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	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	ref_context	gc_content	COSMIC_n_overlapping_mutations	ESP_AvgAAsampleReadDepth	ESP_AvgEAsampleReadDepth	ESP_AvgSampleReadDepth	ESP_Chromosome	ESP_Position	ESP_TotalAAsamplesCovered	ESP_TotalEAsamplesCovered	ESP_TotalSamplesCovered	Ensembl_so_accession	Ensembl_so_term	HGNC_AccessionNumbers	HGNC_CCDSIDs	HGNC_Chromosome	HGNC_DateModified	HGNC_DateNameChanged	HGNC_DateSymbolChanged	HGNC_EnsemblGeneID	HGNC_EnsemblIDsuppliedbyEnsembl	HGNC_Genefamilydescription	HGNC_HGNCID	HGNC_LocusGroup	HGNC_LocusType	HGNC_NameSynonyms	HGNC_OMIMIDsuppliedbyNCBI	HGNC_PreviousNames	HGNC_PreviousSymbols	HGNC_PubmedIDs	HGNC_RecordType	HGNC_RefSeqsuppliedbyNCBI	HGNC_Status	HGNC_Synonyms	HGNC_UCSCIDsuppliedbyUCSC	HGNC_UniProtIDsuppliedbyUniProt	HGNC_VEGAIDs	HGVS_coding_DNA_change	HGVS_genomic_change	HGVS_protein_change	UniProt_alt_uniprot_accessions	annotation_transcript	build	ccds_id	dbNSFP_1000Gp1_AC	dbNSFP_1000Gp1_AF	dbNSFP_1000Gp1_AFR_AC	dbNSFP_1000Gp1_AFR_AF	dbNSFP_1000Gp1_AMR_AC	dbNSFP_1000Gp1_AMR_AF	dbNSFP_1000Gp1_ASN_AC	dbNSFP_1000Gp1_ASN_AF	dbNSFP_1000Gp1_EUR_AC	dbNSFP_1000Gp1_EUR_AF	dbNSFP_Ancestral_allele	dbNSFP_CADD_phred	dbNSFP_CADD_raw	dbNSFP_CADD_raw_rankscore	dbNSFP_ESP6500_AA_AF	dbNSFP_ESP6500_EA_AF	dbNSFP_Ensembl_geneid	dbNSFP_Ensembl_transcriptid	dbNSFP_FATHMM_pred	dbNSFP_FATHMM_rankscore	dbNSFP_FATHMM_score	dbNSFP_GERP_NR	dbNSFP_GERP_RS	dbNSFP_GERP_RS_rankscore	dbNSFP_Interpro_domain	dbNSFP_LRT_Omega	dbNSFP_LRT_converted_rankscore	dbNSFP_LRT_pred	dbNSFP_LRT_score	dbNSFP_LR_pred	dbNSFP_LR_rankscore	dbNSFP_LR_score	dbNSFP_MutationAssessor_pred	dbNSFP_MutationAssessor_rankscore	dbNSFP_MutationAssessor_score	dbNSFP_MutationTaster_converted_rankscore	dbNSFP_MutationTaster_pred	dbNSFP_MutationTaster_score	dbNSFP_Polyphen2_HDIV_pred	dbNSFP_Polyphen2_HDIV_rankscore	dbNSFP_Polyphen2_HDIV_score	dbNSFP_Polyphen2_HVAR_pred	dbNSFP_Polyphen2_HVAR_rankscore	dbNSFP_Polyphen2_HVAR_score	dbNSFP_RadialSVM_pred	dbNSFP_RadialSVM_rankscore	dbNSFP_RadialSVM_score	dbNSFP_Reliability_index	dbNSFP_SIFT_converted_rankscore	dbNSFP_SIFT_pred	dbNSFP_SIFT_score	dbNSFP_SLR_test_statistic	dbNSFP_SiPhy_29way_logOdds	dbNSFP_SiPhy_29way_logOdds_rankscore	dbNSFP_SiPhy_29way_pi	dbNSFP_UniSNP_ids	dbNSFP_Uniprot_aapos	dbNSFP_Uniprot_acc	dbNSFP_Uniprot_id	dbNSFP_aaalt	dbNSFP_aapos	dbNSFP_aapos_FATHMM	dbNSFP_aapos_SIFT	dbNSFP_aaref	dbNSFP_cds_strand	dbNSFP_codonpos	dbNSFP_folddegenerate	dbNSFP_genename	dbNSFP_hg18_pos1coor	dbNSFP_phastCons100way_vertebrate	dbNSFP_phastCons100way_vertebrate_rankscore	dbNSFP_phastCons46way_placental	dbNSFP_phastCons46way_placental_rankscore	dbNSFP_phastCons46way_primate	dbNSFP_phastCons46way_primate_rankscore	dbNSFP_phyloP100way_vertebrate	dbNSFP_phyloP100way_vertebrate_rankscore	dbNSFP_phyloP46way_placental	dbNSFP_phyloP46way_placental_rankscore	dbNSFP_phyloP46way_primate	dbNSFP_phyloP46way_primate_rankscore	dbNSFP_refcodon	gencode_transcript_name	gencode_transcript_status	gencode_transcript_tags	gencode_transcript_type	gene_type	havana_transcript	init_n_lod	init_t_lod	isArtifactMode	n_alt_count	n_ref_count	oxoGCut	pox	pox_cutoff	qox	refseq_mrna_id	t_alt_count	t_lod_fstar	t_ref_count	tumor_f
NFATC2	4773	broad.mit.edu	hg19	20	50090554	50090554	+	Silent	SNP	G	G	T			TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d	g.chr20:50090554G>T	ENST00000371564.3	-	5	1890	c.1671C>A	c.(1669-1671)atC>atA	p.I557I	NFATC2_ENST00000609507.1_Silent_p.I338I|NFATC2_ENST00000414705.1_Silent_p.I537I|NFATC2_ENST00000396009.3_Silent_p.I557I|NFATC2_ENST00000610033.1_Silent_p.I338I|NFATC2_ENST00000609943.1_Silent_p.I537I	NM_001258296.1|NM_012340.4	NP_001245225.1|NP_036472.2	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	557	RHD.	