.(11239-11241)atG>atT	p.M3747I		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	3747	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)	p.M3747I(2)		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)					CTGTGTCAATGCCCATGGAAA	0.473																																																	2	Substitution - Missense(2)	large_intestine(1)|kidney(1)											231.0	219.0	223.0					7																	100685938		2203	4300	6503	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.11241G>T	7.37:g.100685938G>T	ENSP00000302716:p.Met3747Ile	Somatic		WXS	Illumina HiSeq	Phase_I	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	g	0.015	-1.568913	0.00895	.	.	ENSG00000169876	ENST00000306151	T	0.01854	4.6	2.18	-4.37	0.03633	.	.	.	.	.	T	0.01156	0.0038	N	0.08118	0	0.09310	N	1	B	0.17852	0.024	B	0.21546	0.035	T	0.44251	-0.9340	9	0.36615	T	0.2	.	1.8825	0.03231	0.2822:0.1252:0.4285:0.164	.	3747	Q685J3	MUC17_HUMAN	I	3747	ENSP00000302716:M3747I	ENSP00000302716:M3747I	M	+	3	0	MUC17	100472658	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.017000	0.03630	-2.879000	0.00320	-2.111000	0.00353	ATG		0.473	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1		NM_001040105	
MYCBP2	23077	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	77835374	77835374	+	Missense_Mutation	SNP	A	A	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr13:77835374A>T	ENST00000544440.2	-	12	1687	c.1670T>A	c.(1669-1671)cTt>cAt	p.L557H	MYCBP2_ENST00000407578.2_Missense_Mutation_p.L595H|MYCBP2_ENST00000360084.5_5'UTR|MYCBP2_ENST00000357337.6_Missense_Mutation_p.L557H					MYC binding protein 2, E3 ubiquitin protein ligase									p.L557H(2)|p.L595H(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		TGCAACTAAAAGGGCGTGAGA	0.403																																																	3	Substitution - Missense(3)	kidney(3)											133.0	121.0	125.0					13																	77835374		2203	4300	6503	SO:0001583	missense	23077			AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"""MYC binding protein 2"""			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.1670T>A	13.37:g.77835374A>T	ENSP00000444596:p.Leu557His	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000544440.2	37		.	.	.	.	.	.	.	.	.	.	A	24.3	4.511846	0.85389	.	.	ENSG00000005810	ENST00000357337;ENST00000407578;ENST00000544440	D;D;D	0.82803	-1.65;-1.65;-1.65	5.62	5.62	0.85841	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.64402	D	0.000004	D	0.89061	0.6608	L	0.55481	1.735	0.58432	D	0.999995	D	0.76494	0.999	D	0.77557	0.99	D	0.90126	0.4203	10	0.87932	D	0	.	15.8183	0.78621	1.0:0.0:0.0:0.0	.	557	O75592	MYCB2_HUMAN	H	557;595;557	ENSP00000349892:L557H;ENSP00000384288:L595H;ENSP00000444596:L557H	ENSP00000349892:L557H	L	-	2	0	MYCBP2	76733375	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	9.228000	0.95250	2.143000	0.66587	0.477000	0.44152	CTT		0.403	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1		NM_015057	
NBN	4683	broad.mit.edu;ucsc.edu	37	8	90955480	90955481	+	Splice_Site	DEL	CC	CC	-			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	CC	CC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr8:90955480_90955481delCC	ENST00000265433.3	-	14	2338_2339	c.2184_2185delGG	c.(2182-2187)gaggta>gata	p.EV728fs	NBN_ENST00000409330.1_Splice_Site_p.EV646fs	NM_002485.4	NP_002476.2	O60934	NBN_HUMAN	nibrin	728					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)			TTCCTACTAACCTCCATTTCCT	0.401								Homologous recombination																																									0																																										SO:0001630	splice_region_variant	4683			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.2184+1GG>-	8.37:g.90955480_90955481delCC		Somatic		WXS	Illumina GAIIx	Phase_I	B2R626|B2RNC5|O60672|Q32NF7|Q53FM6|Q63HR6|Q7LDM2	Splice_Site	DEL	ENST00000265433.3	37	CCDS6249.1																																																																																				0.401	NBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331583.3		NM_001024688	Frame_Shift_Del
NETO1	81832	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	18	70417575	70417575	+	Silent	SNP	C	C	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr18:70417575C>T	ENST00000327305.6	-	9	1920	c.1263G>A	c.(1261-1263)cgG>cgA	p.R421R	NETO1_ENST00000583169.1_Silent_p.R421R|NETO1_ENST00000299430.2_Silent_p.R420R|RNA5SP460_ENST00000516789.1_RNA	NM_138966.3	NP_620416	Q8TDF5	NETO1_HUMAN	neuropilin (NRP) and tolloid (TLL)-like 1	421					memory (GO:0007613)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|receptor localization to synapse (GO:0097120)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|visual learning (GO:0008542)	cell junction (GO:0030054)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|kainate selective glutamate receptor complex (GO:0032983)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)		p.R421R(1)		NS(3)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(36)|ovary(2)|prostate(3)|skin(3)|stomach(1)	63		Esophageal squamous(42;0.129)		READ - Rectum adenocarcinoma(1;0.0487)		AAGATGACCTCCGCAGTTTAT	0.463																																																	1	Substitution - coding silent(1)	kidney(1)											105.0	95.0	98.0					18																	70417575		2203	4300	6503	SO:0001819	synonymous_variant	81832			AF448838	CCDS12000.1, CCDS42444.1	18q22.2	2008-08-01			ENSG00000166342	ENSG00000166342			13823	protein-coding gene	gene with protein product		607973				11943477, 12810072	Standard	NM_138999		Approved	BTCL1, BCTL1	uc002lkw.3	Q8TDF5	OTTHUMG00000132834	ENST00000327305.6:c.1263G>A	18.37:g.70417575C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q86W85|Q8ND78|Q8TDF4	Silent	SNP	ENST00000327305.6	37	CCDS12000.1																																																																																				0.463	NETO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256301.2		NM_138999	
NLRP8	126205	hgsc.bcm.edu;ucsc.edu	37	19	56487556	56487557	+	Frame_Shift_Ins	INS	-	-	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr19:56487556_56487557insA	ENST00000291971.3	+	8	2834_2835	c.2763_2764insA	c.(2764-2766)aaafs	p.K922fs	NLRP8_ENST00000590542.1_Frame_Shift_Ins_p.K903fs	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	922					neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		CTGCGCTCTGTAAAAATAAAAC	0.411																																																	0																																										SO:0001589	frameshift_variant	126205			AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"""Nucleotide-binding domain and leucine rich repeat containing"""	22940	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"""	609659	"""NACHT, leucine rich repeat and PYD containing 8"""	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.2768dupA	19.37:g.56487561_56487561dupA	ENSP00000291971:p.Lys922fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q7RTR4	Frame_Shift_Ins	INS	ENST00000291971.3	37	CCDS12937.1																																																																																				0.411	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1		NM_176811	
OR4P4	81300	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	55405910	55405910	+	Missense_Mutation	SNP	T	T	C			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr11:55405910T>C	ENST00000314612.2	+	1	77	c.77T>C	c.(76-78)tTt>tCt	p.F26S		NM_001004124.1	NP_001004124.1	Q8NGL7	OR4P4_HUMAN	olfactory receptor, family 4, subfamily P, member 4	26						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F26S(1)		autonomic_ganglia(1)|central_nervous_system(1)|kidney(4)|large_intestine(4)|lung(28)|ovary(1)|upper_aerodigestive_tract(1)	40						GTCCTCTGCTTTGTATTATTT	0.353																																																	1	Substitution - Missense(1)	kidney(1)											125.0	116.0	119.0					11																	55405910		2181	4027	6208	SO:0001583	missense	81300			AB065775	CCDS31504.1	11q11	2012-08-09			ENSG00000181927	ENSG00000181927		"""GPCR / Class A : Olfactory receptors"""	15180	protein-coding gene	gene with protein product				OR4P3P			Standard	NM_001004124		Approved		uc010rij.2	Q8NGL7	OTTHUMG00000165300	ENST00000314612.2:c.77T>C	11.37:g.55405910T>C	ENSP00000324831:p.Phe26Ser	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000314612.2	37	CCDS31504.1	.	.	.	.	.	.	.	.	.	.	T	12.83	2.056135	0.36277	.	.	ENSG00000181927	ENST00000314612	T	0.04551	3.6	5.02	3.89	0.44902	.	0.000000	0.41938	D	0.000783	T	0.16342	0.0393	M	0.71296	2.17	0.23611	N	0.9973	D	0.58620	0.983	D	0.65773	0.938	T	0.02339	-1.1174	10	0.56958	D	0.05	-16.6902	9.6549	0.39919	0.0:0.0841:0.0:0.9158	.	26	Q8NGL7	OR4P4_HUMAN	S	26	ENSP00000324831:F26S	ENSP00000324831:F26S	F	+	2	0	OR4P4	55162486	0.999000	0.42202	0.084000	0.20598	0.222000	0.24845	3.586000	0.53950	0.773000	0.33404	0.509000	0.49947	TTT		0.353	OR4P4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383356.1		NM_001004124	
