#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
ACO1	48	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	32433772	32433772	+	Missense_Mutation	SNP	T	T	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr9:32433772T>A	ENST00000309951.6	+	16	2036	c.1898T>A	c.(1897-1899)cTg>cAg	p.L633Q	ACO1_ENST00000379923.1_Missense_Mutation_p.L633Q|ACO1_ENST00000541043.1_Missense_Mutation_p.L534Q	NM_002197.2	NP_002188.1	P21399	ACOC_HUMAN	aconitase 1, soluble	633					cellular iron ion homeostasis (GO:0006879)|citrate metabolic process (GO:0006101)|intestinal absorption (GO:0050892)|post-embryonic development (GO:0009791)|regulation of translation (GO:0006417)|response to iron(II) ion (GO:0010040)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|aconitate hydratase activity (GO:0003994)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			breast(1)|endometrium(7)|kidney(5)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	30			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;3.94e-06)		TCAGATAAGCTGTTTTTCTGG	0.343																																																	0													110.0	111.0	110.0					9																	32433772		2203	4300	6503	SO:0001583	missense	48			M58510	CCDS6525.1	9p21.1	2013-05-21			ENSG00000122729	ENSG00000122729	4.2.1.3		117	protein-coding gene	gene with protein product	"""aconitate hydratase, cytoplasmic"""	100880		IREB1		2172968, 2771641	Standard	NM_002197		Approved	IRP1, IREBP	uc003zqw.4	P21399	OTTHUMG00000019740	ENST00000309951.6:c.1898T>A	9.37:g.32433772T>A	ENSP00000309477:p.Leu633Gln	Somatic		WXS	Illumina HiSeq	Phase_I	D3DRK7|Q14652|Q5VZA7	Missense_Mutation	SNP	ENST00000309951.6	37	CCDS6525.1	.	.	.	.	.	.	.	.	.	.	T	17.14	3.313726	0.60414	.	.	ENSG00000122729	ENST00000432017;ENST00000309951;ENST00000379923;ENST00000541043	T;T;T	0.38401	1.14;1.14;2.16	5.19	5.19	0.71726	Aconitase/3-isopropylmalate dehydratase, swivel (1);	0.000000	0.64402	D	0.000002	T	0.45094	0.1325	M	0.73319	2.225	0.80722	D	1	D;B	0.58268	0.982;0.435	P;B	0.46885	0.53;0.197	T	0.51787	-0.8661	10	0.62326	D	0.03	-10.6577	14.0185	0.64539	0.0:0.0:0.0:1.0	.	669;633	Q59FI0;P21399	.;ACOC_HUMAN	Q	669;633;633;534	ENSP00000309477:L633Q;ENSP00000369255:L633Q;ENSP00000438733:L534Q	ENSP00000309477:L633Q	L	+	2	0	ACO1	32423772	1.000000	0.71417	0.989000	0.46669	0.388000	0.30384	8.040000	0.89188	1.964000	0.57103	0.460000	0.39030	CTG		0.343	ACO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051998.3		NM_002197	
AGAP4	119016	hgsc.bcm.edu	37	10	46342585	46342585	+	Frame_Shift_Del	DEL	C	C	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr10:46342585delC	ENST00000448048.2	-	1	336	c.211delG	c.(211-213)gagfs	p.E71fs	AGAP4_ENST00000430779.2_5'UTR	NM_133446.2	NP_597703.2	Q96P64	AGAP4_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 4	71					regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			central_nervous_system(1)|lung(1)|ovary(1)	3						TCAGGCATCTCCCGGTCACGA	0.592																																																	0													1.0	1.0	1.0					10																	46342585		24	58	82	SO:0001589	frameshift_variant	119016			AF411132	CCDS7215.1	10q11.21	2014-06-19	2008-09-22	2008-09-22	ENSG00000188234	ENSG00000188234		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	23459	protein-coding gene	gene with protein product			"""centaurin, gamma-like family, member 1"", ""ArfGAP with GTPase domain, ankyrin repeat and PH domain 8"", ""centaurin, gamma-like family, member 5"""	CTGLF1, AGAP8, CTGLF5		12477932	Standard	XM_005271797		Approved	Em:AC012044.1, MRIP2	uc001jcx.4	Q96P64	OTTHUMG00000018088	ENST00000448048.2:c.211delG	10.37:g.46342585delC	ENSP00000392513:p.Glu71fs	Somatic		WXS	Illumina HiSeq	Phase_I		Frame_Shift_Del	DEL	ENST00000448048.2	37	CCDS7215.1																																																																																				0.592	AGAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047799.1		NM_133446	
ALLC	55821	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	3727534	3727534	+	Missense_Mutation	SNP	C	C	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr2:3727534C>T	ENST00000252505.3	+	5	410	c.248C>T	c.(247-249)aCg>aTg	p.T83M		NM_018436.3	NP_060906.3	Q8N6M5	ALLC_HUMAN	allantoicase	102					allantoin catabolic process (GO:0000256)		allantoicase activity (GO:0004037)	p.T83M(2)		breast(4)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	30	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.088)	all_cancers(51;0.24)		OV - Ovarian serous cystadenocarcinoma(76;0.088)|all cancers(51;0.151)|Epithelial(75;0.206)		TCTTACTTCACGGGAGATTAC	0.532										HNSCC(21;0.051)																																							2	Substitution - Missense(2)	large_intestine(1)|kidney(1)											137.0	144.0	142.0					2																	3727534		2075	4214	6289	SO:0001583	missense	55821			AF215924	CCDS46223.1	2p25.3	2008-02-05			ENSG00000151360	ENSG00000151360			17377	protein-coding gene	gene with protein product		612396				11054555	Standard	NM_018436		Approved	ALC	uc010ewt.3	Q8N6M5	OTTHUMG00000151485	ENST00000252505.3:c.248C>T	2.37:g.3727534C>T	ENSP00000252505:p.Thr83Met	Somatic		WXS	Illumina HiSeq	Phase_I	Q53T95|Q5RL81|Q96RE6|Q9NZA7	Missense_Mutation	SNP	ENST00000252505.3	37	CCDS46223.1	.	.	.	.	.	.	.	.	.	.	C	8.179	0.793502	0.16327	.	.	ENSG00000151360	ENST00000252505	.	.	.	5.77	-3.07	0.05363	Allantoicase domain (1);Galactose-binding domain-like (1);	0.782013	0.12462	N	0.466774	T	0.31389	0.0795	M	0.64260	1.97	0.09310	N	1	P	0.52170	0.951	P	0.44696	0.458	T	0.18713	-1.0328	9	0.59425	D	0.04	-6.5612	4.4518	0.11624	0.2443:0.378:0.0:0.3777	.	102	Q8N6M5	ALLC_HUMAN	M	83	.	ENSP00000252505:T83M	T	+	2	0	ALLC	3705409	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-0.173000	0.09854	-0.616000	0.05671	-1.268000	0.01426	ACG		0.532	ALLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322855.1			
USP34	9736	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	61413601	61413601	+	IGR	SNP	C	C	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr2:61413601C>G	ENST00000398571.2	-	0	11357				AHSA2_ENST00000489653.1_3'UTR|AHSA2_ENST00000410073.1_Missense_Mutation_p.I80M|AHSA2_ENST00000357022.2_Missense_Mutation_p.I71M|AHSA2_ENST00000394457.3_Missense_Mutation_p.I71M	NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34						positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			AGAAGATCATCATGAAATGGA	0.363																																																	0													101.0	105.0	104.0					2																	61413601		2203	4300	6503	SO:0001628	intergenic_variant	130872			AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"""Ubiquitin-specific peptidases"""	20066	protein-coding gene	gene with protein product		615295	"""ubiquitin specific protease 34"""			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265		2.37:g.61413601C>G		Somatic		WXS	Illumina HiSeq	Phase_I	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Missense_Mutation	SNP	ENST00000398571.2	37	CCDS42686.1	.	.	.	.	.	.	.	.	.	.	.	13.47	2.247606	0.39697	.	.	ENSG00000173209	ENST00000357022;ENST00000394457;ENST00000430934;ENST00000410073	.	.	.	5.92	4.95	0.65309	.	0.382752	0.25132	N	0.032897	T	0.31482	0.0798	L	0.29908	0.895	0.22489	N	0.999054	B	0.34103	0.437	B	0.35353	0.201	T	0.31166	-0.9953	9	0.72032	D	0.01	.	9.5772	0.39465	0.0:0.8739:0.0:0.1261	.	233	Q719I0	AHSA2_HUMAN	M	71;71;234;80	.	ENSP00000349525:I71M	I	+	3	3	AHSA2	61267105	1.000000	0.71417	0.999000	0.59377	0.694000	0.40290	1.470000	0.35354	2.818000	0.97014	0.655000	0.94253	ATC		0.363	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			
ANK2	287	broad.mit.edu;ucsc.edu	37	4	114213643	114213643	+	Silent	SNP	T	T	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr4:114213643T>C	ENST00000357077.4	+	21	2402	c.2349T>C	c.(2347-2349)caT>caC	p.H783H	ANK2_ENST00000264366.6_Silent_p.H783H|ANK2_ENST00000506722.1_Silent_p.H762H|ANK2_ENST00000509550.1_5'Flank|ANK2_ENST00000394537.3_Silent_p.H783H	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	783					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		TGCTCCAGCATGGGGCCAAGC	0.617																																																	0													56.0	40.0	45.0					4																	114213643		2203	4300	6503	SO:0001819	synonymous_variant	287			M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"""Ankyrin repeat domain containing"""	493	protein-coding gene	gene with protein product		106410	"""long (electrocardiographic) QT syndrome 4"""	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.2349T>C	4.37:g.114213643T>C		Somatic		WXS	Illumina GAIIx	Phase_I	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Silent	SNP	ENST00000357077.4	37	CCDS3702.1																																																																																				0.617	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2		NM_001148	
ARHGAP39	80728	hgsc.bcm.edu	37	8	145773342	145773344	+	In_Frame_Del	DEL	CTG	CTG	-	rs138155129	byFrequency	TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	CTG	CTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr8:145773342_145773344delCTG	ENST00000276826.5	-	4	1327_1329	c.1126_1128delCAG	c.(1126-1128)cagdel	p.Q376del	ARHGAP39_ENST00000540274.1_In_Frame_Del_p.Q376del|ARHGAP39_ENST00000377307.2_In_Frame_Del_p.Q376del|ARHGAP39_ENST00000528810.1_5'Flank			Q9C0H5	RHG39_HUMAN	Rho GTPase activating protein 39	376					axon guidance (GO:0007411)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	22						CGGGACACTTCTGCTTGGTGAGC	0.704														89	0.0177716	0.0045	0.0187	5008	,	,		14552	0.0		0.0626	False		,,,				2504	0.0072																0										76,4134		6,64,2035						5.4	1.0		dbSNP_131	14	592,7572		48,496,3538	no	coding	ARHGAP39	NM_025251.1		54,560,5573	A1A1,A1R,RR		7.2513,1.8052,5.3984				668,11706				SO:0001651	inframe_deletion	80728				CCDS34971.1	8q24.3	2011-06-29			ENSG00000147799	ENSG00000147799		"""Rho GTPase activating proteins"""	29351	protein-coding gene	gene with protein product	"""RhoGAP93B homolog (Drosophila)"", ""crossGAP homolog (Drosophila)"""	615880				15755809	Standard	XM_005272344		Approved	KIAA1688, Vilse, CrGAP	uc003zds.1	Q9C0H5	OTTHUMG00000165182	ENST00000276826.5:c.1126_1128delCAG	8.37:g.145773342_145773344delCTG	ENSP00000276826:p.Gln376del	Somatic		WXS	Illumina HiSeq	Phase_I	B4E1I1	In_Frame_Del	DEL	ENST00000276826.5	37																																																																																					0.704	ARHGAP39-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382509.1			
ASH1L	55870	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	155450216	155450216	+	Silent	SNP	G	G	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr1:155450216G>C	ENST00000368346.3	-	3	3084	c.2445C>G	c.(2443-2445)gtC>gtG	p.V815V	ASH1L_ENST00000392403.3_Silent_p.V815V			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	815					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)			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)			GGTCACTAGAGACACACATAC	0.408																																																	0													82.0	82.0	82.0					1																	155450216		2203	4299	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.2445C>G	1.37:g.155450216G>C		Somatic		WXS	Illumina HiSeq	Phase_I	Q59GP1|Q5T714|Q5T715|Q9P2C7	Silent	SNP	ENST00000368346.3	37																																																																																					0.408	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1		NM_018489	
ATAD5	79915	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	29161396	29161396	+	Silent	SNP	G	G	T	rs114289357	byFrequency	TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr17:29161396G>T	ENST00000321990.4	+	2	675	c.297G>T	c.(295-297)acG>acT	p.T99T	CTD-2349P21.11_ENST00000580873.1_RNA	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	99					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				AAGACTGTACGACACCTTTGG	0.343																																																	0													89.0	93.0	91.0					17																	29161396		2203	4299	6502	SO:0001819	synonymous_variant	79915				CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"""ATPases / AAA-type"""	25752	protein-coding gene	gene with protein product	"""enhanced level of genomic instability 1 homolog (S. cerevisiae)"""	609534	"""chromosome 17 open reading frame 41"""	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.297G>T	17.37:g.29161396G>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q05DH0|Q69YR6|Q9H9I1	Silent	SNP	ENST00000321990.4	37	CCDS11260.1																																																																																				0.343	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2		NM_024857	
B3GALTL	145173	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	31903770	31903770	+	Missense_Mutation	SNP	C	C	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr13:31903770C>A	ENST00000343307.4	+	15	1611	c.1462C>A	c.(1462-1464)Cag>Aag	p.Q488K		NM_194318.3	NP_919299.3	Q6Y288	B3GLT_HUMAN	beta 1,3-galactosyltransferase-like	488					fucose metabolic process (GO:0006004)|protein glycosylation (GO:0006486)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19		Lung SC(185;0.0257)		all cancers(112;0.00436)|Epithelial(112;0.0285)|OV - Ovarian serous cystadenocarcinoma(117;0.0512)|GBM - Glioblastoma multiforme(144;0.184)		CAAAGCCAGGCAGGAGACACA	0.502																																																	0													121.0	125.0	123.0					13																	31903770		2203	4300	6503	SO:0001583	missense	145173			AB101481	CCDS9341.1	13q12.3	2014-03-24			ENSG00000187676	ENSG00000187676		"""Beta 3-glycosyltransferases"""	20207	protein-coding gene	gene with protein product		610308				12943678, 16899492, 17032646	Standard	NM_194318		Approved	B3GTL, B3Glc-T	uc010aaz.3	Q6Y288	OTTHUMG00000016688	ENST00000343307.4:c.1462C>A	13.37:g.31903770C>A	ENSP00000343002:p.Gln488Lys	Somatic		WXS	Illumina HiSeq	Phase_I	A8K5F8|Q5W0H2|Q6NUI3	Missense_Mutation	SNP	ENST00000343307.4	37	CCDS9341.1	.	.	.	.	.	.	.	.	.	.	C	8.775	0.926803	0.18056	.	.	ENSG00000187676	ENST00000343307	T	0.72167	-0.63	5.85	4.03	0.46877	.	0.869891	0.10415	N	0.677475	T	0.63438	0.2511	L	0.54323	1.7	0.09310	N	1	B	0.19583	0.037	B	0.12837	0.008	T	0.50039	-0.8874	10	0.18276	T	0.48	-4.8265	9.5222	0.39143	0.2558:0.6777:0.0:0.0665	.	488	Q6Y288	B3GLT_HUMAN	K	488	ENSP00000343002:Q488K	ENSP00000343002:Q488K	Q	+	1	0	B3GALTL	30801770	0.000000	0.05858	0.003000	0.11579	0.118000	0.20060	0.050000	0.14120	1.438000	0.47492	0.585000	0.79938	CAG		0.502	B3GALTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044396.3		NM_194318	
ATP7B	540	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	52518307	52518307	+	Missense_Mutation	SNP	C	C	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr13:52518307C>T	ENST00000242839.4	-	14	3337	c.3181G>A	c.(3181-3183)Ggg>Agg	p.G1061R	ATP7B_ENST00000448424.2_Missense_Mutation_p.G983R|ATP7B_ENST00000400366.3_Missense_Mutation_p.G950R|ATP7B_ENST00000344297.5_Missense_Mutation_p.G854R|ATP7B_ENST00000482841.1_5'UTR|ATP7B_ENST00000417240.2_Intron|ATP7B_ENST00000400370.3_Missense_Mutation_p.G631R|ATP7B_ENST00000418097.2_Missense_Mutation_p.G996R	NM_000053.3	NP_000044.2	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	1061			G -> E (in WD). {ECO:0000269|PubMed:10544227, ECO:0000269|PubMed:11216666, ECO:0000269|PubMed:15952988}.		cellular copper ion homeostasis (GO:0006878)|cellular zinc ion homeostasis (GO:0006882)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|intracellular copper ion transport (GO:0015680)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|response to copper ion (GO:0046688)|sequestering of calcium ion (GO:0051208)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|mitochondrion (GO:0005739)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper-exporting ATPase activity (GO:0004008)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(23)|ovary(1)|prostate(3)|skin(4)|stomach(2)	55		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)	Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	TCCGCAGTCCCCACCACAGCC	0.637									Wilson disease																																								0													39.0	43.0	42.0					13																	52518307		2051	4200	6251	SO:0001583	missense	540	Familial Cancer Database		U11700	CCDS41892.1, CCDS45049.1, CCDS58293.1	13q14.3	2012-10-22	2005-11-29		ENSG00000123191	ENSG00000123191	3.6.3.4	"""ATPases / P-type"""	870	protein-coding gene	gene with protein product	"""Wilson disease"", ""copper pump 2"", ""copper-transporting ATPase 2"""	606882	"""ATPase, Cu++ transporting, beta polypeptide (Wilson disease)"""	WND		8298641, 8298639	Standard	NM_000053		Approved		uc001vfw.2	P35670	OTTHUMG00000017406	ENST00000242839.4:c.3181G>A	13.37:g.52518307C>T	ENSP00000242839:p.Gly1061Arg	Somatic		WXS	Illumina HiSeq	Phase_I	Q16318|Q16319|Q4U3V3|Q59FJ9|Q5T7X7	Missense_Mutation	SNP	ENST00000242839.4	37	CCDS41892.1	.	.	.	.	.	.	.	.	.	.	C	19.66	3.868965	0.72065	.	.	ENSG00000123191	ENST00000242839;ENST00000400366;ENST00000344297;ENST00000448424;ENST00000400370;ENST00000418097	D;D;D;D;D;D	0.95788	-3.81;-3.81;-3.81;-3.81;-3.81;-3.81	5.43	4.59	0.56863	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.044904	0.85682	D	0.000000	D	0.97077	0.9045	M	0.64080	1.96	0.80722	D	1	D;D;D;D;B;D;D	0.89917	0.991;1.0;1.0;1.0;0.381;1.0;1.0	D;D;D;D;B;D;D	0.97110	0.959;0.998;1.0;1.0;0.127;1.0;0.999	D	0.97646	1.0151	10	0.87932	D	0	-16.5576	15.7562	0.78030	0.1376:0.8624:0.0:0.0	.	983;1013;996;631;950;854;1061	E7ET55;B7ZLR4;F5H748;F5H562;P35670-3;P35670-2;P35670	.;.;.;.;.;.;ATP7B_HUMAN	R	1061;950;854;983;631;996	ENSP00000242839:G1061R;ENSP00000383217:G950R;ENSP00000342559:G854R;ENSP00000416738:G983R;ENSP00000383221:G631R;ENSP00000393343:G996R	ENSP00000242839:G1061R	G	-	1	0	ATP7B	51416308	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.770000	0.85390	1.326000	0.45319	-0.219000	0.12488	GGG		0.637	ATP7B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045981.1		NM_000053	
KIAA1551	55196	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	32137779	32137779	+	Missense_Mutation	SNP	T	T	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr12:32137779T>G	ENST00000312561.4	+	4	4304	c.3890T>G	c.(3889-3891)tTg>tGg	p.L1297W	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	1297																	AGAAAAAAATTGAGGTTTCAC	0.358																																																	0													51.0	52.0	52.0					12																	32137779		2203	4300	6503	SO:0001583	missense	0			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.3890T>G	12.37:g.32137779T>G	ENSP00000310338:p.Leu1297Trp	Somatic		WXS	Illumina HiSeq	Phase_I	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Missense_Mutation	SNP	ENST00000312561.4	37	CCDS8725.2	.	.	.	.	.	.	.	.	.	.	T	14.70	2.613156	0.46631	.	.	ENSG00000174718	ENST00000312561	T	0.15834	2.39	5.21	1.33	0.21861	.	1.081500	0.07286	N	0.871642	T	0.14700	0.0355	L	0.29908	0.895	0.09310	N	1	P	0.49862	0.929	P	0.45577	0.486	T	0.22173	-1.0224	9	.	.	.	.	5.5617	0.17148	0.0:0.1424:0.1491:0.7085	.	1297	Q9HCM1	CL035_HUMAN	W	1297	ENSP00000310338:L1297W	.	L	+	2	0	C12orf35	32029046	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	0.332000	0.19751	-0.017000	0.14103	0.460000	0.39030	TTG		0.358	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2		NM_018169	
SZT2	23334	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	43868851	43868851	+	Missense_Mutation	SNP	G	G	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr1:43868851G>A	ENST00000562955.1	+	2	31	c.31G>A	c.(31-33)Gaa>Aaa	p.E11K	SZT2_ENST00000310739.4_Missense_Mutation_p.E11K|SZT2_ENST00000372450.4_Missense_Mutation_p.E11K	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	11					central nervous system development (GO:0007417)|corpus callosum morphogenesis (GO:0021540)|embryo development (GO:0009790)|pigmentation (GO:0043473)|post-embryonic development (GO:0009791)|regulation of superoxide dismutase activity (GO:1901668)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)		p.E11*(2)		NS(2)|breast(9)|central_nervous_system(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(39)|ovary(4)|pancreas(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	113						TTCCCAGGTGGAAGAAGCTGG	0.448																																																	2	Substitution - Nonsense(2)	endometrium(2)											117.0	114.0	115.0					1																	43868851		2203	4300	6503	SO:0001583	missense	0			AB007936	CCDS30694.1, CCDS30694.2	1p34.2	2012-11-19	2011-06-10	2011-06-10	ENSG00000198198	ENSG00000198198			29040	protein-coding gene	gene with protein product	"""seizure threshold 2 homolog A (mouse)"", ""seizure threshold 2 homolog B (mouse)"""	615463	"""chromosome 1 open reading frame 84"", ""KIAA0467"""	C1orf84, KIAA0467		9455484	Standard	NM_015284		Approved	FLJ10387, SZT2B, RP11-506B15.1, FLJ34502, SZT2A	uc001cjk.3	Q5T011	OTTHUMG00000007423	ENST00000562955.1:c.31G>A	1.37:g.43868851G>A	ENSP00000457168:p.Glu11Lys	Somatic		WXS	Illumina HiSeq	Phase_I	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Missense_Mutation	SNP	ENST00000562955.1	37	CCDS30694.2	.	.	.	.	.	.	.	.	.	.	G	12.29	1.894121	0.33442	.	.	ENSG00000223526	ENST00000372450;ENST00000310739;ENST00000357658	.	.	.	5.72	5.72	0.89469	.	.	.	.	.	T	0.58409	0.2120	N	0.22421	0.69	0.80722	D	1	P;D	0.55605	0.827;0.972	P;P	0.53912	0.52;0.737	T	0.53464	-0.8435	8	0.27785	T	0.31	.	19.8786	0.96886	0.0:0.0:1.0:0.0	.	11;11	Q5T011-4;Q5T011-7	.;.	K	11	.	ENSP00000312234:E11K	E	+	1	0	AL139289.1	43641438	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.838000	0.92115	2.693000	0.91896	0.655000	0.94253	GAA		0.448	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3		NM_015284	
