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
RABL6	55684	broad.mit.edu	hg19	9	139734309	139734309	+	Missense_Mutation	SNP	G	G	C			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr9:139734309G>C	ENST00000371675.3	+	13	2462	c.1577G>C	c.(1576-1578)aGt>aCt	p.S526T	RABL6_ENST00000357466.2_Intron|RABL6_ENST00000371663.4_Missense_Mutation_p.S642T|RABL6_ENST00000311502.7_Missense_Mutation_p.S641T|RABL6_ENST00000432842.2_3'UTR					RAB, member RAS oncogene family-like 6												AAGGAGAGCAGTGAGGAAGGT	0.682	0	18.0	23.0	22.0	9	139734309	1961	4127	6088	SO:0001583	missense	AK094382	CCDS48058.1, CCDS55352.1, CCDS55353.1	9q34.3	2012-06-28	2012-06-28	2012-06-28	ENSG00000196642	ENSG00000196642		24703	protein-coding gene	gene with protein product	"""Rab-like protein 1"", ""partner of ARF"""	610615	"""chromosome 9 open reading frame 86"""	C9orf86	14702039, 16582619, 17962191, 19433581	Standard	NM_024718	Approved	FLJ10101, FLJ13045, pp8875, bA216L13.9, Parf, RBEL1	uc004cjj.1	Q3YEC7	OTTHUMG00000020947	ENST00000311502.7:c.1922G>C	9.37:g.139734309G>C	ENSP00000311134:p.Ser641Thr	A8QVZ7|A8QVZ8|C6K8I4|C6K8I5|Q4F968|Q5T5R7|Q8IWK1|Q8TCL4|Q8WU94|Q96SR8|Q9BU21|Q9H935	ENST00000311502.7	37	CCDS48058.1	.	.	.	.	.	.	.	.	.	.	.	11.74	1.728562	0.30593	.	.	ENSG00000196642	ENST00000371663;ENST00000311502;ENST00000371675;ENST00000435930	T;T;T;T	0.73152	-0.61;-0.63;-0.62;-0.72	4.72	4.72	0.59763	.	0.338891	0.33127	N	0.005251	T	0.78635	0.4314	M	0.71581	2.175	0.46298	D	0.998971	D;D;P	0.71674	0.998;0.965;0.941	D;P;P	0.63703	0.917;0.655;0.453	T	0.77135	-0.2699	10	0.33940	T	0.23	-14.0842	8.9208	0.35610	0.1028:0.0:0.8972:0.0	.	435;642;641	B1AMX5;Q3YEC7-2;Q3YEC7	.;.;PARF_HUMAN	T	642;641;526;435	ENSP00000360727:S642T;ENSP00000311134:S641T;ENSP00000360740:S526T;ENSP00000408442:S435T	ENSP00000311134:S641T	S	+	2	0	C9orf86	138854130	1.000000	0.71417	0.169000	0.22859	0.034000	0.12701	6.146000	0.71777	2.162000	0.67917	0.561000	0.74099	AGT	RABL6-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055141.4		33.755183	0	0	17	0	0	1	0	NM_024718	10	34.331778	4	0.714286
RAB3GAP2	25782	broad.mit.edu	hg19	1	220364491	220364491	+	Missense_Mutation	SNP	G	G	A	rs151225064		TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr1:220364491G>A	ENST00000358951.2	-	14	1522	c.1406C>T	c.(1405-1407)gCg>gTg	p.A469V		NM_012414.3	NP_036546.2	Q9H2M9	RBGPR_HUMAN	RAB3 GTPase activating protein subunit 2 (non-catalytic)	469		intracellular protein transport	cytoplasm|soluble fraction	GTPase activator activity|protein heterodimerization activity	breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(1)	39				GBM - Glioblastoma multiforme(131;0.0443)	CCTTCTTGGCGCATAGATCAC	0.493	1	137.0	134.0	135.0	1	220364491	2203	4300	6503	SO:0001583	missense	AB020646	CCDS31028.1	1q41	2014-03-03			ENSG00000118873	ENSG00000118873		17168	protein-coding gene	gene with protein product		609275			15696165, 16532399, 24482476	Standard	NM_012414	Approved	RAB3-GAP150, KIAA0839, DKFZP434D245, SPG69	uc010puk.1	Q9H2M9	OTTHUMG00000037139	ENST00000358951.2:c.1406C>T	1.37:g.220364491G>A	ENSP00000351832:p.Ala469Val	A6H8V0|O75872|Q9HAB0|Q9UFJ7|Q9UQ15	ENST00000358951.2	37	CCDS31028.1	.	.	.	.	.	.	.	.	.	.	G	35	5.508939	0.96386	0.0	2.33E-4	ENSG00000118873	ENST00000358951	D	0.90444	-2.67	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	D	0.94925	0.8359	M	0.65975	2.015	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.94568	0.7768	10	0.56958	D	0.05	.	19.7176	0.96129	0.0:0.0:1.0:0.0	.	469	Q9H2M9	RBGPR_HUMAN	V	469	ENSP00000351832:A469V	ENSP00000351832:A469V	A	-	2	0	RAB3GAP2	218431114	1.000000	0.71417	0.907000	0.35723	0.936000	0.57629	9.090000	0.94144	2.670000	0.90874	0.563000	0.77884	GCG	RAB3GAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090205.2		-21.343212	0	13	125	0	0	1	0	NM_012414	5	9.723141	129	0.037313