OR7D2	162998	hgsc.bcm.edu;ucsc.edu	37	19	9297034	9297034	+	Frame_Shift_Del	DEL	T	T	-			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr19:9297034delT	ENST00000344248.2	+	1	756	c.577delT	c.(577-579)ttcfs	p.F193fs		NM_175883.2	NP_787079.1	Q96RA2	OR7D2_HUMAN	olfactory receptor, family 7, subfamily D, member 2	193					regulation of transcription, DNA-templated (GO:0006355)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|upper_aerodigestive_tract(2)	20						CTCTGATACCTTCCTGAACAG	0.418																																																	0													185.0	174.0	178.0					19																	9297034		2203	4300	6503	SO:0001589	frameshift_variant	162998			AK095468	CCDS32900.1	19p13.2	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	8378	protein-coding gene	gene with protein product							Standard	NM_175883		Approved	OR19-4, HTPCRH03, FLJ38149	uc002mkz.1	Q96RA2		ENST00000344248.2:c.577delT	19.37:g.9297034delT	ENSP00000345563:p.Phe193fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q6IFJ7|Q8N133	Frame_Shift_Del	DEL	ENST00000344248.2	37	CCDS32900.1																																																																																				0.418	OR7D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449002.1			
PBRM1	55193	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	52651419	52651419	+	Nonsense_Mutation	SNP	A	A	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr3:52651419A>T	ENST00000296302.7	-	14	1678	c.1677T>A	c.(1675-1677)taT>taA	p.Y559*	PBRM1_ENST00000409114.3_Nonsense_Mutation_p.Y574*|PBRM1_ENST00000394830.3_Nonsense_Mutation_p.Y559*|PBRM1_ENST00000337303.4_Nonsense_Mutation_p.Y559*|PBRM1_ENST00000356770.4_Nonsense_Mutation_p.Y527*|PBRM1_ENST00000409057.1_Nonsense_Mutation_p.Y559*|PBRM1_ENST00000409767.1_Nonsense_Mutation_p.Y574*|PBRM1_ENST00000410007.1_Nonsense_Mutation_p.Y559*			Q86U86	PB1_HUMAN	polybromo 1	559	Bromo 4. {ECO:0000255|PROSITE- ProRule:PRU00035}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.Y559*(2)|p.Y527*(1)		breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		AGATGATTTTATAATAATCAG	0.378			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																			Rec	yes		3	3p21	55193	polybromo 1		E	3	Substitution - Nonsense(3)	kidney(3)											110.0	111.0	111.0					3																	52651419		2203	4300	6503	SO:0001587	stop_gained	55193			BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.1677T>A	3.37:g.52651419A>T	ENSP00000296302:p.Tyr559*	Somatic		WXS	Illumina HiSeq	Phase_I	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Nonsense_Mutation	SNP	ENST00000296302.7	37		.	.	.	.	.	.	.	.	.	.	A	37	6.568650	0.97671	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351;ENST00000446103	.	.	.	5.84	3.16	0.36331	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-28.4785	9.6974	0.40165	0.7618:0.0:0.2382:0.0	.	.	.	.	X	527;559;559;559;559;559;574;574;559;518	.	ENSP00000296302:Y559X	Y	-	3	2	PBRM1	52626459	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.943000	0.40253	1.045000	0.40225	0.533000	0.62120	TAT		0.378	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1		NM_018165	
PCDHGA11	56105	broad.mit.edu;hgsc.bcm.edu	37	5	140802703	140802703	+	Missense_Mutation	SNP	G	G	C			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr5:140802703G>C	ENST00000398587.2	+	1	1942	c.1909G>C	c.(1909-1911)Gac>Cac	p.D637H	PCDHGA5_ENST00000518069.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA8_ENST00000398604.2_Intron	NM_018914.2|NM_032092.1	NP_061737.1|NP_114481.1	Q9Y5H2	PCDGB_HUMAN	protocadherin gamma subfamily A, 11	637	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)	p.D637H(1)		breast(3)|endometrium(8)|kidney(3)|large_intestine(9)|lung(22)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCTGGACAGAGACGCGCTCAA	0.697																																																	1	Substitution - Missense(1)	kidney(1)											44.0	53.0	50.0					5																	140802703		2203	4299	6502	SO:0001583	missense	56105			AF152505	CCDS47294.1, CCDS54930.1, CCDS75345.1	5q31	2010-01-26			ENSG00000253873	ENSG00000253873		"""Cadherins / Protocadherins : Clustered"""	8698	other	protocadherin		606298				10380929	Standard	NM_018914		Approved	PCDH-GAMMA-A11		Q9Y5H2	OTTHUMG00000164055	ENST00000398587.2:c.1909G>C	5.37:g.140802703G>C	ENSP00000381589:p.Asp637His	Somatic		WXS	Illumina HiSeq	Phase_I	B7ZVY8|Q9Y5D8|Q9Y5D9	Missense_Mutation	SNP	ENST00000398587.2	37	CCDS47294.1	.	.	.	.	.	.	.	.	.	.	g	18.63	3.666111	0.67700	.	.	ENSG00000253873	ENST00000398587	T	0.52754	0.65	5.33	5.33	0.75918	Cadherin (4);Cadherin-like (1);	0.000000	0.29624	U	0.011638	T	0.71484	0.3345	M	0.78801	2.425	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.991	T	0.75105	-0.3435	10	0.87932	D	0	.	19.0887	0.93217	0.0:0.0:1.0:0.0	.	637;637	Q9Y5H2;Q9Y5H2-2	PCDGB_HUMAN;.	H	637	ENSP00000381589:D637H	ENSP00000381589:D637H	D	+	1	0	PCDHGA11	140782887	1.000000	0.71417	0.994000	0.49952	0.708000	0.40852	6.654000	0.74387	2.520000	0.84964	0.556000	0.70494	GAC		0.697	PCDHGA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376974.1		NM_018914	
PCLO	27445	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	82430893	82430893	+	Missense_Mutation	SNP	T	T	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr7:82430893T>A	ENST00000333891.9	-	22	15285	c.14948A>T	c.(14947-14949)cAg>cTg	p.Q4983L		NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.Q4983L(2)		breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TTGTCCATTCTGTCCCATCTT	0.348																																																	2	Substitution - Missense(2)	kidney(2)											102.0	99.0	100.0					7																	82430893		1818	4079	5897	SO:0001583	missense	27445			AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.14948A>T	7.37:g.82430893T>A	ENSP00000334319:p.Gln4983Leu	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	T	14.96	2.690464	0.48097	.	.	ENSG00000186472	ENST00000333891	T	0.17691	2.26	5.66	5.66	0.87406	.	.	.	.	.	T	0.20333	0.0489	N	0.24115	0.695	0.80722	D	1	P	0.46142	0.873	P	0.49047	0.599	T	0.01420	-1.1359	9	0.87932	D	0	.	15.8952	0.79329	0.0:0.0:0.0:1.0	.	4983	Q9Y6V0-5	.	L	4983	ENSP00000334319:Q4983L	ENSP00000334319:Q4983L	Q	-	2	0	PCLO	82268829	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.505000	0.66981	2.162000	0.67917	0.397000	0.26171	CAG		0.348	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5		NM_014510	
PCNXL2	80003	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	233386509	233386509	+	Missense_Mutation	SNP	T	T	C			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr1:233386509T>C	ENST00000258229.9	-	8	2432	c.2198A>G	c.(2197-2199)aAt>aGt	p.N733S	PCNXL2_ENST00000430153.1_Missense_Mutation_p.N32S	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	733						integral component of membrane (GO:0016021)		p.N733S(1)		NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(7)|large_intestine(19)|lung(30)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86		all_cancers(173;0.0347)|Prostate(94;0.137)				ACAGTCATTATTTGATGGTAG	0.413																																																	1	Substitution - Missense(1)	kidney(1)											68.0	68.0	68.0					1																	233386509		1888	4103	5991	SO:0001583	missense	80003			AK055374	CCDS44335.1	1q42.2	2008-02-05	2001-11-28		ENSG00000135749	ENSG00000135749			8736	protein-coding gene	gene with protein product			"""pecanex (Drosophila)-like 2"""			12477932	Standard	NM_014801		Approved	KIAA0435, FLJ11383	uc001hvl.2	A6NKB5	OTTHUMG00000037824	ENST00000258229.9:c.2198A>G	1.37:g.233386509T>C	ENSP00000258229:p.Asn733Ser	Somatic		WXS	Illumina HiSeq	Phase_I	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	Missense_Mutation	SNP	ENST00000258229.9	37	CCDS44335.1	.	.	.	.	.	.	.	.	.	.	T	11.48	1.651930	0.29336	.	.	ENSG00000135749	ENST00000258229;ENST00000430153	T;T	0.32988	1.43;1.43	5.74	2.25	0.28309	.	0.000000	0.36972	U	0.002316	T	0.15435	0.0372	L	0.27053	0.805	0.09310	N	1	B;B	0.16802	0.019;0.008	B;B	0.14023	0.01;0.003	T	0.33854	-0.9852	10	0.02654	T	1	.	7.9015	0.29738	0.0:0.2252:0.0:0.7748	.	32;733	A6NKB5-2;A6NKB5	.;PCX2_HUMAN	S	733;32	ENSP00000258229:N733S;ENSP00000394703:N32S	ENSP00000258229:N733S	N	-	2	0	PCNXL2	231453132	0.107000	0.21998	0.007000	0.13788	0.004000	0.04260	1.584000	0.36589	0.461000	0.27071	0.459000	0.35465	AAT		0.413	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092480.3		NM_014801	