C1S	716	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	7174353	7174353	+	Missense_Mutation	SNP	G	G	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr12:7174353G>A	ENST00000406697.1	+	12	1626	c.998G>A	c.(997-999)gGt>gAt	p.G333D	C1S_ENST00000402681.3_Missense_Mutation_p.G166D|C1S_ENST00000328916.3_Missense_Mutation_p.G333D|C1S_ENST00000360817.5_Missense_Mutation_p.G333D			P09871	C1S_HUMAN	complement component 1, s subcomponent	333	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(5)|kidney(2)|large_intestine(8)|liver(4)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	33					Abciximab(DB00054)|Adalimumab(DB00051)|Basiliximab(DB00074)|Cetuximab(DB00002)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Muromonab(DB00075)|Rituximab(DB00073)|Trastuzumab(DB00072)	GGACGTGTTGGTGCAACATCT	0.383																																					GBM(156;750 1943 12971 24779 31015)												0													150.0	137.0	141.0					12																	7174353		2203	4300	6503	SO:0001583	missense	716				CCDS31735.1	12p13	2014-09-17			ENSG00000182326	ENSG00000182326	3.4.21.42	"""Complement system"""	1247	protein-coding gene	gene with protein product		120580					Standard	NM_201442		Approved		uc001qsl.3	P09871	OTTHUMG00000150305	ENST00000406697.1:c.998G>A	12.37:g.7174353G>A	ENSP00000385035:p.Gly333Asp	Somatic		WXS	Illumina HiSeq	Phase_I	D3DUT4|Q9UCU7|Q9UCU8|Q9UCU9|Q9UCV0|Q9UCV1|Q9UCV2|Q9UCV3|Q9UCV4|Q9UCV5|Q9UM14	Missense_Mutation	SNP	ENST00000406697.1	37	CCDS31735.1	.	.	.	.	.	.	.	.	.	.	G	8.046	0.765039	0.15914	.	.	ENSG00000182326	ENST00000406697;ENST00000328916;ENST00000360817;ENST00000382222;ENST00000402681	T;T;T;T	0.76316	-1.01;-1.01;-1.01;-1.01	5.74	4.86	0.63082	Complement control module (2);Sushi/SCR/CCP (3);	0.342239	0.21537	N	0.072959	T	0.69024	0.3065	L	0.51422	1.61	0.09310	N	1	B	0.10296	0.003	B	0.12837	0.008	T	0.52931	-0.8509	10	0.12766	T	0.61	.	10.5159	0.44889	0.0885:0.0:0.9115:0.0	.	333	P09871	C1S_HUMAN	D	333;333;333;321;166	ENSP00000385035:G333D;ENSP00000328173:G333D;ENSP00000354057:G333D;ENSP00000384171:G166D	ENSP00000328173:G333D	G	+	2	0	C1S	7044614	0.010000	0.17322	0.034000	0.17996	0.324000	0.28378	1.642000	0.37207	1.433000	0.47394	0.561000	0.74099	GGT		0.383	C1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317481.1		NM_001734	
CEP85L	387119	hgsc.bcm.edu	37	6	118812811	118812813	+	Intron	DEL	TGT	TGT	-	rs71866282	byFrequency	TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	TGT	TGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr6:118812811_118812813delTGT	ENST00000368491.3	-	6	2059				CEP85L_ENST00000360290.3_In_Frame_Del_p.Q389del|CEP85L_ENST00000392500.3_In_Frame_Del_p.Q494del|CEP85L_ENST00000419517.2_In_Frame_Del_p.Q491del|CEP85L_ENST00000368488.5_Intron	NM_001042475.2	NP_001035940.1	Q5SZL2	CE85L_HUMAN	centrosomal protein 85kDa-like							centrosome (GO:0005813)|cytoplasm (GO:0005737)											GCTGAGGAAATGTTGTTGACCTA	0.32														166	0.033147	0.059	0.0173	5008	,	,		18299	0.0		0.0189	False		,,,				2504	0.0583																0									,,	241,4015		6,229,1893					,,	3.5	0.0		dbSNP_130	43	164,8084		2,160,3962	no	coding,intron,intron	C6orf204	NM_206921.2,NM_001178035.1,NM_001042475.2	,,	8,389,5855	A1A1,A1R,RR		1.9884,5.6626,3.239	,,	,,		405,12099				SO:0001627	intron_variant	0			AF308284	CCDS5119.2, CCDS43498.1, CCDS55052.1	6q22.31	2011-11-25	2011-11-25	2011-11-25	ENSG00000111860	ENSG00000111860			21638	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 204"""	C6orf204			Standard	NM_206921		Approved	NY-BR-15, bA57K17.2	uc003pya.2	Q5SZL2	OTTHUMG00000015465	ENST00000368491.3:c.1437+35ACA>-	6.37:g.118812814_118812816delTGT		Somatic		WXS	Illumina HiSeq	Phase_I	A1A4E1|A2A3P2|A2IDE5|F8W6J2|G3V0H3|Q2TAM2|Q5T323|Q7Z5K7|Q9H289	In_Frame_Del	DEL	ENST00000368491.3	37	CCDS43498.1																																																																																				0.320	CEP85L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041996.2		NM_001042475	
CC2D2A	57545	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	15556749	15556749	+	Silent	SNP	C	C	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr4:15556749C>T	ENST00000503292.1	+	21	2721	c.2541C>T	c.(2539-2541)gaC>gaT	p.D847D	CC2D2A_ENST00000389652.5_Silent_p.D798D|CC2D2A_ENST00000424120.1_Silent_p.D847D|CC2D2A_ENST00000413206.1_Silent_p.D847D	NM_001080522.2	NP_001073991.2	Q9P2K1	C2D2A_HUMAN	coiled-coil and C2 domain containing 2A	847					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|TCTN-B9D complex (GO:0036038)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|urinary_tract(2)	32						GACTGACAGACATGAAAAAAT	0.473																																																	0													95.0	99.0	98.0					4																	15556749		1972	4152	6124	SO:0001819	synonymous_variant	57545			AB037766, EU450799	CCDS47026.1, CCDS47027.1, CCDS47027.2, CCDS54744.1	4p15.33	2014-09-17	2007-10-19		ENSG00000048342	ENSG00000048342			29253	protein-coding gene	gene with protein product	"""Meckel syndrome, type 6"""	612013				10718198, 18513680	Standard	NM_001080522		Approved	KIAA1345, MKS6, JBTS9	uc010idv.2	Q9P2K1	OTTHUMG00000160255	ENST00000503292.1:c.2541C>T	4.37:g.15556749C>T		Somatic		WXS	Illumina HiSeq	Phase_I	A6ND97|B3FW08|D6RB72|E7EP21|E9PEV5|Q3SYP3|Q9H8A7	Silent	SNP	ENST00000503292.1	37	CCDS47026.1																																																																																				0.473	CC2D2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359906.2		NM_001080522	
CCDC24	149473	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	44461642	44461642	+	Missense_Mutation	SNP	T	T	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr1:44461642T>A	ENST00000372318.3	+	9	905	c.734T>A	c.(733-735)cTc>cAc	p.L245H	SLC6A9_ENST00000372307.3_Intron|CCDC24_ENST00000479055.1_3'UTR|SLC6A9_ENST00000372306.3_Intron	NM_152499.1	NP_689712.1	Q8N4L8	CCD24_HUMAN	coiled-coil domain containing 24	245										endometrium(3)|large_intestine(2)|lung(3)|stomach(1)	9	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0821)				ACACAGGGCCTCAGACCCCCG	0.642																																																	0													91.0	98.0	96.0					1																	44461642		2203	4300	6503	SO:0001583	missense	149473				CCDS507.1	1p34.1	2008-02-05			ENSG00000159214	ENSG00000159214			28688	protein-coding gene	gene with protein product						12477932	Standard	NM_152499		Approved	MGC45441	uc001clj.3	Q8N4L8	OTTHUMG00000008299	ENST00000372318.3:c.734T>A	1.37:g.44461642T>A	ENSP00000361392:p.Leu245His	Somatic		WXS	Illumina HiSeq	Phase_I	Q6RWT2	Missense_Mutation	SNP	ENST00000372318.3	37	CCDS507.1	.	.	.	.	.	.	.	.	.	.	T	12.13	1.847050	0.32606	.	.	ENSG00000159214	ENST00000372318	.	.	.	4.78	-0.808	0.10868	.	0.410133	0.17781	N	0.162256	T	0.22704	0.0548	N	0.24115	0.695	0.09310	N	0.999998	B;B	0.20261	0.043;0.043	B;B	0.23018	0.043;0.043	T	0.10800	-1.0614	9	0.40728	T	0.16	-34.6466	3.7519	0.08570	0.1553:0.294:0.0:0.5507	.	209;245	Q8N4L8-2;Q8N4L8	.;CCD24_HUMAN	H	245	.	ENSP00000361392:L245H	L	+	2	0	CCDC24	44234229	0.000000	0.05858	0.000000	0.03702	0.635000	0.38103	-0.246000	0.08878	-0.344000	0.08338	0.421000	0.28195	CTC		0.642	CCDC24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022865.1		NM_152499	
CDH11	1009	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	65038653	65038653	+	Silent	SNP	C	C	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr16:65038653C>T	ENST00000268603.4	-	3	735	c.120G>A	c.(118-120)gaG>gaA	p.E40E	CDH11_ENST00000394156.3_Silent_p.E40E|CDH11_ENST00000569624.1_5'UTR|CDH11_ENST00000566827.1_Intron	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	40					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		CCTTGCCCTTCTCATGGTGCC	0.652			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)																														Dom	yes		16	16q22.1	1009	"""cadherin 11, type 2, OB-cadherin (osteoblast)"""		M	0													41.0	35.0	37.0					16																	65038653		2202	4300	6502	SO:0001819	synonymous_variant	1009			D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"""Cadherins / Major cadherins"""	1750	protein-coding gene	gene with protein product	"""OB-Cadherin"""	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.120G>A	16.37:g.65038653C>T		Somatic		WXS	Illumina HiSeq	Phase_I	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Silent	SNP	ENST00000268603.4	37	CCDS10803.1																																																																																				0.652	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1		NM_033664	
CHD1	1105	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	98228309	98228309	+	Silent	SNP	T	T	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr5:98228309T>C	ENST00000284049.3	-	14	2249	c.2100A>G	c.(2098-2100)aaA>aaG	p.K700K	RNU6-402P_ENST00000410678.1_RNA	NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	700					chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	49		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	TTTCCACATCTTTCTTAACTC	0.403																																																	0													133.0	135.0	134.0					5																	98228309		2202	4300	6502	SO:0001819	synonymous_variant	1105			AF006513	CCDS34204.1	5q15-q21	2008-07-18			ENSG00000153922	ENSG00000153922			1915	protein-coding gene	gene with protein product		602118				8460153, 9326634	Standard	XM_005271866		Approved		uc003knf.3	O14646	OTTHUMG00000162744	ENST00000284049.3:c.2100A>G	5.37:g.98228309T>C		Somatic		WXS	Illumina HiSeq	Phase_I	Q17RZ3	Silent	SNP	ENST00000284049.3	37	CCDS34204.1																																																																																				0.403	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1		NM_001270	
CNNM4	26504	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	97475200	97475200	+	Silent	SNP	T	T	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr2:97475200T>G	ENST00000377075.2	+	7	2372	c.2274T>G	c.(2272-2274)ctT>ctG	p.L758L	RP11-353K11.1_ENST00000608609.1_lincRNA|CNNM4_ENST00000540067.1_3'UTR	NM_020184.3	NP_064569.3	Q6P4Q7	CNNM4_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 4	758					biomineral tissue development (GO:0031214)|ion transport (GO:0006811)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)			breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)	20						CCACAACTCTTCTCAACGAGC	0.622																																																	0													119.0	94.0	103.0					2																	97475200		2203	4300	6503	SO:0001819	synonymous_variant	26504			AB046812	CCDS2024.2	2q11.2	2014-08-08	2014-08-07		ENSG00000158158	ENSG00000158158			105	protein-coding gene	gene with protein product		607805	"""cyclin M4"""	ACDP4		21393841, 24194943	Standard	XM_005263914		Approved	KIAA1592	uc002swx.3	Q6P4Q7	OTTHUMG00000130532	ENST00000377075.2:c.2274T>G	2.37:g.97475200T>G		Somatic		WXS	Illumina HiSeq	Phase_I	B7Z1U0|C7SQM3|C7SQM4|C7SQM5|Q53RE5|Q9H9G3|Q9HCI0|Q9NRN1	Silent	SNP	ENST00000377075.2	37	CCDS2024.2																																																																																				0.622	CNNM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252954.1		NM_020184	
DNAJB4	11080	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	78470926	78470926	+	Missense_Mutation	SNP	A	A	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr1:78470926A>T	ENST00000370763.5	+	1	389	c.132A>T	c.(130-132)aaA>aaT	p.K44N	DNAJB4_ENST00000487931.1_Intron|GIPC2_ENST00000476882.1_Intron|RP11-386I14.4_ENST00000608684.1_RNA	NM_007034.3	NP_008965.2	Q9UDY4	DNJB4_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 4	44	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				protein folding (GO:0006457)|response to heat (GO:0009408)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chaperone binding (GO:0051087)|unfolded protein binding (GO:0051082)			endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	10						CAGAGGAAAAATTTAAAGAGG	0.373																																																	0													60.0	67.0	65.0					1																	78470926		2200	4300	6500	SO:0001583	missense	11080			U40992	CCDS684.1	1p31.1	2011-09-02			ENSG00000162616	ENSG00000162616		"""Heat shock proteins / DNAJ (HSP40)"""	14886	protein-coding gene	gene with protein product		611327				9546042, 11147971	Standard	NM_007034		Approved	HLJ1	uc001dij.3	Q9UDY4	OTTHUMG00000040905	ENST00000370763.5:c.132A>T	1.37:g.78470926A>T	ENSP00000359799:p.Lys44Asn	Somatic		WXS	Illumina HiSeq	Phase_I	B2R824|Q13431	Missense_Mutation	SNP	ENST00000370763.5	37	CCDS684.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.087216	0.76642	.	.	ENSG00000162616	ENST00000426517;ENST00000370763	T;T	0.35048	1.33;1.33	5.69	5.69	0.88448	Heat shock protein DnaJ, N-terminal (5);	0.090883	0.85682	D	0.000000	T	0.34978	0.0916	L	0.28504	0.86	0.80722	D	1	D	0.71674	0.998	D	0.77557	0.99	T	0.33574	-0.9863	10	0.59425	D	0.04	.	10.3037	0.43667	0.9263:0.0:0.0737:0.0	.	44	Q9UDY4	DNJB4_HUMAN	N	44	ENSP00000399494:K44N;ENSP00000359799:K44N	ENSP00000359799:K44N	K	+	3	2	DNAJB4	78243514	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.304000	0.59104	2.149000	0.67028	0.528000	0.53228	AAA		0.373	DNAJB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098248.3			
ELMO1	9844	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	37262227	37262227	+	Missense_Mutation	SNP	C	C	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr7:37262227C>G	ENST00000310758.4	-	10	1420	c.773G>C	c.(772-774)aGg>aCg	p.R258T	ELMO1_ENST00000448602.1_Missense_Mutation_p.R258T|ELMO1_ENST00000442504.1_Missense_Mutation_p.R258T	NM_001206480.1|NM_014800.10	NP_001193409.1|NP_055615.8	Q92556	ELMO1_HUMAN	engulfment and cell motility 1	258					actin cytoskeleton organization (GO:0030036)|apoptotic process (GO:0006915)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|phagocytosis, engulfment (GO:0006911)|Rac protein signal transduction (GO:0016601)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(28)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	58						TACCTGCCTCCTCTCATCAGG	0.428																																																	0													138.0	128.0	132.0					7																	37262227		2203	4300	6503	SO:0001583	missense	9844			AF398885	CCDS5449.1, CCDS5450.1	7p14.1	2012-07-10	2006-01-20		ENSG00000155849	ENSG00000155849		"""Engulfment and cell motility proteins"""	16286	protein-coding gene	gene with protein product		606420	"""engulfment and cell motility 1 (ced-12 homolog, C. elegans)"""			11595183	Standard	NM_001039459		Approved	KIAA0281, CED12, ELMO-1, CED-12	uc003tfk.2	Q92556	OTTHUMG00000023701	ENST00000310758.4:c.773G>C	7.37:g.37262227C>G	ENSP00000312185:p.Arg258Thr	Somatic		WXS	Illumina HiSeq	Phase_I	A4D1X6|Q29R79|Q6ZTJ0|Q96PB0|Q9H0I1	Missense_Mutation	SNP	ENST00000310758.4	37	CCDS5449.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.43|13.43	2.235613|2.235613	0.39498|0.39498	.|.	.|.	ENSG00000155849|ENSG00000155849	ENST00000433246|ENST00000310758;ENST00000361912;ENST00000442504;ENST00000448602	.|T;T;T	.|0.51817	.|0.69;0.69;0.69	5.66|5.66	2.85|2.85	0.33270|0.33270	.|Armadillo-like helical (1);Armadillo-type fold (1);	.|0.104540	.|0.64402	.|D	.|0.000004	T|T	0.41673|0.41673	0.1169|0.1169	L|L	0.38175|0.38175	1.15|1.15	0.80722|0.80722	D|D	1|1	.|B	.|0.27286	.|0.174	.|B	.|0.38655	.|0.278	T|T	0.29458|0.29458	-1.0011|-1.0011	5|10	.|0.39692	.|T	.|0.17	.|.	9.4712|9.4712	0.38844|0.38844	0.0:0.6495:0.0:0.3505|0.0:0.6495:0.0:0.3505	.|.	.|258	.|Q92556	.|ELMO1_HUMAN	R|T	23|258;162;258;258	.|ENSP00000312185:R258T;ENSP00000406952:R258T;ENSP00000394458:R258T	.|ENSP00000312185:R258T	G|R	-|-	1|2	0|0	ELMO1|ELMO1	37228752|37228752	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.693000|0.693000	0.40251|0.40251	1.617000|1.617000	0.36943|0.36943	0.866000|0.866000	0.35629|0.35629	0.655000|0.655000	0.94253|0.94253	GGA|AGG		0.428	ELMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219830.4		NM_130442	
ERC1	23085	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	1299182	1299182	+	Missense_Mutation	SNP	A	A	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr12:1299182A>G	ENST00000397203.2	+	12	2721	c.2315A>G	c.(2314-2316)aAg>aGg	p.K772R	ERC1_ENST00000360905.4_Missense_Mutation_p.K772R|ERC1_ENST00000355446.5_Missense_Mutation_p.K772R|ERC1_ENST00000543086.3_Missense_Mutation_p.K744R|ERC1_ENST00000546231.2_Missense_Mutation_p.K772R|ERC1_ENST00000589028.1_Missense_Mutation_p.K772R|ERC1_ENST00000536573.2_3'UTR			Q8IUD2	RB6I2_HUMAN	ELKS/RAB6-interacting/CAST family member 1	772					I-kappaB phosphorylation (GO:0007252)|multicellular organismal development (GO:0007275)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|IkappaB kinase complex (GO:0008385)|presynaptic membrane (GO:0042734)	leucine zipper domain binding (GO:0043522)			NS(1)|breast(2)|cervix(2)|endometrium(2)|large_intestine(8)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	38	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)			GAAAATGAGAAGAATGACAAA	0.403																																																	0													113.0	115.0	114.0					12																	1299182		2203	4300	6503	SO:0001583	missense	23085			AB015617	CCDS8508.1, CCDS53732.1	12p13.3	2008-02-05	2006-08-14	2006-08-14	ENSG00000082805	ENSG00000082805			17072	protein-coding gene	gene with protein product		607127	"""RAB6 interacting protein 2"""	RAB6IP2		10697956, 11929610	Standard	NM_178040		Approved	ELKS, KIAA1081, CAST2, MGC12974	uc001qjb.2	Q8IUD2	OTTHUMG00000130138	ENST00000397203.2:c.2315A>G	12.37:g.1299182A>G	ENSP00000380386:p.Lys772Arg	Somatic		WXS	Illumina HiSeq	Phase_I	A2RU77|A7E295|D3DUP7|D3DUP8|Q6NVK2|Q8IUD3|Q8IUD4|Q8IUD5|Q8NAS1|Q9NXN5|Q9UIK7|Q9UPS1	Missense_Mutation	SNP	ENST00000397203.2	37	CCDS8508.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.415522	0.83449	.	.	ENSG00000082805	ENST00000347735;ENST00000397203;ENST00000454194;ENST00000537890;ENST00000299183;ENST00000543086;ENST00000542302;ENST00000545948;ENST00000546231;ENST00000355446;ENST00000360905;ENST00000440394;ENST00000538971;ENST00000536573	T;T;T;T;T;T;T;T	0.39787	1.06;1.06;1.06;1.06;1.06;1.06;1.06;1.06	5.88	5.88	0.94601	.	0.049592	0.85682	D	0.000000	T	0.60327	0.2260	M	0.61703	1.905	0.80722	D	1	D;D;D;D;D	0.76494	0.999;0.997;0.999;0.999;0.994	D;D;D;D;D	0.87578	0.998;0.983;0.994;0.994;0.993	T	0.55029	-0.8204	10	0.16420	T	0.52	-23.2937	16.2792	0.82664	1.0:0.0:0.0:0.0	.	520;412;744;744;772	F5H327;F5GZU8;Q8IUD2-2;Q8IUD2-3;Q8IUD2	.;.;.;.;RB6I2_HUMAN	R	744;772;744;744;472;744;744;472;772;772;772;744;520;412	ENSP00000340054:K744R;ENSP00000380386:K772R;ENSP00000438546:K744R;ENSP00000442976:K472R;ENSP00000442739:K772R;ENSP00000347621:K772R;ENSP00000354158:K772R;ENSP00000410064:K744R	ENSP00000299183:K472R	K	+	2	0	ERC1	1169443	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.339000	0.96797	2.243000	0.73865	0.533000	0.62120	AAG		0.403	ERC1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398380.2		NM_015064	
EVC	2121	broad.mit.edu;hgsc.bcm.edu	37	4	5733355	5733355	+	Silent	SNP	C	C	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr4:5733355C>T	ENST00000264956.6	+	4	772	c.588C>T	c.(586-588)aaC>aaT	p.N196N	EVC_ENST00000509451.1_Silent_p.N196N|EVC_ENST00000382674.2_Silent_p.N196N	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	196					cartilage development (GO:0051216)|endochondral bone growth (GO:0003416)|muscle organ development (GO:0007517)|positive regulation of smoothened signaling pathway (GO:0045880)|skeletal system development (GO:0001501)|smoothened signaling pathway (GO:0007224)	ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|stomach(1)	28		Myeloproliferative disorder(84;0.117)				TCCGGGTGAACGCCTTCCCTG	0.617																																																	0													58.0	48.0	51.0					4																	5733355		2203	4300	6503	SO:0001819	synonymous_variant	2121			AF216184	CCDS3383.1	4p16	2008-07-03			ENSG00000072840	ENSG00000072840			3497	protein-coding gene	gene with protein product		604831				10700184	Standard	NM_153717		Approved	DWF-1	uc003gil.1	P57679	OTTHUMG00000090427	ENST00000264956.6:c.588C>T	4.37:g.5733355C>T		Somatic		WXS	Illumina HiSeq	Phase_I		Silent	SNP	ENST00000264956.6	37	CCDS3383.1																																																																																				0.617	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1			
BRINP2	57795	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	177249921	177249921	+	Missense_Mutation	SNP	C	C	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr1:177249921C>T	ENST00000361539.4	+	8	1921	c.1609C>T	c.(1609-1611)Cgg>Tgg	p.R537W	BRINP2_ENST00000478325.1_3'UTR	NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	537					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	extracellular region (GO:0005576)											CAATGACATGCGGCTGGGCAG	0.557																																																	0													44.0	38.0	40.0					1																	177249921		2203	4300	6503	SO:0001583	missense	57795				CCDS1320.1	1q24	2013-08-06	2013-08-06	2013-07-31	ENSG00000198797	ENSG00000198797			13746	protein-coding gene	gene with protein product			"""family with sequence similarity 5, member B"""	FAM5B		15193423	Standard	NM_021165		Approved	DBCCR1L2	uc001glf.3	Q9C0B6	OTTHUMG00000034953	ENST00000361539.4:c.1609C>T	1.37:g.177249921C>T	ENSP00000354481:p.Arg537Trp	Somatic		WXS	Illumina HiSeq	Phase_I	O95560|Q6ZWC1|Q7LCZ9|Q8N360	Missense_Mutation	SNP	ENST00000361539.4	37	CCDS1320.1	.	.	.	.	.	.	.	.	.	.	C	17.31	3.357216	0.61293	.	.	ENSG00000198797	ENST00000536589;ENST00000361539	T	0.21543	2.0	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.47525	0.1450	M	0.79475	2.455	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	T	0.49380	-0.8946	10	0.87932	D	0	-12.0386	13.6412	0.62253	0.1549:0.8451:0.0:0.0	.	432;537	Q9C0B6-2;Q9C0B6	.;FAM5B_HUMAN	W	290;537	ENSP00000354481:R537W	ENSP00000354481:R537W	R	+	1	2	FAM5B	175516544	1.000000	0.71417	0.999000	0.59377	0.858000	0.48976	3.698000	0.54771	2.514000	0.84764	0.313000	0.20887	CGG		0.557	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084599.1		NM_021165	
GPR98	84059	broad.mit.edu;hgsc.bcm.edu	37	5	90079095	90079095	+	Silent	SNP	G	G	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr5:90079095G>A	ENST00000405460.2	+	66	13482	c.13386G>A	c.(13384-13386)ggG>ggA	p.G4462G	GPR98_ENST00000425867.2_Silent_p.G123G	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	4462	Calx-beta 30. {ECO:0000255}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TTCAGCATGGGCAAAACTTAA	0.388																																																	0													84.0	80.0	81.0					5																	90079095		1885	4126	6011	SO:0001819	synonymous_variant	84059			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.13386G>A	5.37:g.90079095G>A		Somatic		WXS	Illumina HiSeq	Phase_I	O75171|Q8TF58|Q9H0X5|Q9UL61	Silent	SNP	ENST00000405460.2	37	CCDS47246.1																																																																																				0.388	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2		NM_032119	