LRRTM3	347731	broad.mit.edu	hg19	10	68687631	68687631	+	Missense_Mutation	SNP	T	T	A			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr10:68687631T>A	ENST00000361320.4	+	2	1535	c.957T>A	c.(955-957)aaT>aaA	p.N319K	CTNNA3_ENST00000373744.4_Intron|CTNNA3_ENST00000433211.2_Intron	NM_178011.3	NP_821079.3	Q86VH5	LRRT3_HUMAN	leucine rich repeat transmembrane neuronal 3	319	LRRCT.		integral to membrane		breast(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	41					GCAGCAGAAATATTTGCTCCC	0.398	0	77.0	84.0	82.0	10	68687631	2203	4300	6503	SO:0001583	missense	BX640611	CCDS7270.1	10q22.1	2007-01-22				ENSG00000198739		19410	protein-coding gene	gene with protein product		610869			12676565	Standard	XR_247527	Approved		uc001jmz.1	Q86VH5		ENST00000361320.4:c.957T>A	10.37:g.68687631T>A	ENSP00000355187:p.Asn319Lys	A8K2A3|Q2NKX7|Q6N0A3	ENST00000361320.4	37	CCDS7270.1	.	.	.	.	.	.	.	.	.	.	T	2.049	-0.418154	0.04766	.	.	ENSG00000198739	ENST00000361320;ENST00000373722	T	0.04317	3.65	5.8	0.496	0.16896	.	0.000000	0.85682	D	0.000000	T	0.02610	0.0079	N	0.13043	0.29	0.42989	D	0.994482	B;B	0.20459	0.007;0.045	B;B	0.21360	0.009;0.034	T	0.50048	-0.8873	10	0.10636	T	0.68	.	9.5846	0.39508	0.0:0.3875:0.0:0.6125	.	319;319	Q86VH5;Q86VH5-2	LRRT3_HUMAN;.	K	319	ENSP00000355187:N319K	ENSP00000355187:N319K	N	+	3	2	LRRTM3	68357637	1.000000	0.71417	0.999000	0.59377	0.983000	0.72400	1.623000	0.37008	0.058000	0.16222	-0.280000	0.10049	AAT	LRRTM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048277.2		32.011942	0	16	89	0	0	1	0	NM_178011	14	38.279393	58	0.194444
GNA11	2767	broad.mit.edu	hg19	19	3118942	3118942	+	Missense_Mutation	SNP	A	A	T			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr19:3118942A>T	ENST00000078429.4	+	5	868	c.626A>T	c.(625-627)cAg>cTg	p.Q209L	AC005262.3_ENST00000587701.1_RNA|GNA11_ENST00000586180.1_3'UTR	NM_002067.2	NP_002058.2	P29992	GNA11_HUMAN	guanine nucleotide binding protein (G protein), alpha 11 (Gq class)	209		activation of phospholipase C activity by dopamine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|platelet activation|protein ADP-ribosylation|regulation of action potential	cytoplasm|heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity	endometrium(2)|eye(132)|kidney(1)|large_intestine(2)|lung(1)|meninges(5)|ovary(1)|prostate(1)|skin(16)	161		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.79e-05)|OV - Ovarian serous cystadenocarcinoma(105;2.68e-113)|Epithelial(107;1.22e-111)|all cancers(105;5.78e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00141)|STAD - Stomach adenocarcinoma(1328;0.181)	GTGGGGGGCCAGCGGTCGGAG	0.612	82	104.0	89.0	94.0	19	3118942	2203	4300	6503	SO:0001583	missense	AF493900	CCDS12103.1	19p13.3	2014-02-04			ENSG00000088256	ENSG00000088256		4379	protein-coding gene	gene with protein product		139313	"""hypocalciuric hypercalcemia 2"""	HHC2	1302014, 23802516	Standard	NM_002067	Approved	FBH, FBH2, FHH2	uc002lxd.3	P29992	OTTHUMG00000180631	ENST00000078429.4:c.626A>T	19.37:g.3118942A>T	ENSP00000078429:p.Gln209Leu	O15109|Q14350|Q6IB00	ENST00000078429.4	37	CCDS12103.1	.	