B cell receptor signaling pathway|positive regulation of B cell proliferation|response to DNA damage stimulus|response to drug	actin cytoskeleton|nucleus|plasma membrane	protein binding|sequence-specific DNA binding transcription factor activity	breast(2)|endometrium(7)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	53	Hepatocellular(150;0.248)				GTAAAGAGACGATTCTGCCAC	0.567	0	141.0	113.0	122.0	20	50090554	2203	4300	6503	SO:0001819	synonymous_variant	U43342, U43341	CCDS13437.1, CCDS33488.1, CCDS46614.1, CCDS68156.1, CCDS68157.1	20q13.2	2009-11-24			ENSG00000101096	ENSG00000101096	"""Nuclear factor of activated T-cells"""	7776	protein-coding gene	gene with protein product		600490			8202141	Standard	NM_012340	Approved	NF-ATP, NFATp, NFAT1	uc002xwd.4	Q13469	OTTHUMG00000032747	ENST00000396009.3:c.1671C>A	20.37:g.50090554G>T		B5B2N8|B5B2N9|B5B2P0|B5B2P2|B5B2P3|Q13468|Q5TFW7|Q5TFW8|Q9NPX6|Q9NQH3|Q9UJR2	ENST00000396009.3	37	CCDS13437.1																																																																																			NFATC2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079730.2		-0.607734	1	-9	44	0	1	1	1	NM_012340	3	7.072249	38	0.073171
ATG9A	79065	hgsc.bcm.edu	hg19	2	220086024	220086024	+	Missense_Mutation	SNP	G	G	C			TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d																										TGCTTGTGGAGCTGGAGAAAT	0.602	0	11.0	12.0	12.0	2	220086024	1985	4155	6140	SO:0001630	splice_region_variant	AK021732	CCDS42820.1	2q35	2014-02-12	2012-06-06	2005-09-11	ENSG00000198925	ENSG00000198925		22408	protein-coding gene	gene with protein product		612204	"""APG9 autophagy 9-like 1 (S. cerevisiae)"", ""ATG9 autophagy related 9 homolog A (S. cerevisiae)"""	APG9L1		Standard	NM_024085	Approved	FLJ22169	uc002vkf.1	Q7Z3C6	OTTHUMG00000154557	ENST00000409618.1:c.2146-1C>G	2.37:g.220086024G>C		Q3ZAQ6|Q6P0N7|Q7Z317|Q7Z320|Q8NDK6|Q8WU65|Q9BVL5|Q9H6L1|Q9HAG7	ENST00000409618.1	37	CCDS42820.1	.	.	.	.	.	.	.	.	.	.	G	12.21	1.870543	0.33069	.	.	ENSG00000198925	ENST00000396761;ENST00000409618;ENST00000361242;ENST00000409422	T;T;T;T	0.53857	1.0;1.0;1.0;0.6	5.3	4.35	0.52113	.	0.142087	0.47093	D	0.000253	T	0.34745	0.0908	L	0.42686	1.345	0.43457	D	0.995656	P	0.37955	0.612	B	0.32533	0.147	T	0.11867	-1.0570	10	0.22109	T	0.4	-16.7292	4.3548	0.11172	0.2818:0.0:0.7182:0.0	.	716	Q7Z3C6	ATG9A_HUMAN	V	716;716;716;655	ENSP00000379983:L716V;ENSP00000386710:L716V;ENSP00000355173:L716V;ENSP00000386535:L655V	ENSP00000355173:L716V	L	-	1	0	ATG9A	219794268	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.397000	0.34543	2.757000	0.94681	0.591000	0.81541	CTC	ATG9A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335930.1				1	18					NM_024085	5		12	
AIM1L	55057	broad.mit.edu	hg19	1	26655240	26655240	+	Missense_Mutation	SNP	C	C	T			TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d	g.chr1:26655240C>T	ENST00000527815.1	-	15	1866	c.1817G>A	c.(1816-1818)cGg>cAg	p.R606Q	AIM1L_ENST00000308182.5_Missense_Mutation_p.R435Q	NM_001039775.3	NP_001034864.2	Q8N1P7	AIM1L_HUMAN	absent in melanoma 1-like	435	Ricin B-type lectin.			sugar binding	endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|pancreas(1)|skin(2)	12		all_cancers(24;4.67e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.51e-27)|Colorectal(126;1.61e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000792)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.00858)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.165)|LUSC - Lung squamous cell carcinoma(448;0.239)	CCCCTTGATCCGCACAGACAG	0.617	0	153.0	129.0	137.0	1	26655240	2203	4300	6503	SO:0001583	missense			1p35	2010-07-14			ENSG00000176092	ENSG00000176092		17295	protein-coding gene	gene with protein product	"""beta-gamma crystallin domain containing 2"""					Standard	NM_001039775	Approved	CRYBG2, FLJ38020	uc001bmd.4	Q8N1P7	OTTHUMG00000003490	ENST00000527815.1:c.1817G>A	1.37:g.26655240C>T	ENSP00000433931:p.Arg606Gln	B2RNG3|Q5T137|Q5T150	ENST00000527815.1	37		.	.	.	.	.	.	.	.	.	.	C	9.021	0.984904	0.18889	.	.	