#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_ORegAnno_bin	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
ALCAM	214	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	105266275	105266275	+	Missense_Mutation	SNP	G	G	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr3:105266275G>A	ENST00000306107.5	+	11	1782	c.1282G>A	c.(1282-1284)Gga>Aga	p.G428R	ALCAM_ENST00000486979.2_Missense_Mutation_p.G377R|ALCAM_ENST00000389927.4_Missense_Mutation_p.G150R|ALCAM_ENST00000472644.2_Missense_Mutation_p.G428R	NM_001627.3	NP_001618.2	Q13740	CD166_HUMAN	activated leukocyte cell adhesion molecule	428	Ig-like C2-type 3.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|motor neuron axon guidance (GO:0008045)|signal transduction (GO:0007165)	axon (GO:0030424)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	receptor binding (GO:0005102)	p.G428R(1)		breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	28						TGATCCCAGTGGACTATCTAA	0.353																																																	1	Substitution - Missense(1)	kidney(1)											64.0	61.0	62.0					3																	105266275		2203	4298	6501	SO:0001583	missense	214			AK054632	CCDS33810.1, CCDS58841.1	3q13.1	2013-01-29	2002-08-08		ENSG00000170017	ENSG00000170017		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	400	protein-coding gene	gene with protein product		601662	"""activated leucocyte cell adhesion molecule"""			7760007	Standard	NM_001627		Approved	CD166, MEMD	uc003dvx.3	Q13740	OTTHUMG00000159192	ENST00000306107.5:c.1282G>A	3.37:g.105266275G>A	ENSP00000305988:p.Gly428Arg		B2RNS3|B4DTU0|O60892|Q1HGM8|Q1HGM9|Q6PEY4|Q6ZS95	Missense_Mutation	SNP	ENST00000306107.5	37	CCDS33810.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.17|19.17	3.776267|3.776267	0.70107|0.70107	.|.	.|.	ENSG00000170017|ENSG00000170017	ENST00000306107;ENST00000472644;ENST00000486979;ENST00000389927|ENST00000465413	T;T;T;T|.	0.23348|.	2.12;2.12;2.12;1.91|.	5.6|5.6	5.6|5.6	0.85130|0.85130	Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	0.200409|.	0.51477|.	D|.	0.000089|.	T|.	0.56731|.	0.2005|.	L|L	0.36672|0.36672	1.1|1.1	0.46260|0.46260	D|D	0.998953|0.998953	D;D;D|.	0.69078|.	0.995;0.997;0.997|.	D;D;D|.	0.67231|.	0.95;0.949;0.949|.	T|.	0.51903|.	-0.8646|.	10|.	0.87932|.	D|.	0|.	-16.0087|-16.0087	13.3274|13.3274	0.60467|0.60467	0.0817:0.0:0.9183:0.0|0.0817:0.0:0.9183:0.0	.|.	150;428;428|.	Q6ZS95;B4DTU0;Q13740|.	.;.;CD166_HUMAN|.	R|X	428;428;377;150|188	ENSP00000305988:G428R;ENSP00000419236:G428R;ENSP00000418213:G377R;ENSP00000374577:G150R|.	ENSP00000305988:G428R|.	G|W	+|+	1|2	0|0	ALCAM|ALCAM	106748965|106748965	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.954000|0.954000	0.61252|0.61252	4.802000|4.802000	0.62539|0.62539	2.639000|2.639000	0.89480|0.89480	0.460000|0.460000	0.39030|0.39030	GGA|TGG		0.353	ALCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353764.1		NM_001627	
ANKHD1	54882	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	139905891	139905891	+	Silent	SNP	C	C	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr5:139905891C>T	ENST00000360839.2	+	26	4957	c.4803C>T	c.(4801-4803)tgC>tgT	p.C1601C	ANKHD1-EIF4EBP3_ENST00000532219.1_Silent_p.C1601C|ANKHD1_ENST00000297183.6_Silent_p.C1601C|ANKHD1_ENST00000544120.1_5'UTR|SNORD45_ENST00000363181.1_RNA	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	1601						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.C1601C(2)		breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCACAGACTGCAACAGTGAGA	0.423																																																	2	Substitution - coding silent(2)	kidney(2)											135.0	149.0	144.0					5																	139905891		2203	4300	6503	SO:0001819	synonymous_variant	54882			AF521882	CCDS4225.1, CCDS43371.1, CCDS43372.1, CCDS75319.1	5q31.3	2013-01-10			ENSG00000131503	ENSG00000131503		"""Ankyrin repeat domain containing"""	24714	protein-coding gene	gene with protein product		610500				10470851, 11230166, 16098192	Standard	NM_017747		Approved	MASK, FLJ20288, FLJ11979, FLJ10042, FLJ14127, KIAA1085		Q8IWZ3	OTTHUMG00000161610	ENST00000360839.2:c.4803C>T	5.37:g.139905891C>T			A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Silent	SNP	ENST00000360839.2	37	CCDS4225.1	.	.	.	.	.	.	.	.	.	.	C	9.059	0.994064	0.19043	.	.	ENSG00000131503	ENST00000435794;ENST00000432301	.	.	.	5.41	4.34	0.51931	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0219	0.71637	0.0:0.9196:0.0:0.0804	.	.	.	.	X	92;52	.	.	Q	+	1	0	ANKHD1	139886075	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.367000	0.44213	2.542000	0.85734	0.557000	0.71058	CAA		0.423	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1		NM_017747	
ARIH1	25820	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	72847625	72847625	+	Missense_Mutation	SNP	T	T	G			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr15:72847625T>G	ENST00000379887.4	+	4	916	c.602T>G	c.(601-603)cTt>cGt	p.L201R		NM_005744.3	NP_005735.2	Q9Y4X5	ARI1_HUMAN	ariadne RBR E3 ubiquitin protein ligase 1	201	Interaction with UBE2L3.				cytokine-mediated signaling pathway (GO:0019221)|protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|ubiquitin ligase complex (GO:0000151)	small conjugating protein ligase activity (GO:0019787)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.L201R(1)		endometrium(1)|kidney(4)|large_intestine(3)|lung(4)|prostate(1)|skin(1)	14						TTCACTGGCCTTGAATGTGGA	0.353																																																	1	Substitution - Missense(1)	kidney(1)											137.0	130.0	132.0					15																	72847625		2198	4297	6495	SO:0001583	missense	25820			AF072832	CCDS10244.1	15q24	2013-10-03	2013-10-03		ENSG00000166233	ENSG00000166233			689	protein-coding gene	gene with protein product	"""ariadne, Drosophila, homolog of"""	605624	"""ariadne (Drosophila) homolog, ubiquitin-conjugating enzyme E2-binding protein, 1"", ""ariadne homolog, ubiquitin-conjugating enzyme E2 binding protein, 1 (Drosophila)"""			10521492, 24058416	Standard	NM_005744		Approved	HARI, HHARI, UBCH7BP, ARI	uc002aut.4	Q9Y4X5	OTTHUMG00000133474	ENST00000379887.4:c.602T>G	15.37:g.72847625T>G	ENSP00000369217:p.Leu201Arg		B2R6U3|O76026|Q9H3T6|Q9UEN0|Q9UP39	Missense_Mutation	SNP	ENST00000379887.4	37	CCDS10244.1	.	