PEX5	5830	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	7360264	7360264	+	Missense_Mutation	SNP	T	T	G			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr12:7360264T>G	ENST00000455147.2	+	12	1556	c.976T>G	c.(976-978)Ttt>Gtt	p.F326V	PEX5_ENST00000266564.3_Missense_Mutation_p.F318V|PEX5_ENST00000412720.2_Missense_Mutation_p.F347V|PEX5_ENST00000420616.2_Missense_Mutation_p.F326V|PEX5_ENST00000266563.5_Missense_Mutation_p.F289V|PEX5_ENST00000434354.2_Missense_Mutation_p.F341V	NM_001131026.1	NP_001124498.1	P50542	PEX5_HUMAN	peroxisomal biogenesis factor 5	326					cell development (GO:0048468)|cerebral cortex cell migration (GO:0021795)|cerebral cortex neuron differentiation (GO:0021895)|endoplasmic reticulum organization (GO:0007029)|fatty acid beta-oxidation (GO:0006635)|mitochondrial membrane organization (GO:0007006)|negative regulation of protein homotetramerization (GO:1901094)|neuromuscular process (GO:0050905)|neuron migration (GO:0001764)|positive regulation of multicellular organism growth (GO:0040018)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome matrix, docking (GO:0016560)|protein import into peroxisome matrix, translocation (GO:0016561)|protein import into peroxisome membrane (GO:0045046)|protein targeting to peroxisome (GO:0006625)|protein tetramerization (GO:0051262)|very long-chain fatty acid metabolic process (GO:0000038)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)	enzyme binding (GO:0019899)|peroxisome matrix targeting signal-1 binding (GO:0005052)|peroxisome targeting sequence binding (GO:0000268)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|small GTPase binding (GO:0031267)	p.F318V(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)	21						GGGGTACCAGTTTGAGGAGGA	0.557																																																	1	Substitution - Missense(1)	kidney(1)											83.0	84.0	84.0					12																	7360264		2203	4300	6503	SO:0001583	missense	5830			U19721	CCDS8576.1, CCDS44822.1, CCDS44823.1, CCDS44824.1, CCDS73433.1	12p	2013-01-10	2004-03-17	2004-03-19		ENSG00000139197		"""Tetratricopeptide (TTC) repeat domain containing"""	9719	protein-coding gene	gene with protein product		600414	"""peroxisome receptor 1"""	PXR1			Standard	NM_000319		Approved	PTS1R	uc010sgc.2	P50542		ENST00000455147.2:c.976T>G	12.37:g.7360264T>G	ENSP00000400647:p.Phe326Val	Somatic		WXS	Illumina HiSeq	Phase_I	A8K891|B4DZ45|B7ZAD5|D3DUT8|Q15115|Q15266|Q96FN7	Missense_Mutation	SNP	ENST00000455147.2	37	CCDS44823.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.556555	0.86231	.	.	ENSG00000139197	ENST00000455147;ENST00000266563;ENST00000434354;ENST00000420616;ENST00000412720;ENST00000396637;ENST00000266564	T;T;T;T;T;T;T	0.80738	-1.41;-1.41;-1.41;-1.41;-1.41;-1.41;-1.41	4.95	4.95	0.65309	Tetratricopeptide-like helical (1);	0.100153	0.64402	D	0.000001	D	0.87617	0.6222	L	0.61036	1.89	0.80722	D	1	B;D;D;D;D	0.57899	0.332;0.981;0.962;0.978;0.978	B;D;D;D;D	0.71414	0.256;0.94;0.94;0.973;0.973	D	0.89008	0.3426	10	0.87932	D	0	.	14.7772	0.69738	0.0:0.0:0.0:1.0	.	347;341;326;318;289	B4E0T2;B4DZ45;P50542;P50542-3;P50542-2	.;.;PEX5_HUMAN;.;.	V	326;289;341;326;347;296;318	ENSP00000400647:F326V;ENSP00000266563:F289V;ENSP00000407401:F341V;ENSP00000410159:F326V;ENSP00000391601:F347V;ENSP00000379877:F296V;ENSP00000266564:F318V	ENSP00000266563:F289V	F	+	1	0	PEX5	7251531	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	7.776000	0.85560	2.079000	0.62486	0.402000	0.26972	TTT		0.557	PEX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398611.1		NM_000319	
PLA2G7	7941	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	46684241	46684241	+	Missense_Mutation	SNP	G	G	C			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr6:46684241G>C	ENST00000274793.7	-	4	452	c.256C>G	c.(256-258)Cca>Gca	p.P86A	PLA2G7_ENST00000537365.1_Missense_Mutation_p.P86A|PLA2G7_ENST00000541026.1_Intron|PLA2G7_ENST00000538237.1_Missense_Mutation_p.P41A	NM_005084.3	NP_005075.3	Q13093	PAFA_HUMAN	phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)	86					cellular protein metabolic process (GO:0044267)|lipid catabolic process (GO:0016042)|lipid oxidation (GO:0034440)|low-density lipoprotein particle remodeling (GO:0034374)|plasma lipoprotein particle oxidation (GO:0034441)|positive regulation of inflammatory response (GO:0050729)|positive regulation of monocyte chemotaxis (GO:0090026)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|low-density lipoprotein particle (GO:0034362)	1-alkyl-2-acetylglycerophosphocholine esterase activity (GO:0003847)|calcium-independent phospholipase A2 activity (GO:0047499)|phospholipid binding (GO:0005543)	p.P86A(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|skin(1)|soft_tissue(1)	14			Lung(136;0.192)			TCTTGGGATGGATAATATAAA	0.368																																																	1	Substitution - Missense(1)	kidney(1)											94.0	93.0	93.0					6																	46684241		2203	4300	6503	SO:0001583	missense	7941			U20157	CCDS4917.1	6p21.2-p12	2008-09-19			ENSG00000146070	ENSG00000146070	3.1.1.4		9040	protein-coding gene	gene with protein product		601690				7700381, 8624782	Standard	NM_005084		Approved	PAFAH, LDL-PLA2	uc021zae.1	Q13093	OTTHUMG00000014789	ENST00000274793.7:c.256C>G	6.37:g.46684241G>C	ENSP00000274793:p.Pro86Ala	Somatic		WXS	Illumina HiSeq	Phase_I	A5HTT5|Q15692|Q5VTT1|Q8IVA2	Missense_Mutation	SNP	ENST00000274793.7	37	CCDS4917.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.028537	0.75390	.	.	ENSG00000146070	ENST00000274793;ENST00000537365;ENST00000538237	T;T;T	0.63096	-0.02;-0.02;-0.02	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	T	0.80276	0.4593	M	0.90705	3.14	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79784	0.993;0.985;0.985	D	0.84132	0.0412	10	0.87932	D	0	.	16.2297	0.82323	0.0:0.0:1.0:0.0	.	41;86;86	F5GYY6;A8K2W6;Q13093	.;.;PAFA_HUMAN	A	86;86;41	ENSP00000274793:P86A;ENSP00000445666:P86A;ENSP00000441416:P41A	ENSP00000274793:P86A	P	-	1	0	PLA2G7	46792200	1.000000	0.71417	1.000000	0.80357	0.689000	0.40095	7.728000	0.84847	2.622000	0.88805	0.563000	0.77884	CCA		0.368	PLA2G7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040802.1			
PNPLA6	10908	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	7605595	7605595	+	Splice_Site	SNP	C	C	G			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr19:7605595C>G	ENST00000221249.6	+	9	1108	c.677C>G	c.(676-678)aCc>aGc	p.T226S	PNPLA6_ENST00000414982.3_Splice_Site_p.T274S|PNPLA6_ENST00000600737.1_Splice_Site_p.T265S|PNPLA6_ENST00000545201.2_Splice_Site_p.T226S|PNPLA6_ENST00000450331.3_Splice_Site_p.T226S	NM_006702.4	NP_006693.3	Q8IY17	PLPL6_HUMAN	patatin-like phospholipase domain containing 6	265					angiogenesis (GO:0001525)|cell death (GO:0008219)|lipid catabolic process (GO:0016042)|organ morphogenesis (GO:0009887)|phosphatidylcholine metabolic process (GO:0046470)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	lysophospholipase activity (GO:0004622)	p.T226S(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)	35						GATGTCATCACCGTGAGTGAC	0.577																																																	1	Substitution - Missense(1)	kidney(1)											182.0	141.0	155.0					19																	7605595		2203	4300	6503	SO:0001630	splice_region_variant	10908			AJ004832	CCDS32891.1, CCDS54206.1, CCDS54207.1, CCDS59343.1	19p13.2	2013-09-11						"""Patatin-like phospholipase domain containing"""	16268	protein-coding gene	gene with protein product	"""neuropathy target esterase"""	603197				9576844, 16799181, 19029121	Standard	NM_006702		Approved	NTE, sws, iPLA2delta, SPG39	uc010xjq.2	Q8IY17		ENST00000221249.6:c.678+1C>G	19.37:g.7605595C>G		Somatic		WXS	Illumina HiSeq	Phase_I	A6NGQ0|B4DFB9|B7Z7T2|F5H5K9|J3KQS3|O60859|Q86W58|Q9UG58	Missense_Mutation	SNP	ENST00000221249.6	37	CCDS32891.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.588661	0.86851	.	.	ENSG00000032444	ENST00000221249;ENST00000545201;ENST00000414982;ENST00000544207;ENST00000450331	T;T;T;T	0.04758	3.61;3.56;3.59;3.61	5.2	5.2	0.72013	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.000000	0.85682	D	0.000000	T	0.13670	0.0331	L	0.42487	1.325	0.80722	D	1	D;D;D;D	0.64830	0.988;0.97;0.985;0.994	D;P;P;P	0.63877	0.919;0.779;0.868;0.858	T	0.03157	-1.1066	10	0.33940	T	0.23	.	16.2158	0.82217	0.0:1.0:0.0:0.0	.	265;226;265;226	Q8IY17;F5H5K9;Q8IY17-3;Q8IY17-2	PLPL6_HUMAN;.;.;.	S	226;226;274;163;226	ENSP00000221249:T226S;ENSP00000443323:T226S;ENSP00000407509:T274S;ENSP00000394348:T226S	ENSP00000221249:T226S	T	+	2	0	PNPLA6	7511595	0.998000	0.40836	0.977000	0.42913	0.855000	0.48748	3.954000	0.56708	2.441000	0.82636	0.491000	0.48974	ACC		0.577	PNPLA6-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459275.1		NM_006702	Missense_Mutation
PRELP	5549	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	203452939	203452939	+	Silent	SNP	C	C	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr1:203452939C>T	ENST00000343110.2	+	2	754	c.627C>T	c.(625-627)gaC>gaT	p.D209D		NM_002725.3|NM_201348.1	NP_002716.1|NP_958505.1	P51888	PRELP_HUMAN	proline/arginine-rich end leucine-rich repeat protein	209					carbohydrate metabolic process (GO:0005975)|cell aging (GO:0007569)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)	p.D209D(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			BRCA - Breast invasive adenocarcinoma(75;0.109)			GGCTGAGCGACGGCGTCTTCA	0.597																																																	1	Substitution - coding silent(1)	kidney(1)											117.0	118.0	118.0					1																	203452939		2203	4300	6503	SO:0001819	synonymous_variant	5549			BC032498	CCDS1438.1	1q32	2008-02-05	2005-07-24		ENSG00000188783	ENSG00000188783		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	9357	protein-coding gene	gene with protein product	"""prolargin proteoglycan"""	601914	"""proline arginine-rich end leucine-rich repeat protein"""				Standard	NM_002725		Approved	SLRR2A, prolargin	uc001gzt.3	P51888	OTTHUMG00000035911	ENST00000343110.2:c.627C>T	1.37:g.203452939C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q6FG38	Silent	SNP	ENST00000343110.2	37	CCDS1438.1																																																																																				0.597	PRELP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087474.1		NM_002725	