.	.	.	.	.	.	.	.	.	.	15.05	2.718086	0.48622	.	.	ENSG00000088256	ENST00000078429	D	0.91237	-2.81	3.26	3.26	0.37387	.	0.000000	0.64402	U	0.000006	D	0.96950	0.9004	H	0.99357	4.53	0.80722	D	1	D	0.59767	0.986	D	0.68483	0.958	D	0.96823	0.9605	10	0.87932	D	0	.	10.7338	0.46113	1.0:0.0:0.0:0.0	.	209	P29992	GNA11_HUMAN	L	209	ENSP00000078429:Q209L	ENSP00000078429:Q209L	Q	+	2	0	GNA11	3069942	1.000000	0.71417	0.438000	0.26821	0.027000	0.11550	9.104000	0.94239	1.256000	0.44068	0.379000	0.24179	CAG	GNA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452261.2		76.588246	0	-11	70	0	0	1	0	NM_002067	25	76.823517	33	0.431034
CSMD3	114788	broad.mit.edu	hg19	8	113694820	113694820	+	Missense_Mutation	SNP	G	G	A			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr8:113694820G>A	ENST00000297405.5	-	16	2772	c.2528C>T	c.(2527-2529)gCa>gTa	p.A843V	CSMD3_ENST00000455883.2_Missense_Mutation_p.A739V|CSMD3_ENST00000343508.3_Missense_Mutation_p.A803V|CSMD3_ENST00000352409.3_Missense_Mutation_p.A843V	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	843	Sushi 4.		integral to membrane|plasma membrane		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646					AAACCGCCGTGCATTGATTGG	0.348	0	99.0	99.0	99.0	8	113694820	2203	4300	6503	SO:0001583	missense	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796		19291	protein-coding gene	gene with protein product		608399				Standard	NM_052900	Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.2528C>T	8.37:g.113694820G>A	ENSP00000297405:p.Ala843Val	Q96PZ3	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.769141	0.90020	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.25912	1.77;1.77;1.77;1.77;1.77	5.58	5.58	0.84498	Complement control module (2);Sushi/SCR/CCP (3);	0.075478	0.52532	D	0.000071	T	0.50446	0.1616	L	0.60904	1.88	0.40393	D	0.979562	D;D;D	0.76494	0.999;0.999;0.989	D;D;D	0.91635	0.998;0.999;0.921	T	0.48387	-0.9040	10	0.59425	D	0.04	.	19.557	0.95354	0.0:0.0:1.0:0.0	.	739;843;803	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	V	803;843;183;739;843	ENSP00000345799:A803V;ENSP00000297405:A843V;ENSP00000341558:A183V;ENSP00000412263:A739V;ENSP00000343124:A843V	ENSP00000297405:A843V	A	-	2	0	CSMD3	113763996	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	4.687000	0.61708	2.623000	0.88846	0.650000	0.86243	GCA	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1		59.911682	0	27	130	0	0	1	0	NM_052900	28	72.871382	118	0.191781
APEH	327	broad.mit.edu	hg19	3	49716365	49716365	+	Missense_Mutation	SNP	G	G	A			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr3:49716365G>A	ENST00000296456.5	+	12	1541	c.1141G>A	c.(1141-1143)Gct>Act	p.A381T	APEH_ENST00000438011.1_Missense_Mutation_p.A381T	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase	381		proteolysis	cytoplasm|nuclear membrane	serine-type endopeptidase activity	endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)	CTTTGACTCGGCTCAGCGCAG	0.607	0	77.0	72.0	74.0	3	49716365	2203	4300	6503	SO:0001583	missense	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062		586	protein-coding gene	gene with protein product	"""acylaminoacyl-peptidase"""	102645	"""N-acylaminoacyl-peptide hydrolase"""	D3F15S2, DNF15S2, D3S48E	2392324	Standard	NM_001640	Approved		uc003cxf.3	P13798	OTTHUMG00000156882	ENST00000296456.5:c.1141G>A	3.37:g.49716365G>A	ENSP00000296456:p.Ala381Thr	Q9BQ33|Q9P0Y2	ENST00000296456.5	37	CCDS2801.1	.	