ENSG00000176092	ENST00000527815;ENST00000308182	T;T	0.77489	-1.1;-1.1	5.03	1.05	0.20165	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.354241	0.30791	N	0.008866	T	0.63792	0.2541	L	0.46947	1.48	0.80722	D	1	B	0.13594	0.008	B	0.12837	0.008	T	0.52533	-0.8563	10	0.05833	T	0.94	.	9.9776	0.41793	0.0:0.7148:0.0:0.2852	.	435	Q8N1P7	AIM1L_HUMAN	Q	606;435	ENSP00000433931:R606Q;ENSP00000310435:R435Q	ENSP00000310435:R435Q	R	-	2	0	AIM1L	26527827	0.854000	0.29725	0.999000	0.59377	0.711000	0.40976	1.418000	0.34782	0.316000	0.23135	-0.258000	0.10820	CGG	AIM1L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000009703.5		89.225668	0	-12	97	0	0	1	0	NM_001039775.2	30	91.192938	58	0.340909
CTD-2620I22.1	0	broad.mit.edu	hg19	19	53473365	53473365	+	RNA	SNP	G	G	C			TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d	g.chr19:53473365G>C	ENST00000600068.1	-	0	489				ZNF702P_ENST00000270443.4_RNA																	CATTACACTTGTGAGGTTTCT	0.383	0	62.0	55.0	57.0	19	53473365	692	1591	2283																												19.37:g.53473365G>C			ENST00000600068.1	37																																																																																				CTD-2620I22.1-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000463881.1		7.615242	0	-17	46	0	0	1	0		3	9.078323	13	0.187500
GNAQ	2776	broad.mit.edu	hg19	9	80409488	80409488	+	Missense_Mutation	SNP	T	T	G	rs121913492		TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d	g.chr9:80409488T>G	ENST00000286548.4	-	5	848	c.626A>C	c.(625-627)cAa>cCa	p.Q209P	GNAQ_ENST00000397476.3_Missense_Mutation_p.Q7P	NM_002072.3	NP_002063.2	P50148	GNAQ_HUMAN	guanine nucleotide binding protein (G protein), q polypeptide	209		activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|glutamate signaling pathway|negative regulation of protein kinase activity|platelet activation|protein ADP-ribosylation|protein stabilization|regulation of action potential|regulation of catenin import into nucleus	cytoplasm|heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activator activity|GTPase activity|signal transducer activity	NS(1)|endometrium(3)|eye(229)|kidney(1)|large_intestine(4)|lung(6)|meninges(11)|ovary(1)|prostate(1)|skin(44)|upper_aerodigestive_tract(1)	302					CTCTGACCTTTGGCCCCCTAC	0.348	153	108.0	105.0	106.0	9	80409488	2203	4300	6503	SO:0001583	missense		CCDS6658.1	9q21	2010-03-17			ENSG00000156052	ENSG00000156052		4390	protein-coding gene	gene with protein product		600998			8825633	Standard	NM_002072	Approved	G-ALPHA-q, GAQ	uc004akw.3	P50148	OTTHUMG00000020059	ENST00000286548.4:c.626A>C	9.37:g.80409488T>G	ENSP00000286548:p.Gln209Pro	O15108|Q13462|Q6NT27|Q92471|Q9BZB9	ENST00000286548.4	37	CCDS6658.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.614273	0.87359	.	.	ENSG00000156052	ENST00000286548;ENST00000397476	D;D	0.91237	-2.81;-2.81	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	D	0.97164	0.9073	H	0.97291	3.975	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.98607	1.0661	10	0.87932	D	0	.	15.9502	0.79827	0.0:0.0:0.0:1.0	.	209	P50148	GNAQ_HUMAN	P	209;7	ENSP00000286548:Q209P;ENSP00000443197:Q7P	ENSP00000286548:Q209P	Q	-	2	0	GNAQ	79599308	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	8.040000	0.89188	2.167000	0.68274	0.460000	0.39030	CAA	GNAQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052761.1		99.843706	0	-8	104	0	0	1	0	NM_002072	30	100.048327	38	0.441176