RBM33	155435	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	155473515	155473515	+	Silent	SNP	A	A	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr7:155473515A>T	ENST00000401878.3	+	5	678	c.480A>T	c.(478-480)atA>atT	p.I160I	RBM33_ENST00000392759.3_Silent_p.I160I|RBM33_ENST00000287912.3_Silent_p.I160I	NM_053043.2	NP_444271.2	Q96EV2	RBM33_HUMAN	RNA binding motif protein 33	160	Glu-rich.						nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.I160I(3)		breast(3)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	27	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)		AAGACCAAATAGAATATGTGG	0.403																																																	3	Substitution - coding silent(3)	kidney(3)											90.0	90.0	90.0					7																	155473515		1980	4173	6153	SO:0001819	synonymous_variant	155435			AL832196	CCDS5941.2	7q36.3	2013-02-12			ENSG00000184863	ENSG00000184863		"""RNA binding motif (RRM) containing"""	27223	protein-coding gene	gene with protein product			"""proline rich 8"""	PRR8			Standard	NM_053043		Approved	DKFZp686F102, MGC20460, DKFZp434D1319	uc010lqk.1	Q96EV2	OTTHUMG00000150260	ENST00000401878.3:c.480A>T	7.37:g.155473515A>T		Somatic		WXS	Illumina HiSeq	Phase_I	A4D244|B5MC24|Q52LF5|Q75LN9|Q75ML5|Q9NSV0	Silent	SNP	ENST00000401878.3	37	CCDS5941.2																																																																																				0.403	RBM33-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317225.3		NM_001008408	
RGL2	5863	broad.mit.edu;hgsc.bcm.edu	37	6	33259865	33259865	+	3'UTR	SNP	A	A	G	rs370640530		TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr6:33259865A>G	ENST00000497454.1	-	0	2843				WDR46_ENST00000477718.1_5'Flank|WDR46_ENST00000374617.4_5'Flank|RGL2_ENST00000437840.2_5'UTR|PFDN6_ENST00000463584.1_Intron	NM_001243738.1|NM_004761.4	NP_001230667.1|NP_004752.1	O15211	RGL2_HUMAN	ral guanine nucleotide dissociation stimulator-like 2						positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)	intracellular (GO:0005622)	Ras guanyl-nucleotide exchange factor activity (GO:0005088)			breast(2)|cervix(2)|endometrium(7)|kidney(2)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	34						CTGTAAGCCAACGGGGCTTCC	0.532													A|||	1	0.000199681	0.0008	0.0	5008	,	,		22020	0.0		0.0	False		,,,				2504	0.0																0								A		4,4400	8.1+/-20.4	0,4,2198	44.0	39.0	41.0			-2.2	0.0	6		41	0,8600		0,0,4300	no	utr-3	RGL2	NM_004761.4		0,4,6498	GG,GA,AA		0.0,0.0908,0.0308			33259865	4,13000	2202	4300	6502	SO:0001624	3_prime_UTR_variant	5863				CCDS4774.1	6p21.3	2010-02-17	2004-06-11	2004-06-16	ENSG00000237441	ENSG00000237441			9769	protein-coding gene	gene with protein product		602306	"""RAB2, member RAS oncogene family-like"""	RAB2L		8976381	Standard	NM_001243738		Approved	KE1.5, HKE1.5	uc003odv.3	O15211	OTTHUMG00000031072	ENST00000497454.1:c.*14T>C	6.37:g.33259865A>G		Somatic		WXS	Illumina HiSeq	Phase_I	B4DG72|Q5STK0|Q9Y3F3	RNA	SNP	ENST00000497454.1	37	CCDS4774.1																																																																																				0.532	RGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076098.2			
RNF180	285671	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	63509694	63509694	+	Missense_Mutation	SNP	G	G	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr5:63509694G>T	ENST00000389100.4	+	4	613	c.541G>T	c.(541-543)Gca>Tca	p.A181S	RNF180_ENST00000296615.6_Missense_Mutation_p.A181S|RNF180_ENST00000381081.2_Intron	NM_001113561.1	NP_001107033.1	Q86T96	RN180_HUMAN	ring finger protein 180	181					adult behavior (GO:0030534)|norepinephrine metabolic process (GO:0042415)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein polyubiquitination (GO:0000209)|regulation of catalytic activity (GO:0050790)|serotonin metabolic process (GO:0042428)	integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.A181S(2)		breast(1)|kidney(1)|large_intestine(4)|lung(9)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	20		Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0848)|Colorectal(97;0.234)		Lung(70;0.114)		ATTAACAGAAGCACTCTGCCT	0.443																																																	2	Substitution - Missense(2)	kidney(2)											60.0	67.0	65.0					5																	63509694		2203	4300	6503	SO:0001583	missense	285671			AK090756	CCDS34169.1, CCDS47219.1	5q12.3	2013-01-09			ENSG00000164197	ENSG00000164197		"""RING-type (C3HC4) zinc fingers"""	27752	protein-coding gene	gene with protein product							Standard	NM_178532		Approved		uc003jti.3	Q86T96	OTTHUMG00000162278	ENST00000389100.4:c.541G>T	5.37:g.63509694G>T	ENSP00000373752:p.Ala181Ser	Somatic		WXS	Illumina HiSeq	Phase_I	Q0JSU3|Q495A8|Q8NBD1	Missense_Mutation	SNP	ENST00000389100.4	37	CCDS47219.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.262080	0.80358	.	.	ENSG00000164197	ENST00000296615;ENST00000389100	T	0.62105	0.05	6.08	6.08	0.98989	.	0.160135	0.56097	D	0.000036	T	0.78855	0.4349	M	0.64997	1.995	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.996;0.999	T	0.78695	-0.2104	10	0.87932	D	0	-12.8039	19.6529	0.95825	0.0:0.0:1.0:0.0	.	181;181	Q86T96;Q86T96-2	RN180_HUMAN;.	S	181	ENSP00000373752:A181S	ENSP00000296615:A181S	A	+	1	0	RNF180	63545450	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.122000	0.77169	2.890000	0.99128	0.655000	0.94253	GCA		0.443	RNF180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368394.1		NM_178532	
RORA	6095	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	60789779	60789779	+	Nonsense_Mutation	SNP	G	G	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr15:60789779G>A	ENST00000335670.6	-	11	1547	c.1447C>T	c.(1447-1449)Cga>Tga	p.R483*	RORA_ENST00000449337.2_Nonsense_Mutation_p.R428*|RP11-219B17.1_ENST00000558140.1_RNA|RP11-219B17.1_ENST00000559824.1_RNA|RP11-219B17.1_ENST00000501579.2_RNA|RORA_ENST00000309157.4_Nonsense_Mutation_p.R508*|RP11-219B17.1_ENST00000558235.1_RNA|RORA_ENST00000261523.5_Nonsense_Mutation_p.R516*	NM_134261.2	NP_599023.1	P35398	RORA_HUMAN	RAR-related orphan receptor A	483	Ligand-binding.				angiogenesis (GO:0001525)|cellular response to hypoxia (GO:0071456)|cellular response to sterol (GO:0036315)|cerebellar granule cell precursor proliferation (GO:0021930)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|circadian regulation of gene expression (GO:0032922)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|muscle cell differentiation (GO:0042692)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|nitric oxide biosynthetic process (GO:0006809)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of cholesterol homeostasis (GO:2000188)|regulation of glucose metabolic process (GO:0010906)|regulation of macrophage activation (GO:0043030)|regulation of smoothened signaling pathway (GO:0008589)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription involved in cell fate commitment (GO:0060850)|regulation of transcription, DNA-templated (GO:0006355)|T-helper 17 cell differentiation (GO:0072539)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)|xenobiotic metabolic process (GO:0006805)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	direct ligand regulated sequence-specific DNA binding transcription factor activity (GO:0098531)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|oxysterol binding (GO:0008142)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator binding (GO:0001223)|transcription corepressor binding (GO:0001222)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.R483*(1)|p.R516*(1)|p.R508*(1)		endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	21						TCTGTATGTCGTCCACATAAG	0.398																																																	3	Substitution - Nonsense(3)	kidney(3)											166.0	142.0	151.0					15																	60789779		2203	4300	6503	SO:0001587	stop_gained	6095			U04897	CCDS10177.1, CCDS10178.1, CCDS10179.1, CCDS45271.1	15q21-q22	2013-01-16			ENSG00000069667	ENSG00000069667		"""Nuclear hormone receptors"""	10258	protein-coding gene	gene with protein product		600825				7926749	Standard	NM_134261		Approved	RZRA, ROR1, ROR2, ROR3, NR1F1	uc002agv.3	P35398	OTTHUMG00000132769	ENST00000335670.6:c.1447C>T	15.37:g.60789779G>A	ENSP00000335087:p.Arg483*	Somatic		WXS	Illumina HiSeq	Phase_I	P35397|P35399|P45445|Q495X4|Q96H83	Nonsense_Mutation	SNP	ENST00000335670.6	37	CCDS10177.1	.	.	.	.	.	.	.	.	.	.	G	36	5.802127	0.96960	.	.	ENSG00000069667	ENST00000335670;ENST00000449337;ENST00000309157;ENST00000261523	.	.	.	5.96	5.96	0.96718	.	0.058151	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05959	T	0.93	.	20.4008	0.98991	0.0:0.0:1.0:0.0	.	.	.	.	X	483;428;508;516	.	ENSP00000261523:R516X	R	-	1	2	RORA	58577071	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.773000	0.68898	2.826000	0.97356	0.655000	0.94253	CGA		0.398	RORA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256142.2			