.	.	.	.	.	.	.	.	.	T	15.45	2.838376	0.51057	.	.	ENSG00000166233	ENST00000379887;ENST00000299305	D	0.86694	-2.16	5.22	5.22	0.72569	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);	0.000000	0.85682	D	0.000000	D	0.95175	0.8436	H	0.94423	3.535	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	D	0.96451	0.9334	10	0.87932	D	0	.	15.0391	0.71774	0.0:0.0:0.0:1.0	.	201	Q9Y4X5	ARI1_HUMAN	R	201;171	ENSP00000369217:L201R	ENSP00000299305:L171R	L	+	2	0	ARIH1	70634679	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.555000	0.82223	2.091000	0.63221	0.477000	0.44152	CTT		0.353	ARIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257350.1		NM_005744	
PHF7	51533	hgsc.bcm.edu;ucsc.edu	37	3	52443623	52443647	+	5'Flank	DEL	ACCTGCGATGAGGAAAGGAAAGCAG	ACCTGCGATGAGGAAAGGAAAGCAG	-	rs141802003		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	ACCTGCGATGAGGAAAGGAAAGCAG	ACCTGCGATGAGGAAAGGAAAGCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr3:52443623_52443647delACCTGCGATGAGGAAAGGAAAGCAG	ENST00000327906.3	+	0	0				PHF7_ENST00000347025.2_5'Flank|BAP1_ENST00000460680.1_Splice_Site_p.A23fs|BAP1_ENST00000296288.5_Splice_Site_p.A23fs	NM_016483.4	NP_057567.3	Q9BWX1	PHF7_HUMAN	PHD finger protein 7							Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			breast(2)|large_intestine(4)|lung(3)	9				BRCA - Breast invasive adenocarcinoma(193;1.71e-05)|Kidney(197;0.00178)|KIRC - Kidney renal clear cell carcinoma(197;0.00201)|OV - Ovarian serous cystadenocarcinoma(275;0.0275)		CCCCCTTGACACCTGCGATGAGGAAAGGAAAGCAGTAGGGAAGGA	0.604																																																	0																																										SO:0001631	upstream_gene_variant	8314			AY014283	CCDS2854.1, CCDS2855.1	3p21.31	2013-01-28			ENSG00000010318	ENSG00000010318		"""Zinc fingers, PHD-type"""	18458	protein-coding gene	gene with protein product						11042152, 11829468	Standard	NM_016483		Approved	NYD-SP6, HSPC226	uc003ddy.3	Q9BWX1	OTTHUMG00000158495		3.37:g.52443623_52443647delACCTGCGATGAGGAAAGGAAAGCAG	Exception_encountered		K4DI82	In_Frame_Del	DEL	ENST00000327906.3	37	CCDS2854.1																																																																																				0.604	PHF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351155.1		NM_016483	
CACNA1I	8911	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	22	40062013	40062013	+	Splice_Site	SNP	T	T	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr22:40062013T>A	ENST00000402142.3	+	23	4104		c.e23+2		CACNA1I_ENST00000404898.1_Splice_Site|CACNA1I_ENST00000407673.1_Splice_Site|CACNA1I_ENST00000401624.1_Splice_Site|CACNA1I_ENST00000336649.4_Splice_Site|CACNA1I_ENST00000400164.3_Splice_Site	NM_021096.3	NP_066919.2	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type, alpha 1I subunit						axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|signal transduction (GO:0007165)|sleep (GO:0030431)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)	p.?(2)		breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(2)|lung(27)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Melanoma(58;0.0749)				Cinnarizine(DB00568)|Flunarizine(DB04841)|Paramethadione(DB00617)|Spironolactone(DB00421)|Verapamil(DB00661)|Zonisamide(DB00909)	CTGGGCCAGGTGAGCACCACC	0.602																																																	2	Unknown(2)	kidney(2)											69.0	72.0	71.0					22																	40062013		2144	4231	6375	SO:0001630	splice_region_variant	8911			AF129133	CCDS46710.1, CCDS46711.1	22q13.1	2012-03-07	2007-02-16		ENSG00000100346	ENSG00000100346		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1396	protein-coding gene	gene with protein product		608230				10454147, 16382099	Standard	NM_021096		Approved	Cav3.3	uc003ayd.3	Q9P0X4	OTTHUMG00000151096	ENST00000402142.3:c.4104+2T>A	22.37:g.40062013T>A			B0QY12|B0QY13|B0QY14|O95504|Q5JZ88|Q7Z6S9|Q8NFX6|Q9NZC8|Q9UH15|Q9UH30|Q9ULU9|Q9UNE6	Splice_Site	SNP	ENST00000402142.3	37	CCDS46710.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.129275	0.77549	.	.	ENSG00000100346	ENST00000402142;ENST00000404898;ENST00000401624;ENST00000407673;ENST00000336649;ENST00000400164	.	.	.	4.3	4.3	0.51218	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.0379	0.42139	0.1506:0.0:0.0:0.8494	.	.	.	.	.	-1	.	.	.	+	.	.	CACNA1I	38391959	1.000000	0.71417	0.990000	0.47175	0.878000	0.50629	6.206000	0.72154	1.560000	0.49568	0.379000	0.24179	.		0.602	CACNA1I-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321290.1		NM_001003406	Intron
CCDC120	90060	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	48923285	48923285	+	Missense_Mutation	SNP	C	C	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chrX:48923285C>T	ENST00000376396.3	+	9	1084	c.865C>T	c.(865-867)Cgc>Tgc	p.R289C	CCDC120_ENST00000536628.2_Missense_Mutation_p.R277C|CCDC120_ENST00000597275.1_Missense_Mutation_p.R289C|CCDC120_ENST00000422185.2_Missense_Mutation_p.R289C|CCDC120_ENST00000603986.1_Missense_Mutation_p.R324C|CCDC120_ENST00000496529.2_Missense_Mutation_p.R289C	NM_001271835.1|NM_001271836.1|NM_033626.2	NP_001258764.1|NP_001258765.1|NP_296375.1	Q96HB5	CC120_HUMAN	coiled-coil domain containing 120	289								p.R289C(1)		breast(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	14						TAGCCCCACACGCTCGCTGCC	0.647																																																	1	Substitution - Missense(1)	kidney(1)											40.0	25.0	30.0					X																	48923285		2166	4227	6393	SO:0001583	missense	90060			BC008769	CCDS14316.1, CCDS55413.1, CCDS55414.1, CCDS55414.2	Xp11.23	2008-02-05			ENSG00000147144	ENSG00000147144			28910	protein-coding gene	gene with protein product						12477932	Standard	NM_033626		Approved	JM11	uc011mmr.3	Q96HB5	OTTHUMG00000021509	ENST00000376396.3:c.865C>T	X.37:g.48923285C>T	ENSP00000365577:p.Arg289Cys		B4DFC1|B4DTU2|F5GZU4	Missense_Mutation	SNP	ENST00000376396.3	37	CCDS14316.1	.	