OR56A3	390083	broad.mit.edu	hg19	11	5968660	5968660	+	Silent	SNP	G	G	A			TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d	g.chr11:5968660G>A	ENST00000329564.6	+	1	91	c.84G>A	c.(82-84)caG>caA	p.Q28Q		NM_001003443.2	NP_001003443.2	Q8NH54	O56A3_HUMAN	olfactory receptor, family 56, subfamily A, member 3	28		sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(27)|stomach(1)|upper_aerodigestive_tract(1)	41		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;9.41e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)	CCAGCTGGCAGCACTGGCTGT	0.537	0	91.0	97.0	95.0	11	5968660	2200	4296	6496	SO:0001819	synonymous_variant		CCDS41614.1	11p15.4	2012-08-09		2004-03-10	ENSG00000184478	ENSG00000184478	"""GPCR / Class A : Olfactory receptors"""	14786	protein-coding gene	gene with protein product				OR56A6, OR56A3P		Standard	NM_001003443	Approved		uc010qzt.2	Q8NH54	OTTHUMG00000165373	ENST00000329564.6:c.84G>A	11.37:g.5968660G>A		A6NN77|Q6IFF7	ENST00000329564.6	37	CCDS41614.1																																																																																			OR56A3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383753.1		-3.417803	0	22	77	0	0	1	0	NM_001003443	3	6.705186	47	0.060000
SLC18B1	116843	broad.mit.edu	hg19	6	133105166	133105166	+	Silent	SNP	C	C	T			TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d	g.chr6:133105166C>T	ENST00000275227.4	-	6	660	c.564G>A	c.(562-564)ttG>ttA	p.L188L	SLC18B1_ENST00000367918.1_Intron|SLC18B1_ENST00000538764.1_Silent_p.L62L	NM_052831.2	NP_439896.1	Q6NT16	CF192_HUMAN	solute carrier family 18, subfamily B, member 1	188		transmembrane transport	integral to membrane								AGGATTGATACAAAAAGCCAC	0.368	0	111.0	115.0	114.0	6	133105166	2203	4300	6503	SO:0001819	synonymous_variant	AK124442	CCDS5163.1	6q22.3-q23.3	2013-05-22	2012-03-09	2012-03-09	ENSG00000146409	ENSG00000146409	"""Solute carriers"""	21573	protein-coding gene	gene with protein product		613361	"""chromosome 6 open reading frame 192"""	C6orf192	19697161	Standard	XM_006715328	Approved	dJ55C23.6	uc003qdw.1	Q6NT16	OTTHUMG00000015595	ENST00000275227.4:c.564G>A	6.37:g.133105166C>T		A8K1K3|B3KW77|Q6ISF2	ENST00000275227.4	37	CCDS5163.1																																																																																			SLC18B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042273.1		27.433068	0	-14	94	0	0	1	0	NM_052831	13	33.495437	55	0.191176
KIAA1244	57221	broad.mit.edu	hg19	6	138608050	138608050	+	Missense_Mutation	SNP	C	C	G			TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d	g.chr6:138608050C>G	ENST00000251691.4	+	16	2948	c.2782C>G	c.(2782-2784)Cta>Gta	p.L928V		NM_020340.4	NP_065073.3	Q5TH69	BIG3_HUMAN	KIAA1244	928		regulation of ARF protein signal transduction	cytoplasm|integral to membrane	ARF guanyl-nucleotide exchange factor activity	NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)	GAGCTGCGCTCTAGGTACCAG	0.622	0	33.0	31.0	32.0	6	138608050	2203	4300	6503	SO:0001583	missense	AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379	"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	21213	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 33"""		"""chromosome 6 open reading frame 92"""	C6orf92		Standard	NM_020340	Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.2782C>G	6.37:g.138608050C>G	ENSP00000251691:p.Leu928Val		ENST00000251691.4	37	CCDS5189.2	.	.	.	.	.	.	.	.	.	.	C	17.60	3.429550	0.62844	.	.	ENSG00000112379	ENST00000251691	T	0.57273	0.41	5.25	4.31	0.51392	.	0.068008	0.64402	D	0.000018	T	0.64216	0.2578	M	0.75777	2.31	0.80722	D	1	D	0.69078	0.997	D	0.78314	0.991	T	0.66689	-0.5860	10	0.72032	D	0.01	-11.2175	11.8879	0.52613	0.0:0.8647:0.0:0.1353	.	928	Q5TH69	BIG3_HUMAN	V	928	ENSP00000251691:L928V	ENSP00000251691:L928V	L	+	1	2	KIAA1244	138649743	0.953000	0.32496	0.978000	0.43139	0.744000	0.42396	2.136000	0.42121	2.738000	0.93877	0.655000	0.94253	CTA	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4		12.497831	0	0	26	0	0	1	0	NM_020340	4	12.585346	6	0.400000