SAMD14	201191	broad.mit.edu;ucsc.edu	37	17	48195543	48195543	+	Silent	SNP	C	C	T	rs538760933		TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr17:48195543C>T	ENST00000330175.4	-	3	509	c.192G>A	c.(190-192)tcG>tcA	p.S64S	SAMD14_ENST00000503131.1_Silent_p.S64S|SAMD14_ENST00000503734.1_5'UTR	NM_001257359.1	NP_001244288.1	Q8IZD0	SAM14_HUMAN	sterile alpha motif domain containing 14	64								p.S64S(1)		breast(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(3)|prostate(1)|urinary_tract(1)	15						CGGGCCCATCCGAGCCTTCAC	0.637																																																	1	Substitution - coding silent(1)	kidney(1)											49.0	52.0	51.0					17																	48195543		2203	4300	6503	SO:0001819	synonymous_variant	201191				CCDS11560.1, CCDS58562.1	17q21.33	2013-01-10				ENSG00000167100		"""Sterile alpha motif (SAM) domain containing"""	27312	protein-coding gene	gene with protein product						8619474	Standard	NM_174920		Approved	FLJ36890	uc002iqg.4	Q8IZD0		ENST00000330175.4:c.192G>A	17.37:g.48195543C>T		Somatic		WXS	Illumina GAIIx	Phase_I	A5D8V1|Q8N2X0	Silent	SNP	ENST00000330175.4	37	CCDS58562.1																																																																																				0.637	SAMD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366661.1		NM_174920	
SKA1	220134	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	18	47906545	47906545	+	Silent	SNP	C	C	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr18:47906545C>A	ENST00000285116.3	+	3	349	c.138C>A	c.(136-138)atC>atA	p.I46I	SKA1_ENST00000417656.2_Silent_p.I46I|SKA1_ENST00000488454.1_Intron|SKA1_ENST00000398452.2_Silent_p.I46I	NM_001039535.2|NM_145060.3	NP_001034624.1|NP_659497.1	Q96BD8	SKA1_HUMAN	spindle and kinetochore associated complex subunit 1	46					cell division (GO:0051301)|chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of microtubule polymerization or depolymerization (GO:0031110)	condensed chromosome outer kinetochore (GO:0000940)|cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|spindle microtubule (GO:0005876)	microtubule binding (GO:0008017)	p.I46I(1)		breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|lung(6)|ovary(1)|prostate(1)	13						GAGATGAGATCATTGTAATAA	0.294																																																	1	Substitution - coding silent(1)	kidney(1)											51.0	60.0	57.0					18																	47906545		2196	4283	6479	SO:0001819	synonymous_variant	220134			BC015706	CCDS11946.1	18q21.1	2013-01-17	2009-08-19	2009-08-19	ENSG00000154839	ENSG00000154839			28109	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 24"""	C18orf24		17093495	Standard	NM_145060		Approved	MGC10200	uc002leu.3	Q96BD8	OTTHUMG00000132685	ENST00000285116.3:c.138C>A	18.37:g.47906545C>A		Somatic		WXS	Illumina HiSeq	Phase_I	B2R9Y6|B4E0P4	Silent	SNP	ENST00000285116.3	37	CCDS11946.1																																																																																				0.294	SKA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255982.2		NM_145060	
SPAG16	79582	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	214239769	214239769	+	Missense_Mutation	SNP	G	G	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr2:214239769G>A	ENST00000331683.5	+	9	963	c.868G>A	c.(868-870)Ggt>Agt	p.G290S	SPAG16_ENST00000272898.7_Missense_Mutation_p.G290S|SPAG16_ENST00000447990.1_Missense_Mutation_p.G290S|SPAG16_ENST00000374309.3_Missense_Mutation_p.G196S	NM_024532.4	NP_078808.3	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16	290					cilium assembly (GO:0042384)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|microtubule cytoskeleton (GO:0015630)|motile cilium (GO:0031514)|nucleus (GO:0005634)		p.G290S(1)		endometrium(4)|kidney(1)|large_intestine(15)|lung(27)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	56		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)		TGCACCAGAAGGTCCTACTCA	0.318																																																	1	Substitution - Missense(1)	kidney(1)											86.0	81.0	83.0					2																	214239769		2203	4300	6503	SO:0001583	missense	79582			AF310672	CCDS2396.1, CCDS46508.1	2q34	2013-05-21			ENSG00000144451	ENSG00000144451		"""WD repeat domain containing"""	23225	protein-coding gene	gene with protein product		612173				12391165, 11867345	Standard	NM_024532		Approved	PF20, FLJ22724, DKFZp666P1710, WDR29	uc002veq.4	Q8N0X2	OTTHUMG00000133015	ENST00000331683.5:c.868G>A	2.37:g.214239769G>A	ENSP00000332592:p.Gly290Ser	Somatic		WXS	Illumina HiSeq	Phase_I	Q498B7|Q658W1|Q68DB3|Q6I9Z6|Q8N9C7|Q9H601	Missense_Mutation	SNP	ENST00000331683.5	37	CCDS2396.1	.	.	.	.	.	.	.	.	.	.	G	10.52	1.374171	0.24857	.	.	ENSG00000144451	ENST00000331683;ENST00000272898;ENST00000447990;ENST00000374309	T;T	0.56275	0.52;0.47	5.0	4.12	0.48240	WD40/YVTN repeat-like-containing domain (1);	0.324591	0.29321	N	0.012483	T	0.56863	0.2014	L	0.42686	1.345	0.30529	N	0.767608	D;P;B;D	0.69078	0.997;0.734;0.397;0.993	P;B;B;P	0.56751	0.805;0.301;0.093;0.805	T	0.59327	-0.7475	10	0.46703	T	0.11	.	11.2799	0.49188	0.0:0.1838:0.8162:0.0	.	196;141;230;290	B4DYB5;Q8N0X2-2;Q4G1A2;Q8N0X2	.;.;.;SPG16_HUMAN	S	290;290;290;196	ENSP00000332592:G290S;ENSP00000363428:G196S	ENSP00000272898:G290S	G	+	1	0	SPAG16	213948014	1.000000	0.71417	1.000000	0.80357	0.318000	0.28184	3.012000	0.49575	1.300000	0.44818	-0.305000	0.09177	GGT		0.318	SPAG16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256601.2		NM_024532	
SPG11	80208	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	44858475	44858475	+	Silent	SNP	C	C	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr15:44858475C>T	ENST00000261866.7	-	37	6799	c.6783G>A	c.(6781-6783)ctG>ctA	p.L2261L	SPG11_ENST00000535302.2_Silent_p.L2148L|SPG11_ENST00000427534.2_Intron	NM_025137.3	NP_079413.3	Q96JI7	SPTCS_HUMAN	spastic paraplegia 11 (autosomal recessive)	2261					cell death (GO:0008219)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)		p.L2261L(1)		autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	72		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		GCAGTTGTTTCAGCTGGTGCC	0.502																																																	1	Substitution - coding silent(1)	kidney(1)											84.0	74.0	77.0					15																	44858475		2198	4298	6496	SO:0001819	synonymous_variant	80208				CCDS10112.1, CCDS53939.1	15q13-q15	2007-11-13			ENSG00000104133	ENSG00000104133			11226	protein-coding gene	gene with protein product	"""spatacsin"""	610844	"""KIAA1840"""	KIAA1840		10408536, 17322883	Standard	NM_001160227		Approved	FLJ21439	uc001ztx.3	Q96JI7	OTTHUMG00000131199	ENST00000261866.7:c.6783G>A	15.37:g.44858475C>T		Somatic		WXS	Illumina HiSeq	Phase_I	A8KAX9|B9EK60|F5H3N6|Q4VC11|Q58G86|Q69YG6|Q6NW01|Q8N270|Q8TBU9|Q9H734	Silent	SNP	ENST00000261866.7	37	CCDS10112.1																																																																																				0.502	SPG11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253927.1			
SPTY2D1	144108	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	18636763	18636763	+	Missense_Mutation	SNP	G	G	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr11:18636763G>A	ENST00000336349.5	-	3	1293	c.1058C>T	c.(1057-1059)cCt>cTt	p.P353L	SPTY2D1_ENST00000543776.1_5'Flank	NM_194285.2	NP_919261.2	Q68D10	SPT2_HUMAN	SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae)	353	Ser-rich.							p.P353L(1)		breast(4)|cervix(3)|endometrium(2)|kidney(3)|large_intestine(7)|lung(9)|skin(1)|stomach(1)	30						CATGGGCCCAGGCCTGGAATG	0.557																																																	1	Substitution - Missense(1)	kidney(1)											112.0	122.0	118.0					11																	18636763		2199	4293	6492	SO:0001583	missense	144108			BX647798	CCDS31441.1	11p15.1	2005-10-28			ENSG00000179119	ENSG00000179119			26818	protein-coding gene	gene with protein product							Standard	NM_194285		Approved	FLJ39441, DKFZp686I068	uc001moy.3	Q68D10	OTTHUMG00000167733	ENST00000336349.5:c.1058C>T	11.37:g.18636763G>A	ENSP00000337991:p.Pro353Leu	Somatic		WXS	Illumina HiSeq	Phase_I	Q6AWA5|Q6MZI5|Q7Z390|Q7Z470|Q86VG8|Q8N3E7|Q8N417|Q8N8I3	Missense_Mutation	SNP	ENST00000336349.5	37	CCDS31441.1	.	.	.	.	.	.	.	.	.	.	G	17.46	3.396315	0.62177	.	.	ENSG00000179119	ENST00000336349	T	0.16743	2.32	5.84	5.84	0.93424	.	0.344807	0.31123	N	0.008211	T	0.16085	0.0387	L	0.34521	1.04	0.49389	D	0.999789	P	0.42785	0.79	B	0.41571	0.36	T	0.00942	-1.1506	10	0.45353	T	0.12	-5.7793	13.3441	0.60561	0.0721:0.0:0.9279:0.0	.	353	Q68D10	SPT2_HUMAN	L	353	ENSP00000337991:P353L	ENSP00000337991:P353L	P	-	2	0	SPTY2D1	18593339	0.553000	0.26513	1.000000	0.80357	0.777000	0.43975	1.392000	0.34486	2.762000	0.94881	0.563000	0.77884	CCT		0.557	SPTY2D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395941.1		NM_194285	