GPRC5C	55890	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	72443073	72443073	+	Missense_Mutation	SNP	A	A	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr17:72443073A>G	ENST00000392627.1	+	4	2493	c.1367A>G	c.(1366-1368)gAa>gGa	p.E456G	GPRC5C_ENST00000481232.1_3'UTR|GPRC5C_ENST00000582873.1_3'UTR|GPRC5C_ENST00000392629.2_Missense_Mutation_p.E423G|GPRC5C_ENST00000342648.5_Missense_Mutation_p.E96G	NM_022036.2	NP_071319.2	Q9NQ84	GPC5C_HUMAN	G protein-coupled receptor, class C, group 5, member C	411					G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)|vesicle (GO:0031982)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|large_intestine(3)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	17						CTGCGGGCTGAAGACATGTAC	0.602																																																	0													73.0	76.0	75.0					17																	72443073		2203	4300	6503	SO:0001583	missense	55890			AF207989	CCDS11699.1, CCDS42378.1	17q25	2014-01-30	2014-01-30		ENSG00000170412	ENSG00000170412		"""GPCR / Class C : Orphans"""	13309	protein-coding gene	gene with protein product		605949	"""G protein-coupled receptor, family C, group 5, member C"""			10945465	Standard	NM_022036		Approved	RAIG-3	uc002jkr.3	Q9NQ84	OTTHUMG00000067613	ENST00000392627.1:c.1367A>G	17.37:g.72443073A>G	ENSP00000376403:p.Glu456Gly	Somatic		WXS	Illumina HiSeq	Phase_I	B5BUN4|Q2NL85|Q9NZG5	Missense_Mutation	SNP	ENST00000392627.1	37	CCDS11699.1	.	.	.	.	.	.	.	.	.	.	A	25.6	4.652769	0.88056	.	.	ENSG00000170412	ENST00000392627;ENST00000342648;ENST00000262616;ENST00000392629;ENST00000392628	T	0.22743	1.94	5.48	5.48	0.80851	.	0.380726	0.24229	N	0.040367	T	0.37972	0.1023	L	0.43152	1.355	0.46774	D	0.999191	D;P;P;P	0.76494	0.999;0.842;0.842;0.902	D;B;B;P	0.69479	0.964;0.321;0.395;0.6	T	0.11155	-1.0599	10	0.66056	D	0.02	-27.403	14.4052	0.67079	1.0:0.0:0.0:0.0	.	122;411;411;423	Q9NXI0;A8MXZ4;Q9NQ84;Q9NQ84-2	.;.;GPC5C_HUMAN;.	G	411;456;122;423;411	ENSP00000376405:E423G	ENSP00000262616:E122G	E	+	2	0	GPRC5C	69954668	1.000000	0.71417	0.957000	0.39632	0.959000	0.62525	6.476000	0.73587	2.094000	0.63399	0.459000	0.35465	GAA		0.602	GPRC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145094.2			
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33054014	33054014	+	Stop_Codon_Del	DEL	A	A	-	rs67523850	byFrequency	TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr6:33054014delA	ENST00000418931.2	+	0	892					NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1						antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						GGATCTGCATAAACAGGTAAT	0.423													|||unknown(NO_COVERAGE)	391	0.0780751	0.0968	0.0677	5008	,	,		20380	0.0863		0.0437	False		,,,				2504	0.0869																0										358,3906		18,322,1792	167.0	183.0	177.0			-2.0	0.0	6	dbSNP_130	185	318,7936		7,304,3816	no	frameshift	HLA-DPB1	NM_002121.5		25,626,5608	A1A1,A1R,RR		3.8527,8.3959,5.4002			33054014	676,11842	2202	4299	6501	SO:0001567	stop_retained_variant	3115				CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	Exception_encountered	6.37:g.33054014delA		Somatic		WXS	Illumina HiSeq	Phase_I	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Frame_Shift_Del	DEL	ENST00000418931.2	37	CCDS4765.1																																																																																				0.423	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2		NM_002121	
HS1BP3	64342	broad.mit.edu;ucsc.edu	37	2	20823713	20823713	+	Missense_Mutation	SNP	T	T	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr2:20823713T>A	ENST00000304031.3	-	6	888	c.863A>T	c.(862-864)gAg>gTg	p.E288V		NM_022460.3	NP_071905.3	Q53T59	H1BP3_HUMAN	HCLS1 binding protein 3	288							phosphatidylinositol binding (GO:0035091)			endometrium(4)|large_intestine(1)|lung(7)|ovary(1)|skin(2)	15	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCCTCCACTCTCACAGGCGGC	0.652																																																	0													30.0	33.0	32.0					2																	20823713		2202	4299	6501	SO:0001583	missense	64342				CCDS1700.1	2p24.1	2006-08-15			ENSG00000118960	ENSG00000118960			24979	protein-coding gene	gene with protein product		609359				10590261, 15699368	Standard	NM_022460		Approved	HS1-BP3,FLJ14249	uc002rdw.1	Q53T59	OTTHUMG00000122099	ENST00000304031.3:c.863A>T	2.37:g.20823713T>A	ENSP00000305193:p.Glu288Val	Somatic		WXS	Illumina GAIIx	Phase_I	B2RAW2|D6W529|Q86VC2|Q8N367	Missense_Mutation	SNP	ENST00000304031.3	37	CCDS1700.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	15.02|15.02|15.02	2.709736|2.709736|2.709736	0.48517|0.48517|0.48517	.|.|.	.|.|.	ENSG00000118960|ENSG00000118960|ENSG00000118960	ENST00000304031;ENST00000458740|ENST00000415264|ENST00000445102	T;T|.|.	0.38077|.|.	2.04;1.16|.|.	4.46|4.46|4.46	0.637|0.637|0.637	0.17735|0.17735|0.17735	.|.|.	0.764210|.|.	0.12312|.|.	N|.|.	0.480135|.|.	T|.|.	0.41558|.|.	0.1164|.|.	L|L|L	0.59436|0.59436|0.59436	1.845|1.845|1.845	0.09310|0.09310|0.09310	N|N|N	1|1|1	B|.|.	0.30482|.|.	0.281|.|.	B|.|.	0.22601|.|.	0.04|.|.	T|.|.	0.33137|.|.	-0.9880|.|.	10|.|.	0.32370|.|.	T|.|.	0.25|.|.	-3.0905|-3.0905|-3.0905	6.5368|6.5368|6.5368	0.22359|0.22359|0.22359	0.0:0.3011:0.0:0.6989|0.0:0.3011:0.0:0.6989|0.0:0.3011:0.0:0.6989	.|.|.	288|.|.	Q53T59|.|.	H1BP3_HUMAN|.|.	V|X|C	288;107|41|80	ENSP00000305193:E288V;ENSP00000392203:E107V|.|.	ENSP00000305193:E288V|.|.	E|R|X	-|-|-	2|1|3	0|2|0	HS1BP3|HS1BP3|HS1BP3	20687194|20687194|20687194	0.000000|0.000000|0.000000	0.05858|0.05858|0.05858	0.000000|0.000000|0.000000	0.03702|0.03702|0.03702	0.039000|0.039000|0.039000	0.13416|0.13416|0.13416	-0.135000|-0.135000|-0.135000	0.10420|0.10420|0.10420	-0.035000|-0.035000|-0.035000	0.13691|0.13691|0.13691	0.459000|0.459000|0.459000	0.35465|0.35465|0.35465	GAG|AGA|TGA		0.652	HS1BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242863.1		NM_022460	
KIAA0355	9710	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	34791500	34791500	+	Missense_Mutation	SNP	T	T	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr19:34791500T>C	ENST00000299505.6	+	2	995	c.122T>C	c.(121-123)cTg>cCg	p.L41P		NM_014686.3	NP_055501.2	O15063	K0355_HUMAN	KIAA0355	41										breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	41	Esophageal squamous(110;0.162)					GGCCGAGCACTGAGTGCTCCC	0.637																																																	0													42.0	36.0	38.0					19																	34791500		2203	4300	6503	SO:0001583	missense	9710				CCDS12436.1	19q13.12	2012-11-29			ENSG00000166398	ENSG00000166398			29016	protein-coding gene	gene with protein product						9205841	Standard	NM_014686		Approved		uc002nvd.4	O15063	OTTHUMG00000180505	ENST00000299505.6:c.122T>C	19.37:g.34791500T>C	ENSP00000299505:p.Leu41Pro	Somatic		WXS	Illumina HiSeq	Phase_I	Q2M3W4	Missense_Mutation	SNP	ENST00000299505.6	37	CCDS12436.1	.	.	.	.	.	.	.	.	.	.	T	19.16	3.772845	0.69992	.	.	ENSG00000166398	ENST00000299505	.	.	.	5.25	5.25	0.73442	.	0.000000	0.64402	D	0.000001	T	0.65502	0.2697	L	0.27053	0.805	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	T	0.70167	-0.4946	9	0.87932	D	0	.	15.4502	0.75268	0.0:0.0:0.0:1.0	.	41	O15063	K0355_HUMAN	P	41	.	ENSP00000299505:L41P	L	+	2	0	KIAA0355	39483340	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.648000	0.83479	2.107000	0.64212	0.459000	0.35465	CTG		0.637	KIAA0355-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451678.4		NM_014686	
KLF12	11278	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	74420129	74420129	+	Missense_Mutation	SNP	G	G	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr13:74420129G>T	ENST00000377669.2	-	3	531	c.505C>A	c.(505-507)Cct>Act	p.P169T	KLF12_ENST00000377666.4_Missense_Mutation_p.P169T|KLF12_ENST00000472022.1_5'UTR	NM_007249.4	NP_009180.3	Q9Y4X4	KLF12_HUMAN	Kruppel-like factor 12	169					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	16		Prostate(6;0.00217)|Breast(118;0.0838)		GBM - Glioblastoma multiforme(99;0.00677)		GGACTTGAAGGCGGTACGGGA	0.512																																																	0													103.0	88.0	93.0					13																	74420129		2203	4300	6503	SO:0001583	missense	11278			AJ243274	CCDS9449.1	13q22	2013-01-08			ENSG00000118922	ENSG00000118922		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	6346	protein-coding gene	gene with protein product	"""KLF12 zinc finger transcriptional repressor"", ""AP-2rep transcription factor"", ""AP-2 repressor"""	607531				10704285	Standard	NM_007249		Approved	AP-2rep, HSPC122, AP2REP	uc001vjf.3	Q9Y4X4	OTTHUMG00000017078	ENST00000377669.2:c.505C>A	13.37:g.74420129G>T	ENSP00000366897:p.Pro169Thr	Somatic		WXS	Illumina HiSeq	Phase_I	A8K5T2|L0R3J4|Q5VZM7|Q9UHZ0	Missense_Mutation	SNP	ENST00000377669.2	37	CCDS9449.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.605734	0.87157	.	.	ENSG00000118922	ENST00000377669;ENST00000342812;ENST00000377666	T;T	0.01379	4.96;4.96	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.07098	0.0180	L	0.55481	1.735	0.80722	D	1	D	0.71674	0.998	D	0.73708	0.981	T	0.32640	-0.9899	10	0.38643	T	0.18	.	19.5289	0.95219	0.0:0.0:1.0:0.0	.	169	Q9Y4X4	KLF12_HUMAN	T	169	ENSP00000366897:P169T;ENSP00000366894:P169T	ENSP00000344057:P169T	P	-	1	0	KLF12	73318130	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.574000	0.60900	2.865000	0.98341	0.655000	0.94253	CCT		0.512	KLF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045271.2		NM_007249	
KLHL4	56062	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	86890606	86890606	+	Frame_Shift_Del	DEL	T	T	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chrX:86890606delT	ENST00000373119.4	+	9	1901	c.1756delT	c.(1756-1758)tcafs	p.S586fs	KLHL4_ENST00000373114.4_Frame_Shift_Del_p.S586fs	NM_019117.4	NP_061990.2	Q9C0H6	KLHL4_HUMAN	kelch-like family member 4	586						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(29)|ovary(2)|prostate(1)|skin(1)	67						CTGCCTCAAATCAATGGAATA	0.398																																																	0													127.0	106.0	114.0					X																	86890606		2203	4300	6503	SO:0001589	frameshift_variant	56062			AF284765	CCDS14456.1, CCDS14457.1	Xq21.3	2013-01-30	2013-01-30		ENSG00000102271	ENSG00000102271		"""Kelch-like"", ""BTB/POZ domain containing"""	6355	protein-coding gene	gene with protein product		300348	"""kelch (Drosophila)-like 4"", ""kelch-like 4 (Drosophila)"""			11401425	Standard	NM_019117		Approved	KIAA1687, DKELCHL, KHL4	uc004efa.2	Q9C0H6	OTTHUMG00000021946	ENST00000373119.4:c.1756delT	X.37:g.86890606delT	ENSP00000362211:p.Ser586fs	Somatic		WXS	Illumina HiSeq	Phase_I	B2RTW2|Q9Y3J5	Frame_Shift_Del	DEL	ENST00000373119.4	37	CCDS14457.1																																																																																				0.398	KLHL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057413.1			
KLK6	5653	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	51466690	51466690	+	Nonsense_Mutation	SNP	G	G	A	rs577792048		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr19:51466690G>A	ENST00000376851.3	-	4	752	c.313C>T	c.(313-315)Cag>Tag	p.Q105*	KLK6_ENST00000391808.1_5'UTR|KLK6_ENST00000310157.2_Nonsense_Mutation_p.Q105*|CTB-147C22.8_ENST00000601506.1_RNA|KLK6_ENST00000376853.4_Intron|KLK6_ENST00000594641.1_Nonsense_Mutation_p.Q105*|KLK6_ENST00000456750.2_5'Flank	NM_001012964.1	NP_001012982.1	Q92876	KLK6_HUMAN	kallikrein-related peptidase 6	105	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				amyloid precursor protein metabolic process (GO:0042982)|central nervous system development (GO:0007417)|collagen catabolic process (GO:0030574)|hormone metabolic process (GO:0042445)|myelination (GO:0042552)|neuron death (GO:0070997)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|protein autoprocessing (GO:0016540)|regulation of cell differentiation (GO:0045595)|regulation of neuron projection development (GO:0010975)|response to wounding (GO:0009611)|tissue regeneration (GO:0042246)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)			endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|skin(4)	13		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00372)|GBM - Glioblastoma multiforme(134;0.00871)		ATGATGTCCTGGTCATGGCTG	0.597																																																	0													84.0	63.0	70.0					19																	51466690		2203	4300	6503	SO:0001587	stop_gained	5653			U62801	CCDS12811.1, CCDS42599.1	19q13.3	2011-09-07	2006-10-27			ENSG00000167755		"""Kallikreins"", ""Serine peptidases / Serine peptidases"""	6367	protein-coding gene	gene with protein product		602652	"""protease, serine, 18"", ""kallikrein 6 (neurosin, zyme)"""	PRSS9, PRSS18		9003450, 16800724, 16800723	Standard	NM_002774		Approved	Bssp, Klk7, neurosin	uc002pui.3	Q92876		ENST00000376851.3:c.313C>T	19.37:g.51466690G>A	ENSP00000366047:p.Gln105*	Somatic		WXS	Illumina HiSeq	Phase_I	A6NJA1|A8MW09|Q6H301	Nonsense_Mutation	SNP	ENST00000376851.3	37	CCDS12811.1	.	.	.	.	.	.	.	.	.	.	N	35	5.434001	0.96150	.	.	ENSG00000167755	ENST00000310157;ENST00000376851	.	.	.	4.69	0.976	0.19727	.	0.636305	0.13118	N	0.412478	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	7.7023	0.28630	0.0:0.1441:0.3918:0.4641	.	.	.	.	X	105	.	ENSP00000309148:Q105X	Q	-	1	0	KLK6	56158502	0.996000	0.38824	0.999000	0.59377	0.571000	0.35966	0.436000	0.21526	0.516000	0.28340	-0.492000	0.04666	CAG		0.597	KLK6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465060.1		NM_002774	
LARGE	9215	broad.mit.edu;hgsc.bcm.edu	37	22	33700423	33700423	+	Missense_Mutation	SNP	C	C	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr22:33700423C>T	ENST00000354992.2	-	13	2093	c.1522G>A	c.(1522-1524)Gcc>Acc	p.A508T	LARGE_ENST00000452586.2_Missense_Mutation_p.A307T|LARGE_ENST00000397394.2_Missense_Mutation_p.A508T|LARGE_ENST00000437602.2_Missense_Mutation_p.A508T|LARGE_ENST00000337431.2_Missense_Mutation_p.A456T|LARGE_ENST00000402320.1_Missense_Mutation_p.A456T	NM_004737.4	NP_004728.1	O95461	LARGE_HUMAN	like-glycosyltransferase	508					glycoprotein biosynthetic process (GO:0009101)|glycosphingolipid biosynthetic process (GO:0006688)|muscle cell cellular homeostasis (GO:0046716)|N-acetylglucosamine metabolic process (GO:0006044)|protein glycosylation (GO:0006486)	integral component of Golgi membrane (GO:0030173)	acetylglucosaminyltransferase activity (GO:0008375)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(23)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(1;0.219)				TGGGCCTCGGCGTCTGACAGG	0.637																																					Colon(70;397 1175 4573 19089 45288)												0													51.0	43.0	46.0					22																	33700423		2203	4300	6503	SO:0001583	missense	9215			AJ007583	CCDS13912.1	22q12.3	2013-02-22			ENSG00000133424	ENSG00000133424		"""Glycosyltransferase family 8 domain containing"""	6511	protein-coding gene	gene with protein product		603590				9892679, 10591208, 12966029	Standard	NM_004737		Approved	KIAA0609	uc003ane.4	O95461	OTTHUMG00000150914	ENST00000354992.2:c.1522G>A	22.37:g.33700423C>T	ENSP00000347088:p.Ala508Thr	Somatic		WXS	Illumina HiSeq	Phase_I	B0QXZ7|O60348|Q17R80|Q9UGD1|Q9UGE7|Q9UGG3|Q9UGZ8|Q9UH22	Missense_Mutation	SNP	ENST00000354992.2	37	CCDS13912.1	.	.	.	.	.	.	.	.	.	.	C	15.98	2.993419	0.54041	.	.	ENSG00000133424	ENST00000443693;ENST00000429788;ENST00000354992;ENST00000337431;ENST00000397394;ENST00000402320;ENST00000452586;ENST00000437602	T;T;T;T;T;T	0.52057	1.13;1.18;1.13;1.18;0.68;2.06	5.27	4.24	0.50183	.	0.000000	0.85682	D	0.000000	T	0.50582	0.1624	L	0.47716	1.5	0.80722	D	1	P;B;P;D	0.54397	0.873;0.147;0.839;0.966	B;B;B;P	0.51229	0.392;0.021;0.334;0.663	T	0.44802	-0.9304	10	0.28530	T	0.3	-0.0252	15.2024	0.73150	0.142:0.858:0.0:0.0	.	508;307;456;508	B7Z2I9;E9PH73;O95461-2;O95461	.;.;.;LARGE_HUMAN	T	185;185;508;456;508;456;307;508	ENSP00000347088:A508T;ENSP00000336636:A456T;ENSP00000380549:A508T;ENSP00000385223:A456T;ENSP00000407917:A307T;ENSP00000388544:A508T	ENSP00000336636:A456T	A	-	1	0	LARGE	32030423	1.000000	0.71417	0.893000	0.35052	0.771000	0.43674	7.257000	0.78362	1.204000	0.43247	-0.181000	0.13052	GCC		0.637	LARGE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320515.2		NM_133642	
LARS	51520	hgsc.bcm.edu	37	5	145543912	145543913	+	Frame_Shift_Ins	INS	-	-	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr5:145543912_145543913insG	ENST00000394434.2	-	6	720_721	c.554_555insC	c.(553-555)ccgfs	p.P185fs	LARS_ENST00000274562.9_Frame_Shift_Ins_p.P158fs|LARS_ENST00000545646.1_Frame_Shift_Ins_p.P139fs|LARS_ENST00000510191.1_Frame_Shift_Ins_p.P131fs|LARS_ENST00000511505.1_5'UTR	NM_020117.9	NP_064502.9	Q9P2J5	SYLC_HUMAN	leucyl-tRNA synthetase	185					gene expression (GO:0010467)|leucyl-tRNA aminoacylation (GO:0006429)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|leucine-tRNA ligase activity (GO:0004823)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|prostate(1)|skin(2)|stomach(8)	34			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Leucine(DB00149)	TAGCCAGTGGCGGGAAATAATC	0.366																																																	0																																										SO:0001589	frameshift_variant	51520			AF151026	CCDS34265.1	5q32	2012-10-02			ENSG00000133706	ENSG00000133706	6.1.1.4	"""Aminoacyl tRNA synthetases / Class I"""	6512	protein-coding gene	gene with protein product	"""leucine tRNA ligase 1, cytoplasmic"""	151350				6933703	Standard	NM_020117		Approved	HSPC192, FLJ10595, FLJ21788, LARS1, LEUS, RNTLS	uc003lnx.1	Q9P2J5	OTTHUMG00000163429	ENST00000394434.2:c.555dupC	5.37:g.145543915_145543915dupG	ENSP00000377954:p.Pro185fs	Somatic		WXS	Illumina HiSeq	Phase_I	A2RRR4|A7E266|B4DJ10|Q2TU79|Q9NSE1	Frame_Shift_Ins	INS	ENST00000394434.2	37	CCDS34265.1																																																																																				0.366	LARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000373367.1		NM_020117	
LRP5	4041	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	68193567	68193567	+	Silent	SNP	C	C	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr11:68193567C>G	ENST00000294304.7	+	16	3655	c.3549C>G	c.(3547-3549)acC>acG	p.T1183T		NM_002335.2	NP_002326.2	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein 5	1183	Beta-propeller 4.				adipose tissue development (GO:0060612)|anatomical structure regression (GO:0060033)|anterior/posterior pattern specification (GO:0009952)|apoptotic process involved in patterning of blood vessels (GO:1902262)|bone marrow development (GO:0048539)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|cell migration involved in gastrulation (GO:0042074)|cell-cell signaling involved in mammary gland development (GO:0060764)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic limb morphogenesis (GO:0030326)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocytosis (GO:0006897)|extracellular matrix-cell signaling (GO:0035426)|gastrulation with mouth forming second (GO:0001702)|glucose catabolic process (GO:0006007)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|osteoblast development (GO:0002076)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mitosis (GO:0045840)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of bone remodeling (GO:0046850)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to peptide hormone (GO:0043434)|retina morphogenesis in camera-type eye (GO:0060042)|retinal blood vessel morphogenesis (GO:0061304)|somatic stem cell maintenance (GO:0035019)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	coreceptor activity (GO:0015026)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(24)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TGGAGAAGACCACCGGGGACA	0.622																																																	0													106.0	92.0	97.0					11																	68193567		2200	4294	6494	SO:0001819	synonymous_variant	4041			AF064548	CCDS8181.1	11q13.4	2014-01-28	2003-03-12		ENSG00000162337	ENSG00000162337		"""Low density lipoprotein receptors"""	6697	protein-coding gene	gene with protein product		603506	"""osteoporosis pseudoglioma syndrome"", ""exudative vitreoretinopathy 1"""	LRP7, OPPG, EVR1		9714764, 10049586	Standard	XM_005273994		Approved	LR3, BMND1, HBM, OPS, OPTA1, VBCH2, EVR4	uc001ont.3	O75197	OTTHUMG00000167570	ENST00000294304.7:c.3549C>G	11.37:g.68193567C>G		Somatic		WXS	Illumina HiSeq	Phase_I	Q96TD6|Q9UES7|Q9UP66	Silent	SNP	ENST00000294304.7	37	CCDS8181.1																																																																																				0.622	LRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395088.1		NM_002335	
LRRC42	115353	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	54428053	54428053	+	Missense_Mutation	SNP	A	A	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr1:54428053A>G	ENST00000371370.3	+	7	1419	c.898A>G	c.(898-900)Aac>Gac	p.N300D	LRRC42_ENST00000477905.1_3'UTR|LRRC42_ENST00000319223.4_Missense_Mutation_p.N300D	NM_001256409.1	NP_001243338.1	Q9Y546	LRC42_HUMAN	leucine rich repeat containing 42	300										breast(2)|kidney(1)|large_intestine(1)|lung(5)	9						TGATCATAGTAACTGCAAGAC	0.463																																																	0													98.0	97.0	97.0					1																	54428053		2203	4300	6503	SO:0001583	missense	115353			AK075201	CCDS585.1	1p33-p32.1	2014-02-12			ENSG00000116212	ENSG00000116212			28792	protein-coding gene	gene with protein product						12477932	Standard	NM_001256409		Approved	MGC8974	uc001cwj.2	Q9Y546	OTTHUMG00000008436	ENST00000371370.3:c.898A>G	1.37:g.54428053A>G	ENSP00000360421:p.Asn300Asp	Somatic		WXS	Illumina HiSeq	Phase_I	D3DQ46|Q8N2Q8	Missense_Mutation	SNP	ENST00000371370.3	37	CCDS585.1	.	.	.	.	.	.	.	.	.	.	A	12.60	1.987466	0.35036	.	.	ENSG00000116212	ENST00000371370;ENST00000319223	.	.	.	6.08	6.08	0.98989	.	0.223526	0.51477	D	0.000081	T	0.40448	0.1117	L	0.29908	0.895	0.35863	D	0.827619	P	0.36282	0.546	B	0.30401	0.115	T	0.49588	-0.8924	9	0.27785	T	0.31	-24.5232	16.6438	0.85155	1.0:0.0:0.0:0.0	.	300	Q9Y546	LRC42_HUMAN	D	300	.	ENSP00000318185:N300D	N	+	1	0	LRRC42	54200641	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.494000	0.53273	2.333000	0.79357	0.533000	0.62120	AAC		0.463	LRRC42-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023250.1		NM_052940	