.	.	.	.	.	.	.	.	.	G	15.57	2.871281	0.51695	.	.	ENSG00000164062	ENST00000296456;ENST00000442186;ENST00000438011	T;T	0.43294	0.95;0.95	5.62	4.72	0.59763	Six-bladed beta-propeller, TolB-like (1);Peptidase S9A/B/C, oligopeptidase, N-terminal beta-propeller (1);	0.405904	0.28322	N	0.015780	T	0.38427	0.1040	L	0.56280	1.765	0.31060	N	0.714217	B;B	0.18968	0.032;0.014	B;B	0.19946	0.027;0.017	T	0.38650	-0.9651	10	0.12766	T	0.61	-24.1998	15.3547	0.74418	0.0:0.2638:0.7362:0.0	.	381;381	C9JIF9;P13798	.;ACPH_HUMAN	T	381;306;381	ENSP00000296456:A381T;ENSP00000415862:A381T	ENSP00000296456:A381T	A	+	1	0	APEH	49691369	0.220000	0.23631	0.766000	0.31476	0.910000	0.53928	1.111000	0.31159	1.306000	0.44926	0.561000	0.74099	GCT	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2		-6.438822	0	0	124	0	0	1	0		4	7.957368	66	0.057143
BLOC1S6	26258	broad.mit.edu	hg19	15	45884472	45884472	+	Silent	SNP	C	C	T			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr15:45884472C>T	ENST00000220531.3	+	2	543	c.222C>T	c.(220-222)ctC>ctT	p.L74L	BLOC1S6_ENST00000568816.1_5'UTR|BLOC1S6_ENST00000565323.1_Silent_p.L79L|BLOC1S6_ENST00000562384.1_Intron|RP11-96O20.4_ENST00000564080.1_Intron|BLOC1S6_ENST00000566753.1_Silent_p.L74L|BLOC1S6_ENST00000567461.1_Intron|BLOC1S6_ENST00000565216.1_Intron|BLOC1S6_ENST00000567740.1_Intron|BLOC1S6_ENST00000565409.1_5'UTR|BLOC1S6_ENST00000564765.1_5'UTR	NM_012388.2	NP_036520.1			biogenesis of lysosomal organelles complex-1, subunit 6, pallidin												TCCAGGAACTCACGTAAGCTA	0.363	0	80.0	81.0	80.0	15	45884472	2198	4298	6496	SO:0001819	synonymous_variant	AF080470	CCDS10126.1	15q21.1	2013-09-27	2012-08-07	2012-08-01	ENSG00000104164	ENSG00000104164	"""Biogenesis of lysosomal organelles complex-1 subunits"""	8549	protein-coding gene	gene with protein product		604310	"""pallid (mouse) homolog, pallidin"", ""pallidin homolog (mouse)"""	PA, PLDN	10610180	Standard	NM_012388	Approved	HPS9	uc001zvq.3	Q9UL45	OTTHUMG00000131477	ENST00000220531.3:c.222C>T	15.37:g.45884472C>T			ENST00000220531.3	37	CCDS10126.1																																																																																			BLOC1S6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254320.2		64.470688	0	-2	60	0	0	1	0	NM_012388	21	64.546318	25	0.456522
SLC23A3	151295	broad.mit.edu	hg19	2	220033409	220033409	+	Silent	SNP	G	G	C			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr2:220033409G>C	ENST00000455516.2	-	5	710	c.663C>G	c.(661-663)gcC>gcG	p.A221A	SLC23A3_ENST00000396775.3_Intron|SLC23A3_ENST00000295738.7_Silent_p.A213A|SLC23A3_ENST00000409878.3_Silent_p.A213A	NM_001144890.1	NP_001138362.1	Q6PIS1	S23A3_HUMAN	solute carrier family 23, member 3	213		transmembrane transport	integral to membrane	protein binding|transporter activity	endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	11		Renal(207;0.0474)		Epithelial(149;9.27e-07)|all cancers(144;0.000156)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	AGCAGAACTGGGCTACCTCCC	0.672	0	29.0	34.0	32.0	2	220033409	1993	4161	6154	SO:0001819	synonymous_variant	BC030243	CCDS42819.1, CCDS46517.1, CCDS46518.1	2q35	2013-07-18	2013-07-18		ENSG00000213901	ENSG00000213901	"""Solute carriers"""	20601	protein-coding gene	gene with protein product						Standard	NM_144712	Approved	SVCT3, FLJ31168, Yspl1	uc010zkr.2	Q6PIS1	OTTHUMG00000154616	ENST00000409878.3:c.639C>G	2.37:g.220033409G>C		B7Z512|Q2PYN6|Q96NA6	ENST00000409878.3	37	CCDS46518.1																																																																																			SLC23A3-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336331.2		22.392425	0	5	30	0	0	1	0	NM_144712	8	22.862795	15	0.347826