BAP1	8314	broad.mit.edu	hg19	3	52443574	52443574	+	Nonsense_Mutation	SNP	G	G	A			TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d	g.chr3:52443574G>A	ENST00000460680.1	-	3	589	c.118C>T	c.(118-120)Cag>Tag	p.Q40*	BAP1_ENST00000296288.5_Nonsense_Mutation_p.Q40*	NM_004656.2	NP_004647.1	Q92560	BAP1_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	40		monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|PR-DUB complex	chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity	NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)	ACTCACCCCTGACATTTGCTC	0.582	2	218.0	228.0	224.0	3	52443574	2203	4300	6503	SO:0001587	stop_gained	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930		950	protein-coding gene	gene with protein product		603089			9528852	Standard	NM_004656	Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.118C>T	3.37:g.52443574G>A	ENSP00000417132:p.Gln40*	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	ENST00000460680.1	37	CCDS2853.1	.	.	.	.	.	.	.	.	.	.	G	34	5.352033	0.95830	.	.	ENSG00000163930	ENST00000460680;ENST00000296288	.	.	.	4.97	4.97	0.65823	.	0.114511	0.64402	D	0.000010	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	.	18.2399	0.89963	0.0:0.0:1.0:0.0	.	.	.	.	X	40	.	ENSP00000296288:Q40X	Q	-	1	0	BAP1	52418614	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.607000	0.82883	2.312000	0.78011	0.655000	0.94253	CAG	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1		277.919426	0	-46	233	0	0	1	0		85	287.318056	20	0.809524
SSFA2	6744	broad.mit.edu	hg19	2	182786871	182786871	+	Missense_Mutation	SNP	G	G	A			TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d	g.chr2:182786871G>A	ENST00000431877.2	+	16	3586	c.3407G>A	c.(3406-3408)gGc>gAc	p.G1136D	SSFA2_ENST00000409136.1_Missense_Mutation_p.G645D|SSFA2_ENST00000467172.2_3'UTR|SSFA2_ENST00000409001.1_Missense_Mutation_p.G1114D|SSFA2_ENST00000428267.2_Missense_Mutation_p.G961D|SSFA2_ENST00000320370.7_Missense_Mutation_p.G1136D	NM_001130445.1	NP_001123917.1	P28290	SSFA2_HUMAN	sperm specific antigen 2	1136			cytoplasm|plasma membrane	actin binding	breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(18)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	38			OV - Ovarian serous cystadenocarcinoma(117;0.0856)		GCCTCAGTGGGCAAATCCAAA	0.478	0	118.0	122.0	121.0	2	182786871	2203	4300	6503	SO:0001583	missense	M61199	CCDS2284.1, CCDS46467.1, CCDS74611.1	2q32.1	2012-02-01			ENSG00000138434	ENSG00000138434		11319	protein-coding gene	gene with protein product	"""cleavage signal-1 protein"", ""KRAS-induced actin-interacting protein"", ""sperm associated antigen 13"""	118990			1555770	Standard	XM_005246812	Approved	CS-1, SPAG13, KRAP, KIAA1927	uc002uoh.3	P28290	OTTHUMG00000132584	ENST00000409136.1:c.1934G>A	2.37:g.182786871G>A	ENSP00000386916:p.Gly645Asp	A8K6T0|Q68DA6|Q7Z7L2|Q8N1L3|Q8N263|Q8N7H2|Q8NEN5|Q96E36|Q96PW1	ENST00000409136.1	37		.	.	.	.	.	.	.	.	.	.	G	10.89	1.477171	0.26511	.	.	ENSG00000138434	ENST00000431877;ENST00000320370;ENST00000409001;ENST00000428267;ENST00000409136;ENST00000451836	T;T;T;T;T	0.15603	2.65;2.41;2.59;2.6;2.46	5.95	0.965	0.19661	.	0.984794	0.08352	N	0.959120	T	0.17916	0.0430	L	0.55103	1.725	0.09310	N	1	P;P;P;P;P	0.49185	0.92;0.92;0.649;0.649;0.775	P;P;B;B;B	0.48030	0.564;0.564;0.344;0.344;0.344	T	0.14504	-1.0470	10	0.27082	T	0.32	0.6002	0.9245	0.01321	0.264:0.117:0.3785:0.2406	.	961;645;1114;1136;1136	E7END2;E7EUL7;E9PHV5;P28290;P28290-3	.;.;.;SSFA2_HUMAN;.	D	1136;1136;1114;961;645;81	ENSP00000388731:G1136D;ENSP00000314669:G1136D;ENSP00000387319:G1114D;ENSP00000409867:G961D;ENSP00000386916:G645D	ENSP00000314669:G1136D	G	+	2	0	SSFA2	182495116	0.950000	0.32346	0.012000	0.15200	0.409000	0.31022	1.168000	0.31859	-0.095000	0.12351	-0.253000	0.11424	GGC	SSFA2-009	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000334804.1		-17.531433	0	-10	82	0	0	1	0	NM_006751	4	7.771451	105	0.036697