.	.	.	.	.	.	.	.	.	C	18.79	3.699162	0.68501	.	.	ENSG00000147144	ENST00000376396;ENST00000422185;ENST00000536628	.	.	.	5.47	4.56	0.56223	.	0.052500	0.85682	D	0.000000	T	0.69744	0.3145	L	0.55990	1.75	0.58432	D	0.999996	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.76575	0.982;0.988;0.988;0.988	T	0.72367	-0.4315	9	0.87932	D	0	-27.394	12.4219	0.55524	0.1667:0.8333:0.0:0.0	.	277;324;277;289	B4DTU2;B4DFC1;B4DF24;Q96HB5	.;.;.;CC120_HUMAN	C	289;289;277	.	ENSP00000365577:R289C	R	+	1	0	CCDC120	48810229	0.894000	0.30519	1.000000	0.80357	0.963000	0.63663	1.302000	0.33459	2.426000	0.82243	0.600000	0.82982	CGC		0.647	CCDC120-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056528.1		NM_033626	
CHL1	10752	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	367660	367660	+	Missense_Mutation	SNP	T	T	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr3:367660T>A	ENST00000256509.2	+	4	752	c.110T>A	c.(109-111)aTc>aAc	p.I37N	CHL1_ENST00000397491.2_Missense_Mutation_p.I37N	NM_001253387.1|NM_001253388.1|NM_006614.3	NP_001240316.1|NP_001240317.1|NP_006605.2	Q96FC9	DDX11_HUMAN	cell adhesion molecule L1-like	0	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)	p.I37N(1)		NS(1)|central_nervous_system(5)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|lung(31)|ovary(1)|prostate(4)|skin(10)|stomach(1)	93		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		GTTCCAACAATCATAAAACAG	0.333																																																	1	Substitution - Missense(1)	kidney(1)											81.0	82.0	82.0					3																	367660		2203	4300	6503	SO:0001583	missense	10752			AF002246	CCDS2556.1, CCDS58812.1, CCDS74887.1	3p26	2013-05-01	2013-05-01		ENSG00000134121	ENSG00000134121		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	1939	protein-coding gene	gene with protein product	"""neural cell adhesion molecule"", ""close homolog of L1"""	607416	"""cell adhesion molecule with homology to L1CAM (close homologue of L1)"", ""cell adhesion molecule with homology to L1CAM (close homolog of L1)"""			9799093	Standard	NM_006614		Approved	CALL, L1CAM2, FLJ44930, MGC132578	uc003bot.3	O00533	OTTHUMG00000090601	ENST00000256509.2:c.110T>A	3.37:g.367660T>A	ENSP00000256509:p.Ile37Asn		Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000256509.2	37	CCDS2556.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.229709	0.79688	.	.	ENSG00000134121	ENST00000256509;ENST00000397491;ENST00000427688;ENST00000421198;ENST00000435603;ENST00000449294	T;T;T;D;T;D	0.96913	1.06;1.06;-0.45;-4.17;-0.94;-4.17	5.8	5.8	0.92144	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.059300	0.64402	D	0.000003	D	0.98429	0.9477	M	0.91612	3.225	0.53005	D	0.999962	D;D;D	0.89917	1.0;0.999;0.996	D;D;D	0.91635	0.999;0.976;0.966	D	0.99544	1.0964	10	0.87932	D	0	.	14.7433	0.69472	0.0:0.0:0.0:1.0	.	37;37;37	B3KX75;O00533;O00533-2	.;CHL1_HUMAN;.	N	37	ENSP00000256509:I37N;ENSP00000380628:I37N;ENSP00000403311:I37N;ENSP00000413628:I37N;ENSP00000397445:I37N;ENSP00000390440:I37N	ENSP00000256509:I37N	I	+	2	0	CHL1	342660	1.000000	0.71417	0.404000	0.26397	0.998000	0.95712	6.400000	0.73252	2.209000	0.71365	0.524000	0.50904	ATC		0.333	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2		NM_006614	
CHMP4B	128866	hgsc.bcm.edu;ucsc.edu	37	20	32436409	32436409	+	Frame_Shift_Del	DEL	G	G	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr20:32436409delG	ENST00000217402.2	+	2	492	c.327delG	c.(325-327)atgfs	p.M109fs		NM_176812.4	NP_789782.1	Q9H444	CHM4B_HUMAN	charged multivesicular body protein 4B	109					endosomal transport (GO:0016197)|membrane organization (GO:0061024)|negative regulation of autophagic vacuole assembly (GO:1902902)|negative regulation of neuron death (GO:1901215)|positive regulation of viral release from host cell (GO:1902188)|posttranslational protein targeting to membrane (GO:0006620)|protein homooligomerization (GO:0051260)|regulation of viral process (GO:0050792)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|ESCRT III complex (GO:0000815)|extracellular vesicular exosome (GO:0070062)|midbody (GO:0030496)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	13						TCAAGAACATGGGCTATGCCG	0.607																																																	0													116.0	73.0	87.0					20																	32436409		2203	4300	6503	SO:0001589	frameshift_variant	128866			AL050349	CCDS13228.1	20q11.22	2011-09-21	2011-09-21	2005-04-04	ENSG00000101421	ENSG00000101421		"""Charged multivesicular body proteins"""	16171	protein-coding gene	gene with protein product		610897	"""chromosome 20 open reading frame 178"", ""chromatin modifying protein 4B"""	C20orf178		14678797	Standard	NM_176812		Approved	dJ553F4.4, Shax1, SNF7-2, VPS32B	uc002xaa.3	Q9H444	OTTHUMG00000032272	ENST00000217402.2:c.327delG	20.37:g.32436409delG	ENSP00000217402:p.Met109fs		E1P5N4|Q53ZD6	Frame_Shift_Del	DEL	ENST00000217402.2	37	CCDS13228.1																																																																																				0.607	CHMP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078738.2			