TBX3	6926	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	115117393	115117393	+	Silent	SNP	A	A	G			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr12:115117393A>G	ENST00000257566.3	-	4	1170	c.781T>C	c.(781-783)Ttg>Ctg	p.L261L	TBX3_ENST00000349155.2_Silent_p.L241L	NM_016569.3	NP_057653.3	O15119	TBX3_HUMAN	T-box 3	261					anterior/posterior axis specification, embryo (GO:0008595)|atrioventricular bundle cell differentiation (GO:0003167)|blood vessel development (GO:0001568)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cardiac muscle cell fate commitment (GO:0060923)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|female genitalia development (GO:0030540)|follicle-stimulating hormone secretion (GO:0046884)|forelimb morphogenesis (GO:0035136)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|limbic system development (GO:0021761)|luteinizing hormone secretion (GO:0032275)|male genitalia development (GO:0030539)|mammary gland development (GO:0030879)|mammary placode formation (GO:0060596)|mesoderm morphogenesis (GO:0048332)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sinoatrial node cell development (GO:0060931)|skeletal system development (GO:0001501)|specification of organ position (GO:0010159)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum morphogenesis (GO:0060412)	nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.L261L(1)		breast(5)|endometrium(1)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)		GGGAGTTTCAAGATGTCATTG	0.438																																																	1	Substitution - coding silent(1)	kidney(1)											190.0	186.0	188.0					12																	115117393		2203	4300	6503	SO:0001819	synonymous_variant	6926			BC025258	CCDS9175.1, CCDS9176.1	12q24.21	2013-09-05	2008-07-31		ENSG00000135111	ENSG00000135111		"""T-boxes"""	11602	protein-coding gene	gene with protein product		601621	"""ulnar mammary syndrome"""	UMS		8988164	Standard	NM_005996		Approved	TBX3-ISO, XHL	uc001tvt.1	O15119	OTTHUMG00000169586	ENST00000257566.3:c.781T>C	12.37:g.115117393A>G		Somatic		WXS	Illumina HiSeq	Phase_I	Q8TB20|Q9UKF8	Silent	SNP	ENST00000257566.3	37	CCDS9176.1																																																																																				0.438	TBX3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404947.2		NM_016569, NM_005996	
TMEM145	284339	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	42820894	42820894	+	Splice_Site	SNP	T	T	C			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr19:42820894T>C	ENST00000301204.3	+	10	847		c.e10+2		TMEM145_ENST00000598766.1_Splice_Site	NM_173633.2	NP_775904.2	Q8NBT3	TM145_HUMAN	transmembrane protein 145						G-protein coupled receptor signaling pathway (GO:0007186)|response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)		p.?(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(11)|prostate(4)|skin(1)|urinary_tract(1)	27		Prostate(69;0.00682)				GGTGACACGGTGCCCGGGCAG	0.682																																																	1	Unknown(1)	kidney(1)											64.0	62.0	63.0					19																	42820894		2203	4300	6503	SO:0001630	splice_region_variant	284339			AK075286	CCDS12603.1	19q13.2	2008-02-05				ENSG00000167619			26912	protein-coding gene	gene with protein product							Standard	NM_173633		Approved	FLJ90805	uc002otk.1	Q8NBT3		ENST00000301204.3:c.806+2T>C	19.37:g.42820894T>C		Somatic		WXS	Illumina HiSeq	Phase_I		Splice_Site	SNP	ENST00000301204.3	37	CCDS12603.1	.	.	.	.	.	.	.	.	.	.	T	19.00	3.742576	0.69418	.	.	ENSG00000167619	ENST00000301204	.	.	.	3.76	3.76	0.43208	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.7581	0.46249	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	TMEM145	47512734	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	6.295000	0.72744	1.500000	0.48636	0.374000	0.22700	.		0.682	TMEM145-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463737.1		NM_173633	Intron
TNRC18	84629	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	5391579	5391580	+	Missense_Mutation	DNP	CC	CC	AA			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr7:5391579_5391580CC>AA	ENST00000430969.1	-	17	5688_5689	c.5340_5341GG>TT	c.(5338-5343)agGGgc>agTTgc	p.1780_1781RG>SC	TNRC18_ENST00000399537.4_Missense_Mutation_p.1780_1781RG>SC	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	1780							chromatin binding (GO:0003682)	p.G1781C(2)|p.R1780S(2)|p.R1780_G1781>SC(2)|p.G836C(1)|p.R835_G836>SC(1)|p.R835S(1)		central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		GCCGCCAGGCCCCTCTTGGTCA	0.649																																																	9	Substitution - Missense(6)|Complex - compound substitution(3)	kidney(9)																																								SO:0001583	missense	84629			U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"""Trinucleotide (CAG) repeat containing"""	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.5340_5341delinsAA	7.37:g.5391579_5391580delinsAA	ENSP00000395538:p.R1780_G1781delinsSC	Somatic		WXS	Illumina HiSeq	Phase_I	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	37	CCDS47534.1																																																																																				0.649	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				
TRPC4	7223	broad.mit.edu;ucsc.edu	37	13	38320157	38320157	+	Silent	SNP	G	G	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr13:38320157G>T	ENST00000379705.3	-	3	1671	c.814C>A	c.(814-816)Cga>Aga	p.R272R	TRPC4_ENST00000338947.5_Intron|TRPC4_ENST00000358477.2_Silent_p.R272R|TRPC4_ENST00000379681.3_Silent_p.R272R|TRPC4_ENST00000379679.1_Intron|TRPC4_ENST00000355779.2_Silent_p.R272R|TRPC4_ENST00000447043.1_Silent_p.R272R|TRPC4_ENST00000426868.2_Silent_p.R272R|TRPC4_ENST00000379673.2_Silent_p.R272R			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4	272	Multimerization domain. {ECO:0000250}.				axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|gamma-aminobutyric acid secretion (GO:0014051)|ion transmembrane transport (GO:0034220)|oligodendrocyte differentiation (GO:0048709)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|calcium channel complex (GO:0034704)|caveola (GO:0005901)|cell surface (GO:0009986)|cortical cytoskeleton (GO:0030863)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)	p.R272*(2)|p.R272R(2)		NS(2)|breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(26)|lung(30)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	83				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		TTGTCATCTCGGTAATTAAGA	0.418																																																	4	Substitution - Nonsense(2)|Substitution - coding silent(2)	urinary_tract(2)|kidney(2)											189.0	179.0	183.0					13																	38320157		2203	4300	6503	SO:0001819	synonymous_variant	7223			U40983	CCDS9365.1, CCDS45035.1, CCDS45036.1, CCDS45038.1, CCDS45039.1	13q13.3	2013-01-10			ENSG00000133107	ENSG00000133107		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	12336	protein-coding gene	gene with protein product		603651				8646775, 16382100	Standard	NM_016179		Approved	HTRP4, TRP4	uc010abx.3	Q9UBN4	OTTHUMG00000016752	ENST00000379705.3:c.814C>A	13.37:g.38320157G>T		Somatic		WXS	Illumina GAIIx	Phase_I	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Silent	SNP	ENST00000379705.3	37	CCDS9365.1																																																																																				0.418	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2		NM_003306	
TTC17	55761	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	43429097	43429097	+	Silent	SNP	A	A	G			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr11:43429097A>G	ENST00000039989.4	+	15	2048	c.2034A>G	c.(2032-2034)ctA>ctG	p.L678L	TTC17_ENST00000526774.1_3'UTR|TTC17_ENST00000299240.6_Silent_p.L678L	NM_018259.5	NP_060729.2	Q96AE7	TTC17_HUMAN	tetratricopeptide repeat domain 17	678					actin filament polymerization (GO:0030041)|cilium organization (GO:0044782)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)		p.L678L(1)		breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(27)|ovary(5)|prostate(3)|skin(3)	53						CTAAGCTGCTACTTCAAGCTT	0.388																																																	1	Substitution - coding silent(1)	kidney(1)											75.0	67.0	70.0					11																	43429097		2203	4299	6502	SO:0001819	synonymous_variant	55761			AK001540	CCDS31466.1	11p11.2	2013-01-10			ENSG00000052841	ENSG00000052841		"""Tetratricopeptide (TTC) repeat domain containing"""	25596	protein-coding gene	gene with protein product						12477932	Standard	NM_018259		Approved	FLJ10890	uc001mxi.3	Q96AE7	OTTHUMG00000166398	ENST00000039989.4:c.2034A>G	11.37:g.43429097A>G		Somatic		WXS	Illumina HiSeq	Phase_I	G3XAB3|Q8NEC0	Silent	SNP	ENST00000039989.4	37	CCDS31466.1																																																																																				0.388	TTC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389577.2		NM_018259	
VPS13C	54832	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	62241747	62241747	+	Missense_Mutation	SNP	C	C	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr15:62241747C>T	ENST00000261517.5	-	42	4727	c.4654G>A	c.(4654-4656)Gat>Aat	p.D1552N	VPS13C_ENST00000395898.3_Missense_Mutation_p.D1509N|VPS13C_ENST00000395896.4_Missense_Mutation_p.D1552N|VPS13C_ENST00000249837.3_Missense_Mutation_p.D1509N	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)									p.D1552N(2)		NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						GATAAAAAATCCATGAAGGAA	0.408																																																	2	Substitution - Missense(2)	kidney(2)											80.0	81.0	81.0					15																	62241747		2203	4300	6503	SO:0001583	missense	54832			AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"""vacuolar protein sorting 13C (yeast)"""				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.4654G>A	15.37:g.62241747C>T	ENSP00000261517:p.Asp1552Asn	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	C	7.819	0.717312	0.15372	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T;T	0.26810	2.44;2.44;2.44;1.71	5.77	5.77	0.91146	.	0.231068	0.45606	D	0.000354	T	0.07098	0.0180	N	0.00408	-1.53	0.43342	D	0.995396	B;B;B;B	0.06786	0.0;0.0;0.0;0.001	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.38067	-0.9678	10	0.16896	T	0.51	.	10.9576	0.47366	0.0:0.9149:0.0:0.0851	.	1509;1552;1509;1552	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	N	1509;1552;1552;1552	ENSP00000249837:D1509N;ENSP00000261517:D1552N;ENSP00000379233:D1552N;ENSP00000379235:D1552N	ENSP00000249837:D1509N	D	-	1	0	VPS13C	60029039	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.342000	0.33919	2.729000	0.93468	0.655000	0.94253	GAT		0.408	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1		NM_017684	