LRRTM1	347730	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	80530941	80530941	+	Missense_Mutation	SNP	C	C	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr2:80530941C>G	ENST00000295057.3	-	2	660	c.4G>C	c.(4-6)Gat>Cat	p.D2H	LRRTM1_ENST00000409148.1_Missense_Mutation_p.D2H|CTNNA2_ENST00000466387.1_Intron|CTNNA2_ENST00000402739.4_Intron|CTNNA2_ENST00000496558.1_Intron|CTNNA2_ENST00000361291.4_Intron|CTNNA2_ENST00000541047.1_Intron|CTNNA2_ENST00000540488.1_Intron	NM_178839.4	NP_849161.2	Q86UE6	LRRT1_HUMAN	leucine rich repeat transmembrane neuronal 1	2					exploration behavior (GO:0035640)|locomotory behavior (GO:0007626)|long-term synaptic potentiation (GO:0060291)|negative regulation of receptor internalization (GO:0002091)|protein localization to synapse (GO:0035418)|synapse organization (GO:0050808)	axon (GO:0030424)|cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				NS(1)|breast(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(33)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	63						AGCAGGAAATCCATTAGCGAG	0.562										HNSCC(69;0.2)																																							0													26.0	29.0	28.0					2																	80530941		2018	4150	6168	SO:0001583	missense	347730			AY358310	CCDS1966.1	2p12	2004-06-22			ENSG00000162951	ENSG00000162951			19408	protein-coding gene	gene with protein product		610867				12676565	Standard	XR_244930		Approved	FLJ32082	uc002sok.1	Q86UE6	OTTHUMG00000130021	ENST00000295057.3:c.4G>C	2.37:g.80530941C>G	ENSP00000295057:p.Asp2His	Somatic		WXS	Illumina HiSeq	Phase_I	A8K397|D6W5K1|Q96DN1	Missense_Mutation	SNP	ENST00000295057.3	37	CCDS1966.1	.	.	.	.	.	.	.	.	.	.	C	14.08	2.428036	0.43122	.	.	ENSG00000162951	ENST00000295057;ENST00000409148;ENST00000416268;ENST00000452811;ENST00000415098	T;T;T;T;T	0.57595	0.79;0.79;0.56;0.39;1.32	4.46	3.59	0.41128	.	0.000000	0.85682	U	0.000000	T	0.64091	0.2567	L	0.51422	1.61	0.58432	D	0.999999	D	0.76494	0.999	D	0.79784	0.993	T	0.61584	-0.7033	9	.	.	.	.	12.246	0.54571	0.0:0.9162:0.0:0.0838	.	2	Q86UE6	LRRT1_HUMAN	H	2	ENSP00000295057:D2H;ENSP00000386646:D2H;ENSP00000415368:D2H;ENSP00000389473:D2H;ENSP00000404557:D2H	.	D	-	1	0	LRRTM1	80384452	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	7.462000	0.80851	0.865000	0.35603	0.185000	0.17295	GAT		0.562	LRRTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313614.1		NM_178839	
MAP1S	55201	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	17838790	17838790	+	Missense_Mutation	SNP	T	T	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr19:17838790T>C	ENST00000324096.4	+	5	2748	c.2597T>C	c.(2596-2598)cTg>cCg	p.L866P	MAP1S_ENST00000597681.1_3'UTR|MAP1S_ENST00000544059.2_Missense_Mutation_p.L840P|CTD-3149D2.4_ENST00000595363.1_RNA	NM_018174.4	NP_060644.4	Q66K74	MAP1S_HUMAN	microtubule-associated protein 1S	866	Necessary for association with microtubules.|Necessary for interaction with RASSF1 isoform A and isoform C.				apoptotic DNA fragmentation (GO:0006309)|brain development (GO:0007420)|execution phase of apoptosis (GO:0097194)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|nervous system development (GO:0007399)|neuron projection morphogenesis (GO:0048812)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	actin filament binding (GO:0051015)|beta-tubulin binding (GO:0048487)|DNA binding (GO:0003677)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	25						CGGAAGCCCCTGGCCCGCCCC	0.677																																																	0													10.0	12.0	11.0					19																	17838790		2174	4258	6432	SO:0001583	missense	55201			BC067115	CCDS32954.1	19p13.12	2008-02-05	2006-07-04	2006-07-04		ENSG00000130479			15715	protein-coding gene	gene with protein product		607573	"""chromosome 19 open reading frame 5"", ""VCY2 interacting protein 1"", ""BPY2 interacting protein 1"""	C19orf5, VCY2IP1, BPY2IP1		11827465, 15528209, 16297881, 14627543	Standard	NM_018174		Approved	FLJ10669, MAP8	uc002nhe.1	Q66K74		ENST00000324096.4:c.2597T>C	19.37:g.17838790T>C	ENSP00000325313:p.Leu866Pro	Somatic		WXS	Illumina HiSeq	Phase_I	B4DH53|Q27QB1|Q6NXF1|Q8N3L8|Q8N3W5|Q8NI88|Q96H94|Q96IT4|Q96SP8|Q9BRC6|Q9H928|Q9NVK7	Missense_Mutation	SNP	ENST00000324096.4	37	CCDS32954.1	.	.	.	.	.	.	.	.	.	.	T	9.678	1.148494	0.21288	.	.	ENSG00000130479	ENST00000324096;ENST00000544059	T;T	0.19394	2.15;2.16	4.57	-3.3	0.05003	.	0.925652	0.08909	N	0.876155	T	0.08492	0.0211	N	0.10874	0.06	0.09310	N	1	B;B	0.14805	0.001;0.011	B;B	0.09377	0.002;0.004	T	0.29427	-1.0012	10	0.44086	T	0.13	-9.1757	2.2267	0.03986	0.1241:0.3324:0.1268:0.4168	.	840;866	B4DH53;Q66K74	.;MAP1S_HUMAN	P	866;840	ENSP00000325313:L866P;ENSP00000439243:L840P	ENSP00000325313:L866P	L	+	2	0	MAP1S	17699790	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.391000	0.07323	-0.720000	0.04935	-0.353000	0.07706	CTG		0.677	MAP1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466027.1		NM_018174	
MAP1S	55201	broad.mit.edu;hgsc.bcm.edu	37	19	17838796	17838796	+	Missense_Mutation	SNP	G	G	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr19:17838796G>C	ENST00000324096.4	+	5	2754	c.2603G>C	c.(2602-2604)cGc>cCc	p.R868P	MAP1S_ENST00000597681.1_3'UTR|MAP1S_ENST00000544059.2_Missense_Mutation_p.R842P|CTD-3149D2.4_ENST00000595363.1_RNA	NM_018174.4	NP_060644.4	Q66K74	MAP1S_HUMAN	microtubule-associated protein 1S	868	Necessary for association with microtubules.|Necessary for interaction with RASSF1 isoform A and isoform C.				apoptotic DNA fragmentation (GO:0006309)|brain development (GO:0007420)|execution phase of apoptosis (GO:0097194)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|nervous system development (GO:0007399)|neuron projection morphogenesis (GO:0048812)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	actin filament binding (GO:0051015)|beta-tubulin binding (GO:0048487)|DNA binding (GO:0003677)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	25						CCCCTGGCCCGCCCCAACTCA	0.677																																																	0													9.0	11.0	10.0					19																	17838796		2166	4236	6402	SO:0001583	missense	55201			BC067115	CCDS32954.1	19p13.12	2008-02-05	2006-07-04	2006-07-04		ENSG00000130479			15715	protein-coding gene	gene with protein product		607573	"""chromosome 19 open reading frame 5"", ""VCY2 interacting protein 1"", ""BPY2 interacting protein 1"""	C19orf5, VCY2IP1, BPY2IP1		11827465, 15528209, 16297881, 14627543	Standard	NM_018174		Approved	FLJ10669, MAP8	uc002nhe.1	Q66K74		ENST00000324096.4:c.2603G>C	19.37:g.17838796G>C	ENSP00000325313:p.Arg868Pro	Somatic		WXS	Illumina HiSeq	Phase_I	B4DH53|Q27QB1|Q6NXF1|Q8N3L8|Q8N3W5|Q8NI88|Q96H94|Q96IT4|Q96SP8|Q9BRC6|Q9H928|Q9NVK7	Missense_Mutation	SNP	ENST00000324096.4	37	CCDS32954.1	.	.	.	.	.	.	.	.	.	.	G	15.80	2.939738	0.52972	.	.	ENSG00000130479	ENST00000324096;ENST00000544059	T;T	0.19938	2.11;2.12	4.66	3.62	0.41486	.	0.132996	0.31909	N	0.006866	T	0.36082	0.0954	L	0.53249	1.67	0.09310	N	1	D;D	0.76494	0.999;0.998	D;P	0.68943	0.961;0.899	T	0.06006	-1.0851	10	0.52906	T	0.07	-31.341	9.245	0.37520	0.1038:0.0:0.8962:0.0	.	842;868	B4DH53;Q66K74	.;MAP1S_HUMAN	P	868;842	ENSP00000325313:R868P;ENSP00000439243:R842P	ENSP00000325313:R868P	R	+	2	0	MAP1S	17699796	0.510000	0.26171	0.083000	0.20561	0.009000	0.06853	4.101000	0.57769	1.091000	0.41335	-0.150000	0.13652	CGC		0.677	MAP1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466027.1		NM_018174	
MARCKS	4082	hgsc.bcm.edu	37	6	114181301	114181302	+	In_Frame_Ins	INS	-	-	TGAGGC			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr6:114181301_114181302insTGAGGC	ENST00000368635.4	+	2	926_927	c.545_546insTGAGGC	c.(544-549)ggtgag>ggTGAGGCtgag	p.185_186insAE		NM_002356.5	NP_002347.5	P29966	MARCS_HUMAN	myristoylated alanine-rich protein kinase C substrate	185					energy reserve metabolic process (GO:0006112)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|centrosome (GO:0005813)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|germinal vesicle (GO:0042585)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|calmodulin binding (GO:0005516)			breast(1)|kidney(1)|large_intestine(1)|lung(1)	4		all_cancers(87;7.65e-05)|all_epithelial(87;0.000296)|all_hematologic(75;0.0172)|Colorectal(196;0.0317)|all_lung(197;0.198)		Epithelial(106;1.59e-07)|all cancers(137;9.85e-07)|OV - Ovarian serous cystadenocarcinoma(136;0.000322)		GGAGAAGGCGGTGAGGCTGAGG	0.649																																																	0										3,3535		0,3,1766						1.9	0.8			10	31,7489		1,29,3730	no	coding	MARCKS	NM_002356.5		1,32,5496	A1A1,A1R,RR		0.4122,0.0848,0.3075				34,11024				SO:0001652	inframe_insertion	4082			M68956	CCDS5101.1	6q21	2014-04-10	2001-12-17	2001-12-20	ENSG00000155130	ENSG00000277443			6759	protein-coding gene	gene with protein product		177061	"""myristoylated alanine-rich protein kinase C substrate (MARCKS, 80K-L)"""	MACS		1560845, 8420923	Standard	NM_002356		Approved	PKCSL, 80K-L	uc003pvy.4	P29966	OTTHUMG00000188327	ENST00000368635.4:c.552_557dupTGAGGC	6.37:g.114181302_114181307dupTGAGGC	ENSP00000357624:p.Ala184_Glu185dup	Somatic		WXS	Illumina HiSeq	Phase_I	E1P560|Q2LA83|Q5TDB7	In_Frame_Ins	INS	ENST00000368635.4	37	CCDS5101.1																																																																																				0.649	MARCKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041903.1		NM_002356	
MEI1	150365	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	22	42172238	42172238	+	Missense_Mutation	SNP	C	C	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr22:42172238C>A	ENST00000401548.3	+	21	2717	c.2677C>A	c.(2677-2679)Ctg>Atg	p.L893M	MEI1_ENST00000540880.1_Missense_Mutation_p.L211M|MEI1_ENST00000300398.4_5'UTR|MEI1_ENST00000400107.1_Missense_Mutation_p.L261M	NM_152513.3	NP_689726.3			meiosis inhibitor 1											breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						CCTGCAGCGTCTGCTAGTGGA	0.557																																																	0													71.0	70.0	70.0					22																	42172238		2068	4216	6284	SO:0001583	missense	150365			AK092934	CCDS46718.1	22q13.2	2013-10-11			ENSG00000167077	ENSG00000167077			28613	protein-coding gene	gene with protein product	"""spermatogenesis associated 38"""	608797				16683055	Standard	XM_006724154		Approved	MGC40042, SPATA38	uc003baz.1	Q5TIA1	OTTHUMG00000030083	ENST00000401548.3:c.2677C>A	22.37:g.42172238C>A	ENSP00000384115:p.Leu893Met	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000401548.3	37	CCDS46718.1	.	.	.	.	.	.	.	.	.	.	C	16.15	3.042098	0.55003	.	.	ENSG00000167077	ENST00000401548;ENST00000400107;ENST00000540880	T;T;T	0.74842	-0.82;-0.88;0.38	5.8	3.65	0.41850	.	0.242826	0.34879	N	0.003601	T	0.81197	0.4772	L	0.59436	1.845	0.41510	D	0.988331	D;B;P;P	0.89917	1.0;0.356;0.587;0.587	D;B;B;B	0.81914	0.995;0.197;0.266;0.177	T	0.80141	-0.1506	10	0.56958	D	0.05	.	8.9026	0.35503	0.3024:0.5514:0.1462:0.0	.	261;136;261;893	Q5TIA1-3;Q5TIA1-5;Q5TIA1-2;Q5TIA1	.;.;.;MEI1_HUMAN	M	893;261;211	ENSP00000384115:L893M;ENSP00000382978:L261M;ENSP00000437436:L211M	ENSP00000382978:L261M	L	+	1	2	MEI1	40502184	1.000000	0.71417	0.819000	0.32651	0.809000	0.45718	2.018000	0.40991	0.738000	0.32606	0.650000	0.86243	CTG		0.557	MEI1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000074937.3		NM_152513	
MEX3A	92312	broad.mit.edu;ucsc.edu	37	1	156047265	156047265	+	Silent	SNP	G	G	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr1:156047265G>A	ENST00000532414.2	-	2	662	c.663C>T	c.(661-663)ccC>ccT	p.P221P	AL355388.1_ENST00000410679.1_RNA|MEX3A_ENST00000442784.1_5'UTR	NM_001093725.1	NP_001087194.1	A1L020	MEX3A_HUMAN	mex-3 RNA binding family member A	221						cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(3)|lung(3)	9	Hepatocellular(266;0.158)|all_neural(408;0.195)					TCACCTGGCCGGGCAGAGCAG	0.652																																																	0													48.0	58.0	54.0					1																	156047265		2161	4272	6433	SO:0001819	synonymous_variant	92312			AK024097	CCDS53377.1	1q22	2013-09-24	2013-08-21	2007-07-18	ENSG00000254726	ENSG00000254726		"""RING-type (C3HC4) zinc fingers"", ""Mex-3 homologs"""	33482	protein-coding gene	gene with protein product		611007	"""ring finger and KH domain containing 4"", ""mex-3 homolog A (C. elegans)"""	RKHD4		17267406	Standard	NM_001093725		Approved		uc001fnd.4	A1L020	OTTHUMG00000017465	ENST00000532414.2:c.663C>T	1.37:g.156047265G>A		Somatic		WXS	Illumina GAIIx	Phase_I		Silent	SNP	ENST00000532414.2	37	CCDS53377.1																																																																																				0.652	MEX3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046218.3		NM_001093725	
MEX3B	84206	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	82336581	82336581	+	Missense_Mutation	SNP	C	C	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr15:82336581C>A	ENST00000329713.4	-	2	1065	c.630G>T	c.(628-630)atG>atT	p.M210I	AC026956.1_ENST00000410589.1_RNA|MEX3B_ENST00000558133.1_3'UTR	NM_032246.4	NP_115622.2	Q6ZN04	MEX3B_HUMAN	mex-3 RNA binding family member B	210	KH 2. {ECO:0000255|PROSITE- ProRule:PRU00117}.				protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|upper_aerodigestive_tract(1)	19						CGTTCTCTGGCATGCCGGTCA	0.612																																																	0													140.0	130.0	133.0					15																	82336581		2203	4300	6503	SO:0001583	missense	84206			AK131424	CCDS10319.1	15q25.1	2013-08-21	2013-08-21	2007-07-18	ENSG00000183496	ENSG00000183496		"""RING-type (C3HC4) zinc fingers"", ""Mex-3 homologs"""	25297	protein-coding gene	gene with protein product		611008	"""ring finger and KH domain containing 3"", ""mex-3 homolog B (C. elegans)"""	RKHD3		11230166, 17267406	Standard	NM_032246		Approved	DKFZp434J0617, RNF195	uc002bgq.2	Q6ZN04	OTTHUMG00000147356	ENST00000329713.4:c.630G>T	15.37:g.82336581C>A	ENSP00000329918:p.Met210Ile	Somatic		WXS	Illumina HiSeq	Phase_I	Q4G0W1|Q8IVG2|Q9H0J0	Missense_Mutation	SNP	ENST00000329713.4	37	CCDS10319.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.920577	0.92249	.	.	ENSG00000183496	ENST00000329713	T	0.28666	1.6	4.98	4.98	0.66077	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.044747	0.85682	D	0.000000	T	0.43919	0.1269	L	0.44542	1.39	0.80722	D	1	P	0.41947	0.766	P	0.54499	0.754	T	0.21449	-1.0245	10	0.49607	T	0.09	-36.0099	17.1854	0.86865	0.0:1.0:0.0:0.0	.	210	Q6ZN04	MEX3B_HUMAN	I	210	ENSP00000329918:M210I	ENSP00000329918:M210I	M	-	3	0	MEX3B	80123636	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.604000	0.67626	2.584000	0.87258	0.655000	0.94253	ATG		0.612	MEX3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304000.1		XM_290645	
MICAL3	57553	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	22	18368682	18368682	+	Nonsense_Mutation	SNP	C	C	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr22:18368682C>A	ENST00000441493.2	-	16	2555	c.2203G>T	c.(2203-2205)Gag>Tag	p.E735*	MICAL3_ENST00000207726.7_Nonsense_Mutation_p.E735*|MICAL3_ENST00000400561.2_Nonsense_Mutation_p.E735*|MICAL3_ENST00000414725.2_Nonsense_Mutation_p.E735*|MICAL3_ENST00000429452.1_Nonsense_Mutation_p.E735*|MICAL3_ENST00000383094.3_Nonsense_Mutation_p.E735*|MICAL3_ENST00000444520.1_Nonsense_Mutation_p.E735*|MICAL3_ENST00000585038.1_Nonsense_Mutation_p.E735*	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	735					actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|exocytosis (GO:0006887)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		GGCGCATTCTCTTCAAATTTG	0.562																																																	0													166.0	152.0	156.0					22																	18368682		1568	3582	5150	SO:0001587	stop_gained	57553			AB037785	CCDS46659.1, CCDS46660.1, CCDS46661.1	22q11.21	2013-03-26	2013-03-26		ENSG00000243156	ENSG00000243156			24694	protein-coding gene	gene with protein product		608882				12110185	Standard	NM_015241		Approved	KIAA0819	uc002zng.4	Q7RTP6	OTTHUMG00000150067	ENST00000441493.2:c.2203G>T	22.37:g.18368682C>A	ENSP00000416015:p.Glu735*	Somatic		WXS	Illumina HiSeq	Phase_I	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Nonsense_Mutation	SNP	ENST00000441493.2	37	CCDS46659.1	.	.	.	.	.	.	.	.	.	.	C	44	10.597159	0.99434	.	.	ENSG00000093100;ENSG00000093100;ENSG00000243156;ENSG00000243156;ENSG00000243156;ENSG00000243156;ENSG00000243156	ENST00000441493;ENST00000429452;ENST00000400561;ENST00000444520;ENST00000414725;ENST00000383094;ENST00000207726	.	.	.	5.93	5.93	0.95920	.	0.052862	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	.	20.3437	0.98782	0.0:1.0:0.0:0.0	.	.	.	.	X	735	.	ENSP00000207726:E735X	E	-	1	0	XXbac-B461K10.4;MICAL3	16748682	1.000000	0.71417	1.000000	0.80357	0.671000	0.39405	7.731000	0.84895	2.815000	0.96918	0.561000	0.74099	GAG		0.562	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1			
DNM3	26052	broad.mit.edu;hgsc.bcm.edu	37	1	172113783	172113783	+	Intron	SNP	C	C	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr1:172113783C>T	ENST00000355305.5	+	15	1846				DNM3_ENST00000367731.1_Intron|DNM3OS_ENST00000417354.1_RNA|MIR199A2_ENST00000385289.1_RNA|DNM3_ENST00000520906.1_Intron|DNM3_ENST00000358155.4_Intron			Q9UQ16	DYN3_HUMAN	dynamin 3						endocytosis (GO:0006897)|filopodium assembly (GO:0046847)|GTP catabolic process (GO:0006184)|synapse assembly (GO:0007416)	dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(16)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						CAGAAGCTTCCTTCTATGTAC	0.532																																																	0													64.0	59.0	61.0					1																	172113783		1568	3582	5150	SO:0001627	intron_variant	406977			AL136712	CCDS44276.1, CCDS60356.1	1q24.1	2013-01-10			ENSG00000197959	ENSG00000197959		"""Pleckstrin homology (PH) domain containing"""	29125	protein-coding gene	gene with protein product	"""Dyna III"""	611445				10048485	Standard	NM_015569		Approved	KIAA0820	uc001gie.4	Q9UQ16	OTTHUMG00000034913	ENST00000355305.5:c.1689+13355C>T	1.37:g.172113783C>T		Somatic		WXS	Illumina HiSeq	Phase_I	A9Z1Y1|O14982|O95555|Q1MTM8|Q5W129|Q6P2G1|Q9H0P3|Q9H548|Q9NQ68|Q9NQN6	RNA	SNP	ENST00000355305.5	37																																																																																					0.532	DNM3-003	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000084531.1		NM_015569	
NSRP1	84081	broad.mit.edu;hgsc.bcm.edu	37	17	28444131	28444131	+	Intron	SNP	A	A	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr17:28444131A>G	ENST00000247026.5	+	1	83				NSRP1_ENST00000584423.1_Intron|NSRP1_ENST00000479218.2_Intron|RP11-1148O4.2_ENST00000582938.1_RNA|MIR3184_ENST00000586878.1_RNA|NSRP1_ENST00000540900.3_Intron|MIR423_ENST00000362201.2_RNA	NM_001261467.1|NM_032141.3	NP_001248396.1|NP_115517.1	Q9H0G5	NSRP1_HUMAN	nuclear speckle splicing regulatory protein 1						developmental process (GO:0032502)|mRNA processing (GO:0006397)|nucleocytoplasmic transport (GO:0006913)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	14						AGAGAGCGAGACTTTTCTATT	0.532																																																	0													32.0	33.0	33.0					17																	28444131		1568	3582	5150	SO:0001627	intron_variant	100423003			AL136806	CCDS11255.1, CCDS74025.1	17q11.2	2011-05-24	2011-05-24	2011-05-24	ENSG00000126653	ENSG00000126653			25305	protein-coding gene	gene with protein product			"""coiled-coil domain containing 55"""	CCDC55		11230166	Standard	NM_032141		Approved	DKFZP434K1421, NSrp70	uc002heu.4	Q9H0G5	OTTHUMG00000132754	ENST00000247026.5:c.20+250A>G	17.37:g.28444131A>G		Somatic		WXS	Illumina HiSeq	Phase_I	Q6FI71	RNA	SNP	ENST00000247026.5	37	CCDS11255.1																																																																																				0.532	NSRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256121.2		NM_032141	
DPM1	8813	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	49576416	49576416	+	5'Flank	SNP	A	A	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr20:49576416A>T	ENST00000371588.5	-	0	0				DPM1_ENST00000466152.1_5'Flank|DPM1_ENST00000371582.4_5'Flank|DPM1_ENST00000371583.5_5'Flank|MOCS3_ENST00000244051.1_Missense_Mutation_p.D346V	NM_003859.1	NP_003850.1	O60762	DPM1_HUMAN	dolichyl-phosphate mannosyltransferase polypeptide 1, catalytic subunit						C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|dolichol metabolic process (GO:0019348)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose metabolic process (GO:0019673)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|protein mannosylation (GO:0035268)|protein N-linked glycosylation via asparagine (GO:0018279)|protein O-linked mannosylation (GO:0035269)	dolichol-phosphate-mannose synthase complex (GO:0033185)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nucleus (GO:0005634)	alcohol binding (GO:0043178)|dolichyl-phosphate beta-D-mannosyltransferase activity (GO:0004582)|dolichyl-phosphate-mannose-protein mannosyltransferase activity (GO:0004169)|mannose binding (GO:0005537)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	7						CGACTGCTGGATTCTGGGGCA	0.542																																																	0													177.0	176.0	176.0					20																	49576416		2203	4300	6503	SO:0001631	upstream_gene_variant	27304			AF007875	CCDS13434.1	20q13.1	2013-02-26			ENSG00000000419	ENSG00000000419	2.4.1.83	"""Glycosyltransferase family 2 domain containing"""	3005	protein-coding gene	gene with protein product	"""DPM synthase complex, catalytic subunit"""	603503				9223280, 9535917	Standard	NM_003859		Approved	MPDS, CDGIE	uc002xvw.1	O60762	OTTHUMG00000032742		20.37:g.49576416A>T	Exception_encountered	Somatic		WXS	Illumina HiSeq	Phase_I	O15157|Q6IB78|Q96HK0	Missense_Mutation	SNP	ENST00000371588.5	37	CCDS13434.1	.	.	.	.	.	.	.	.	.	.	A	14.47	2.543903	0.45280	.	.	ENSG00000124217	ENST00000244051	T	0.29917	1.55	5.01	5.01	0.66863	Rhodanese-like (2);Molybdenum cofactor biosynthesis, MoeB (1);	0.051267	0.85682	D	0.000000	T	0.43875	0.1267	M	0.85542	2.76	0.80722	D	1	B	0.33135	0.399	B	0.39465	0.3	T	0.44112	-0.9349	9	.	.	.	-17.9186	13.4412	0.61114	1.0:0.0:0.0:0.0	.	346	O95396	MOCS3_HUMAN	V	346	ENSP00000244051:D346V	.	D	+	2	0	MOCS3	49009823	1.000000	0.71417	0.995000	0.50966	0.773000	0.43773	4.775000	0.62346	2.110000	0.64415	0.459000	0.35465	GAT		0.542	DPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079716.1		NM_003859	
MPND	84954	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	4352949	4352949	+	Missense_Mutation	SNP	A	A	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr19:4352949A>G	ENST00000262966.8	+	4	654	c.587A>G	c.(586-588)gAc>gGc	p.D196G	MPND_ENST00000359935.4_Missense_Mutation_p.D196G|MPND_ENST00000599840.1_Missense_Mutation_p.D196G|AC007292.4_ENST00000594776.1_RNA	NM_032868.4	NP_116257.2	Q8N594	MPND_HUMAN	MPN domain containing	196							peptidase activity (GO:0008233)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(1)	8				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)		gaggaggaggaCGTTCTGGCA	0.657																																																	0													31.0	34.0	33.0					19																	4352949		2005	4165	6170	SO:0001583	missense	84954				CCDS42470.1, CCDS54200.1, CCDS74261.1	19p13.3	2014-08-12			ENSG00000008382				25934	protein-coding gene	gene with protein product							Standard	XM_005259663		Approved	FLJ14981	uc002mae.3	Q8N594	OTTHUMG00000181914	ENST00000262966.8:c.587A>G	19.37:g.4352949A>G	ENSP00000262966:p.Asp196Gly	Somatic		WXS	Illumina HiSeq	Phase_I	Q96SJ0|Q9Y2P1|Q9Y2P2	Missense_Mutation	SNP	ENST00000262966.8	37	CCDS42470.1	.	.	.	.	.	.	.	.	.	.	a	6.109	0.388446	0.11581	.	.	ENSG00000008382	ENST00000262966;ENST00000359935	.	.	.	3.55	3.55	0.40652	.	0.961025	0.08673	N	0.910633	T	0.22627	0.0546	N	0.04880	-0.145	0.31673	N	0.64414	B;B;B	0.09022	0.002;0.001;0.0	B;B;B	0.08055	0.003;0.002;0.001	T	0.17228	-1.0376	9	0.27082	T	0.32	-11.2763	8.7919	0.34857	1.0:0.0:0.0:0.0	.	196;196;196	Q8N594-2;A6NI36;Q8N594	.;.;MPND_HUMAN	G	196	.	ENSP00000262966:D196G	D	+	2	0	MPND	4303949	0.749000	0.28305	0.918000	0.36340	0.690000	0.40134	1.043000	0.30316	1.860000	0.53959	0.393000	0.25936	GAC		0.657	MPND-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458292.1		NM_032868	