CLCN1	1180	hgsc.bcm.edu;ucsc.edu	37	7	143020428	143020428	+	Silent	SNP	C	C	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr7:143020428C>A	ENST00000343257.2	+	6	810	c.723C>A	c.(721-723)atC>atA	p.I241I	CLCN1_ENST00000495612.1_Intron	NM_000083.2	NP_000074	P35523	CLCN1_HUMAN	chloride channel, voltage-sensitive 1	241					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|neuronal action potential propagation (GO:0019227)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	adenyl nucleotide binding (GO:0030554)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(4)|central_nervous_system(1)|endometrium(1)|large_intestine(11)|lung(26)|ovary(3)|prostate(2)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	58	Melanoma(164;0.205)					TTGCCAGCATCTGTGCTGCTG	0.572																																																	0													103.0	92.0	96.0					7																	143020428		2203	4300	6503	SO:0001819	synonymous_variant	1180			Z25884	CCDS5881.1	7q12	2012-09-26	2012-02-23		ENSG00000188037	ENSG00000188037		"""Ion channels / Chloride channels : Voltage-sensitive"""	2019	protein-coding gene	gene with protein product	"""Thomsen disease, autosomal dominant"""	118425	"""chloride channel 1, skeletal muscle"""			1379744	Standard	NM_000083		Approved	CLC1, ClC-1	uc003wcr.1	P35523	OTTHUMG00000152695	ENST00000343257.2:c.723C>A	7.37:g.143020428C>A			A4D2H5|Q2M202	Silent	SNP	ENST00000343257.2	37	CCDS5881.1																																																																																				0.572	CLCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327420.1		NM_000083	
DAB1	1600	broad.mit.edu	37	1	57481090	57481090	+	Missense_Mutation	SNP	C	C	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr1:57481090C>T	ENST00000371231.1	-	13	1043	c.1009G>A	c.(1009-1011)Ggc>Agc	p.G337S	DAB1_ENST00000485760.1_5'UTR|DAB1_ENST00000420954.2_Missense_Mutation_p.G302S|DAB1_ENST00000414851.2_Missense_Mutation_p.G286S|DAB1_ENST00000371234.4_Missense_Mutation_p.G304S|DAB1_ENST00000371236.2_Missense_Mutation_p.G304S|DAB1_ENST00000439789.2_Missense_Mutation_p.G218S			O75553	DAB1_HUMAN	Dab, reelin signal transducer, homolog 1 (Drosophila)	337					adult walking behavior (GO:0007628)|cell-cell adhesion involved in neuronal-glial interactions involved in cerebral cortex radial glia guided migration (GO:0021813)|cerebellum structural organization (GO:0021589)|dendrite development (GO:0016358)|Golgi localization (GO:0051645)|lateral motor column neuron migration (GO:0097477)|midgut development (GO:0007494)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell adhesion (GO:0007162)|negative regulation of JAK-STAT cascade (GO:0046426)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein kinase activity (GO:0045860)|radial glia guided migration of Purkinje cell (GO:0021942)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|ventral spinal cord development (GO:0021517)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)		p.G304S(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(28)|ovary(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(5)	64						AGGACAGCGCCCATTGCAACG	0.567																																																	1	Substitution - Missense(1)	kidney(1)											23.0	26.0	25.0					1																	57481090		2199	4288	6487	SO:0001583	missense	1600			BC067445	CCDS607.1	1p32-p31	2013-10-03	2013-10-03		ENSG00000173406	ENSG00000173406			2661	protein-coding gene	gene with protein product		603448	"""disabled (Drosophila) homolog 1"", ""disabled homolog 1 (Drosophila)"", ""Dab, reelin signal transducer, homolog 1 (Drosophila)"", ""Dab reelin signal transducer 1"""			9790777	Standard	NM_021080		Approved		uc001cys.1	O75553	OTTHUMG00000008391	ENST00000371231.1:c.1009G>A	1.37:g.57481090C>T	ENSP00000360275:p.Gly337Ser		A4FU90|B3KTG3|Q4LE59|Q5T6M6|Q5T6M9|Q5T835|Q5T836|Q5T837|Q6NWS9|Q6NWT0|Q6NWT1|Q9NYA8	Missense_Mutation	SNP	ENST00000371231.1	37		.	.	.	.	.	.	.	.	.	.	C	27.5	4.841514	0.91197	.	.	ENSG00000173406	ENST00000371236;ENST00000371233;ENST00000371234;ENST00000420954;ENST00000414851;ENST00000439789;ENST00000371231;ENST00000371232	T;T;T;T;T;T;T	0.74632	0.58;0.58;0.53;0.64;1.14;0.44;-0.86	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	D	0.84986	0.5594	L	0.59436	1.845	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.997;0.998;0.999;1.0	D	0.84989	0.0893	10	0.66056	D	0.02	-41.0347	19.6787	0.95950	0.0:1.0:0.0:0.0	.	286;337;304;218;302	O75553-4;O75553;O75553-6;O75553-3;O75553-5	.;DAB1_HUMAN;.;.;.	S	304;304;304;302;286;218;337;218	ENSP00000360280:G304S;ENSP00000360278:G304S;ENSP00000395296:G302S;ENSP00000387581:G286S;ENSP00000409328:G218S;ENSP00000360275:G337S;ENSP00000360276:G218S	ENSP00000360275:G337S	G	-	1	0	DAB1	57253678	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.320000	0.79064	2.890000	0.99128	0.650000	0.86243	GGC		0.567	DAB1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000027962.1		NM_021080	
DAPK3	1613	hgsc.bcm.edu;ucsc.edu	37	19	3964350	3964350	+	Missense_Mutation	SNP	C	C	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr19:3964350C>T	ENST00000545797.2	-	4	688	c.445G>A	c.(445-447)Gac>Aac	p.D149N	DAPK3_ENST00000301264.3_Missense_Mutation_p.D149N|MIR637_ENST00000385000.1_RNA			O43293	DAPK3_HUMAN	death-associated protein kinase 3	149	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|chromatin modification (GO:0016568)|cytokinesis (GO:0000910)|intracellular signal transduction (GO:0035556)|negative regulation of translation (GO:0017148)|neuron differentiation (GO:0030182)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of cell motility (GO:2000145)|regulation of focal adhesion assembly (GO:0051893)|regulation of mitosis (GO:0007088)|regulation of mitotic cell cycle (GO:0007346)|regulation of smooth muscle contraction (GO:0006940)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|leucine zipper domain binding (GO:0043522)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(1)|skin(2)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)		ACGTTCTTGTCCAGCAGCATG	0.617																																																	0													203.0	115.0	145.0					19																	3964350		2203	4300	6503	SO:0001583	missense	1613			AB007144	CCDS12116.1	19p13.3	2008-02-05				ENSG00000167657			2676	protein-coding gene	gene with protein product		603289				9488481	Standard	XM_005259508		Approved	ZIP, ZIPK	uc002lzc.1	O43293		ENST00000545797.2:c.445G>A	19.37:g.3964350C>T	ENSP00000442973:p.Asp149Asn		A0AVN4|B3KQE2|Q05JY4	Missense_Mutation	SNP	ENST00000545797.2	37	CCDS12116.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.055780	0.76074	.	.	ENSG00000167657	ENST00000301264;ENST00000545797;ENST00000442766	T;T	0.64085	-0.08;-0.08	5.47	5.47	0.80525	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.055925	0.64402	D	0.000002	T	0.51890	0.1701	L	0.28054	0.825	0.80722	D	1	B	0.20988	0.05	B	0.27796	0.083	T	0.44982	-0.9292	10	0.15499	T	0.54	.	18.3088	0.90192	0.0:1.0:0.0:0.0	.	149	O43293	DAPK3_HUMAN	N	149;149;4	ENSP00000301264:D149N;ENSP00000442973:D149N	ENSP00000301264:D149N	D	-	1	0	DAPK3	3915350	1.000000	0.71417	0.996000	0.52242	0.551000	0.35334	5.807000	0.69157	2.572000	0.86782	0.549000	0.68633	GAC		0.617	DAPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457817.2		NM_001348	