RPTN	126638	broad.mit.edu	hg19	1	152128689	152128689	+	Missense_Mutation	SNP	C	C	T			TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d	g.chr1:152128689C>T	ENST00000316073.3	-	3	950	c.886G>A	c.(886-888)Ggt>Agt	p.G296S		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	296	Gln-rich.		proteinaceous extracellular matrix	calcium ion binding	breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59					TCCGTCTGACCGTAGTGGGAA	0.498	0	597.0	514.0	540.0	1	152128689	1568	3582	5150	SO:0001583	missense	AK096436	CCDS41397.1	1q21.3	2013-01-10			ENSG00000215853	ENSG00000215853	"""EF-hand domain containing"""	26809	protein-coding gene	gene with protein product		613259			15854042	Standard	NM_001122965	Approved	FLJ39117	uc001ezs.1	Q6XPR3	OTTHUMG00000154095	ENST00000316073.3:c.886G>A	1.37:g.152128689C>T	ENSP00000317895:p.Gly296Ser	B7ZBZ3	ENST00000316073.3	37	CCDS41397.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	16.30	3.083172	0.55861	.	.	ENSG00000215853	ENST00000316073	T	0.12984	2.63	4.73	-0.515	0.11954	.	.	.	.	.	T	0.07098	0.0180	L	0.33792	1.035	0.09310	N	1	D	0.65815	0.995	P	0.54140	0.743	T	0.25398	-1.0133	9	0.49607	T	0.09	-8.2231	8.1514	0.31143	0.0:0.4582:0.0:0.5418	.	296	Q6XPR3	RPTN_HUMAN	S	296	ENSP00000317895:G296S	ENSP00000317895:G296S	G	-	1	0	RPTN	150395313	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.770000	0.04705	0.098000	0.17522	-0.409000	0.06214	GGT	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1		-83.795869	0	-97	454	0	0	1	0	XM_371312	4	6.426938	327	0.012085
TNFRSF1A	7132	broad.mit.edu	hg19	12	6439098	6439098	+	Silent	SNP	G	G	A			TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d	g.chr12:6439098G>A	ENST00000162749.2	-	9	1202	c.903C>T	c.(901-903)ccC>ccT	p.P301P	TNFRSF1A_ENST00000540022.1_Silent_p.P258P	NM_001065.3	NP_001056.1	P19438	TNR1A_HUMAN	tumor necrosis factor receptor superfamily, member 1A	301		apoptosis|cellular response to mechanical stimulus|induction of apoptosis by extracellular signals|inflammatory response|interspecies interaction between organisms|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of inflammatory response|positive regulation of transcription from RNA polymerase II promoter|prostaglandin metabolic process	extracellular region|integral to plasma membrane|membrane raft	tumor necrosis factor receptor activity	endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	19					GACAGTCACCGGGGGTATAGG	0.652	0	27.0	29.0	28.0	12	6439098	2194	4268	6462	SO:0001819	synonymous_variant	M75866	CCDS8542.1	12p13.2	2014-09-17			ENSG00000067182	ENSG00000067182	"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11916	protein-coding gene	gene with protein product		191190		TNFR1	1655358, 2158863	Standard	NM_001065	Approved	TNF-R, TNFAR, TNFR60, TNF-R-I, CD120a, TNF-R55	uc001qnu.3	P19438	OTTHUMG00000168267	ENST00000162749.2:c.903C>T	12.37:g.6439098G>A		A8K4X3|B2RDE4|B3KPQ1|B4DQB7|B4E309|B5M0B5|D3DUR1|Q9UCA4	ENST00000162749.2	37	CCDS8542.1																																																																																			TNFRSF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399038.1		16.576834	0	1	10	0	0	1	0	NM_001065	5	16.686552	3	0.625000
PDE4DIP	9659	broad.mit.edu	hg19	1	144856945	144856945	+	Silent	SNP	G	G	A			TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d	g.chr1:144856945G>A	ENST00000369359.4	-	43	6986	c.6948C>T	c.(6946-6948)gtC>gtT	p.V2316V	PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000530740.1_Silent_p.V2265V|PDE4DIP_ENST00000369354.3_Silent_p.V2180V|PDE4DIP_ENST00000369356.4_Silent_p.V2180V|PDE4DIP_ENST00000313382.9_Silent_p.V2074V			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2180		cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding	NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)	TGTGGCCAATGACATGGCGGC	0.512	0	47.0	46.0	46.0	1	144856945	2202	4292	6494	SO:0001819	synonymous_variant	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104		15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2	9455484, 11134006	Standard	NM_022359	Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000530740.1:c.6795C>T	1.37:g.144856945G>A		A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	ENST00000530740.1	37		.	.	.	.	.	.	.	.	.	.	.	10.45	1.354175	0.24512	.	.	ENSG00000178104	ENST00000530130	.	.	.	4.48	-2.2	0.06994	.	.	.	.	.	T	0.32823	0.0842	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35076	-0.9803	4	.	.	.	.	5.6072	0.17387	0.0861:0.4289:0.3666:0.1185	.	.	.	.	L	257	.	.	S	-	2	0	PDE4DIP	143568302	0.976000	0.34144	0.985000	0.45067	0.975000	0.68041	-0.034000	0.12225	-0.122000	0.11766	0.449000	0.29647	TCA	PDE4DIP-036	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000384663.2		51.534355	0	-6	74	0	0	1	0	NM_022359	21	55.619767	59	0.262500