MTFR1	9650	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	66619369	66619369	+	Silent	SNP	A	A	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr8:66619369A>G	ENST00000262146.4	+	6	768	c.642A>G	c.(640-642)cgA>cgG	p.R214R	MTFR1_ENST00000517944.1_3'UTR|MTFR1_ENST00000458689.2_Silent_p.R181R	NM_014637.3	NP_055452.3	Q15390	MTFR1_HUMAN	mitochondrial fission regulator 1	214	Necessary and sufficient to promote mitochondrial fission. {ECO:0000250}.				aerobic respiration (GO:0009060)|mitochondrial fission (GO:0000266)|mitochondrion organization (GO:0007005)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(1)|pancreas(1)|urinary_tract(1)	11			Epithelial(68;0.0526)|BRCA - Breast invasive adenocarcinoma(89;0.156)|all cancers(69;0.171)|OV - Ovarian serous cystadenocarcinoma(28;0.194)			TTAAAGAACGAAGAGAGAAAA	0.483																																																	0													72.0	72.0	72.0					8																	66619369		2203	4300	6503	SO:0001819	synonymous_variant	9650				CCDS6182.1, CCDS55240.1	8q13.1	2012-11-30							29510	protein-coding gene	gene with protein product	"""likely ortholog of chicken chondrocyte protein with a poly proline region"""					7584026, 7584028, 15389597	Standard	NM_014637		Approved	CHPPR, KIAA0009, FAM54A2	uc003xvn.2	Q15390		ENST00000262146.4:c.642A>G	8.37:g.66619369A>G		Somatic		WXS	Illumina HiSeq	Phase_I	E7EP84|Q6IB94|Q7Z669|Q86XH5|Q8IVD7	Silent	SNP	ENST00000262146.4	37	CCDS6182.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	3.298|3.298	-0.143444|-0.143444	0.06669|0.06669	.|.	.|.	ENSG00000066855|ENSG00000066855	ENST00000518800|ENST00000527155	.|.	.|.	.|.	5.49|5.49	-2.02|-2.02	0.07388|0.07388	.|.	.|.	.|.	.|.	.|.	T|T	0.38931|0.38931	0.1059|0.1059	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.30794|0.30794	-0.9966|-0.9966	4|4	.|.	.|.	.|.	-2.8036|-2.8036	1.1072|1.1072	0.01697|0.01697	0.3553:0.116:0.3027:0.2259|0.3553:0.116:0.3027:0.2259	.|.	.|.	.|.	.|.	G|E	172|28	.|.	.|.	E|K	+|+	2|1	0|0	MTFR1|MTFR1	66781923|66781923	0.987000|0.987000	0.35691|0.35691	0.404000|0.404000	0.26397|0.26397	0.237000|0.237000	0.25408|0.25408	0.221000|0.221000	0.17680|0.17680	-0.226000|-0.226000	0.09899|0.09899	-0.256000|-0.256000	0.11100|0.11100	GAA|AAG		0.483	MTFR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378894.1		NM_014637	
MYO15A	51168	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	18062259	18062259	+	Missense_Mutation	SNP	C	C	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr17:18062259C>T	ENST00000205890.5	+	53	9442	c.9104C>T	c.(9103-9105)tCc>tTc	p.S3035F	MYO15A_ENST00000418233.3_Missense_Mutation_p.S299F|MYO15A_ENST00000451725.2_5'Flank	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	3035	Tail.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					AGGCTGAAATCCAAGGAGCCT	0.557																																																	0													66.0	73.0	71.0					17																	18062259		1981	4166	6147	SO:0001583	missense	51168			AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"""Myosins / Myosin superfamily : Class XV"""	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.9104C>T	17.37:g.18062259C>T	ENSP00000205890:p.Ser3035Phe	Somatic		WXS	Illumina HiSeq	Phase_I	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	37	CCDS42271.1	.	.	.	.	.	.	.	.	.	.	C	13.10	2.135155	0.37728	.	.	ENSG00000091536	ENST00000205890;ENST00000418233	D	0.89050	-2.46	4.74	3.74	0.42951	.	.	.	.	.	D	0.88097	0.6345	M	0.61703	1.905	0.80722	D	1	P;P;P	0.48998	0.918;0.604;0.736	P;B;B	0.45167	0.472;0.24;0.28	D	0.88129	0.2837	9	0.72032	D	0.01	.	12.0808	0.53669	0.0:0.8257:0.1743:0.0	.	24;299;3035	B4DLV9;B4DFC7;Q9UKN7	.;.;MYO15_HUMAN	F	3035;24	ENSP00000205890:S3035F	ENSP00000205890:S3035F	S	+	2	0	MYO15A	18002984	0.376000	0.25098	0.986000	0.45419	0.947000	0.59692	0.481000	0.22260	1.084000	0.41184	0.462000	0.41574	TCC		0.557	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1		NM_016239	
NDST2	8509	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	75563696	75563696	+	Missense_Mutation	SNP	T	T	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr10:75563696T>C	ENST00000309979.6	-	10	2478	c.1922A>G	c.(1921-1923)gAg>gGg	p.E641G	ZSWIM8-AS1_ENST00000456638.2_RNA|RP11-574K11.31_ENST00000603027.1_Missense_Mutation_p.E641G|NDST2_ENST00000299641.4_Missense_Mutation_p.E518G			P52849	NDST2_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 2	641	Heparan sulfate N-sulfotransferase 2.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|hydrolase activity (GO:0016787)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(11)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	30	Prostate(51;0.0112)					GAACTGAATCTCCTCAAATGT	0.493																																																	0													151.0	150.0	150.0					10																	75563696		2203	4300	6503	SO:0001583	missense	8509			U36601	CCDS7335.1	10q22	2007-03-14			ENSG00000166507	ENSG00000166507		"""Sulfotransferases, membrane-bound"""	7681	protein-coding gene	gene with protein product		603268				9601056	Standard	NM_003635		Approved	NST2, HSST2	uc001jvk.2	P52849	OTTHUMG00000018489	ENST00000309979.6:c.1922A>G	10.37:g.75563696T>C	ENSP00000310657:p.Glu641Gly	Somatic		WXS	Illumina HiSeq	Phase_I	Q2TB32|Q59H89	Missense_Mutation	SNP	ENST00000309979.6	37	CCDS7335.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.519118	0.85495	.	.	ENSG00000166507	ENST00000309979;ENST00000299641	T;T	0.66995	-0.24;-0.24	5.95	5.95	0.96441	Sulfotransferase domain (1);	0.000000	0.85682	D	0.000000	D	0.88562	0.6470	H	0.97758	4.07	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;0.999;1.0	D	0.92486	0.5996	10	0.87932	D	0	.	16.4159	0.83738	0.0:0.0:0.0:1.0	.	518;311;164;641	B4E139;B4DQU1;B4DE98;P52849	.;.;.;NDST2_HUMAN	G	641;518	ENSP00000310657:E641G;ENSP00000299641:E518G	ENSP00000299641:E518G	E	-	2	0	NDST2	75233702	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.279000	0.76181	0.533000	0.62120	GAG		0.493	NDST2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048710.1		NM_003635	
NFASC	23114	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	204943409	204943409	+	Missense_Mutation	SNP	C	C	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr1:204943409C>T	ENST00000401399.1	+	12	1581	c.1382C>T	c.(1381-1383)aCa>aTa	p.T461I	NFASC_ENST00000367169.4_Missense_Mutation_p.T461I|NFASC_ENST00000338586.6_Missense_Mutation_p.T461I|NFASC_ENST00000338515.6_Missense_Mutation_p.T461I|NFASC_ENST00000403080.1_Missense_Mutation_p.T461I|NFASC_ENST00000513543.1_Missense_Mutation_p.T472I|NFASC_ENST00000367172.4_Missense_Mutation_p.T461I|NFASC_ENST00000539706.1_Missense_Mutation_p.T472I|NFASC_ENST00000367171.4_Missense_Mutation_p.T461I|NFASC_ENST00000360049.4_Missense_Mutation_p.T472I|NFASC_ENST00000367170.4_Missense_Mutation_p.T461I|NFASC_ENST00000339876.6_Missense_Mutation_p.T461I|NFASC_ENST00000404907.1_Missense_Mutation_p.T472I|NFASC_ENST00000404076.1_Missense_Mutation_p.T455I			O94856	NFASC_HUMAN	neurofascin	461	Ig-like C2-type 5.				axon guidance (GO:0007411)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|myelination (GO:0042552)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|synapse organization (GO:0050808)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|node of Ranvier (GO:0033268)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	81	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			CCCATCCCCACACTGCGATGG	0.577																																																	0													72.0	48.0	56.0					1																	204943409		2203	4300	6503	SO:0001583	missense	23114			AK027553	CCDS30982.1, CCDS53460.1, CCDS53461.1, CCDS53462.1	1q32.1	2013-02-11	2010-06-24		ENSG00000163531	ENSG00000163531		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	29866	protein-coding gene	gene with protein product		609145	"""neurofascin homolog (chicken)"""			1377696, 8672144	Standard	NM_015090		Approved	NRCAML, KIAA0756, FLJ46866, NF	uc001hbj.3	O94856	OTTHUMG00000151697	ENST00000401399.1:c.1382C>T	1.37:g.204943409C>T	ENSP00000385637:p.Thr461Ile	Somatic		WXS	Illumina HiSeq	Phase_I	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Missense_Mutation	SNP	ENST00000401399.1	37	CCDS53460.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.08|15.08	2.726620|2.726620	0.48833|0.48833	.|.	.|.	ENSG00000163531|ENSG00000163531	ENST00000367173|ENST00000367172;ENST00000367171;ENST00000367170;ENST00000338515;ENST00000339876;ENST00000338586;ENST00000295776;ENST00000539706;ENST00000360049;ENST00000367169;ENST00000403080;ENST00000404076;ENST00000401399;ENST00000404907;ENST00000513543;ENST00000430393	.|T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	.|0.68181	.|-0.31;-0.31;-0.31;-0.31;-0.31;-0.31;-0.31;-0.31;-0.31;-0.31;-0.31;-0.31;-0.31;-0.31;-0.31	5.54|5.54	5.54|5.54	0.83059|0.83059	.|.	.|0.000000	.|0.53938	.|D	.|0.000044	T|T	0.70298|0.70298	0.3208|0.3208	L|L	0.49126|0.49126	1.545|1.545	0.38611|0.38611	D|D	0.950913|0.950913	.|P;P;P;B;B;P;P	.|0.47106	.|0.867;0.584;0.89;0.452;0.109;0.882;0.575	.|P;B;P;B;B;P;B	.|0.48488	.|0.563;0.201;0.579;0.202;0.027;0.498;0.312	T|T	0.71823|0.71823	-0.4476|-0.4476	5|10	.|0.41790	.|T	.|0.15	.|.	19.0836|19.0836	0.93192|0.93192	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|472;472;557;461;461;472;461	.|O94856-11;O94856-8;B4DRH7;F8W791;O94856-9;O94856-3;O94856-2	.|.;.;.;.;.;.;.	Y|I	431|461;461;461;461;461;461;472;472;472;461;461;455;461;472;472;448	.|ENSP00000356140:T461I;ENSP00000356139:T461I;ENSP00000356138:T461I;ENSP00000342128:T461I;ENSP00000344786:T461I;ENSP00000343509:T461I;ENSP00000438614:T472I;ENSP00000353154:T472I;ENSP00000356137:T461I;ENSP00000384875:T461I;ENSP00000385676:T455I;ENSP00000385637:T461I;ENSP00000384061:T472I;ENSP00000425908:T472I;ENSP00000415031:T448I	.|ENSP00000295776:T472I	H|T	+|+	1|2	0|0	NFASC|NFASC	203210032|203210032	1.000000|1.000000	0.71417|0.71417	0.971000|0.971000	0.41717|0.41717	0.902000|0.902000	0.53008|0.53008	4.454000|4.454000	0.60068|0.60068	2.612000|2.612000	0.88384|0.88384	0.585000|0.585000	0.79938|0.79938	CAC|ACA		0.577	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1		NM_001005388	
PCCB	5096	broad.mit.edu;hgsc.bcm.edu	37	3	136046479	136046479	+	Missense_Mutation	SNP	T	T	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr3:136046479T>C	ENST00000251654.4	+	13	1373	c.1303T>C	c.(1303-1305)Tat>Cat	p.Y435H	PCCB_ENST00000471595.1_Missense_Mutation_p.Y435H|PCCB_ENST00000462637.1_Missense_Mutation_p.Y412H|PCCB_ENST00000478469.1_Intron|PCCB_ENST00000490504.1_Missense_Mutation_p.Y378H|PCCB_ENST00000474833.1_3'UTR|PCCB_ENST00000469217.1_Missense_Mutation_p.Y455H|PCCB_ENST00000482086.1_Missense_Mutation_p.Y319H|PCCB_ENST00000468777.1_Missense_Mutation_p.Y466H|PCCB_ENST00000483687.1_Missense_Mutation_p.Y416H|PCCB_ENST00000466072.1_Missense_Mutation_p.Y455H	NM_000532.4	NP_000523.2	P05166	PCCB_HUMAN	propionyl CoA carboxylase, beta polypeptide	435	Carboxyltransferase.		Y -> C (in PA-2). {ECO:0000269|PubMed:12189489}.		biotin metabolic process (GO:0006768)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|propionyl-CoA carboxylase activity (GO:0004658)			breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|urinary_tract(1)	25					Biotin(DB00121)|L-Valine(DB00161)	GTTTTAGGCCTATGGAGGTGC	0.493																																																	0													122.0	102.0	109.0					3																	136046479		2203	4300	6503	SO:0001583	missense	5096				CCDS3089.1, CCDS54643.1	3q21-q22	2010-07-01	2010-04-30		ENSG00000114054	ENSG00000114054	6.4.1.3		8654	protein-coding gene	gene with protein product		232050	"""propionyl Coenzyme A carboxylase, beta polypeptide"""			2895916	Standard	NM_000532		Approved		uc003eqy.2	P05166	OTTHUMG00000159792	ENST00000251654.4:c.1303T>C	3.37:g.136046479T>C	ENSP00000251654:p.Tyr435His	Somatic		WXS	Illumina HiSeq	Phase_I	B7Z2Z4|Q16813|Q96CX0	Missense_Mutation	SNP	ENST00000251654.4	37	CCDS3089.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.333312	0.81801	.	.	ENSG00000114054	ENST00000251654;ENST00000490504;ENST00000483687;ENST00000468777;ENST00000462637;ENST00000466072;ENST00000482086;ENST00000471595;ENST00000469217	D;D;D;D;D;T;D;D;D	0.98012	-4.66;-4.66;-4.66;-4.66;-4.66;1.34;-4.66;-4.66;-4.66	4.64	4.64	0.57946	Acetyl-coenzyme A carboxyltransferase, C-terminal (1);Carboxyl transferase (1);	0.000000	0.85682	D	0.000000	D	0.99133	0.9701	H	0.97158	3.95	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.85130	0.992;0.997;0.997	D	0.99072	1.0834	10	0.87932	D	0	.	14.2246	0.65850	0.0:0.0:0.0:1.0	.	455;435;435	B7Z2Z4;E9PDR0;P05166	.;.;PCCB_HUMAN	H	435;378;416;466;412;455;319;435;455	ENSP00000251654:Y435H;ENSP00000418307:Y378H;ENSP00000420639:Y416H;ENSP00000419129:Y466H;ENSP00000420391:Y412H;ENSP00000420158:Y455H;ENSP00000417253:Y319H;ENSP00000417549:Y435H;ENSP00000419027:Y455H	ENSP00000251654:Y435H	Y	+	1	0	PCCB	137529169	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	7.448000	0.80631	1.952000	0.56665	0.402000	0.26972	TAT		0.493	PCCB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000357335.1			
PCDH7	5099	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	30724623	30724623	+	Missense_Mutation	SNP	G	G	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr4:30724623G>T	ENST00000361762.2	+	1	2587	c.1579G>T	c.(1579-1581)Gac>Tac	p.D527Y	PCDH7_ENST00000543491.1_Missense_Mutation_p.D527Y	NM_002589.2	NP_002580.2	O60245	PCDH7_HUMAN	protocadherin 7	527	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(8)|liver(1)|lung(26)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	55						CAAGGTGGGAGACACCAACGA	0.622																																																	0													59.0	54.0	56.0					4																	30724623		2203	4300	6503	SO:0001583	missense	5099			AB006755	CCDS33971.1, CCDS75116.1	4p15	2014-06-13	2007-02-12			ENSG00000169851		"""Cadherins / Protocadherins : Non-clustered"""	8659	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 120"""	602988	"""BH-protocadherin (brain-heart)"""			9615233	Standard	NM_002589		Approved	BH-Pcdh, PPP1R120	uc021xnd.1	O60245		ENST00000361762.2:c.1579G>T	4.37:g.30724623G>T	ENSP00000355243:p.Asp527Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	O60246|O60247|Q4W5C4	Missense_Mutation	SNP	ENST00000361762.2	37	CCDS33971.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.22|16.22	3.060643|3.060643	0.55432|0.55432	.|.	.|.	ENSG00000169851|ENSG00000169851	ENST00000361762;ENST00000543491;ENST00000333135|ENST00000511884	T;T|.	0.74632|.	-0.86;-0.86|.	5.26|5.26	5.26|5.26	0.73747|0.73747	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);|.	.|.	.|.	.|.	.|.	D|D	0.90920|0.90920	0.7146|0.7146	H|H	0.98682|0.98682	4.3|4.3	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	1.0;1.0;0.999|.	D|D	0.94122|0.94122	0.7380|0.7380	9|5	0.87932|.	D|.	0|.	.|.	19.0611|19.0611	0.93093|0.93093	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	527;480;527|.	F5GWJ1;O60245-3;O60245|.	.;.;PCDH7_HUMAN|.	Y|I	527;527;480|216	ENSP00000355243:D527Y;ENSP00000441802:D527Y|.	ENSP00000330302:D480Y|.	D|R	+|+	1|2	0|0	PCDH7|PCDH7	30333721|30333721	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.606000|0.606000	0.37113|0.37113	9.657000|9.657000	0.98554|0.98554	2.735000|2.735000	0.93741|0.93741	0.655000|0.655000	0.94253|0.94253	GAC|AGA		0.622	PCDH7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360366.1		NM_032457, NM_002589	
PPP6R3	55291	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	68355413	68355413	+	Missense_Mutation	SNP	A	A	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr11:68355413A>G	ENST00000393800.2	+	16	1905	c.1651A>G	c.(1651-1653)Atg>Gtg	p.M551V	PPP6R3_ENST00000265637.4_Intron|PPP6R3_ENST00000534534.1_Missense_Mutation_p.M319V|PPP6R3_ENST00000529710.1_Missense_Mutation_p.M471V|PPP6R3_ENST00000393799.2_Missense_Mutation_p.M551V|PPP6R3_ENST00000265636.5_Missense_Mutation_p.M471V|PPP6R3_ENST00000527403.2_Splice_Site_p.M516V|PPP6R3_ENST00000524845.1_Missense_Mutation_p.M522V|PPP6R3_ENST00000393801.3_Missense_Mutation_p.M551V|PPP6R3_ENST00000524904.1_Splice_Site_p.M545V	NM_001164161.1|NM_001164162.1|NM_001164163.1	NP_001157633.1|NP_001157634.1|NP_001157635.1	Q5H9R7	PP6R3_HUMAN	protein phosphatase 6, regulatory subunit 3	551					regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)			breast(2)|endometrium(6)|kidney(3)|large_intestine(10)|liver(2)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						TGATTATCAGATGCAACAAAT	0.383																																																	0													218.0	193.0	201.0					11																	68355413		2200	4294	6494	SO:0001583	missense	55291			AF264779	CCDS8182.1, CCDS53671.1, CCDS53672.1, CCDS53673.1, CCDS53674.1, CCDS53675.1	11q13	2012-04-17	2010-06-28	2010-06-28	ENSG00000110075	ENSG00000110075		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"""	1173	protein-coding gene	gene with protein product	"""sporulation-induced transcript 4-associated protein"""	610879	"""chromosome 11 open reading frame 23"", ""SAPS domain family, member 3"""	C11orf23, SAPS3		11401438, 16769727	Standard	NM_018312		Approved	SAPLa, DKFZp781E2374, DKFZp781O2362, DKFZp781E17107, SAP190, SAPL, PP6R3, FLJ11058, FLJ43065, KIAA1558, MGC125711, MGC125712	uc001onv.3	Q5H9R7		ENST00000393800.2:c.1651A>G	11.37:g.68355413A>G	ENSP00000377389:p.Met551Val	Somatic		WXS	Illumina HiSeq	Phase_I	Q3B7I1|Q3I4Y0|Q3KR35|Q68CR3|Q7L4R8|Q8N3B2|Q96MB2|Q9H2K5|Q9H2K6|Q9HCL4|Q9NUY3	Missense_Mutation	SNP	ENST00000393800.2	37	CCDS53672.1	.	.	.	.	.	.	.	.	.	.	A	18.05	3.537311	0.65085	.	.	ENSG00000110075	ENST00000393799;ENST00000393800;ENST00000534534;ENST00000524845;ENST00000524904;ENST00000393801;ENST00000265636;ENST00000529710;ENST00000527403;ENST00000534190	T;T;T;T;T;T;T;T;T;T	0.24908	1.91;1.91;1.9;1.85;1.91;1.91;1.83;1.83;1.96;1.84	5.97	5.97	0.96955	.	0.039520	0.85682	D	0.000000	T	0.36908	0.0984	L	0.33485	1.01	0.58432	D	0.999998	D;D;B;B;B;B;D;B	0.63880	0.989;0.969;0.178;0.178;0.328;0.22;0.993;0.178	D;D;B;B;B;B;D;B	0.73708	0.958;0.914;0.108;0.108;0.155;0.074;0.981;0.076	T	0.06625	-1.0816	10	0.07990	T	0.79	.	16.4473	0.83942	1.0:0.0:0.0:0.0	.	234;319;471;522;545;551;551;471	B4DYU6;E9PQP7;Q5H9R7-3;Q5H9R7-6;Q5H9R7-2;Q5H9R7;Q5H9R7-5;Q5H9R7-4	.;.;.;.;.;PP6R3_HUMAN;.;.	V	551;551;319;522;545;551;471;471;516;258	ENSP00000377388:M551V;ENSP00000377389:M551V;ENSP00000434429:M319V;ENSP00000431415:M522V;ENSP00000433058:M545V;ENSP00000377390:M551V;ENSP00000265636:M471V;ENSP00000437329:M471V;ENSP00000433565:M516V;ENSP00000436209:M258V	ENSP00000265636:M471V	M	+	1	0	PPP6R3	68111989	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.228000	0.95250	2.281000	0.76405	0.533000	0.62120	ATG		0.383	PPP6R3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395275.1		NM_018312	
PREX1	57580	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	47266546	47266546	+	Missense_Mutation	SNP	C	C	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr20:47266546C>G	ENST00000371941.3	-	24	3038	c.3016G>C	c.(3016-3018)Gac>Cac	p.D1006H	PREX1_ENST00000396220.1_Missense_Mutation_p.D1006H	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	1006					actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			TGCTCCGGGTCAAGGCCGATG	0.532																																																	0													73.0	69.0	70.0					20																	47266546		2203	4300	6503	SO:0001583	missense	57580			AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.3016G>C	20.37:g.47266546C>G	ENSP00000361009:p.Asp1006His	Somatic		WXS	Illumina HiSeq	Phase_I	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	37	CCDS13410.1	.	.	.	.	.	.	.	.	.	.	C	14.98	2.697715	0.48307	.	.	ENSG00000124126	ENST00000371941;ENST00000396220	T;T	0.52754	0.65;0.65	5.71	5.71	0.89125	.	0.000000	0.56097	U	0.000028	T	0.67515	0.2901	L	0.59436	1.845	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.75484	0.969;0.986	T	0.67031	-0.5773	10	0.59425	D	0.04	.	19.8677	0.96824	0.0:1.0:0.0:0.0	.	1006;303	Q8TCU6;Q8TCU6-2	PREX1_HUMAN;.	H	1006	ENSP00000361009:D1006H;ENSP00000379522:D1006H	ENSP00000361009:D1006H	D	-	1	0	PREX1	46699953	1.000000	0.71417	0.993000	0.49108	0.805000	0.45488	4.285000	0.58989	2.709000	0.92574	0.655000	0.94253	GAC		0.532	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1		NM_020820	
RAD54L2	23132	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	51667705	51667705	+	Nonsense_Mutation	SNP	T	T	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr3:51667705T>A	ENST00000409535.2	+	7	1063	c.938T>A	c.(937-939)tTg>tAg	p.L313*	RAD54L2_ENST00000296477.3_Nonsense_Mutation_p.L7*	NM_015106.2	NP_055921.2	Q9Y4B4	ARIP4_HUMAN	RAD54-like 2 (S. cerevisiae)	313	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|transcription cofactor activity (GO:0003712)			NS(2)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|liver(2)|lung(9)|ovary(4)|skin(2)	31				BRCA - Breast invasive adenocarcinoma(193;0.000102)|Kidney(197;0.000758)|KIRC - Kidney renal clear cell carcinoma(197;0.000896)		GGGAAAACTTTGCAAGTGATC	0.512																																																	0													101.0	106.0	104.0					3																	51667705		2203	4300	6503	SO:0001587	stop_gained	23132			AB018352	CCDS33765.2	3p21.2	2006-01-17			ENSG00000164080	ENSG00000164080			29123	protein-coding gene	gene with protein product						9872452	Standard	NM_015106		Approved	KIAA0809, SRISNF2L	uc011bdt.2	Q9Y4B4	OTTHUMG00000152936	ENST00000409535.2:c.938T>A	3.37:g.51667705T>A	ENSP00000386520:p.Leu313*	Somatic		WXS	Illumina HiSeq	Phase_I	Q8TB57|Q9BV54	Nonsense_Mutation	SNP	ENST00000409535.2	37	CCDS33765.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	40|40	7.941851|7.941851	0.98574|0.98574	.|.	.|.	ENSG00000164080|ENSG00000164080	ENST00000432863|ENST00000409535;ENST00000296477	.|.	.|.	.|.	5.55|5.55	5.55|5.55	0.83447|0.83447	.|.	.|0.068615	.|0.64402	.|D	.|0.000012	T|.	0.37073|.	0.0990|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.35943|.	-0.9768|.	3|.	.|0.02654	.|T	.|1	-4.9891|-4.9891	14.8726|14.8726	0.70471|0.70471	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|.	.|.	.|.	L|X	141|313;7	.|.	.|ENSP00000296477:L7X	F|L	+|+	3|2	2|0	RAD54L2|RAD54L2	51642745|51642745	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.973000|0.973000	0.67179|0.67179	8.036000|8.036000	0.88901|0.88901	2.103000|2.103000	0.63969|0.63969	0.533000|0.533000	0.62120|0.62120	TTT|TTG		0.512	RAD54L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328700.2		NM_015106	