FEM1C	56929	broad.mit.edu;ucsc.edu	37	5	114860153	114860153	+	Missense_Mutation	SNP	T	T	C			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr5:114860153T>C	ENST00000274457.3	-	3	2267	c.1706A>G	c.(1705-1707)gAt>gGt	p.D569G		NM_020177.2	NP_064562.1	Q96JP0	FEM1C_HUMAN	fem-1 homolog c (C. elegans)	569					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)		p.D569G(1)		breast(5)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|liver(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	18		all_cancers(142;0.000575)|all_epithelial(76;9.98e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;2.5e-07)|Epithelial(69;2.66e-07)|all cancers(49;1.39e-05)		TTCCTTCTCATCCAGCAAGTC	0.363																																																	1	Substitution - Missense(1)	kidney(1)											134.0	131.0	132.0					5																	114860153		2202	4300	6502	SO:0001583	missense	56929				CCDS4118.1	5q22	2013-01-10	2006-11-08		ENSG00000145780	ENSG00000145780		"""Ankyrin repeat domain containing"""	16933	protein-coding gene	gene with protein product		608767				14527725, 11733146	Standard	NM_020177		Approved	KIAA1785, EUROIMAGE686608, EUROIMAGE783647, FEM1A	uc003krb.1	Q96JP0	OTTHUMG00000128895	ENST00000274457.3:c.1706A>G	5.37:g.114860153T>C	ENSP00000274457:p.Asp569Gly		B2RE47|Q8N3V8|Q9H704|Q9NPL6|Q9NPL9	Missense_Mutation	SNP	ENST00000274457.3	37	CCDS4118.1	.	.	.	.	.	.	.	.	.	.	T	11.05	1.525305	0.27299	.	.	ENSG00000145780	ENST00000274457	T	0.67523	-0.27	4.98	4.98	0.66077	Ankyrin repeat-containing domain (2);	0.051111	0.85682	D	0.000000	T	0.63686	0.2532	M	0.72479	2.2	0.58432	D	0.999998	P	0.41041	0.736	B	0.35550	0.205	T	0.66972	-0.5788	10	0.38643	T	0.18	-22.4393	14.6749	0.68972	0.0:0.0:0.0:1.0	.	569	Q96JP0	FEM1C_HUMAN	G	569	ENSP00000274457:D569G	ENSP00000274457:D569G	D	-	2	0	FEM1C	114888052	1.000000	0.71417	0.996000	0.52242	0.969000	0.65631	7.990000	0.88215	1.864000	0.54056	0.460000	0.39030	GAT		0.363	FEM1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250857.3		NM_020177	
CMTR1	23070	broad.mit.edu;ucsc.edu	37	6	37447813	37447813	+	Missense_Mutation	SNP	C	C	G			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr6:37447813C>G	ENST00000373451.4	+	24	2564	c.2400C>G	c.(2398-2400)ttC>ttG	p.F800L		NM_015050.2	NP_055865.1	Q8N1G2	CMTR1_HUMAN	cap methyltransferase 1	800	Interaction with POLR2A.				7-methylguanosine mRNA capping (GO:0006370)|cap1 mRNA methylation (GO:0097309)|mRNA methylation (GO:0080009)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA (nucleoside-2'-O-)-methyltransferase activity (GO:0004483)|nucleic acid binding (GO:0003676)	p.F800L(1)									GCCGGCTCTTCTGGGAGTGGG	0.577																																																	1	Substitution - Missense(1)	kidney(1)											110.0	105.0	107.0					6																	37447813		2203	4300	6503	SO:0001583	missense	23070			BC031890	CCDS4835.1	6p21.2	2013-07-23	2013-07-23	2013-07-23	ENSG00000137200	ENSG00000137200	2.1.1.57	"""G patch domain containing"""	21077	protein-coding gene	gene with protein product			"""KIAA0082"", ""FtsJ methyltransferase domain containing 2"""	KIAA0082, FTSJD2		20713356	Standard	NM_015050		Approved	MTr1, ISG95	uc003ons.3	Q8N1G2	OTTHUMG00000014624	ENST00000373451.4:c.2400C>G	6.37:g.37447813C>G	ENSP00000362550:p.Phe800Leu		A8K949|Q14670|Q96FJ9	Missense_Mutation	SNP	ENST00000373451.4	37	CCDS4835.1	.	.	.	.	.	.	.	.	.	.	C	5.850	0.341018	0.11069	.	.	ENSG00000137200	ENST00000373451	.	.	.	5.16	4.3	0.51218	.	0.000000	0.85682	D	0.000000	T	0.22322	0.0538	L	0.43923	1.385	0.42723	D	0.993687	B	0.09022	0.002	B	0.06405	0.002	T	0.16689	-1.0394	9	0.02654	T	1	-20.4543	9.3472	0.38115	0.0:0.9039:0.0:0.0961	.	800	Q8N1G2	MTR1_HUMAN	L	800	.	ENSP00000362550:F800L	F	+	3	2	FTSJD2	37555791	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	3.547000	0.53663	1.416000	0.47057	0.561000	0.74099	TTC		0.577	CMTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040408.1		NM_015050	
FZD9	8326	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	72849270	72849270	+	Silent	SNP	G	G	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr7:72849270G>A	ENST00000344575.3	+	1	1162	c.933G>A	c.(931-933)acG>acA	p.T311T		NM_003508.2	NP_003499.1	O00144	FZD9_HUMAN	frizzled class receptor 9	311					B cell differentiation (GO:0030183)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|gonad development (GO:0008406)|learning or memory (GO:0007611)|nervous system development (GO:0007399)|neuroblast proliferation (GO:0007405)|vasculature development (GO:0001944)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.T311T(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(4)|prostate(2)|skin(1)	14		Lung NSC(55;0.0659)|all_lung(88;0.152)				TGGAGAACACGGGCTGCACGC	0.667																																					Pancreas(144;909 1878 36867 38226 39554)												1	Substitution - coding silent(1)	kidney(1)											104.0	94.0	97.0					7																	72849270		2202	4300	6502	SO:0001819	synonymous_variant	8326			U82169	CCDS5548.1	7q11.23	2014-01-29	2014-01-29		ENSG00000188763	ENSG00000188763		"""GPCR / Class F : Frizzled receptors"", ""CD molecules"""	4047	protein-coding gene	gene with protein product		601766	"""frizzled (Drosophila) homolog 9"", ""frizzled homolog 9 (Drosophila)"", ""frizzled 9, seven transmembrane spanning receptor"", ""frizzled family receptor 9"""			9147651, 10198163	Standard	NM_003508		Approved	FZD3, CD349	uc003tyb.3	O00144	OTTHUMG00000023051	ENST00000344575.3:c.933G>A	7.37:g.72849270G>A				Silent	SNP	ENST00000344575.3	37	CCDS5548.1																																																																																				0.667	FZD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252120.1			