WDR35	57539	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	20162080	20162080	+	Silent	SNP	G	G	A	rs142103808		TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr2:20162080G>A	ENST00000345530.3	-	11	1318	c.1203C>T	c.(1201-1203)aaC>aaT	p.N401N	WDR35_ENST00000416055.2_Intron|WDR35_ENST00000281405.4_Intron	NM_001006657.1	NP_001006658.1	Q9P2L0	WDR35_HUMAN	WD repeat domain 35	401					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)		p.N401N(1)		breast(1)|endometrium(5)|kidney(8)|large_intestine(8)|lung(16)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCTCCATCTCGTTCTCCTCCT	0.333													G|||	1	0.000199681	0.0	0.0014	5008	,	,		17184	0.0		0.0	False		,,,				2504	0.0																1	Substitution - coding silent(1)	kidney(1)						G	,	1,4405	2.1+/-5.4	0,1,2202	125.0	120.0	122.0		1203,	-0.5	1.0	2	dbSNP_134	122	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,intron	WDR35	NM_001006657.1,NM_020779.3	,	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	,	401/1182,	20162080	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	57539			AB037757	CCDS1695.1, CCDS33152.1	2p24.3	2014-02-21			ENSG00000118965	ENSG00000118965		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	29250	protein-coding gene	gene with protein product		613602				10718198	Standard	NM_001006657		Approved	MGC33196, KIAA1336, IFT121, IFTA1	uc002rdi.3	Q9P2L0	OTTHUMG00000090737	ENST00000345530.3:c.1203C>T	2.37:g.20162080G>A		Somatic		WXS	Illumina HiSeq	Phase_I	B3KVI5|Q4ZG01|Q8NE11	Silent	SNP	ENST00000345530.3	37	CCDS33152.1																																																																																				0.333	WDR35-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000207472.2		NM_020779	
ZDHHC2	51201	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	17067943	17067943	+	Missense_Mutation	SNP	C	C	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr8:17067943C>T	ENST00000262096.8	+	10	1599	c.904C>T	c.(904-906)Cct>Tct	p.P302S		NM_016353.4	NP_057437.1	Q9UIJ5	ZDHC2_HUMAN	zinc finger, DHHC-type containing 2	302					protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|recycling endosome membrane (GO:0055038)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)	p.P302S(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|pancreas(1)|stomach(1)	8				Colorectal(111;0.0697)|COAD - Colon adenocarcinoma(73;0.244)		TAACCAGGATCCTGAACAAGC	0.343																																																	1	Substitution - Missense(1)	kidney(1)											78.0	73.0	75.0					8																	17067943		1839	4096	5935	SO:0001583	missense	51201			AB023584	CCDS47810.1	8p22	2008-05-15			ENSG00000104219	ENSG00000104219		"""Zinc fingers, DHHC-type"""	18469	protein-coding gene	gene with protein product						10918388	Standard	NM_016353		Approved	ZNF372	uc003wxe.3	Q9UIJ5	OTTHUMG00000163860	ENST00000262096.8:c.904C>T	8.37:g.17067943C>T	ENSP00000262096:p.Pro302Ser	Somatic		WXS	Illumina HiSeq	Phase_I	D3DSP5	Missense_Mutation	SNP	ENST00000262096.8	37	CCDS47810.1	.	.	.	.	.	.	.	.	.	.	C	16.98	3.270646	0.59540	.	.	ENSG00000104219	ENST00000262096	T	0.42513	0.97	5.53	5.53	0.82687	.	0.103881	0.64402	D	0.000002	T	0.49712	0.1573	M	0.73962	2.25	0.53688	D	0.999973	P	0.42827	0.791	B	0.43413	0.419	T	0.44267	-0.9339	10	0.15066	T	0.55	-3.4297	19.8416	0.96692	0.0:1.0:0.0:0.0	.	302	Q9UIJ5	ZDHC2_HUMAN	S	302	ENSP00000262096:P302S	ENSP00000262096:P302S	P	+	1	0	ZDHHC2	17112314	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	2.874000	0.48483	2.774000	0.95407	0.585000	0.79938	CCT		0.343	ZDHHC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376014.2		NM_016353	
ZNF721	170960	broad.mit.edu	37	4	420664	420664	+	3'UTR	SNP	G	G	T	rs1053401	byFrequency	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr4:420664G>T	ENST00000506646.1	-	0	848				ABCA11P_ENST00000451020.2_RNA			Q8TF20	ZN721_HUMAN	zinc finger protein 721						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(2)|large_intestine(15)|lung(6)|ovary(1)|skin(1)|stomach(5)|urinary_tract(1)	33						ATCTTCTTCAGGCTCTTCTGG	0.423													G|||	874	0.174521	0.3495	0.0865	5008	,	,		19242	0.1151		0.1064	False		,,,				2504	0.1319																0																																										SO:0001624	3_prime_UTR_variant	79963			AK092362	CCDS46991.1	4p16.3	2013-01-08			ENSG00000182903	ENSG00000182903		"""Zinc fingers, C2H2-type"", ""-"""	29425	protein-coding gene	gene with protein product						11853319	Standard	NM_133474		Approved	KIAA1982	uc003gag.4	Q8TF20		ENST00000506646.1:c.*291C>A	4.37:g.420664G>T		Somatic		WXS	Illumina GAIIx	Phase_I	Q69YG7	Missense_Mutation	SNP	ENST00000506646.1	37																																																																																					0.423	ZNF721-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000357869.2		NM_133474	
CROCCP2	84809	broad.mit.edu	37	1	16946434	16946434	+	lincRNA	SNP	C	C	T	rs367060	byFrequency	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr1:16946434C>T	ENST00000412962.1	-	0	1085				RP5-1182A14.5_ENST00000607700.1_lincRNA			Q86T23	CROL1_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 2						centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)											CTCAGCCTTCCGCCGGGCCAG	0.672													.|||	253	0.0505192	0.115	0.0533	5008	,	,		65734	0.0119		0.0437	False		,,,				2504	0.0082																0																																												0			AK090414		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000215908	ENSG00000215908			28170	pseudogene	pseudogene			"""ciliary rootlet coiled-coil, rootletin-like 1"""	CROCCL1		12477932	Standard	NR_026752		Approved	MGC12760	uc001azf.3	Q86T23	OTTHUMG00000037884		1.37:g.16946434C>T		Somatic		WXS	Illumina GAIIx	Phase_I	Q8NF65|Q96FR5|Q9BRE8	RNA	SNP	ENST00000412962.1	37																																																																																					0.672	CROCCP2-003	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000092784.1		NR_026752.1	
CROCCP2	84809	broad.mit.edu	37	1	16946438	16946438	+	lincRNA	SNP	G	G	A	rs28392876	byFrequency	TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr1:16946438G>A	ENST00000412962.1	-	0	1081				RP5-1182A14.5_ENST00000607700.1_lincRNA			Q86T23	CROL1_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 2						centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)											GCCTTCCGCCGGGCCAGCAGC	0.672																																																	0																																												0			AK090414		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000215908	ENSG00000215908			28170	pseudogene	pseudogene			"""ciliary rootlet coiled-coil, rootletin-like 1"""	CROCCL1		12477932	Standard	NR_026752		Approved	MGC12760	uc001azf.3	Q86T23	OTTHUMG00000037884		1.37:g.16946438G>A		Somatic		WXS	Illumina GAIIx	Phase_I	Q8NF65|Q96FR5|Q9BRE8	RNA	SNP	ENST00000412962.1	37																																																																																					0.672	CROCCP2-003	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000092784.1		NR_026752.1	
FAM50B	26240	broad.mit.edu	37	6	3850384	3850384	+	Silent	SNP	C	C	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr6:3850384C>T	ENST00000380274.1	+	1	765	c.339C>T	c.(337-339)cgC>cgT	p.R113R	FAM50B_ENST00000380272.3_Silent_p.R113R			Q9Y247	FA50B_HUMAN	family with sequence similarity 50, member B	113						nucleus (GO:0005634)		p.R113R(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|pancreas(1)|prostate(3)|urinary_tract(3)	17	Ovarian(93;0.0925)	all_hematologic(90;0.108)				ggcGCGAGCGCAAGCGTAAGA	0.701																																																	1	Substitution - coding silent(1)	kidney(1)											17.0	23.0	21.0					6																	3850384		2201	4296	6497	SO:0001819	synonymous_variant	26240			Y18504	CCDS4487.1	6p25.2	2008-05-15			ENSG00000145945	ENSG00000145945			18789	protein-coding gene	gene with protein product		614686				10534398	Standard	NM_012135		Approved	D6S2654E, X5L	uc003mvu.3	Q9Y247	OTTHUMG00000014147	ENST00000380274.1:c.339C>T	6.37:g.3850384C>T		Somatic		WXS	Illumina GAIIx	Phase_I	Q5T2L6	Silent	SNP	ENST00000380274.1	37	CCDS4487.1																																																																																				0.701	FAM50B-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039693.1		NM_012135	
LRRC37A6P	387646	broad.mit.edu	37	10	27538014	27538014	+	lincRNA	SNP	G	G	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr10:27538014G>T	ENST00000574842.1	+	0	255				LRRC37A6P_ENST00000284414.4_RNA																							TTCTAGTTCAGTAGGTGGACC	0.502																																																	0													30.0	27.0	28.0					10																	27538014		692	1591	2283			0																															10.37:g.27538014G>T		Somatic		WXS	Illumina GAIIx	Phase_I		Missense_Mutation	SNP	ENST00000574842.1	37																																																																																					0.502	RP11-85G18.6-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000436904.1			