RIOK2	55781	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	96503556	96503556	+	Missense_Mutation	SNP	C	C	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr5:96503556C>T	ENST00000283109.3	-	8	1080	c.1012G>A	c.(1012-1014)Gat>Aat	p.D338N	RIOK2_ENST00000508447.1_Missense_Mutation_p.D338N|CTD-2215E18.1_ENST00000509481.1_Intron	NM_018343.2	NP_060813.2	Q9BVS4	RIOK2_HUMAN	RIO kinase 2	338	Protein kinase.						ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|urinary_tract(2)	23		all_cancers(142;0.000125)|all_epithelial(76;8.48e-07)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0676)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0657)		ACTTCTCCATCTGAAAATGAG	0.408																																																	0													151.0	157.0	155.0					5																	96503556		2203	4300	6503	SO:0001583	missense	55781			AK002021	CCDS4089.1, CCDS54884.1	5q14	2012-12-10	2012-12-10		ENSG00000058729	ENSG00000058729			18999	protein-coding gene	gene with protein product			"""RIO kinase 2 (yeast)"""				Standard	NM_018343		Approved	FLJ11159	uc003kmz.3	Q9BVS4	OTTHUMG00000128723	ENST00000283109.3:c.1012G>A	5.37:g.96503556C>T	ENSP00000283109:p.Asp338Asn	Somatic		WXS	Illumina HiSeq	Phase_I	D6RDI3|Q9NUT0	Missense_Mutation	SNP	ENST00000283109.3	37	CCDS4089.1	.	.	.	.	.	.	.	.	.	.	C	12.92	2.082078	0.36758	.	.	ENSG00000058729	ENST00000283109;ENST00000508447	T;T	0.29142	1.58;1.58	5.35	4.43	0.53597	.	1.108030	0.06536	N	0.742344	T	0.31734	0.0806	M	0.63428	1.95	0.41831	D	0.990073	B;B	0.18741	0.03;0.026	B;B	0.14023	0.01;0.008	T	0.26292	-1.0107	10	0.22706	T	0.39	-1.5076	8.0406	0.30519	0.0:0.749:0.1622:0.0888	.	338;338	D6RDI3;Q9BVS4	.;RIOK2_HUMAN	N	338	ENSP00000283109:D338N;ENSP00000420932:D338N	ENSP00000283109:D338N	D	-	1	0	RIOK2	96529312	0.156000	0.22821	1.000000	0.80357	0.154000	0.21943	0.267000	0.18552	2.658000	0.90341	0.460000	0.39030	GAT		0.408	RIOK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250628.1		NM_018343	
RNF14	9604	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	141362998	141362998	+	Missense_Mutation	SNP	A	A	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr5:141362998A>G	ENST00000394520.2	+	7	1426	c.1117A>G	c.(1117-1119)Aga>Gga	p.R373G	RNF14_ENST00000540015.1_Missense_Mutation_p.R70G|RNF14_ENST00000394514.2_Missense_Mutation_p.R247G|AC005740.5_ENST00000520882.1_RNA|RNF14_ENST00000394515.3_Missense_Mutation_p.R197G|RNF14_ENST00000394519.1_Missense_Mutation_p.R373G|RNF14_ENST00000356143.1_Missense_Mutation_p.R373G|RNF14_ENST00000347642.3_Missense_Mutation_p.R373G	NM_001201365.1|NM_004290.4	NP_001188294.1|NP_004281.1	Q9UBS8	RNF14_HUMAN	ring finger protein 14	373	Interaction with androgen receptor.				androgen receptor signaling pathway (GO:0030521)|positive regulation of transcription, DNA-templated (GO:0045893)|protein ubiquitination (GO:0016567)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|small conjugating protein ligase activity (GO:0019787)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15		all_hematologic(541;0.0536)|Ovarian(839;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.0407)		GGCTAATAAAAGACTTTTGGA	0.373																																																	0													79.0	80.0	79.0					5																	141362998		2203	4300	6503	SO:0001583	missense	9604			AF060544	CCDS4270.1, CCDS4271.1	5q23.3-q31.1	2008-02-05			ENSG00000013561	ENSG00000013561		"""RING-type (C3HC4) zinc fingers"""	10058	protein-coding gene	gene with protein product		605675				10085091, 10320776	Standard	NM_183399		Approved	ARA54, HFB30, TRIAD2	uc003lmc.3	Q9UBS8	OTTHUMG00000129660	ENST00000394520.2:c.1117A>G	5.37:g.141362998A>G	ENSP00000378028:p.Arg373Gly	Somatic		WXS	Illumina HiSeq	Phase_I	A0AV26|A6NMR2|A8MTW5|B3KN72|B7ZLV2|D3DQE4|O94793|Q6IBV0	Missense_Mutation	SNP	ENST00000394520.2	37	CCDS4270.1	.	.	.	.	.	.	.	.	.	.	A	15.87	2.959774	0.53400	.	.	ENSG00000013561	ENST00000356143;ENST00000394520;ENST00000347642;ENST00000540015;ENST00000394514;ENST00000512565;ENST00000394515;ENST00000394519	D;D;D;D;D;D;D;D	0.91351	-2.4;-2.4;-2.4;-2.83;-2.42;-2.81;-1.99;-2.4	6.01	4.8	0.61643	.	0.132800	0.64402	D	0.000002	D	0.88130	0.6354	L	0.46157	1.445	0.37890	D	0.93067	B;P;B	0.42248	0.138;0.774;0.415	B;B;B	0.43331	0.082;0.416;0.108	D	0.87911	0.2697	10	0.28530	T	0.3	.	13.6382	0.62235	0.7801:0.2199:0.0:0.0	.	70;197;373	B7Z3J5;B7Z229;Q9UBS8	.;.;RNF14_HUMAN	G	373;373;373;70;247;70;197;373	ENSP00000348462:R373G;ENSP00000378028:R373G;ENSP00000324956:R373G;ENSP00000442490:R70G;ENSP00000378022:R247G;ENSP00000426832:R70G;ENSP00000378023:R197G;ENSP00000378027:R373G	ENSP00000324956:R373G	R	+	1	2	RNF14	141343182	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.307000	0.51888	2.298000	0.77334	0.528000	0.53228	AGA		0.373	RNF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251860.2		NM_004290	
RNF14	9604	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	141363016	141363016	+	Missense_Mutation	SNP	T	T	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr5:141363016T>C	ENST00000394520.2	+	7	1444	c.1135T>C	c.(1135-1137)Tat>Cat	p.Y379H	RNF14_ENST00000540015.1_Missense_Mutation_p.Y76H|RNF14_ENST00000394514.2_Missense_Mutation_p.Y253H|AC005740.5_ENST00000520882.1_RNA|RNF14_ENST00000394515.3_Missense_Mutation_p.Y203H|RNF14_ENST00000394519.1_Missense_Mutation_p.Y379H|RNF14_ENST00000356143.1_Missense_Mutation_p.Y379H|RNF14_ENST00000347642.3_Missense_Mutation_p.Y379H	NM_001201365.1|NM_004290.4	NP_001188294.1|NP_004281.1	Q9UBS8	RNF14_HUMAN	ring finger protein 14	379	Interaction with androgen receptor.				androgen receptor signaling pathway (GO:0030521)|positive regulation of transcription, DNA-templated (GO:0045893)|protein ubiquitination (GO:0016567)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|small conjugating protein ligase activity (GO:0019787)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15		all_hematologic(541;0.0536)|Ovarian(839;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.0407)		GGATCAAAGGTATGGTAAGAG	0.393																																																	0													85.0	85.0	85.0					5																	141363016		2203	4300	6503	SO:0001583	missense	9604			AF060544	CCDS4270.1, CCDS4271.1	5q23.3-q31.1	2008-02-05			ENSG00000013561	ENSG00000013561		"""RING-type (C3HC4) zinc fingers"""	10058	protein-coding gene	gene with protein product		605675				10085091, 10320776	Standard	NM_183399		Approved	ARA54, HFB30, TRIAD2	uc003lmc.3	Q9UBS8	OTTHUMG00000129660	ENST00000394520.2:c.1135T>C	5.37:g.141363016T>C	ENSP00000378028:p.Tyr379His	Somatic		WXS	Illumina HiSeq	Phase_I	A0AV26|A6NMR2|A8MTW5|B3KN72|B7ZLV2|D3DQE4|O94793|Q6IBV0	Missense_Mutation	SNP	ENST00000394520.2	37	CCDS4270.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.468512	0.84533	.	.	ENSG00000013561	ENST00000356143;ENST00000394520;ENST00000347642;ENST00000540015;ENST00000394514;ENST00000512565;ENST00000394515;ENST00000394519	D;D;D;D;D;D;D;D	0.91843	-2.53;-2.53;-2.53;-2.92;-2.53;-1.87;-2.1;-2.53	6.01	4.82	0.62117	.	0.051775	0.85682	D	0.000000	D	0.95918	0.8671	M	0.84683	2.71	0.53005	D	0.999963	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	D	0.95258	0.8366	10	0.46703	T	0.11	.	12.4371	0.55604	0.1259:0.0:0.0:0.8741	.	76;203;379	B7Z3J5;B7Z229;Q9UBS8	.;.;RNF14_HUMAN	H	379;379;379;76;253;76;203;379	ENSP00000348462:Y379H;ENSP00000378028:Y379H;ENSP00000324956:Y379H;ENSP00000442490:Y76H;ENSP00000378022:Y253H;ENSP00000426832:Y76H;ENSP00000378023:Y203H;ENSP00000378027:Y379H	ENSP00000324956:Y379H	Y	+	1	0	RNF14	141343200	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.081000	0.71309	1.052000	0.40392	0.528000	0.53228	TAT		0.393	RNF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251860.2		NM_004290	
SEC31A	22872	broad.mit.edu;hgsc.bcm.edu	37	4	83788105	83788105	+	Silent	SNP	T	T	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr4:83788105T>C	ENST00000395310.2	-	10	1235	c.1053A>G	c.(1051-1053)tcA>tcG	p.S351S	SEC31A_ENST00000326950.5_Silent_p.S351S|SEC31A_ENST00000508479.1_Silent_p.S351S|SEC31A_ENST00000264405.5_Silent_p.S123S|SEC31A_ENST00000508502.1_Silent_p.S351S|SEC31A_ENST00000509142.1_Silent_p.S351S|SEC31A_ENST00000513858.1_Silent_p.S351S|SEC31A_ENST00000436790.2_5'UTR|SEC31A_ENST00000355196.2_Silent_p.S351S|SEC31A_ENST00000505984.1_Silent_p.S351S|SEC31A_ENST00000505472.1_Silent_p.S351S|SEC31A_ENST00000311785.7_Silent_p.S351S|SEC31A_ENST00000348405.4_Silent_p.S351S|SEC31A_ENST00000500777.2_Silent_p.S351S|SEC31A_ENST00000443462.2_Silent_p.S346S|SEC31A_ENST00000432794.1_Silent_p.S351S|SEC31A_ENST00000448323.1_Silent_p.S351S	NM_001077207.2|NM_001077208.2|NM_014933.3	NP_001070675.1|NP_001070676.1|NP_055748.2	O94979	SC31A_HUMAN	SEC31 homolog A (S. cerevisiae)	351	Interaction with SEC13.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)|response to calcium ion (GO:0051592)	COPII vesicle coat (GO:0030127)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle (GO:0030134)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|vesicle coat (GO:0030120)	calcium-dependent protein binding (GO:0048306)		SEC31A/ALK(3)|SEC31A/JAK2(4)	breast(1)	1		Hepatocellular(203;0.114)				TCCCAAAAGATGATGAAAGCT	0.378																																																	0													90.0	93.0	92.0					4																	83788105		2203	4300	6503	SO:0001819	synonymous_variant	22872			AB018358	CCDS3596.1, CCDS3597.1, CCDS43244.1, CCDS47088.1, CCDS54773.1, CCDS75155.1, CCDS75156.1	4q21.3	2013-01-10	2006-10-05	2006-09-07	ENSG00000138674	ENSG00000138674		"""WD repeat domain containing"""	17052	protein-coding gene	gene with protein product		610257	"""SEC31-like 1 (S. cerevisiae)"", ""Sec31 homolog A (S. cerevisiae)"""	SEC31L1		10048485, 10788476	Standard	NM_001077206		Approved	KIAA0905, ABP125, ABP130	uc003hnh.3	O94979	OTTHUMG00000130297	ENST00000395310.2:c.1053A>G	4.37:g.83788105T>C		Somatic		WXS	Illumina HiSeq	Phase_I	B4DIW6|B7ZKZ7|B7ZL00|H7C2W3|Q17RR5|Q5H9P6|Q5XG74|Q659G7|Q6ZU90|Q7LCX9|Q86TJ0|Q8IZH4|Q9P048|Q9P0A6|Q9UM05|Q9UM06	Silent	SNP	ENST00000395310.2	37	CCDS3596.1																																																																																				0.378	SEC31A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252640.1		NM_016211	
SERPINH1	871	broad.mit.edu;hgsc.bcm.edu	37	11	75280027	75280027	+	Silent	SNP	C	C	T	rs369937589		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr11:75280027C>T	ENST00000524558.1	+	4	2200	c.765C>T	c.(763-765)atC>atT	p.I255I	SERPINH1_ENST00000358171.3_Silent_p.I255I|SERPINH1_ENST00000530284.1_Silent_p.I255I|SERPINH1_ENST00000525876.1_Silent_p.I38I|SERPINH1_ENST00000533603.1_Silent_p.I255I			P50454	SERPH_HUMAN	serpin peptidase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)	255				I -> L (in Ref. 1; CAA43795). {ECO:0000305}.	chondrocyte development involved in endochondral bone morphogenesis (GO:0003433)|collagen biosynthetic process (GO:0032964)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|protein maturation (GO:0051604)|regulation of proteolysis (GO:0030162)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(4)|large_intestine(3)|liver(1)|lung(4)|ovary(2)|stomach(1)	15	Ovarian(111;0.11)					AGCTGCAAATCGTGGAGATGC	0.582																																																	0								C	,	0,4400		0,0,2200	105.0	96.0	99.0		765,765	-10.7	0.0	11		99	1,8585	1.2+/-3.3	0,1,4292	no	coding-synonymous,coding-synonymous	SERPINH1	NM_001207014.1,NM_001235.3	,	0,1,6492	TT,TC,CC		0.0116,0.0,0.0077	,	255/419,255/419	75280027	1,12985	2200	4293	6493	SO:0001819	synonymous_variant	871			X61598	CCDS8239.1	11q13.5	2014-02-18	2005-08-18		ENSG00000149257	ENSG00000149257		"""Serine (or cysteine) peptidase inhibitors"""	1546	protein-coding gene	gene with protein product		600943	"""serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 2"", ""serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)"""	CBP1, CBP2, SERPINH2		7656593, 9533029, 24172014	Standard	NM_001207014		Approved	HSP47, colligen	uc001owr.3	P50454	OTTHUMG00000165362	ENST00000524558.1:c.765C>T	11.37:g.75280027C>T		Somatic		WXS	Illumina HiSeq	Phase_I	B3KVJ3|P29043|Q5XPB4|Q6NSJ6|Q8IY96|Q9NP88	Silent	SNP	ENST00000524558.1	37	CCDS8239.1																																																																																				0.582	SERPINH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383610.1		NM_004353	
SGCA	6442	hgsc.bcm.edu;ucsc.edu	37	17	48243426	48243427	+	Frame_Shift_Ins	INS	-	-	AA			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr17:48243426_48243427insAA	ENST00000262018.3	+	1	61_62	c.25_26insAA	c.(25-27)cctfs	p.P9fs	SGCA_ENST00000344627.6_Frame_Shift_Ins_p.P9fs|SGCA_ENST00000513942.1_Intron|SGCA_ENST00000543315.1_Frame_Shift_Ins_p.P9fs|RP11-893F2.14_ENST00000572855.1_RNA|SGCA_ENST00000451235.2_5'UTR	NM_000023.2	NP_000014.1	Q16586	SGCA_HUMAN	sarcoglycan, alpha (50kDa dystrophin-associated glycoprotein)	9					muscle contraction (GO:0006936)|muscle organ development (GO:0007517)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(7)|ovary(2)|skin(1)	14						CTTCTGGACTCCTCTCCTCGTG	0.658																																																	0																																										SO:0001589	frameshift_variant	6442			L34355	CCDS32679.1, CCDS45729.1	17q21	2014-09-17	2002-08-29		ENSG00000108823	ENSG00000108823			10805	protein-coding gene	gene with protein product	"""50kD DAG"", ""Sarcoglycan, alpha (50kD dystrophin-associated glycoprotein; adhalin)"", ""adhalin (limb girdle muscular dystrophy 2D)"""	600119	"""sarcoglycan, alpha (50kD dystrophin-associated glycoprotein)"""	ADL		7937874	Standard	NM_000023		Approved	SCARMD1, LGMD2D, adhalin, DMDA2, A2	uc002iqi.3	Q16586	OTTHUMG00000162024	Exception_encountered	17.37:g.48243426_48243427insAA	ENSP00000262018:p.Pro9fs	Somatic		WXS	Illumina HiSeq	Phase_I	A6NEB8|A8K3K7|Q13710|Q13712	Frame_Shift_Ins	INS	ENST00000262018.3	37	CCDS32679.1																																																																																				0.658	SGCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366841.1		NM_000023	
SGK223	157285	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	8233967	8233967	+	Missense_Mutation	SNP	C	C	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr8:8233967C>G	ENST00000520004.1	-	3	2216	c.1952G>C	c.(1951-1953)aGc>aCc	p.S651T	SGK223_ENST00000330777.4_Missense_Mutation_p.S651T			Q86YV5	SG223_HUMAN		653							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										TCTTCCCCAGCTGTGACTCAG	0.597																																					GBM(34;731 755 10259 33573 33867)												0													125.0	144.0	138.0					8																	8233967		2001	4170	6171	SO:0001583	missense	157285																														ENST00000520004.1:c.1952G>C	8.37:g.8233967C>G	ENSP00000428054:p.Ser651Thr	Somatic		WXS	Illumina HiSeq	Phase_I	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	37	CCDS43706.1	.	.	.	.	.	.	.	.	.	.	C	14.75	2.627195	0.46944	.	.	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.61627	0.09;0.09	4.91	4.91	0.64330	.	0.393217	0.22699	N	0.056714	T	0.45256	0.1333	L	0.29908	0.895	0.30394	N	0.780729	B	0.26672	0.156	B	0.26770	0.073	T	0.47522	-0.9111	10	0.38643	T	0.18	.	12.4936	0.55914	0.0:0.8178:0.1822:0.0	.	651	Q86YV5	SG223_HUMAN	T	651	ENSP00000330930:S651T;ENSP00000428054:S651T	ENSP00000330930:S651T	S	-	2	0	AC068353.1	8271377	0.016000	0.18221	1.000000	0.80357	0.995000	0.86356	1.268000	0.33062	2.665000	0.90641	0.655000	0.94253	AGC		0.597	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1			
SLC15A4	121260	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	129285429	129285430	+	Frame_Shift_Ins	INS	-	-	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr12:129285429_129285430insA	ENST00000266771.5	-	6	1422_1423	c.1383_1384insT	c.(1381-1386)attgggfs	p.G462fs	SLC15A4_ENST00000545031.1_5'UTR|SLC15A4_ENST00000544112.1_Frame_Shift_Ins_p.G125fs	NM_145648.3	NP_663623.1	Q8N697	S15A4_HUMAN	solute carrier family 15 (oligopeptide transporter), member 4	462					ion transport (GO:0006811)|oligopeptide transport (GO:0006857)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	L-histidine transmembrane transporter activity (GO:0005290)|symporter activity (GO:0015293)			endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|skin(1)	22	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.69e-06)|Epithelial(86;1.17e-05)|all cancers(50;5.07e-05)		TCGCTGATCCCAATCAGCAAGT	0.54																																																	0																																										SO:0001589	frameshift_variant	121260			AY038999	CCDS9264.1	12q24.32	2013-07-18	2013-07-18		ENSG00000139370	ENSG00000139370		"""Solute carriers"""	23090	protein-coding gene	gene with protein product		615806	"""solute carrier family 15, member 4"""			11741232	Standard	NM_145648		Approved	PHT1, PTR4	uc001uhu.2	Q8N697	OTTHUMG00000168415	ENST00000266771.5:c.1384dupT	12.37:g.129285431_129285431dupA	ENSP00000266771:p.Gly462fs	Somatic		WXS	Illumina HiSeq	Phase_I	A6H8Y9|B3KTK1|Q71M34|Q7Z5F8|Q8TAH0	Frame_Shift_Ins	INS	ENST00000266771.5	37	CCDS9264.1																																																																																				0.540	SLC15A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399663.1		NM_145648	
SLC5A11	115584	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	24869990	24869990	+	Missense_Mutation	SNP	A	A	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr16:24869990A>G	ENST00000347898.3	+	2	648	c.26A>G	c.(25-27)cAg>cGg	p.Q9R	SLC5A11_ENST00000567758.1_Missense_Mutation_p.Q9R|SLC5A11_ENST00000449109.2_Intron|SLC5A11_ENST00000568579.1_Missense_Mutation_p.Q9R|SLC5A11_ENST00000424767.2_Missense_Mutation_p.Q9R|SLC5A11_ENST00000545376.1_Missense_Mutation_p.Q9R|SLC5A11_ENST00000569071.1_Intron|SLC5A11_ENST00000565769.1_Intron|SLC5A11_ENST00000539472.1_Intron	NM_052944.3	NP_443176.2			solute carrier family 5 (sodium/inositol cotransporter), member 11											endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(30)|ovary(2)|prostate(2)|urinary_tract(1)	49				GBM - Glioblastoma multiforme(48;0.0365)		AGCAGCCCTCAGCCTCCACAG	0.557																																																	0													100.0	81.0	87.0					16																	24869990		2197	4300	6497	SO:0001583	missense	115584			AF292385	CCDS10625.1, CCDS58437.1, CCDS58438.1, CCDS58439.1, CCDS58440.1	16p12.1	2013-07-19	2013-07-19		ENSG00000158865	ENSG00000158865		"""Solute carriers"""	23091	protein-coding gene	gene with protein product		610238	"""solute carrier family 5 (sodium/glucose cotransporter), member 11"""			12039040, 12133831	Standard	NM_001258414		Approved	KST1, SMIT2, SGLT6	uc002dmu.4	Q8WWX8	OTTHUMG00000097003	ENST00000347898.3:c.26A>G	16.37:g.24869990A>G	ENSP00000289932:p.Gln9Arg	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000347898.3	37	CCDS10625.1	.	.	.	.	.	.	.	.	.	.	A	5.448	0.267682	0.10294	.	.	ENSG00000158865	ENST00000347898;ENST00000424767;ENST00000545376	D;D;D	0.86497	-1.99;-2.13;-2.11	5.59	-5.22	0.02806	.	0.908627	0.09681	N	0.769702	T	0.67173	0.2865	N	0.14661	0.345	0.09310	N	0.999996	B;B;B	0.26547	0.039;0.152;0.094	B;B;B	0.18871	0.007;0.023;0.01	T	0.54944	-0.8217	10	0.33940	T	0.23	.	1.5799	0.02632	0.1942:0.4026:0.1629:0.2402	.	9;9;9	B7Z329;Q8WWX8-2;Q8WWX8	.;.;SC5AB_HUMAN	R	9	ENSP00000289932:Q9R;ENSP00000416782:Q9R;ENSP00000441384:Q9R	ENSP00000289932:Q9R	Q	+	2	0	SLC5A11	24777491	0.000000	0.05858	0.018000	0.16275	0.343000	0.28985	-0.866000	0.04245	-0.518000	0.06452	0.459000	0.35465	CAG		0.557	SLC5A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214091.3		NM_052944	
SLCO1B3	28234	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	21036504	21036504	+	Silent	SNP	A	A	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr12:21036504A>G	ENST00000381545.3	+	13	1869	c.1650A>G	c.(1648-1650)acA>acG	p.T550T	SLCO1B3_ENST00000553473.1_Silent_p.T550T|SLCO1B3_ENST00000261196.2_Silent_p.T550T|SLCO1B7_ENST00000554957.1_Intron|LST3_ENST00000540229.1_Silent_p.T550T|LST3_ENST00000381541.3_Intron	NM_019844.3	NP_062818.1	Q9NPD5	SO1B3_HUMAN	solute carrier organic anion transporter family, member 1B3	550					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	organic anion transmembrane transporter activity (GO:0008514)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(23)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(2)	63	Esophageal squamous(101;0.149)				Atorvastatin(DB01076)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Dabrafenib(DB08912)|Digoxin(DB00390)|Docetaxel(DB01248)|Estradiol(DB00783)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Olmesartan(DB00275)|Ouabain(DB01092)|Paclitaxel(DB01229)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Rosuvastatin(DB01098)|Valsartan(DB00177)	TCTCTGCAACAGGAGGTACCA	0.348																																																	0													102.0	101.0	101.0					12																	21036504		2203	4300	6503	SO:0001819	synonymous_variant	28234				CCDS8684.1	12p12	2013-05-22	2003-11-25	2003-11-26		ENSG00000111700		"""Solute carriers"""	10961	protein-coding gene	gene with protein product		605495	"""solute carrier family 21 (organic anion transporter), member 8"""	SLC21A8			Standard	NM_019844		Approved	OATP8, OATP1B3	uc001rel.4	Q9NPD5	OTTHUMG00000169011	ENST00000381545.3:c.1650A>G	12.37:g.21036504A>G		Somatic		WXS	Illumina HiSeq	Phase_I	E7EMT8|Q5JAR4	Silent	SNP	ENST00000381545.3	37	CCDS8684.1																																																																																				0.348	SLCO1B3-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401936.1		NM_019844	