NDUFA5	4698	broad.mit.edu	hg19	7	123190629	123190629	+	Silent	SNP	T	T	A			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr7:123190629T>A	ENST00000471770.1	-	3	212	c.78A>T	c.(76-78)atA>atT	p.I26I	NDUFA5_ENST00000355749.2_Silent_p.I26I|NDUFA5_ENST00000467117.1_5'UTR	NM_001282419.1|NM_001282420.1|NM_001282421.1	NP_001269348.1|NP_001269349.1|NP_001269350.1	Q16718	NDUA5_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 5	26		mitochondrial electron transport, NADH to ubiquinone|transport	mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity	large_intestine(1)|urinary_tract(1)	2					TTGTGTACAATATTCTTAGCC	0.318	0	76.0	83.0	81.0	7	123190629	2202	4299	6501	SO:0001819	synonymous_variant		CCDS5788.1, CCDS64760.1, CCDS75655.1, CCDS75656.1	7q31.33	2013-06-19	2013-06-19		ENSG00000128609	ENSG00000128609	"""Mitochondrial respiratory chain complex / Complex I"""	7688	protein-coding gene	gene with protein product	"""complex I 13kDa subunit B"", ""ubiquinone reductase"", ""type I dehydrogenase"", ""NADH-ubiquinone oxidoreductase 13 kDa-B subunit"""	601677	"""NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 5 (13kD, B13)"", ""NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 5, 13kDa"""		9763677, 9021153	Standard	XM_005250371	Approved	B13, NUFM, CI-13KD-B, UQOR13, CI-13kB	uc003vks.3	Q16718	OTTHUMG00000157348	ENST00000355749.2:c.78A>T	7.37:g.123190629T>A		B2RD98|Q5H9R2|Q6IRX7	ENST00000355749.2	37	CCDS5788.1	.	.	.	.	.	.	.	.	.	.	T	7.828	0.719297	0.15372	.	.	ENSG00000128609	ENST00000378795	.	.	.	5.54	4.35	0.52113	.	.	.	.	.	T	0.64724	0.2624	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63812	-0.6552	5	0.46703	T	0.11	.	11.0704	0.47999	0.1393:0.0:0.0:0.8607	.	.	.	.	F	22	.	ENSP00000368072:I22F	I	-	1	0	NDUFA5	122977865	1.000000	0.71417	0.262000	0.24481	0.710000	0.40934	1.396000	0.34531	0.972000	0.38314	0.533000	0.62120	ATT	NDUFA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348533.1		5.005542	0	13	101	0	0	1	0	NM_005000	6	14.849210	55	0.098361
OTUD4	54726	broad.mit.edu	hg19	4	146059006	146059006	+	Missense_Mutation	SNP	G	G	A			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr4:146059006G>A	ENST00000454497.2	-	21	2863	c.2726C>T	c.(2725-2727)aCt>aTt	p.T909I	OTUD4_ENST00000455611.2_Intron|OTUD4_ENST00000447906.2_Missense_Mutation_p.T974I	NM_001102653.1	NP_001096123.1	Q01804	OTUD4_HUMAN	OTU domain containing 4	973				protein binding	breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(180;0.151)				AACAGGCACAGTTTCTCTCTC	0.463	0	128.0	133.0	131.0	4	146059006	2203	4300	6503	SO:0001583	missense		CCDS3764.1, CCDS47139.1	4q31.21	2014-02-24	2014-02-24		ENSG00000164164	ENSG00000164164	"""OTU domain containing"""	24949	protein-coding gene	gene with protein product		611744	"""OTU domain containing 4"""		1475186, 12727813, 19996094	Standard	NM_001102653	Approved	HSHIN1, KIAA1046, DUBA6	uc003ika.4	Q01804	OTTHUMG00000161480	ENST00000447906.2:c.2921C>T	4.37:g.146059006G>A	ENSP00000395487:p.Thr974Ile	B4DYS4|Q147U2|Q1ZYK1|Q6PG39|Q96MQ5|Q9NT94|Q9UPV6	ENST00000447906.2	37		.	.	.	.	.	.	.	.	.	.	G	13.28	2.191504	0.38707	.	.	ENSG00000164164	ENST00000454497;ENST00000447906	T;T	0.34275	1.37;1.37	6.17	5.33	0.75918	.	