SBDS	51119	broad.mit.edu	hg19	7	66456163	66456163	+	Missense_Mutation	SNP	C	C	A			TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d	g.chr7:66456163C>A	ENST00000246868.2	-	4	768	c.585G>T	c.(583-585)aaG>aaT	p.K195N		NM_016038.2	NP_057122.2	Q9Y3A5	SBDS_HUMAN	Shwachman-Bodian-Diamond syndrome	195		bone marrow development|bone mineralization|leukocyte chemotaxis|mature ribosome assembly|mitotic spindle stabilization|positive regulation of translation|ribosomal large subunit biogenesis|rRNA processing	cytoplasm|nucleolus|nucleoplasm|spindle pole	microtubule binding|ribosome binding|rRNA binding	cervix(1)|endometrium(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	7					TTTCTATGACCTTGATCAGTG	0.363	0	162.0	134.0	144.0	7	66456163	2203	4300	6503	SO:0001583	missense	AF151855	CCDS5537.1	7q11.22	2014-09-17			ENSG00000126524	ENSG00000126524		19440	protein-coding gene	gene with protein product		607444			12496757	Standard	NM_016038	Approved	CGI-97, FLJ10917, SDS, SWDS	uc003tvm.1	Q9Y3A5	OTTHUMG00000023165	ENST00000246868.2:c.585G>T	7.37:g.66456163C>A	ENSP00000246868:p.Lys195Asn	A8K0P4|Q96FX0|Q9NV53	ENST00000246868.2	37	CCDS5537.1	.	.	.	.	.	.	.	.	.	.	C	13.42	2.232682	0.39498	.	.	ENSG00000126524	ENST00000246868	D	0.96073	-3.9	5.04	5.04	0.67666	Ribosome maturation protein SBDS, C-terminal (1);	0.042740	0.85682	D	0.000000	D	0.92708	0.7682	L	0.47716	1.5	0.80722	D	1	B	0.11235	0.004	B	0.19946	0.027	D	0.88911	0.3359	10	0.17832	T	0.49	-17.7777	15.9306	0.79656	0.0:1.0:0.0:0.0	.	195	Q9Y3A5	SBDS_HUMAN	N	195	ENSP00000246868:K195N	ENSP00000246868:K195N	K	-	3	2	SBDS	66093598	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.258000	0.51507	2.641000	0.89580	0.555000	0.69702	AAG	SBDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251746.2		-7.129469	1	-10	93	0	1	1	1	NM_016038	3	6.318062	59	0.048387
PTPN23	25930	broad.mit.edu	hg19	3	47454066	47454066	+	Silent	SNP	T	T	C			TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d	g.chr3:47454066T>C	ENST00000265562.4	+	24	4457	c.4380T>C	c.(4378-4380)caT>caC	p.H1460H	PTPN23_ENST00000431726.1_Silent_p.H1334H	NM_015466.2	NP_056281.1	Q9H3S7	PTN23_HUMAN	protein tyrosine phosphatase, non-receptor type 23	1460		cilium morphogenesis	cilium|cytoplasmic membrane-bounded vesicle|microtubule basal body	protein tyrosine phosphatase activity	breast(3)|central_nervous_system(1)|large_intestine(5)|lung(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.000271)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)	TGCAGCGCCATGGTGTGCCTC	0.612	0	99.0	90.0	93.0	3	47454066	2203	4300	6503	SO:0001819	synonymous_variant	AB025194	CCDS2754.1	3p21.3	2011-06-09			ENSG00000076201	ENSG00000076201	"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	14406	protein-coding gene	gene with protein product		606584			11095967	Standard	NM_015466	Approved	DKFZP564F0923, KIAA1471, HD-PTP	uc003crf.1	Q9H3S7	OTTHUMG00000133520	ENST00000265562.4:c.4380T>C	3.37:g.47454066T>C		A8K0D7|Q7KZF8|Q8N6Z5|Q9BSR5|Q9P257|Q9UG03|Q9UMZ4	ENST00000265562.4	37	CCDS2754.1																																																																																			PTPN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257492.2		33.155504	0	8	54	0	0	1	0	NM_015466	10	34.018621	3	0.769231