SMARCA4	6597	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	11144110	11144110	+	Missense_Mutation	SNP	G	G	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr19:11144110G>A	ENST00000429416.3	+	27	3972	c.3691G>A	c.(3691-3693)Gcc>Acc	p.A1231T	SMARCA4_ENST00000541122.2_Missense_Mutation_p.A1231T|SMARCA4_ENST00000444061.3_Missense_Mutation_p.A1231T|SMARCA4_ENST00000358026.2_Missense_Mutation_p.A1231T|SMARCA4_ENST00000413806.3_Missense_Mutation_p.A1231T|SMARCA4_ENST00000450717.3_Missense_Mutation_p.A1231T|SMARCA4_ENST00000344626.4_Missense_Mutation_p.A1231T|SMARCA4_ENST00000589677.1_Missense_Mutation_p.A1231T|SMARCA4_ENST00000590574.1_Missense_Mutation_p.A1231T	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	1231	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				GGTGATCCAGGCCGGCATGTT	0.632			"""F, N, Mis"""		NSCLC																																			Rec	yes		19	19p13.2	6597	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"""		E	1	Unknown(1)	lung(1)											122.0	117.0	118.0					19																	11144110		2203	4300	6503	SO:0001583	missense	6597			D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"""SNF2-like 4"", ""global transcription activator homologous sequence"", ""sucrose nonfermenting-like 4"", ""mitotic growth and transcription activator"", ""BRM/SWI2-related gene 1"", ""homeotic gene regulator"", ""nuclear protein GRB1"", ""brahma protein-like 1"", ""ATP-dependent helicase SMARCA4"""	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.3691G>A	19.37:g.11144110G>A	ENSP00000395654:p.Ala1231Thr	Somatic		WXS	Illumina HiSeq	Phase_I	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	37	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.741441	0.89573	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	T;T;T;D;D;D;D	0.95447	-1.01;-1.01;-1.01;-3.71;-3.71;-3.71;-3.71	4.74	4.74	0.60224	Helicase, C-terminal (1);	0.061212	0.64402	D	0.000004	D	0.97105	0.9054	M	0.64260	1.97	0.58432	D	0.999999	D;D;D;P;D;D;P	0.89917	1.0;1.0;1.0;0.939;1.0;0.996;0.939	D;D;D;P;D;P;P	0.97110	1.0;1.0;1.0;0.786;0.999;0.844;0.786	D	0.97715	1.0193	10	0.87932	D	0	-29.2939	16.7067	0.85374	0.0:0.0:1.0:0.0	.	1231;1231;1231;1231;1231;451;1231	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;P51532	.;.;.;.;.;.;SMCA4_HUMAN	T	1231;1231;1295;1231;1231;1231;1231;1231	ENSP00000395654:A1231T;ENSP00000350720:A1231T;ENSP00000343896:A1231T;ENSP00000445036:A1231T;ENSP00000392837:A1231T;ENSP00000397783:A1231T;ENSP00000414727:A1231T	ENSP00000343896:A1231T	A	+	1	0	SMARCA4	11005110	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.264000	0.95635	2.488000	0.83962	0.558000	0.71614	GCC		0.632	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2		NM_003072	
SMC1B	27127	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	22	45745648	45745648	+	Missense_Mutation	SNP	A	A	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr22:45745648A>C	ENST00000357450.4	-	23	3455	c.3456T>G	c.(3454-3456)gaT>gaG	p.D1152E	SMC1B_ENST00000404354.3_Intron	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	1152	Ala/Asp-rich (DA-box).				meiotic nuclear division (GO:0007126)|sister chromatid cohesion (GO:0007062)	chromosome, centromeric region (GO:0000775)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		CATCCACTTCATCTAAAACAA	0.338																																																	0													86.0	82.0	83.0					22																	45745648		1855	4097	5952	SO:0001583	missense	27127			AJ504806	CCDS43027.1, CCDS74876.1	22q13	2006-07-06	2006-07-06	2006-07-06	ENSG00000077935	ENSG00000077935		"""Structural maintenance of chromosomes proteins"""	11112	protein-coding gene	gene with protein product		608685	"""SMC1 (structural maintenance of chromosomes 1, yeast)-like 1"", ""SMC1 structural maintenance of chromosomes 1-like 2 (yeast)"""	SMC1L2		10591208, 11564881	Standard	XM_005261566		Approved	bK268H5	uc003bgc.3	Q8NDV3	OTTHUMG00000151334	ENST00000357450.4:c.3456T>G	22.37:g.45745648A>C	ENSP00000350036:p.Asp1152Glu	Somatic		WXS	Illumina HiSeq	Phase_I	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Missense_Mutation	SNP	ENST00000357450.4	37	CCDS43027.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.721163	0.89205	.	.	ENSG00000077935	ENST00000357450	T	0.50277	0.75	5.01	5.01	0.66863	.	0.000000	0.56097	D	0.000026	T	0.74550	0.3731	M	0.91038	3.17	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.81430	-0.0936	10	0.87932	D	0	.	14.3957	0.67010	1.0:0.0:0.0:0.0	.	1152	Q8NDV3-3	.	E	1152	ENSP00000350036:D1152E	ENSP00000350036:D1152E	D	-	3	2	SMC1B	44124312	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.118000	0.57884	1.876000	0.54355	0.377000	0.23210	GAT		0.338	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2		NM_148674	
CNOT11	55571	broad.mit.edu;hgsc.bcm.edu	37	2	101889409	101889409	+	IGR	SNP	A	A	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr2:101889409A>G	ENST00000289382.3	+	0	2599				RNF149_ENST00000485752.1_5'Flank|SNORD89_ENST00000390981.1_RNA	NM_017546.4	NP_060016.3	Q9UKZ1	CNO11_HUMAN	CCR4-NOT transcription complex, subunit 11						cell proliferation (GO:0008283)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytosol (GO:0005829)|nucleus (GO:0005634)											CTGAGGTCAGACTAGTGGTTC	0.443																																																	0													122.0	102.0	108.0					2																	101889409		876	1991	2867	SO:0001628	intergenic_variant	692205			AF103798	CCDS2050.1	2q12.1	2013-01-24	2013-01-24	2013-01-24	ENSG00000158435	ENSG00000158435			25217	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 29"""	C2orf29		10497265, 23232451, 23303381	Standard	NM_017546		Approved	C40	uc002taw.4	Q9UKZ1	OTTHUMG00000130686		2.37:g.101889409A>G		Somatic		WXS	Illumina HiSeq	Phase_I	Q6P2M9|Q8N681	RNA	SNP	ENST00000289382.3	37	CCDS2050.1																																																																																				0.443	CNOT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253181.1		NM_017546	
SPAG1	6674	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	101252794	101252795	+	Frame_Shift_Del	DEL	CT	CT	-	rs4734455	byFrequency	TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr8:101252794_101252795delCT	ENST00000388798.2	+	18	2635_2636	c.2444_2445delCT	c.(2443-2445)gctfs	p.A815fs	SPAG1_ENST00000251809.3_Frame_Shift_Del_p.A815fs	NM_003114.4	NP_003105.2	Q07617	SPAG1_HUMAN	sperm associated antigen 1	815					axonemal dynein complex assembly (GO:0070286)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	GTP binding (GO:0005525)|hydrolase activity (GO:0016787)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	all_cancers(14;2.35e-05)|all_epithelial(15;5.2e-08)|Lung NSC(17;0.000283)|all_lung(17;0.000823)	Breast(495;0.195)	Epithelial(11;1.12e-09)|all cancers(13;1.26e-07)|OV - Ovarian serous cystadenocarcinoma(57;4.37e-05)|STAD - Stomach adenocarcinoma(118;0.0525)	KIRC - Kidney renal clear cell carcinoma(542;0.00178)|READ - Rectum adenocarcinoma(644;0.236)		ATTATAAATGCTCTCAGTACCA	0.426																																																	0																																										SO:0001589	frameshift_variant	6674			AF311312	CCDS34930.1	8q22	2014-01-21			ENSG00000104450	ENSG00000104450		"""Tetratricopeptide (TTC) repeat domain containing"""	11212	protein-coding gene	gene with protein product		603395				16368546	Standard	NM_172218		Approved	SP75, FLJ32920, HSD-3.8, TPIS, CT140	uc003yjh.2	Q07617	OTTHUMG00000164706	ENST00000388798.2:c.2444_2445delCT	8.37:g.101252796_101252797delCT	ENSP00000373450:p.Ala815fs	Somatic		WXS	Illumina HiSeq	Phase_I	A6NP70|B3KQ58|G3XAM3|Q7Z5G1	Frame_Shift_Del	DEL	ENST00000388798.2	37	CCDS34930.1																																																																																				0.426	SPAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379853.2		NM_172218	
SPECC1	92521	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	20000054	20000054	+	Silent	SNP	C	C	T	rs199639674		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr17:20000054C>T	ENST00000261503.5	+	2	141	c.90C>T	c.(88-90)tcC>tcT	p.S30S	SPECC1_ENST00000395527.4_Silent_p.S30S|SPECC1_ENST00000472876.1_Intron|SPECC1_ENST00000395529.3_Silent_p.S30S	NM_001033553.2	NP_001028725.1	Q5M775	CYTSB_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1	30					cell adhesion (GO:0007155)	nucleus (GO:0005634)				breast(1)|large_intestine(3)|ovary(4)	8				KIRC - Kidney renal clear cell carcinoma(2;0.166)|Kidney(2;0.196)		CAGCCTCTTCCGGCATGAAGA	0.602																																																	0													72.0	78.0	76.0					17																	20000054		2203	4300	6503	SO:0001819	synonymous_variant	92521			AY816329, AB041533	CCDS32590.1, CCDS42280.1, CCDS42281.1, CCDS45628.1, CCDS58531.1	17p11.2	2012-11-19	2010-09-17	2010-09-17	ENSG00000128487	ENSG00000128487			30615	protein-coding gene	gene with protein product	"""sperm antigen HCMOGT 1"", ""cytokinesis and spindle organization B"", ""cytospin B"""	608793				15602574, 18763323, 15087372	Standard	NM_001033553		Approved	HCMOGT-1, FLJ36955, NSP, CYTSB	uc002gwq.3	Q5M775	OTTHUMG00000179808	ENST00000261503.5:c.90C>T	17.37:g.20000054C>T		Somatic		WXS	Illumina HiSeq	Phase_I	B4DHH0|B7WNS8|Q5IBP1|Q5IBP2|Q5IBP3|Q5IBP4|Q5M772|Q5M773|Q5M774|Q86XT8|Q8N4U4|Q8WU84|Q9HCQ3	Silent	SNP	ENST00000261503.5	37	CCDS32590.1																																																																																				0.602	SPECC1-018	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441206.1		NM_152904	
SYNRG	11276	hgsc.bcm.edu;ucsc.edu	37	17	35880695	35880695	+	Frame_Shift_Del	DEL	A	A	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr17:35880695delA	ENST00000339208.6	-	20	3863	c.3723delT	c.(3721-3723)aatfs	p.N1241fs	SYNRG_ENST00000345615.4_Frame_Shift_Del_p.N1163fs|SYNRG_ENST00000394378.2_Frame_Shift_Del_p.N1186fs|SYNRG_ENST00000346661.4_Frame_Shift_Del_p.N1241fs|SYNRG_ENST00000585472.1_Frame_Shift_Del_p.N1162fs|SYNRG_ENST00000502449.2_Frame_Shift_Del_p.N1118fs|SYNRG_ENST00000591288.1_Frame_Shift_Del_p.N1035fs	NM_001163544.1|NM_001163545.1|NM_007247.4	NP_001157016.1|NP_001157017.1|NP_009178.3	Q9UMZ2	SYNRG_HUMAN	synergin, gamma	1241					endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)	AP-1 adaptor complex (GO:0030121)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						GCTCCTGAGCATTTTTAATCC	0.512																																																	0													79.0	81.0	80.0					17																	35880695		2203	4300	6503	SO:0001589	frameshift_variant	11276			AF169548	CCDS11321.1, CCDS11322.1, CCDS11322.2, CCDS54113.1, CCDS54114.1, CCDS59284.1, CCDS59285.1	17q12	2014-04-16	2009-07-20	2009-07-20	ENSG00000006114	ENSG00000275066			557	protein-coding gene	gene with protein product	"""gamma-synergin"", ""adaptor-related protein complex 1 gamma subunit-binding protein 1"""	607291	"""AP1 gamma subunit binding protein 1"""	AP1GBP1		10477754	Standard	XM_005256980		Approved	SYNG, MGC104959	uc010wdf.2	Q9UMZ2	OTTHUMG00000188473	ENST00000339208.6:c.3723delT	17.37:g.35880695delA	ENSP00000343610:p.Asn1241fs	Somatic		WXS	Illumina HiSeq	Phase_I	A8MWU4|B7ZKZ2|B7ZKZ3|Q17RI2|Q5BKU5|Q6ZT17	Frame_Shift_Del	DEL	ENST00000339208.6	37	CCDS11321.1																																																																																				0.512	SYNRG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256811.2		NM_007247	
TARS2	80222	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	150459930	150459930	+	Missense_Mutation	SNP	G	G	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr1:150459930G>A	ENST00000369064.3	+	1	38	c.4G>A	c.(4-6)Gcc>Acc	p.A2T	TARS2_ENST00000606933.1_Missense_Mutation_p.A2T|TARS2_ENST00000438568.2_Missense_Mutation_p.A2T|TARS2_ENST00000369054.2_Missense_Mutation_p.A2T	NM_025150.3	NP_079426.2	Q9BW92	SYTM_HUMAN	threonyl-tRNA synthetase 2, mitochondrial (putative)	2					gene expression (GO:0010467)|mitochondrial threonyl-tRNA aminoacylation (GO:0070159)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|threonine-tRNA ligase activity (GO:0004829)			cervix(1)|endometrium(4)|large_intestine(7)|lung(19)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	35	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.51e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)		L-Threonine(DB00156)	AAGGAACATGGCCCTGTATCA	0.547																																																	0													137.0	112.0	121.0					1																	150459930		2203	4300	6503	SO:0001583	missense	80222			BC007824	CCDS952.1, CCDS60251.1, CCDS60252.1	1q21.2	2012-10-26	2007-02-23	2007-02-23	ENSG00000143374	ENSG00000143374	6.1.1.3	"""Aminoacyl tRNA synthetases / Class II"""	30740	protein-coding gene	gene with protein product	"""threonine tRNA ligase 2, mitochondrial"""	612805	"""threonyl-tRNA synthetase-like 1"""	TARSL1			Standard	NM_001271895		Approved	FLJ12528	uc001euq.4	Q9BW92	OTTHUMG00000012809	ENST00000369064.3:c.4G>A	1.37:g.150459930G>A	ENSP00000358060:p.Ala2Thr	Somatic		WXS	Illumina HiSeq	Phase_I	Q53GW7|Q96I50|Q9H9V2	Missense_Mutation	SNP	ENST00000369064.3	37	CCDS952.1	.	.	.	.	.	.	.	.	.	.	G	15.28	2.786221	0.49997	.	.	ENSG00000143374	ENST00000438568;ENST00000369054;ENST00000369064;ENST00000369053	.	.	.	4.94	1.75	0.24633	.	0.549079	0.18346	N	0.144012	T	0.06142	0.0159	N	0.08118	0	0.09310	N	0.999999	B;B	0.17038	0.008;0.02	B;B	0.16722	0.007;0.016	T	0.24693	-1.0153	9	0.87932	D	0	-1.6598	3.9355	0.09304	0.223:0.2009:0.5761:0.0	.	2;2	Q9H9V2;Q9BW92	.;SYTM_HUMAN	T	2	.	ENSP00000358049:A2T	A	+	1	0	TARS2	148726554	0.575000	0.26692	0.907000	0.35723	0.002000	0.02628	0.441000	0.21611	0.655000	0.30866	-0.258000	0.10820	GCC		0.547	TARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035847.1		NM_025150	
TBL1XR1	79718	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	176769354	176769354	+	Missense_Mutation	SNP	C	C	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr3:176769354C>T	ENST00000430069.1	-	5	624	c.365G>A	c.(364-366)gGa>gAa	p.G122E	TBL1XR1_ENST00000457928.2_Missense_Mutation_p.G122E			Q9BZK7	TBL1R_HUMAN	transducin (beta)-like 1 X-linked receptor 1	122					canonical Wnt signaling pathway (GO:0060070)|cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|histone binding (GO:0042393)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(7)|liver(1)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	31	all_cancers(143;1.44e-17)|Ovarian(172;0.00163)|Breast(254;0.214)	Acute lymphoblastic leukemia(1;0.00599)|all_hematologic(1;0.0632)|Prostate(884;0.215)	OV - Ovarian serous cystadenocarcinoma(80;9.83e-31)			TTTTGCAGATCCTTGTTGGCT	0.443																																																	0													82.0	78.0	79.0					3																	176769354		1852	4097	5949	SO:0001583	missense	79718			AK022956	CCDS46961.1	3q26.33	2013-01-10	2008-01-17		ENSG00000177565	ENSG00000177565		"""WD repeat domain containing"""	29529	protein-coding gene	gene with protein product		608628	"""transducin (beta)-like 1X-linked receptor 1"""			11063877, 11931768	Standard	NM_024665		Approved	IRA1, FLJ12894, TBLR1, C21, DC42	uc003fix.4	Q9BZK7	OTTHUMG00000157140	ENST00000430069.1:c.365G>A	3.37:g.176769354C>T	ENSP00000405574:p.Gly122Glu	Somatic		WXS	Illumina HiSeq	Phase_I	D3DNQ9|Q14DC3|Q9H2I1|Q9H9A1	Missense_Mutation	SNP	ENST00000430069.1	37	CCDS46961.1	.	.	.	.	.	.	.	.	.	.	C	4.351	0.064579	0.08388	.	.	ENSG00000177565	ENST00000430069;ENST00000457928;ENST00000536758;ENST00000428970;ENST00000424913;ENST00000352800;ENST00000437738;ENST00000431421	T;T	0.49720	0.77;0.77	5.52	5.52	0.82312	.	0.054083	0.64402	D	0.000001	T	0.33235	0.0856	L	0.34521	1.04	0.45852	D	0.998717	B	0.21309	0.054	B	0.18263	0.021	T	0.13150	-1.0520	10	0.02654	T	1	-6.4114	14.0919	0.64995	0.0:0.8497:0.1503:0.0	.	122	Q9BZK7	TBL1R_HUMAN	E	122;122;35;35;35;122;122;35	ENSP00000405574:G122E;ENSP00000413251:G122E	ENSP00000263964:G122E	G	-	2	0	TBL1XR1	178252048	0.598000	0.26882	0.985000	0.45067	0.780000	0.44128	2.962000	0.49176	2.609000	0.88269	0.557000	0.71058	GGA		0.443	TBL1XR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347587.3		NM_024665	
THRA	7067	hgsc.bcm.edu	37	17	38245611	38245612	+	Intron	INS	-	-	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr17:38245611_38245612insC	ENST00000264637.4	+	9	1690				THRA_ENST00000584985.1_Intron|THRA_ENST00000394121.4_Intron|THRA_ENST00000450525.2_Frame_Shift_Ins_p.A379fs|THRA_ENST00000546243.1_Frame_Shift_Ins_p.A379fs	NM_003250.5	NP_003241.2	P10827	THA_HUMAN	thyroid hormone receptor, alpha						cartilage condensation (GO:0001502)|cytoplasmic sequestering of transcription factor (GO:0042994)|erythrocyte differentiation (GO:0030218)|female courtship behavior (GO:0008050)|gene expression (GO:0010467)|hormone-mediated signaling pathway (GO:0009755)|learning or memory (GO:0007611)|negative regulation of DNA-templated transcription, initiation (GO:2000143)|negative regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0017055)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of female receptivity (GO:0045925)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of heart contraction (GO:0008016)|regulation of lipid catabolic process (GO:0050994)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of thyroid hormone mediated signaling pathway (GO:0002155)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cold (GO:0009409)|thyroid gland development (GO:0030878)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Type I pneumocyte differentiation (GO:0060509)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|steroid receptor RNA activator RNA binding (GO:0002153)|TBP-class protein binding (GO:0017025)|thyroid hormone binding (GO:0070324)|thyroid hormone receptor activity (GO:0004887)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(3)|large_intestine(2)|lung(4)|prostate(1)	11	Colorectal(19;0.000442)	Myeloproliferative disorder(1115;0.0255)			Dextrothyroxine(DB00509)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	CATGATCGGGGCCTGCCACGCC	0.584																																																	0																																										SO:0001627	intron_variant	7067			J03239	CCDS11360.1, CCDS42316.1, CCDS58546.1	17q21.1	2013-01-16	2011-05-19		ENSG00000126351	ENSG00000126351		"""Nuclear hormone receptors"""	11796	protein-coding gene	gene with protein product		190120	"""thyroid hormone receptor, alpha (avian erythroblastic leukemia viral (v-erb-a) oncogene homolog)"", ""thyroid hormone receptor, alpha (erythroblastic leukemia viral (v-erb-a) oncogene homolog, avian)"""	THRA1, THRA2, ERBA1		6323162, 6589608	Standard	NM_003250		Approved	EAR-7.1/EAR-7.2, THRA3, AR7, ERBA, NR1A1	uc002htw.3	P10827	OTTHUMG00000133332	ENST00000264637.4:c.1110+25->C	17.37:g.38245613_38245613dupC		Somatic		WXS	Illumina HiSeq	Phase_I	A8K3B5|P21205|Q8N6A1|Q96H73	Frame_Shift_Ins	INS	ENST00000264637.4	37	CCDS11360.1																																																																																				0.584	THRA-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257160.2			
TMEM180	79847	broad.mit.edu;ucsc.edu	37	10	104231152	104231152	+	Splice_Site	SNP	A	A	G			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr10:104231152A>G	ENST00000238936.4	+	6	1064	c.827A>G	c.(826-828)cAg>cGg	p.Q276R	TMEM180_ENST00000369931.3_Splice_Site_p.Q125R|TMEM180_ENST00000366277.2_Splice_Site_p.Q5R	NM_024789.3	NP_079065.2	Q14CX5	TM180_HUMAN	transmembrane protein 180	276						integral component of membrane (GO:0016021)				breast(3)|endometrium(2)|large_intestine(3)|lung(1)|ovary(3)|skin(1)	13		Colorectal(252;0.122)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		GACCTGGTGCAGGTATGGGGA	0.627																																																	0													74.0	69.0	70.0					10																	104231152		2203	4300	6503	SO:0001630	splice_region_variant	79847			AK026182	CCDS7535.1	10q24.32	2011-02-09	2006-10-12	2006-10-12	ENSG00000138111	ENSG00000138111			26196	protein-coding gene	gene with protein product				C10orf77		12477932	Standard	XM_006717971		Approved	FLJ22529, bA18I14.8	uc001kvt.3	Q14CX5	OTTHUMG00000018961	ENST00000238936.4:c.828+1A>G	10.37:g.104231152A>G		Somatic		WXS	Illumina GAIIx	Phase_I	Q6NWM8|Q6NWM9|Q6PEZ7|Q9H679	Missense_Mutation	SNP	ENST00000238936.4	37	CCDS7535.1	.	.	.	.	.	.	.	.	.	.	A	31	5.100994	0.94245	.	.	ENSG00000138111	ENST00000366277;ENST00000447593;ENST00000238936;ENST00000369931;ENST00000369930	T	0.81415	-1.49	5.52	5.52	0.82312	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	D	0.90038	0.6889	M	0.86651	2.83	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.996	D;D;D	0.87578	0.998;0.997;0.986	D	0.89102	0.3490	10	0.25106	T	0.35	.	14.8081	0.69974	1.0:0.0:0.0:0.0	.	125;276;125	B4DWN6;Q14CX5;Q6UWF4	.;TM180_HUMAN;.	R	5;125;276;125;5	ENSP00000238936:Q276R	ENSP00000238936:Q276R	Q	+	2	0	TMEM180	104221142	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	8.553000	0.90686	2.096000	0.63516	0.459000	0.35465	CAG		0.627	TMEM180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050075.2		NM_024789	Missense_Mutation
TMEM182	130827	broad.mit.edu;hgsc.bcm.edu	37	2	103380788	103380788	+	Splice_Site	SNP	C	C	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr2:103380788C>T	ENST00000412401.2	+	3	438	c.233C>T	c.(232-234)aCc>aTc	p.T78I	TMEM182_ENST00000409528.1_5'UTR|TMEM182_ENST00000409173.1_Splice_Site_p.T35I|TMEM182_ENST00000486293.1_3'UTR	NM_144632.3	NP_653233.3	Q6ZP80	TM182_HUMAN	transmembrane protein 182	78						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)	11						TTCTTCCTAGCCAATCAGCCA	0.468																																																	0													154.0	116.0	129.0					2																	103380788		2203	4300	6503	SO:0001630	splice_region_variant	130827			AK054856	CCDS2064.1	2q12.1	2009-08-25			ENSG00000170417	ENSG00000170417			26391	protein-coding gene	gene with protein product						12477932	Standard	NM_144632		Approved	FLJ30294	uc010fjb.3	Q6ZP80	OTTHUMG00000130779	ENST00000412401.2:c.233-1C>T	2.37:g.103380788C>T		Somatic		WXS	Illumina HiSeq	Phase_I	C9JML7|Q3B7B8|Q53TT9|Q6GMU0|Q8WW45|Q96NR4	Missense_Mutation	SNP	ENST00000412401.2	37	CCDS2064.1	.	.	.	.	.	.	.	.	.	.	C	17.79	3.476443	0.63737	.	.	ENSG00000170417	ENST00000454536;ENST00000409173;ENST00000412401	T;T	0.50277	0.77;0.75	5.83	3.84	0.44239	.	0.249014	0.47093	N	0.000260	T	0.44871	0.1314	M	0.65498	2.005	0.48236	D	0.999618	B;B	0.18741	0.012;0.03	B;B	0.19946	0.027;0.027	T	0.28427	-1.0044	9	.	.	.	.	11.3465	0.49563	0.0:0.8034:0.1239:0.0727	.	78;35	Q6ZP80;B8ZZ71	TM182_HUMAN;.	I	35;35;78	ENSP00000387184:T35I;ENSP00000394178:T78I	.	T	+	2	0	TMEM182	102747220	1.000000	0.71417	0.999000	0.59377	0.804000	0.45430	2.204000	0.42761	0.660000	0.30964	0.655000	0.94253	ACC		0.468	TMEM182-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253293.1		NM_144632	Missense_Mutation