1.059000	0.07258	N	0.867023	T	0.32793	0.0841	N	0.24115	0.695	0.80722	D	1	B;B	0.13145	0.007;0.004	B;B	0.14023	0.01;0.004	T	0.02275	-1.1184	10	0.59425	D	0.04	-0.3286	15.5098	0.75772	0.0658:0.0:0.9342:0.0	.	974;973	G3V0I6;Q01804	.;OTUD4_HUMAN	I	909;974	ENSP00000409279:T909I;ENSP00000395487:T974I	ENSP00000395487:T974I	T	-	2	0	OTUD4	146278456	0.027000	0.19231	0.108000	0.21378	0.880000	0.50808	2.210000	0.42816	1.621000	0.50320	0.655000	0.94253	ACT	OTUD4-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000365117.2		-22.105384	0	45	191	0	0	1	0	NM_017493	4	7.258989	119	0.032520
PCDHB7	0	broad.mit.edu	hg19	5	140554267	140554267	+	Silent	SNP	G	G	A			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr5:140554267G>A	ENST00000231137.3	+	1	2025	c.1851G>A	c.(1849-1851)gtG>gtA	p.V617V		NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN		617	Cadherin 6.	calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	NS(2)|breast(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)		TATTCGGCGTGTGGGCGCACA	0.677	0	33.0	50.0	44.0	5	140554267	2163	4261	6424	SO:0001819	synonymous_variant	AF152500	CCDS4249.1	5q31	2010-01-26			ENSG00000113212	ENSG00000113212	"""Cadherins / Protocadherins : Clustered"""	8692	other	protocadherin		606333			10380929	Standard	NM_018940	Approved	PCDH-BETA7	uc003lit.3	Q9Y5E2	OTTHUMG00000129608	ENST00000231137.3:c.1851G>A	5.37:g.140554267G>A		A1L3Y8	ENST00000231137.3	37	CCDS4249.1																																																																																			PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2		43.051129	0	-23	137	0	0	1	0	NM_018940	23	55.405236	105	0.179687
OR52M1	119772	broad.mit.edu	hg19	11	4567078	4567078	+	Missense_Mutation	SNP	T	T	C			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr11:4567078T>C	ENST00000360213.1	+	1	658	c.658T>C	c.(658-660)Tcc>Ccc	p.S220P		NM_001004137.1	NP_001004137.1	Q8NGK5	O52M1_HUMAN	olfactory receptor, family 52, subfamily M, member 1	220		sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	endometrium(2)|large_intestine(2)|lung(9)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)	TATTGCTGCATCCTATGTGAT	0.522	0	263.0	247.0	252.0	11	4567078	2201	4298	6499	SO:0001583	missense	AB065789	CCDS31353.1	11p15.4	2012-08-09	2002-11-13	2002-11-15	ENSG00000197790	ENSG00000197790	"""GPCR / Class A : Olfactory receptors"""	15225	protein-coding gene	gene with protein product			"""olfactory receptor, family 52, subfamily M, member 1 pseudogene"""	OR52M1P		Standard	NM_001004137	Approved		uc010qyf.2	Q8NGK5	OTTHUMG00000165706	ENST00000360213.1:c.658T>C	11.37:g.4567078T>C	ENSP00000353343:p.Ser220Pro		ENST00000360213.1	37	CCDS31353.1	.	.	.	.	.	.	.	.	.	.	T	15.74	2.922553	0.52653	.	.	ENSG00000197790	ENST00000360213	T	0.46819	0.86	5.01	5.01	0.66863	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47093	D	0.000258	T	0.78130	0.4235	H	0.97516	4.02	0.25075	N	0.990962	D	0.69078	0.997	D	0.67231	0.95	T	0.76713	-0.2858	10	0.87932	D	0	.	13.9773	0.64282	0.0:0.0:0.0:1.0	.	220	Q8NGK5	O52M1_HUMAN	P	220	ENSP00000353343:S220P	ENSP00000353343:S220P	S	+	1	0	OR52M1	4523654	0.957000	0.32711	0.969000	0.41365	0.789000	0.44602	3.065000	0.49994	2.233000	0.73108	0.528000	0.53228	TCC	OR52M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385847.1		-27.830942	0	19	230	0	0	1	0	NM_001004137	4	7.864828	141	0.027586