GALNT9	50614	broad.mit.edu	37	12	132682466	132682466	+	Frame_Shift_Del	DEL	C	C	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr12:132682466delC	ENST00000328957.8	-	10	1535	c.1536delG	c.(1534-1536)gggfs	p.G512fs	GALNT9_ENST00000397325.2_Frame_Shift_Del_p.G146fs|GALNT9_ENST00000541995.1_Frame_Shift_Del_p.G146fs|GALNT9_ENST00000535228.1_Frame_Shift_Del_p.G263fs	NM_001122636.1	NP_001116108.1	Q9HCQ5	GALT9_HUMAN	polypeptide N-acetylgalactosaminyltransferase 9	512	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(1)|endometrium(1)|large_intestine(2)|lung(5)	9	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.49e-08)|Epithelial(86;3.55e-07)|all cancers(50;2.09e-05)		AGCCCAGAGGCCCCAGCTGCA	0.657																																					Colon(186;2147 2752 13553 41466)												0													21.0	28.0	25.0					12																	132682466		2142	4246	6388	SO:0001589	frameshift_variant	50614			AB040672	CCDS41866.1	12q24.33	2014-03-13	2014-03-13		ENSG00000182870	ENSG00000182870	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4131	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 9"""	606251	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 9 (GalNAc-T9)"""			10978536, 12407114	Standard	NM_021808		Approved	GALNAC-T9	uc001ukc.4	Q9HCQ5	OTTHUMG00000168256	ENST00000328957.8:c.1536delG	12.37:g.132682466delC	ENSP00000329846:p.Gly512fs		Q52LR8|Q6NT54|Q8NFR1	Frame_Shift_Del	DEL	ENST00000328957.8	37																																																																																					0.657	GALNT9-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000402967.1		NM_001122636	
GPRIN1	114787	hgsc.bcm.edu	37	5	176026124	176026147	+	In_Frame_Del	DEL	AAGACCCAGGATCCTCCTTCCTCG	AAGACCCAGGATCCTCCTTCCTCG	-	rs79403503|rs200519605|rs386695335|rs550332435|rs77245696|rs142779818|rs371149640|rs199714570|rs373697082|rs201635586	byFrequency	TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	AAGACCCAGGATCCTCCTTCCTCG	AAGACCCAGGATCCTCCTTCCTCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr5:176026124_176026147delAAGACCCAGGATCCTCCTTCCTCG	ENST00000303991.4	-	2	866_889	c.689_712delCGAGGAAGGAGGATCCTGGGTCTT	c.(688-714)ccgaggaaggaggatcctgggtctttg>ctg	p.PRKEDPGS230del		NM_052899.2	NP_443131.2	Q7Z2K8	GRIN1_HUMAN	G protein regulated inducer of neurite outgrowth 1	230					neuron projection development (GO:0031175)	cell projection (GO:0042995)|plasma membrane (GO:0005886)		p.L238L(1)		NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ACCTTTCTCAAAGACCCAGGATCCTCCTTCCTCGGTGACACTGT	0.5																																																	1	Substitution - coding silent(1)	lung(1)																																								SO:0001651	inframe_deletion	114787			AB067480	CCDS4405.1	5q35.2	2008-02-05			ENSG00000169258	ENSG00000169258			24835	protein-coding gene	gene with protein product		611239				11572484	Standard	NM_052899		Approved	GRIN1, KIAA1893	uc003meo.1	Q7Z2K8	OTTHUMG00000130659	ENST00000303991.4:c.689_712delCGAGGAAGGAGGATCCTGGGTCTT	5.37:g.176026124_176026147delAAGACCCAGGATCCTCCTTCCTCG	ENSP00000305839:p.Pro230_Ser237del		C9JM70|Q8ND74|Q96PZ4	In_Frame_Del	DEL	ENST00000303991.4	37	CCDS4405.1																																																																																				0.500	GPRIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253149.1		NM_052899	
GZF1	64412	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	23350858	23350858	+	Missense_Mutation	SNP	T	T	G			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr20:23350858T>G	ENST00000338121.5	+	6	1993	c.1916T>G	c.(1915-1917)cTg>cGg	p.L639R	GZF1_ENST00000377051.2_Missense_Mutation_p.L639R|GZF1_ENST00000542987.1_Missense_Mutation_p.L148R|GZF1_ENST00000544236.1_Missense_Mutation_p.L163R			Q9H116	GZF1_HUMAN	GDNF-inducible zinc finger protein 1	639					branching involved in ureteric bud morphogenesis (GO:0001658)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)|sequence-specific DNA binding (GO:0043565)	p.L639R(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|urinary_tract(2)	24	Lung NSC(19;0.0605)|Colorectal(13;0.0993)|all_lung(19;0.135)					GATAAATTGCTGTCTTTTGCA	0.488																																																	1	Substitution - Missense(1)	kidney(1)											109.0	87.0	94.0					20																	23350858		2203	4300	6503	SO:0001583	missense	64412			AK025447	CCDS13151.1	20p11.21	2013-01-09	2006-09-19	2006-09-19	ENSG00000125812	ENSG00000125812		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	15808	protein-coding gene	gene with protein product		613842	"""zinc finger protein 336"""	ZNF336		14522971, 16049025	Standard	NM_022482		Approved	dJ322G13.2, ZBTB23	uc002wsz.3	Q9H116	OTTHUMG00000032069	ENST00000338121.5:c.1916T>G	20.37:g.23350858T>G	ENSP00000338290:p.Leu639Arg		A8K199|B2RBC3|B3KPL4|B4DF58|D3DW39|Q54A22|Q96N08|Q9BQK9|Q9H117|Q9H6W6	Missense_Mutation	SNP	ENST00000338121.5	37	CCDS13151.1	.	.	.	.	.	.	.	.	.	.	T	15.92	2.975989	0.53720	.	.	ENSG00000125812	ENST00000544236;ENST00000338121;ENST00000542987;ENST00000377051	T;T;T;T	0.10960	2.98;2.82;3.28;2.82	5.77	5.77	0.91146	.	0.000000	0.43579	D	0.000560	T	0.19685	0.0473	L	0.34521	1.04	0.46222	D	0.998937	D	0.76494	0.999	D	0.65233	0.933	T	0.03695	-1.1012	10	0.24483	T	0.36	.	13.8281	0.63363	0.0:0.0:0.0:1.0	.	639	Q9H116	GZF1_HUMAN	R	163;639;148;639	ENSP00000445458:L163R;ENSP00000338290:L639R;ENSP00000445118:L148R;ENSP00000366250:L639R	ENSP00000338290:L639R	L	+	2	0	GZF1	23298858	1.000000	0.71417	1.000000	0.80357	0.174000	0.22865	3.546000	0.53656	2.202000	0.70862	0.533000	0.62120	CTG		0.488	GZF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078333.1		NM_022482	