KIAA1551	55196	broad.mit.edu	hg19	12	32137648	32137648	+	Silent	SNP	C	C	T	rs150095870		TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d	g.chr12:32137648C>T	ENST00000312561.4	+	4	4173	c.3759C>T	c.(3757-3759)gaC>gaT	p.D1253D	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639			KIAA1551												AACTACAAGACGACAGTAGAA	0.353	0	56.0	54.0	55.0	12	32137648	2203	4299	6502	SO:0001819	synonymous_variant	AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718		25559	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 35"""	C12orf35	10997877	Standard	NM_018169	Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.3759C>T	12.37:g.32137648C>T		B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	ENST00000312561.4	37	CCDS8725.2																																																																																			KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2		75.591357	0	12	53	0	0	1	0	NM_018169	24	76.196237	37	0.393443
GLIS3	169792	broad.mit.edu	hg19	9	3856041	3856041	+	Missense_Mutation	SNP	G	G	A			TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d	g.chr9:3856041G>A	ENST00000324333.10	-	8	2169	c.1976C>T	c.(1975-1977)tCt>tTt	p.S659F	GLIS3_ENST00000461870.1_5'UTR|GLIS3_ENST00000381971.3_Missense_Mutation_p.S814F	NM_152629.3	NP_689842.3	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3	659		negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter		DNA binding|zinc ion binding	NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(12)|lung(4)|ovary(2)|prostate(1)|skin(1)	26		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)	TTGAAAAGAAGAGTTTGTTTC	0.443	0	151.0	146.0	147.0	9	3856041	2203	4300	6503	SO:0001583	missense	BC033899	CCDS6451.1, CCDS43784.1	9p24.2	2008-05-02	2004-07-16	2004-07-16	ENSG00000107249	ENSG00000107249	"""Zinc fingers, C2H2-type"""	28510	protein-coding gene	gene with protein product		610192	"""zinc finger protein 515"""	ZNF515	14500813	Standard	NM_152629	Approved	MGC33662	uc003zhx.1	Q8NEA6	OTTHUMG00000019463	ENST00000381971.3:c.2441C>T	9.37:g.3856041G>A	ENSP00000371398:p.Ser814Phe	B1AL19|Q1PHK5	ENST00000381971.3	37	CCDS43784.1	.	.	.	.	.	.	.	.	.	.	g	19.98	3.926811	0.73327	.	.	ENSG00000107249	ENST00000324333;ENST00000381971	T;T	0.11930	2.74;2.73	5.8	4.9	0.64082	.	0.245141	0.27946	N	0.017218	T	0.20047	0.0482	L	0.27053	0.805	0.24718	N	0.993167	D;P;D;P	0.59767	0.974;0.894;0.986;0.956	P;B;P;P	0.54100	0.66;0.365;0.742;0.459	T	0.04855	-1.0922	10	0.72032	D	0.01	.	16.952	0.86248	0.0:0.1277:0.8723:0.0	.	254;327;814;659	Q59FQ6;Q1PHK3;Q8NEA6-2;Q8NEA6	.;.;.;GLIS3_HUMAN	F	659;814	ENSP00000325494:S659F;ENSP00000371398:S814F	ENSP00000325494:S659F	S	-	2	0	GLIS3	3846041	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	4.066000	0.57520	1.454000	0.47793	0.561000	0.74099	TCT	GLIS3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354776.1		145.945991	0	2	93	0	0	1	0	NM_152629	46	145.948368	47	0.494624
DMXL2	23312	broad.mit.edu	hg19	15	51791218	51791219	+	Frame_Shift_Ins	INS	-	-	A			TCGA-V4-A9EX-01A-11D-A39W-08	TCGA-V4-A9EX-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	97116c78-ac2a-4d7f-803b-1d829e737070	de0d7475-70ab-4147-b388-97e0e414bc7d	g.chr15:51791218_51791219insA	ENST00000251076.5	-	18	4489_4490	c.4202_4203insT	c.(4201-4203)gtafs	p.V1401fs	DMXL2_ENST00000543779.2_Frame_Shift_Ins_p.V1401fs|DMXL2_ENST00000449909.3_Intron	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	1401			cell junction|synaptic vesicle membrane	Rab GTPase binding	breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)	TACTGCCACTTACACTAATAGT	0.406	0									SO:0001589	frameshift_variant	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093	"""WD repeat domain containing"""	2938	protein-coding gene	gene with protein product	"""rabconnectin 3"""	612186				Standard	NM_001174116	Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000543779.2:c.4203dupT	15.37:g.51791219_51791219dupA	ENSP00000441858:p.Val1401fs	B2RTR3|B7ZMH3|F5GWF1|O94938	ENST00000543779.2	37	CCDS53946.1																																																																																			DMXL2-014	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000419004.1	.	.		-32	178					NM_015263	79		114	0.41