PYROXD2	84795	broad.mit.edu	hg19	10	100147057	100147057	+	Silent	SNP	A	A	G			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr10:100147057A>G	ENST00000370575.4	-	14	1503	c.1455T>C	c.(1453-1455)gaT>gaC	p.D485D	PYROXD2_ENST00000483923.1_5'UTR	NM_032709.2	NP_116098.2	Q8N2H3	PYRD2_HUMAN	pyridine nucleotide-disulphide oxidoreductase domain 2	485				oxidoreductase activity	central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	12					CCTCGATGCAATCAAACACTG	0.483	0	91.0	86.0	88.0	10	100147057	2203	4300	6503	SO:0001819	synonymous_variant	AK074429	CCDS7474.1	10q24.2	2009-04-22	2009-04-22	2009-04-22	ENSG00000119943	ENSG00000119943		23517	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 33"""	C10orf33		Standard	NM_032709	Approved	FLJ23849	uc001kpc.3	Q8N2H3	OTTHUMG00000018877	ENST00000370575.4:c.1455T>C	10.37:g.100147057A>G		D3DR61|Q5TAA9|Q9BRQ1	ENST00000370575.4	37	CCDS7474.1																																																																																			PYROXD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049782.2		50.793909	0	-19	65	0	0	1	0	NM_032709	16	51.000537	22	0.421053
MUC3A	4584	broad.mit.edu	hg19	7	100609626	100609626	+	Silent	SNP	C	C	A			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr7:100609626C>A	ENST00000319509.7	+	8	2358	c.2358C>A	c.(2356-2358)gcC>gcA	p.A786A	RP11-395B7.2_ENST00000420080.1_RNA					mucin 3A, cell surface associated						breast(3)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(32)|prostate(3)	44					GCCTGACGGCCGGCGCCGCGC	0.766	0	7.0	7.0	7.0	7	100609626	860	1954	2814	SO:0001819	synonymous_variant	AF113616		7q22.1	2012-04-20	2006-03-14		ENSG00000169894	ENSG00000169894	"""Mucins"""	7513	protein-coding gene	gene with protein product		158371	"""mucin 3A, intestinal"""	MUC3	2393399, 10973822	Standard	XM_006710192	Approved		uc003uxl.1	Q02505	OTTHUMG00000157038	ENST00000319509.7:c.2358C>A	7.37:g.100609626C>A		O14650|O14651|O43418|O43421|Q02506|Q6W763|Q9H3Q7|Q9UKW9|Q9UN93|Q9UN94|Q9UN95	ENST00000319509.7	37																																																																																				MUC3A-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000347215.1		7.722693	1	-3	10	0	1	1	1	XM_001725354	3	8.773991	11	0.214286
USP13	8975	broad.mit.edu	hg19	3	179448030	179448030	+	Missense_Mutation	SNP	A	A	T			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr3:179448030A>T	ENST00000263966.3	+	9	1613	c.1142A>T	c.(1141-1143)cAa>cTa	p.Q381L	USP13_ENST00000496897.1_Missense_Mutation_p.Q316L|USP13_ENST00000482333.1_3'UTR	NM_003940.2	NP_003931.2	Q92995	UBP13_HUMAN	ubiquitin specific peptidase 13 (isopeptidase T-3)	381		ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding	central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	46	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)		GATCCAACACAAGATTTCAAC	0.343	0	124.0	122.0	122.0	3	179448030	2203	4300	6503	SO:0001583	missense	U75362	CCDS3235.1	3q26.2-q26.3	2008-04-11	2005-08-08		ENSG00000058056	ENSG00000058056	"""Ubiquitin-specific peptidases"""	12611	protein-coding gene	gene with protein product		603591	"""ubiquitin specific protease 13 (isopeptidase T-3)"""		12838346	Standard	NM_003940	Approved	IsoT-3	uc003fkh.3	Q92995	OTTHUMG00000157783	ENST00000263966.3:c.1142A>T	3.37:g.179448030A>T	ENSP00000263966:p.Gln381Leu	A8K2S3|B4DYF3|D3DNS2|Q96B25	ENST00000263966.3	37	CCDS3235.1	.	.	.	.	.	.	.	.	.	.	A	15.20	2.763128	0.49574	.	.	