LRRC37B	114659	broad.mit.edu	37	17	30357718	30357718	+	Missense_Mutation	SNP	T	T	G			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr17:30357718T>G	ENST00000341671.7	+	4	1872	c.1867T>G	c.(1867-1869)Ttt>Gtt	p.F623V	LRRC37B_ENST00000394713.3_Intron|LRRC37B_ENST00000543378.2_Missense_Mutation_p.F541V|LRRC37B_ENST00000327564.7_Missense_Mutation_p.F650V|LRRC37B_ENST00000584368.1_Intron	NM_052888.2	NP_443120.2	Q96QE4	LR37B_HUMAN	leucine rich repeat containing 37B	623						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)		p.F623V(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	29		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.111)|Ovarian(249;0.182)|Breast(31;0.244)				AAGACAAACATTTGAATCACT	0.254																																																	1	Substitution - Missense(1)	kidney(1)											23.0	17.0	19.0					17																	30357718		2165	4118	6283	SO:0001583	missense	114659			AJ314647	CCDS32609.1	17q11.2	2006-11-29		2005-08-09	ENSG00000185158	ENSG00000185158			29070	protein-coding gene	gene with protein product	"""KIAA0563-related"""					11468690, 10843809	Standard	NM_052888		Approved		uc002hgu.3	Q96QE4	OTTHUMG00000132785	ENST00000341671.7:c.1867T>G	17.37:g.30357718T>G	ENSP00000340519:p.Phe623Val	Somatic		WXS	Illumina GAIIx	Phase_I	Q17RC9|Q5YKG6	Missense_Mutation	SNP	ENST00000341671.7	37	CCDS32609.1	.	.	.	.	.	.	.	.	.	.	N	9.757	1.168952	0.21621	.	.	ENSG00000185158	ENST00000543378;ENST00000327564;ENST00000341671	T;T;T	0.70164	-0.46;-0.46;-0.46	2.14	2.14	0.27477	.	.	.	.	.	T	0.80924	0.4717	M	0.89601	3.045	0.80722	D	1	D	0.69078	0.997	D	0.74023	0.982	T	0.80843	-0.1201	9	0.87932	D	0	.	6.3016	0.21115	0.0:0.0:0.0:1.0	.	623	Q96QE4	LR37B_HUMAN	V	541;650;623	ENSP00000443345:F541V;ENSP00000332536:F650V;ENSP00000340519:F623V	ENSP00000332536:F650V	F	+	1	0	LRRC37B	27381831	1.000000	0.71417	0.984000	0.44739	0.030000	0.12068	3.330000	0.52068	1.234000	0.43709	0.368000	0.22195	TTT		0.254	LRRC37B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446508.1		NM_052888	
NYX	60506	broad.mit.edu	37	X	41307152	41307152	+	Nonsense_Mutation	SNP	C	C	T	rs371622974		TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chrX:41307152C>T	ENST00000342595.2	+	1	466	c.10C>T	c.(10-12)Cga>Tga	p.R4*	NYX_ENST00000378220.1_Nonsense_Mutation_p.R4*	NM_022567.2	NP_072089.1	Q9GZU5	NYX_HUMAN	nyctalopin	4					response to stimulus (GO:0050896)|visual perception (GO:0007601)	intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)		p.R4*(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(11)|upper_aerodigestive_tract(1)	17						GATGAAAGGCCGAGGGATGTT	0.617																																																	1	Substitution - Nonsense(1)	kidney(1)						C	stop/ARG	0,3835		0,0,1632,571	136.0	97.0	110.0		10	-0.7	0.0	X		110	1,6727		0,1,2427,1872	no	stop-gained	NYX	NM_022567.2		0,1,4059,2443	TT,TC,CC,C		0.0149,0.0,0.0095		4/482	41307152	1,10562	2203	4300	6503	SO:0001587	stop_gained	60506			AF254868	CCDS14256.1	Xp11.4	2014-01-28			ENSG00000188937	ENSG00000188937			8082	protein-coding gene	gene with protein product		300278		CSNB1, CSNB4		11062471, 11062472	Standard	NM_022567		Approved	CLRP, CSNB1A	uc004dfh.2	Q9GZU5	OTTHUMG00000021370	ENST00000342595.2:c.10C>T	X.37:g.41307152C>T	ENSP00000340328:p.Arg4*	Somatic		WXS	Illumina GAIIx	Phase_I	D3DWC0|Q2M1S4|Q5H983|Q9H4J0	Nonsense_Mutation	SNP	ENST00000342595.2	37	CCDS14256.1	.	.	.	.	.	.	.	.	.	.	C	19.85	3.903162	0.72754	0.0	1.49E-4	ENSG00000188937	ENST00000342595;ENST00000378220	.	.	.	4.46	-0.663	0.11410	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	0.892	0.01256	0.1622:0.3878:0.1557:0.2944	.	.	.	.	X	4	.	ENSP00000340328:R4X	R	+	1	2	NYX	41192096	0.000000	0.05858	0.000000	0.03702	0.461000	0.32589	-0.231000	0.09069	-0.416000	0.07473	-0.852000	0.03032	CGA		0.617	NYX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056256.1		NM_022567	
PBX2	5089	broad.mit.edu	37	6	32156550	32156550	+	Missense_Mutation	SNP	C	C	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr6:32156550C>T	ENST00000375050.4	-	2	515	c.245G>A	c.(244-246)cGa>cAa	p.R82Q	XXbac-BPG300A18.13_ENST00000559458.1_RNA	NM_002586.4	NP_002577.2	P40425	PBX2_HUMAN	pre-B-cell leukemia homeobox 2	82					embryonic limb morphogenesis (GO:0030326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.R82Q(1)		endometrium(1)|kidney(1)|lung(9)|ovary(1)|prostate(2)	14						AGGCTTCATTCGGTGGCAGTT	0.537																																																	1	Substitution - Missense(1)	kidney(1)											132.0	162.0	151.0					6																	32156550		1511	2709	4220	SO:0001583	missense	5089				CCDS4748.1	6p21.32	2011-06-20	2007-01-30		ENSG00000204304	ENSG00000204304		"""Homeoboxes / TALE class"""	8633	protein-coding gene	gene with protein product		176311	"""pre-B-cell leukemia transcription factor 2"""			7835890	Standard	NM_002586		Approved	G17, HOX12, PBX2MHC	uc003oav.1	P40425	OTTHUMG00000031116	ENST00000375050.4:c.245G>A	6.37:g.32156550C>T	ENSP00000364190:p.Arg82Gln	Somatic		WXS	Illumina GAIIx	Phase_I	A2BFJ2	Missense_Mutation	SNP	ENST00000375050.4	37	CCDS4748.1	.	.	.	.	.	.	.	.	.	.	C	36	5.664631	0.96745	.	.	ENSG00000204304	ENST00000375050	T	0.36340	1.26	4.92	4.92	0.64577	PBX (1);	0.000000	0.56097	D	0.000040	T	0.58481	0.2125	M	0.86573	2.825	0.54753	D	0.999986	D;D	0.89917	0.999;1.0	D;D	0.77557	0.963;0.99	T	0.66858	-0.5817	10	0.66056	D	0.02	-13.9347	15.6112	0.76721	0.0:1.0:0.0:0.0	.	82;82	Q7KZE5;P40425	.;PBX2_HUMAN	Q	82	ENSP00000364190:R82Q	ENSP00000364190:R82Q	R	-	2	0	PBX2	32264528	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.638000	0.67861	2.270000	0.75569	0.561000	0.74099	CGA		0.537	PBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076194.4			
TNRC18	84629	broad.mit.edu	37	7	5427483	5427483	+	Missense_Mutation	SNP	G	G	T			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr7:5427483G>T	ENST00000430969.1	-	5	2320	c.1972C>A	c.(1972-1974)Ccc>Acc	p.P658T	TNRC18_ENST00000399537.4_Missense_Mutation_p.P658T	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	658							chromatin binding (GO:0003682)	p.P658T(2)		central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		GCGCTCTCGGGCCTCTCGGGG	0.736																																																	2	Substitution - Missense(2)	kidney(2)																																								SO:0001583	missense	84629			U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"""Trinucleotide (CAG) repeat containing"""	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.1972C>A	7.37:g.5427483G>T	ENSP00000395538:p.Pro658Thr	Somatic		WXS	Illumina GAIIx	Phase_I	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	37	CCDS47534.1	.	.	.	.	.	.	.	.	.	.	g	12.22	1.872216	0.33069	.	.	ENSG00000182095	ENST00000399537;ENST00000430969;ENST00000413081	T;T	0.16324	2.36;2.35	4.47	4.47	0.54385	.	.	.	.	.	T	0.35098	0.0920	M	0.68593	2.085	0.41549	D	0.98856	D	0.69078	0.997	D	0.64042	0.921	T	0.12811	-1.0533	9	0.72032	D	0.01	.	10.7888	0.46422	0.0878:0.0:0.9122:0.0	.	658	O15417	TNC18_HUMAN	T	658;658;60	ENSP00000382452:P658T;ENSP00000395538:P658T	ENSP00000382452:P658T	P	-	1	0	TNRC18	5394009	1.000000	0.71417	0.998000	0.56505	0.840000	0.47671	7.289000	0.78701	2.016000	0.59253	0.556000	0.70494	CCC		0.736	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				
RN7SL417P	0	broad.mit.edu	37	15	84946555	84946556	+	RNA	INS	-	-	T	rs71453238		TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr15:84946555_84946556insT	ENST00000459938.2	+	0	0									RNA, 7SL, cytoplasmic 417, pseudogene																		CGAAGGGAGGAttttttttttt	0.515																																																	0																																												0					15q25.2	2013-04-02			ENSG00000244056	ENSG00000244056		"""ncRNAs / Small cytoplasmic RNAs"""	46433	pseudogene	RNA, pseudogene							Standard			Approved						15.37:g.84946566_84946566dupT		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	INS	ENST00000459938.2	37																																																																																					0.515	RN7SL417P-201	KNOWN	basic	misc_RNA	misc_RNA				
MIR4477B	100616194	broad.mit.edu	37	9	68413570	68413570	+	RNA	SNP	G	G	A			TCGA-A3-3372-01A-01D-0966-08	TCGA-A3-3372-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f9f50073-a1d3-4c52-be78-529bd05cbce4	eabe41f2-bf96-48bd-98c1-9a001b92bf85	g.chr9:68413570G>A	ENST00000581659.1	+	0	0					NR_039688.1|NR_039689.1				microRNA 4477b																		CCCCAGTGGCGCCGGATCTAG	0.602																																																	0																																												0					9	2011-09-12						"""ncRNAs / Micro RNAs"""	41898	non-coding RNA	RNA, micro							Standard	NR_039689		Approved	hsa-mir-4477b					9.37:g.68413570G>A		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000581659.1	37																																																																																					0.602	MIR4477B-201	KNOWN	basic	miRNA	miRNA			NR_039689	