TRDMT1	1787	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	17195548	17195548	+	Missense_Mutation	SNP	G	G	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr10:17195548G>C	ENST00000377799.3	-	10	1080	c.1033C>G	c.(1033-1035)Cct>Gct	p.P345A	TRDMT1_ENST00000452380.2_5'UTR|TRDMT1_ENST00000412821.3_Missense_Mutation_p.P321A|TRDMT1_ENST00000457442.2_Missense_Mutation_p.P264A|TRDMT1_ENST00000351358.4_Missense_Mutation_p.P299A|TRDMT1_ENST00000377766.5_3'UTR|TRDMT1_ENST00000358282.7_3'UTR|TRDMT1_ENST00000488990.1_Missense_Mutation_p.P222A	NM_004412.5	NP_004403.1	O14717	TRDMT_HUMAN	tRNA aspartic acid methyltransferase 1	345	SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				C-5 methylation of cytosine (GO:0090116)|response to amphetamine (GO:0001975)|tRNA methylation (GO:0030488)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|RNA binding (GO:0003723)|tRNA methyltransferase activity (GO:0008175)			breast(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(4)|ovary(1)|prostate(1)	18					Pentamidine(DB00738)	ATTTCTTTAGGAGTGAAATAT	0.338																																																	0													152.0	143.0	146.0					10																	17195548		2203	4300	6503	SO:0001583	missense	1787			AJ223333	CCDS7114.1	10p15.1	2006-10-23	2006-10-23	2006-10-23	ENSG00000107614	ENSG00000107614	2.1.1.37		2977	protein-coding gene	gene with protein product		602478	"""DNA (cytosine-5-)-methyltransferase 2"""	DNMT2		9425235, 9763678, 16424344	Standard	NM_004412		Approved	RNMT1	uc001iop.3	O14717	OTTHUMG00000017745	ENST00000377799.3:c.1033C>G	10.37:g.17195548G>C	ENSP00000367030:p.Pro345Ala	Somatic		WXS	Illumina HiSeq	Phase_I	B0YJ02|B0YJ03|B0YJ07|B0YJ08|O43669|Q86WW6	Missense_Mutation	SNP	ENST00000377799.3	37	CCDS7114.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.294610	0.81025	.	.	ENSG00000107614	ENST00000377799;ENST00000412821;ENST00000351358;ENST00000457442;ENST00000488990	T;T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3;-0.3	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	D	0.82935	0.5145	M	0.79123	2.44	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;0.999;0.999;0.991;0.996;0.997	D;D;D;P;P;P	0.87578	0.998;0.935;0.974;0.833;0.893;0.894	T	0.81716	-0.0806	10	0.44086	T	0.13	-20.3298	20.0205	0.97499	0.0:0.0:1.0:0.0	.	222;274;264;299;321;345	B7Z8H2;B7Z1Y7;E7EMI8;O14717-3;O14717-2;O14717	.;.;.;.;.;TRDMT_HUMAN	A	345;321;299;264;222	ENSP00000367030:P345A;ENSP00000409354:P321A;ENSP00000324328:P299A;ENSP00000412256:P264A;ENSP00000419625:P222A	ENSP00000324328:P299A	P	-	1	0	TRDMT1	17235554	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.444000	0.90323	2.801000	0.96364	0.650000	0.86243	CCT		0.338	TRDMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047024.3		NM_004412	
TUBB3	10381	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	90001521	90001521	+	Missense_Mutation	SNP	C	C	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr16:90001521C>T	ENST00000315491.7	+	4	785	c.662C>T	c.(661-663)aCc>aTc	p.T221I	TUBB3_ENST00000555576.1_Intron|TUBB3_ENST00000554444.1_Missense_Mutation_p.T149I|TUBB3_ENST00000304984.5_Missense_Mutation_p.T149I|TUBB3_ENST00000556922.1_Missense_Mutation_p.T568I	NM_006086.3	NP_006077.2	Q13509	TBB3_HUMAN	tubulin, beta 3 class III	221					'de novo' posttranslational protein folding (GO:0051084)|axon guidance (GO:0007411)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(3)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	17		all_cancers(9;1.69e-11)|Lung NSC(15;8.94e-06)|all_lung(18;1.39e-05)|all_neural(9;0.00581)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0273)	Ixabepilone(DB04845)	GCCACGCCCACCTACGGGGAC	0.632																																																	0													128.0	100.0	110.0					16																	90001521		2198	4300	6498	SO:0001583	missense	10381			BC000748	CCDS10988.1, CCDS56012.1	16q24.3	2014-02-04	2011-10-10		ENSG00000198211	ENSG00000198211		"""Tubulins"""	20772	protein-coding gene	gene with protein product	"""class III beta-tubulin"""	602661	"""tubulin, beta 3"", ""fibrosis of extraocular muscles, congenital, 3"""	FEOM3		9473684, 8098743, 20074521	Standard	NM_006086		Approved	beta-4, CFEOM3, CFEOM3A	uc002fph.2	Q13509	OTTHUMG00000138985	ENST00000315491.7:c.662C>T	16.37:g.90001521C>T	ENSP00000320295:p.Thr221Ile	Somatic		WXS	Illumina HiSeq	Phase_I	A8K854|Q9BTZ0|Q9BW10	Missense_Mutation	SNP	ENST00000315491.7	37	CCDS10988.1	.	.	.	.	.	.	.	.	.	.	C	17.03	3.285340	0.59867	.	.	ENSG00000258947;ENSG00000258947;ENSG00000258947;ENSG00000198211;ENSG00000198211;ENSG00000198211	ENST00000556922;ENST00000555399;ENST00000304984;ENST00000555810;ENST00000554444;ENST00000315491	T;T;T;T;T	0.71934	-0.61;-0.61;-0.61;-0.61;-0.61	4.67	4.67	0.58626	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.64402	D	0.000015	D	0.88991	0.6588	H	0.96239	3.79	0.53688	D	0.999974	D;D	0.69078	0.997;0.997	D;D	0.70016	0.94;0.967	D	0.92831	0.6280	9	.	.	.	.	17.5189	0.87782	0.0:1.0:0.0:0.0	.	221;221	Q13509;B2RBD5	TBB3_HUMAN;.	I	568;221;149;149;149;221	ENSP00000451560:T568I;ENSP00000302777:T149I;ENSP00000450538:T149I;ENSP00000451617:T149I;ENSP00000320295:T221I	.	T	+	2	0	RP11-566K11.2;TUBB3	88529022	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.639000	0.83342	2.316000	0.78162	0.407000	0.27541	ACC		0.632	TUBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272874.1		NM_006086	
UBE4B	10277	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	10238756	10238758	+	In_Frame_Del	DEL	GGG	GGG	-			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	GGG	GGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr1:10238756_10238758delGGG	ENST00000253251.8	+	25	4032_4034	c.3193_3195delGGG	c.(3193-3195)gggdel	p.G1065del	UBE4B_ENST00000377157.3_In_Frame_Del_p.G949del|UBE4B_ENST00000343090.6_In_Frame_Del_p.G1194del					ubiquitination factor E4B									p.G1065G(1)		NS(3)|breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(14)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	48		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)		GCGGAAGGCAGGGATCAAATCCA	0.453																																																	1	Substitution - coding silent(1)	ovary(1)																																								SO:0001651	inframe_deletion	10277			AF091093	CCDS110.1, CCDS41245.1	1p36.1	2013-01-28	2011-05-19		ENSG00000130939	ENSG00000130939		"""U-box domain containing"""	12500	protein-coding gene	gene with protein product		613565	"""ubiquitination factor E4B (homologous to yeast UFD2)"", ""ubiquitination factor E4B (UFD2 homolog, yeast)"""			9734811, 10089879	Standard	NM_006048		Approved	UBOX3, E4, UFD2, KIAA0684	uc001aqs.4	O95155	OTTHUMG00000001797	ENST00000253251.8:c.3193_3195delGGG	1.37:g.10238756_10238758delGGG	ENSP00000253251:p.Gly1065del	Somatic		WXS	Illumina HiSeq	Phase_I		In_Frame_Del	DEL	ENST00000253251.8	37	CCDS110.1																																																																																				0.453	UBE4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005017.1		NM_006048	
UNC13B	10497	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	35385805	35385805	+	Missense_Mutation	SNP	A	A	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr9:35385805A>T	ENST00000378495.3	+	22	2935	c.2713A>T	c.(2713-2715)Atg>Ttg	p.M905L	UNC13B_ENST00000396787.1_Missense_Mutation_p.M917L|UNC13B_ENST00000378496.4_Missense_Mutation_p.M905L	NM_006377.3	NP_006368.3	O14795	UN13B_HUMAN	unc-13 homolog B (C. elegans)	905					apoptotic process (GO:0006915)|excretion (GO:0007588)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synaptic vesicle priming (GO:0010808)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|terminal bouton (GO:0043195)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(16)|liver(2)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			TTTCTTCAGAATGAAGGTAAG	0.483																																																	0													71.0	73.0	73.0					9																	35385805		2203	4300	6503	SO:0001583	missense	10497			AF020202	CCDS6579.1	9p13.3	2008-05-15	2003-10-17	2003-10-17	ENSG00000198722	ENSG00000198722			12566	protein-coding gene	gene with protein product		605836	"""unc-13-like (C. elegans)"""	UNC13		9607201	Standard	NM_006377		Approved	hmunc13, Unc13h2	uc003zwq.3	O14795	OTTHUMG00000019856	ENST00000378495.3:c.2713A>T	9.37:g.35385805A>T	ENSP00000367756:p.Met905Leu	Somatic		WXS	Illumina HiSeq	Phase_I	Q5VYM8	Missense_Mutation	SNP	ENST00000378495.3	37	CCDS6579.1	.	.	.	.	.	.	.	.	.	.	A	27.1	4.797184	0.90538	.	.	ENSG00000198722	ENST00000396787;ENST00000378495;ENST00000378496;ENST00000535471	D;D;D	0.84442	-1.72;-1.65;-1.85	5.21	5.21	0.72293	.	0.037971	0.85682	D	0.000000	T	0.81711	0.4880	L	0.47078	1.49	0.80722	D	1	B;B	0.17852	0.024;0.004	B;B	0.14578	0.011;0.005	T	0.78497	-0.2181	10	0.52906	T	0.07	-24.2713	15.3729	0.74581	1.0:0.0:0.0:0.0	.	905;905	F8W8M9;O14795	.;UN13B_HUMAN	L	917;905;905;492	ENSP00000380006:M917L;ENSP00000367756:M905L;ENSP00000367757:M905L	ENSP00000367756:M905L	M	+	1	0	UNC13B	35375805	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.875000	0.69660	2.088000	0.63022	0.533000	0.62120	ATG		0.483	UNC13B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052296.1		NM_006377	
USP15	9958	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	62749239	62749239	+	Missense_Mutation	SNP	A	A	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr12:62749239A>C	ENST00000280377.5	+	8	956	c.898A>C	c.(898-900)Atg>Ctg	p.M300L	USP15_ENST00000353364.3_Missense_Mutation_p.M271L|USP15_ENST00000393654.3_Missense_Mutation_p.M275L	NM_001252078.1	NP_001239007.1	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15	300	USP.				BMP signaling pathway (GO:0030509)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|protein deubiquitination (GO:0016579)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|identical protein binding (GO:0042802)|SMAD binding (GO:0046332)|transforming growth factor beta receptor binding (GO:0005160)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(15)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	37			GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)		TACGTGTTTCATGAACTCAGC	0.373																																					Melanoma(181;615 2041 39364 49691 50001)												0													101.0	94.0	97.0					12																	62749239		2203	4300	6503	SO:0001583	missense	9958			AB011101	CCDS8963.1, CCDS58250.1, CCDS58251.1	12q14	2006-07-18	2005-08-08					"""Ubiquitin-specific peptidases"""	12613	protein-coding gene	gene with protein product		604731	"""ubiquitin specific protease 15"""			12838346	Standard	NM_001252078		Approved	KIAA0529, UNPH4	uc001src.2	Q9Y4E8	OTTHUMG00000170186	ENST00000280377.5:c.898A>C	12.37:g.62749239A>C	ENSP00000280377:p.Met300Leu	Somatic		WXS	Illumina HiSeq	Phase_I	Q08AL5|Q9H8G9|Q9HCA6|Q9UNP0|Q9Y5B5	Missense_Mutation	SNP	ENST00000280377.5	37	CCDS58251.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.701957	0.88924	.	.	ENSG00000135655	ENST00000353364;ENST00000280377;ENST00000393654	T;T;T	0.34072	1.38;1.38;1.38	5.6	5.6	0.85130	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site (1);Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.171029	0.64402	D	0.000007	T	0.54431	0.1858	L	0.52573	1.65	0.58432	D	0.999999	D;D	0.76494	0.999;0.999	D;D	0.91635	0.999;0.998	T	0.51044	-0.8755	9	.	.	.	-11.536	15.7844	0.78291	1.0:0.0:0.0:0.0	.	300;271	Q9Y4E8;Q9Y4E8-2	UBP15_HUMAN;.	L	271;300;275	ENSP00000258123:M271L;ENSP00000280377:M300L;ENSP00000377264:M275L	.	M	+	1	0	USP15	61035506	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	8.434000	0.90294	2.141000	0.66446	0.455000	0.32223	ATG		0.373	USP15-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407831.2		NM_006313	
YARS	8565	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	33245096	33245096	+	Missense_Mutation	SNP	G	G	C			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr1:33245096G>C	ENST00000373477.4	-	12	2271	c.1363C>G	c.(1363-1365)Ctg>Gtg	p.L455V	YARS_ENST00000469100.1_5'UTR	NM_003680.3	NP_003671.1	P54577	SYYC_HUMAN	tyrosyl-tRNA synthetase	455	tRNA-binding. {ECO:0000255|PROSITE- ProRule:PRU00209}.				apoptotic process (GO:0006915)|gene expression (GO:0010467)|signal transduction (GO:0007165)|tRNA aminoacylation for protein translation (GO:0006418)|tyrosyl-tRNA aminoacylation (GO:0006437)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	ATP binding (GO:0005524)|interleukin-8 receptor binding (GO:0005153)|poly(A) RNA binding (GO:0044822)|signal transducer activity (GO:0004871)|tRNA binding (GO:0000049)|tyrosine-tRNA ligase activity (GO:0004831)			endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|skin(2)|urinary_tract(1)	15		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)			L-Tyrosine(DB00135)	GGAGGGTCCAGAGGTTCAACC	0.537																																																	0													73.0	72.0	72.0					1																	33245096		2203	4300	6503	SO:0001583	missense	8565			U89436	CCDS368.1	1p35.1	2014-09-17			ENSG00000134684	ENSG00000134684	6.1.1.1	"""Aminoacyl tRNA synthetases / Class I"""	12840	protein-coding gene	gene with protein product	"""tyrosine tRNA ligase 1, cytoplasmic"""	603623				8552597, 9162081	Standard	NM_003680		Approved	YTS, YRS, tyrRS	uc001bvy.1	P54577	OTTHUMG00000003933	ENST00000373477.4:c.1363C>G	1.37:g.33245096G>C	ENSP00000362576:p.Leu455Val	Somatic		WXS	Illumina HiSeq	Phase_I	B3KWK4|D3DPQ4|O43276|Q53EN1	Missense_Mutation	SNP	ENST00000373477.4	37	CCDS368.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.012307	0.75046	.	.	ENSG00000134684	ENST00000373477	T	0.73047	-0.71	5.65	4.73	0.59995	Nucleic acid-binding, OB-fold-like (1);tRNA-binding domain (2);Nucleic acid-binding, OB-fold (1);	0.000000	0.85682	D	0.000000	T	0.79088	0.4387	M	0.64997	1.995	0.80722	D	1	D	0.54964	0.969	P	0.58266	0.836	T	0.79070	-0.1954	10	0.49607	T	0.09	-10.0276	15.6492	0.77078	0.0691:0.0:0.9309:0.0	.	455	P54577	SYYC_HUMAN	V	455	ENSP00000362576:L455V	ENSP00000362576:L455V	L	-	1	2	YARS	33017683	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.418000	0.66429	2.835000	0.97688	0.650000	0.86243	CTG		0.537	YARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011225.1		NM_003680	
ZNF175	7728	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	52084648	52084648	+	Missense_Mutation	SNP	C	C	T			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr19:52084648C>T	ENST00000262259.2	+	3	435	c.77C>T	c.(76-78)tCa>tTa	p.S26L	ZNF175_ENST00000436511.2_Missense_Mutation_p.S26L|ZNF175_ENST00000596504.1_Missense_Mutation_p.S26L	NM_007147.2	NP_009078.1	Q9Y473	ZN175_HUMAN	zinc finger protein 175	26					defense response to virus (GO:0051607)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24		all_neural(266;0.0299)		GBM - Glioblastoma multiforme(134;0.000426)|OV - Ovarian serous cystadenocarcinoma(262;0.0257)		TTACAGGCATCAGTGTCATTT	0.522																																																	0													128.0	100.0	110.0					19																	52084648		2203	4300	6503	SO:0001583	missense	7728			D50419	CCDS12837.1	19q13.4	2013-01-08			ENSG00000105497	ENSG00000105497		"""Zinc fingers, C2H2-type"", ""-"""	12964	protein-coding gene	gene with protein product		601139				8838321	Standard	NM_007147		Approved	OTK18	uc002pxb.3	Q9Y473	OTTHUMG00000167771	ENST00000262259.2:c.77C>T	19.37:g.52084648C>T	ENSP00000262259:p.Ser26Leu	Somatic		WXS	Illumina HiSeq	Phase_I	A8K9H2	Missense_Mutation	SNP	ENST00000262259.2	37	CCDS12837.1	.	.	.	.	.	.	.	.	.	.	C	8.779	0.927691	0.18056	.	.	ENSG00000105497	ENST00000262259;ENST00000436511	T;T	0.00737	5.76;5.76	2.47	0.325	0.15903	Krueppel-associated box (1);	.	.	.	.	T	0.00468	0.0015	N	0.03917	-0.325	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.44128	-0.9348	9	0.34782	T	0.22	.	6.3552	0.21397	0.0:0.7272:0.0:0.2728	.	26	Q9Y473	ZN175_HUMAN	L	26	ENSP00000262259:S26L;ENSP00000440578:S26L	ENSP00000262259:S26L	S	+	2	0	ZNF175	56776460	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.069000	0.03444	0.152000	0.19188	0.655000	0.94253	TCA		0.522	ZNF175-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396205.1		NM_007147	
DIO2	1734	broad.mit.edu	37	14	80669073	80669073	+	Missense_Mutation	SNP	T	T	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr14:80669073T>A	ENST00000557010.1	-	4	1166	c.781A>T	c.(781-783)Aat>Tat	p.N261Y	DIO2_ENST00000557125.1_3'UTR|DIO2_ENST00000555750.1_Missense_Mutation_p.N297Y|DIO2_ENST00000438257.4_Missense_Mutation_p.N261Y|DIO2_ENST00000422005.3_3'UTR	NM_000793.5|NM_001242502.1|NM_001242503.1	NP_000784.2|NP_001229431.1|NP_001229432.1	Q92813	IOD2_HUMAN	deiodinase, iodothyronine, type II	261					cellular nitrogen compound metabolic process (GO:0034641)|hormone biosynthetic process (GO:0042446)|selenocysteine incorporation (GO:0001514)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)|thyroid hormone metabolic process (GO:0042403)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	selenium binding (GO:0008430)|thyroxine 5'-deiodinase activity (GO:0004800)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(14)|skin(1)|stomach(1)	25				BRCA - Breast invasive adenocarcinoma(234;0.0281)		TTGCTGAAATTCTTCTCCAGC	0.383																																																	0													58.0	55.0	56.0					14																	80669073		1840	4094	5934	SO:0001583	missense	1734			AF007144	CCDS45146.1, CCDS55934.1	14q24.2-q24.3	2014-05-02			ENSG00000211448	ENSG00000211448	1.97.1.10		2884	protein-coding gene	gene with protein product	"""thyroxine deiodinase, type II"", ""deiodonase-2"", ""deiodinase-2"""	601413				8755651, 10343107	Standard	NM_001007023		Approved	TXDI2, SelY	uc021rxb.1	Q92813	OTTHUMG00000171443	ENST00000557010.1:c.781A>T	14.37:g.80669073T>A	ENSP00000451419:p.Asn261Tyr	Somatic		WXS	Illumina GAIIx	Phase_I	B9EGK0|G3V315|Q6B0A3|Q9HCP8|Q9P1W4|Q9UDZ1	Missense_Mutation	SNP	ENST00000557010.1	37	CCDS45146.1	.	.	.	.	.	.	.	.	.	.	T	8.534	0.871712	0.17322	.	.	ENSG00000211448	ENST00000438257;ENST00000557010;ENST00000555750	T;T;T	0.27720	1.65;1.65;1.65	5.47	5.47	0.80525	.	0.439325	0.21086	N	0.080406	T	0.34366	0.0895	N	0.22421	0.69	0.80722	D	1	D;D;D	0.71674	0.986;0.989;0.998	P;P;D	0.63381	0.814;0.883;0.914	T	0.03922	-1.0992	10	0.02654	T	1	.	15.837	0.78805	0.0:0.0:0.0:1.0	.	297;261;297	Q92813-2;Q92813;G3V315	.;IOD2_HUMAN;.	Y	261;261;297	ENSP00000405854:N261Y;ENSP00000451419:N261Y;ENSP00000450980:N297Y	ENSP00000405854:N261Y	N	-	1	0	DIO2	79738826	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.569000	0.67391	2.199000	0.70637	0.528000	0.53228	AAT		0.383	DIO2-001	KNOWN	basic|appris_principal|CCDS|seleno	protein_coding	protein_coding	OTTHUMT00000413428.2			
OR7E37P	100506759	broad.mit.edu	37	13	42005884	42005885	+	IGR	INS	-	-	A			TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr13:42005884_42005885insA								NAA16 (54718 upstream) : AL354833.1 (13541 downstream)																							ACTGAGGACAGAAAAAAAAAAG	0.436																																																	0																																										SO:0001628	intergenic_variant	100506759																															13.37:g.42005894_42005894dupA		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	INS		37																																																																																				0	0.436									
PBX2	5089	broad.mit.edu	37	6	32155509	32155509	+	Missense_Mutation	SNP	T	T	A	rs202223627		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr6:32155509T>A	ENST00000375050.4	-	5	1055	c.785A>T	c.(784-786)tAt>tTt	p.Y262F	XXbac-BPG300A18.13_ENST00000559458.1_RNA	NM_002586.4	NP_002577.2	P40425	PBX2_HUMAN	pre-B-cell leukemia homeobox 2	262					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.Y262F(3)		endometrium(1)|kidney(1)|lung(9)|ovary(1)|prostate(2)	14						GGAGTAGAAATACTCATTTAG	0.517																																																	3	Substitution - Missense(3)	lung(3)																																								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.785A>T	6.37:g.32155509T>A	ENSP00000364190:p.Tyr262Phe	Somatic		WXS	Illumina GAIIx	Phase_I	A2BFJ2	Missense_Mutation	SNP	ENST00000375050.4	37	CCDS4748.1	.	.	.	.	.	.	.	.	.	.	T	19.51	3.841111	0.71488	.	.	ENSG00000204304	ENST00000375050	D	0.83673	-1.75	4.63	4.63	0.57726	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.201957	0.34435	N	0.003969	T	0.61837	0.2379	N	0.10629	0.01	0.80722	D	1	P;P	0.42337	0.776;0.502	P;P	0.45232	0.474;0.458	T	0.71314	-0.4630	10	0.49607	T	0.09	-0.8351	12.0363	0.53427	0.0:0.0:0.0:1.0	.	262;262	Q7KZE5;P40425	.;PBX2_HUMAN	F	262	ENSP00000364190:Y262F	ENSP00000364190:Y262F	Y	-	2	0	PBX2	32263487	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	7.505000	0.81655	1.943000	0.56356	0.459000	0.35465	TAT		0.517	PBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076194.4			
TTC3	7267	broad.mit.edu	37	21	38460511	38460517	+	Frame_Shift_Del	DEL	GTATATG	GTATATG	-	rs113425690	byFrequency	TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	GTATATG	GTATATG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr21:38460511_38460517delGTATATG	ENST00000399017.2	+	4	2950_2956	c.203_209delGTATATG	c.(202-210)agtatatggfs	p.SIW68fs	TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000354749.2_Frame_Shift_Del_p.SIW68fs|TTC3_ENST00000540756.1_Intron|TTC3_ENST00000399010.1_Frame_Shift_Del_p.SIW68fs|TTC3_ENST00000355666.1_Frame_Shift_Del_p.SIW68fs	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	68					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				GACATCTGCAGTATATGGTGTAGTAAA	0.295																																					Ovarian(38;194 1649 35661)												0																																										SO:0001589	frameshift_variant	7267			D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"""RING-type (C3HC4) zinc fingers"", ""Tetratricopeptide (TTC) repeat domain containing"""	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.203_209delGTATATG	21.37:g.38460511_38460517delGTATATG	ENSP00000381981:p.Ser68fs	Somatic		WXS	Illumina GAIIx	Phase_I	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Frame_Shift_Del	DEL	ENST00000399017.2	37	CCDS13651.1																																																																																				0.295	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1			
LOC284577	284577	broad.mit.edu	37	1	205437150	205437151	+	lincRNA	INS	-	-	GTGT	rs56245634|rs34140801		TCGA-A3-3319-01A-01D-0966-08	TCGA-A3-3319-11A-01D-0966-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a771a7ad-8dfa-46ee-849d-4478798c46a6	3cf11e36-4249-4b4d-9def-42e9ec38e274	g.chr1:205437150_205437151insGTGT	ENST00000442318.1	+	0	1883_1884																											GGGAAAGAGGAgtgtgtgtgtg	0.411																																																	0																																												0																															1.37:g.205437155_205437158dupGTGT		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	INS	ENST00000442318.1	37																																																																																					0.411	RP11-576D8.4-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000090406.1			