ENSG00000058056	ENST00000263966;ENST00000496897;ENST00000497155	T;T;T	0.33438	1.41;1.41;1.41	5.69	5.69	0.88448	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.48077	0.1480	L	0.61036	1.89	0.80722	D	1	D;B	0.56035	0.974;0.03	P;B	0.57960	0.83;0.036	T	0.36138	-0.9760	10	0.33940	T	0.23	-16.1905	15.9458	0.79792	1.0:0.0:0.0:0.0	.	381;381	Q92995;A8K2S3	UBP13_HUMAN;.	L	381;316;27	ENSP00000263966:Q381L;ENSP00000417146:Q316L;ENSP00000420057:Q27L	ENSP00000263966:Q381L	Q	+	2	0	USP13	180930724	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.339000	0.96797	2.162000	0.67917	0.459000	0.35465	CAA	USP13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349617.1		86.258571	0	31	126	0	0	1	0		29	86.642034	40	0.420290
MGME1	92667	broad.mit.edu	hg19	20	17968940	17968940	+	Splice_Site	SNP	A	A	T			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr20:17968940A>T	ENST00000377710.5	+	4	1151	c.863A>T	c.(862-864)cAg>cTg	p.Q288L	MGME1_ENST00000377709.1_Splice_Site_p.Q208L|MGME1_ENST00000377704.4_Intron|MGME1_ENST00000467391.1_3'UTR	NM_052865.2	NP_443097.1			mitochondrial genome maintenance exonuclease 1												TACAGCTTTCAGGTCAGGACA	0.453	0	96.0	87.0	90.0	20	17968940	2203	4300	6503	SO:0001630	splice_region_variant		CCDS13131.1	20p11.23	2013-08-29	2013-01-11	2013-01-11	ENSG00000125871	ENSG00000125871		16205	protein-coding gene	gene with protein product		615076	"""chromosome 20 open reading frame 72"""	C20orf72	23313956, 23358826, 23434322	Standard	NM_052865	Approved	bA504H3.4, DDK1	uc002wqh.3	Q9BQP7	OTTHUMG00000031955	ENST00000377710.5:c.864+1A>T	20.37:g.17968940A>T			ENST00000377710.5	37	CCDS13131.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.413106	0.83449	.	.	ENSG00000125871	ENST00000377710;ENST00000377709	T;T	0.49720	0.77;0.83	5.62	5.62	0.85841	.	0.102324	0.64402	D	0.000001	T	0.66197	0.2765	M	0.70903	2.155	0.80722	D	1	D	0.76494	0.999	D	0.65874	0.939	T	0.67205	-0.5729	10	0.45353	T	0.12	-12.6793	15.4826	0.75539	1.0:0.0:0.0:0.0	.	288	Q9BQP7	CT072_HUMAN	L	288;208	ENSP00000366939:Q288L;ENSP00000366938:Q208L	ENSP00000366938:Q208L	Q	+	2	0	C20orf72	17916940	1.000000	0.71417	1.000000	0.80357	0.593000	0.36681	8.721000	0.91446	2.137000	0.66172	0.379000	0.24179	CAG	MGME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078139.1		-9.538392	0	9	105	0	0	1	0	NM_052865	3	6.717945	69	0.041667
ALG1L	200810	broad.mit.edu	hg19	3	125651539	125651539	+	Silent	SNP	A	A	C	rs147593769	by1000genomes	TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr3:125651539A>C	ENST00000340333.3	-	3	277	c.114T>G	c.(112-114)ctT>ctG	p.L38L		NM_001015050.2|NM_001195223.1	NP_001015050.2|NP_001182152.1	Q6GMV1	ALG1L_HUMAN	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase-like	38				transferase activity, transferring glycosyl groups	large_intestine(2)|lung(2)	4					CATCAAGAGTAAGTTGTTCAA	0.423	0	89.0	82.0	85.0	3	125651539	2203	4300	6503	SO:0001819	synonymous_variant	BC073816	CCDS33840.1, CCDS74998.1	3q21.2	2013-02-22	2013-02-22		ENSG00000189366	ENSG00000189366	"""Glycosyltransferase group 1 domain containing"""	33721	protein-coding gene	gene with protein product	"""asparagine-linked glycosylation 1-like 1"""		"""asparagine-linked glycosylation 1-like"""			Standard	NM_001015050	Approved	ALG1L1	uc003eig.2	Q6GMV1	OTTHUMG00000159588	ENST00000340333.3:c.114T>G	3.37:g.125651539A>C		D3DNA5	ENST00000340333.3	37	CCDS33840.1																																																																																			ALG1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356347.1		-7.463182	0	5	99	0	0	1	0	NM_001015050	4	9.159825	74	0.051282