HIVEP1	3096	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	12125187	12125187	+	Nonsense_Mutation	SNP	C	C	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr6:12125187C>A	ENST00000379388.2	+	4	5491	c.5159C>A	c.(5158-5160)tCa>tAa	p.S1720*	HIVEP1_ENST00000541134.1_5'Flank	NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	1720					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S1720*(1)		NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				TCTTCTCTATCAGAATCCTTG	0.388																																																	1	Substitution - Nonsense(1)	kidney(1)											63.0	61.0	62.0					6																	12125187		1817	4077	5894	SO:0001587	stop_gained	3096			J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"""Zinc fingers, C2H2-type"""	4920	protein-coding gene	gene with protein product		194540	"""human immunodeficiency virus type I enhancer-binding protein 1"", ""zinc finger protein 40"""	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.5159C>A	6.37:g.12125187C>A	ENSP00000368698:p.Ser1720*		B2RTU3|Q14122|Q5MPB1|Q5VW60	Nonsense_Mutation	SNP	ENST00000379388.2	37	CCDS43426.1	.	.	.	.	.	.	.	.	.	.	C	44	10.904840	0.99486	.	.	ENSG00000095951	ENST00000379388	.	.	.	5.58	3.74	0.42951	.	0.339094	0.16826	N	0.197944	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	.	.	.	-0.2688	7.8768	0.29599	0.0:0.6718:0.0:0.3282	.	.	.	.	X	1720	.	.	S	+	2	0	HIVEP1	12233173	0.000000	0.05858	0.001000	0.08648	0.015000	0.08874	0.403000	0.20982	0.654000	0.30846	0.655000	0.94253	TCA		0.388	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2		NM_002114	
IFT46	56912	hgsc.bcm.edu;ucsc.edu	37	11	118427645	118427647	+	In_Frame_Del	DEL	TCA	TCA	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	TCA	TCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr11:118427645_118427647delTCA	ENST00000264021.3	-	4	577_579	c.159_161delTGA	c.(157-162)gatgaa>gaa	p.D53del	IFT46_ENST00000530872.1_In_Frame_Del_p.D104del|IFT46_ENST00000264020.2_In_Frame_Del_p.D104del	NM_001168618.1	NP_001162089.1	Q9NQC8	IFT46_HUMAN	intraflagellar transport 46	53	Asp/Glu-rich (highly acidic).				cilium assembly (GO:0042384)|intraciliary transport (GO:0042073)|protein stabilization (GO:0050821)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)|motile cilium (GO:0031514)|motile primary cilium (GO:0031512)	protein C-terminus binding (GO:0008022)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)	9						TCCATGCTCTTCATCATCATCAT	0.473																																																	0																																										SO:0001651	inframe_deletion	56912			AL136934	CCDS8399.1, CCDS53718.1	11q23.3	2014-07-18	2014-07-03	2010-04-22	ENSG00000118096	ENSG00000118096		"""Intraflagellar transport homologs"""	26146	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 32"""		"""chromosome 11 open reading frame 60"", ""intraflagellar transport 46 homolog (Chlamydomonas)"""	C11orf60		10873569, 19253336	Standard	NM_020153		Approved	C11orf2, FLJ21827, CFAP32	uc001pto.2	Q9NQC8	OTTHUMG00000166408	ENST00000264021.3:c.159_161delTGA	11.37:g.118427654_118427656delTCA	ENSP00000264021:p.Asp53del		A8K0F6|Q9H6V5	In_Frame_Del	DEL	ENST00000264021.3	37	CCDS53718.1																																																																																				0.473	IFT46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389627.1		NM_020153	
ITGB1	3688	broad.mit.edu;hgsc.bcm.edu	37	10	33199315	33199315	+	Missense_Mutation	SNP	T	T	C			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr10:33199315T>C	ENST00000396033.2	-	14	2135	c.2000A>G	c.(1999-2001)tAt>tGt	p.Y667C	ITGB1_ENST00000374956.4_Missense_Mutation_p.Y667C|ITGB1_ENST00000423113.1_Missense_Mutation_p.Y667C|ITGB1_ENST00000302278.3_Missense_Mutation_p.Y667C	NM_133376.2	NP_596867.1	P05556	ITB1_HUMAN	integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12)	667					axon extension (GO:0048675)|axon guidance (GO:0007411)|B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cardiac muscle cell differentiation (GO:0055007)|cell fate specification (GO:0001708)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular calcium ion homeostasis (GO:0006874)|cellular defense response (GO:0006968)|cellular response to ionizing radiation (GO:0071479)|cellular response to mechanical stimulus (GO:0071260)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|formation of radial glial scaffolds (GO:0021943)|G1/S transition of mitotic cell cycle (GO:0000082)|germ cell migration (GO:0008354)|heterotypic cell-cell adhesion (GO:0034113)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|maternal process involved in female pregnancy (GO:0060135)|mesodermal cell differentiation (GO:0048333)|negative regulation of anoikis (GO:2000811)|negative regulation of cell projection organization (GO:0031345)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of endocytosis (GO:0045807)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein transport within lipid bilayer (GO:0032594)|regulation of cell cycle (GO:0051726)|regulation of collagen catabolic process (GO:0010710)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of immune response (GO:0050776)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|response to transforming growth factor beta (GO:0071559)|sarcomere organization (GO:0045214)|tight junction assembly (GO:0070830)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	acrosomal vesicle (GO:0001669)|basement membrane (GO:0005604)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integrin alpha1-beta1 complex (GO:0034665)|integrin alpha10-beta1 complex (GO:0034680)|integrin alpha11-beta1 complex (GO:0034681)|integrin alpha2-beta1 complex (GO:0034666)|integrin alpha3-beta1 complex (GO:0034667)|integrin alpha7-beta1 complex (GO:0034677)|integrin alpha8-beta1 complex (GO:0034678)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|intercalated disc (GO:0014704)|invadopodium membrane (GO:0071438)|membrane (GO:0016020)|membrane raft (GO:0045121)|myelin sheath abaxonal region (GO:0035748)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|cell adhesion molecule binding (GO:0050839)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)|peptide binding (GO:0042277)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|virus receptor activity (GO:0001618)	p.Y667C(2)		autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Ovarian(717;1.34e-05)|Breast(68;0.0634)			Antithymocyte globulin(DB00098)	AATGTTAAAATAGGAACATTC	0.408																																																	2	Substitution - Missense(2)	kidney(2)											47.0	48.0	48.0					10																	33199315		2203	4296	6499	SO:0001583	missense	3688			BC020057	CCDS7174.1	10p11.2	2010-10-13			ENSG00000150093	ENSG00000150093		"""CD molecules"", ""Integrins"""	6153	protein-coding gene	gene with protein product		135630		FNRB, MSK12, MDF2		2524991	Standard	NM_033668		Approved	CD29, GPIIA	uc001iwt.4	P05556	OTTHUMG00000017928	ENST00000396033.2:c.2000A>G	10.37:g.33199315T>C	ENSP00000379350:p.Tyr667Cys		A8K6N2|D3DRX9|D3DRY3|D3DRY4|D3DRY5|P78466|P78467|Q13089|Q13090|Q13091|Q13212|Q14622|Q14647|Q29RW2|Q7Z3V1|Q8WUM6	Missense_Mutation	SNP	ENST00000396033.2	37	CCDS7174.1	.	.	.	.	.	.	.	.	.	.	T	17.36	3.369533	0.61624	.	.	ENSG00000150093	ENST00000396033;ENST00000423113;ENST00000302278;ENST00000374956	D;D;D;D	0.91894	-2.93;-2.93;-2.93;-2.93	5.65	5.65	0.86999	Integrin beta subunit, tail (2);	0.279243	0.40640	N	0.001052	D	0.94857	0.8338	M	0.75447	2.3	0.31580	N	0.655277	P;P;P;P;P	0.52842	0.931;0.944;0.881;0.502;0.956	P;P;P;B;P	0.58660	0.757;0.843;0.729;0.326;0.774	D	0.94735	0.7913	10	0.44086	T	0.13	.	15.8844	0.79232	0.0:0.0:0.0:1.0	.	667;667;667;667;667	P05556-2;P05556;P05556-5;P05556-3;P05556-4	.;ITB1_HUMAN;.;.;.	C	667	ENSP00000379350:Y667C;ENSP00000388694:Y667C;ENSP00000303351:Y667C;ENSP00000364094:Y667C	ENSP00000303351:Y667C	Y	-	2	0	ITGB1	33239321	0.999000	0.42202	0.722000	0.30670	0.766000	0.43426	5.119000	0.64679	2.163000	0.67991	0.459000	0.35465	TAT		0.408	ITGB1-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047496.1		NM_002211	
JUN	3725	broad.mit.edu;hgsc.bcm.edu	37	1	59248705	59248705	+	Missense_Mutation	SNP	G	G	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr1:59248705G>T	ENST00000371222.2	-	1	1080	c.38C>A	c.(37-39)gCc>gAc	p.A13D	RP4-794H19.2_ENST00000419531.2_lincRNA	NM_002228.3	NP_002219.1	P05412	JUN_HUMAN	jun proto-oncogene	13					aging (GO:0007568)|angiogenesis (GO:0001525)|axon regeneration (GO:0031103)|cellular response to calcium ion (GO:0071277)|cellular response to potassium ion starvation (GO:0051365)|circadian rhythm (GO:0007623)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|leading edge cell differentiation (GO:0035026)|learning (GO:0007612)|liver development (GO:0001889)|membrane depolarization (GO:0051899)|microglial cell activation (GO:0001774)|monocyte differentiation (GO:0030224)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA binding (GO:0043392)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress (GO:1990441)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA replication (GO:0045740)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of monocyte differentiation (GO:0045657)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle (GO:0051726)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|release of cytochrome c from mitochondria (GO:0001836)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|SMAD protein import into nucleus (GO:0007184)|SMAD protein signal transduction (GO:0060395)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nuclear chromosome (GO:0000228)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	cAMP response element binding (GO:0035497)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|R-SMAD binding (GO:0070412)|Rho GTPase activator activity (GO:0005100)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A13D(1)		breast(2)|kidney(2)|lung(5)|skin(1)	10	all_cancers(7;8.55e-07)				Arsenic trioxide(DB01169)|Irbesartan(DB01029)|Pseudoephedrine(DB00852)|Vinblastine(DB00570)	GGCGTTGAGGGCATCGTCATA	0.557			A		sarcoma																																			Dom	yes		1	1p32-p31	3725	jun oncogene		M	1	Substitution - Missense(1)	kidney(1)											102.0	110.0	107.0					1																	59248705		2203	4300	6503	SO:0001583	missense	3725			AY217548	CCDS610.1	1p32-p31	2013-01-10	2010-08-27		ENSG00000177606	ENSG00000177606		"""basic leucine zipper proteins"""	6204	protein-coding gene	gene with protein product		165160	"""v-jun avian sarcoma virus 17 oncogene homolog"", ""v-jun sarcoma virus 17 oncogene homolog (avian)"", ""jun oncogene"""			3194415	Standard	NM_002228		Approved	c-Jun, AP-1	uc001cze.3	P05412	OTTHUMG00000008376	ENST00000371222.2:c.38C>A	1.37:g.59248705G>T	ENSP00000360266:p.Ala13Asp		Q6FHM7|Q96G93	Missense_Mutation	SNP	ENST00000371222.2	37	CCDS610.1	.	.	.	.	.	.	.	.	.	.	G	19.58	3.854552	0.71719	.	.	ENSG00000177606	ENST00000371222	T	0.35048	1.33	4.39	4.39	0.52855	Jun-like transcription factor (1);	0.080529	0.48286	U	0.000196	T	0.27278	0.0669	N	0.16567	0.415	0.58432	D	0.999999	P	0.43231	0.801	B	0.40741	0.339	T	0.12451	-1.0547	10	0.46703	T	0.11	-0.5303	17.1679	0.86821	0.0:0.0:1.0:0.0	.	13	P05412	JUN_HUMAN	D	13	ENSP00000360266:A13D	ENSP00000360266:A13D	A	-	2	0	JUN	59021293	1.000000	0.71417	1.000000	0.80357	0.845000	0.48019	9.160000	0.94734	2.255000	0.74692	0.561000	0.74099	GCC		0.557	JUN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023042.1		NM_002228	
KCNT2	343450	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	196254849	196254849	+	Nonsense_Mutation	SNP	G	G	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr1:196254849G>A	ENST00000294725.9	-	23	3550	c.2635C>T	c.(2635-2637)Cga>Tga	p.R879*	KCNT2_ENST00000609185.1_Nonsense_Mutation_p.R805*|KCNT2_ENST00000367431.4_Nonsense_Mutation_p.R805*|KCNT2_ENST00000367433.5_Nonsense_Mutation_p.R855*|KCNT2_ENST00000498426.1_5'UTR|KCNT2_ENST00000451324.2_3'UTR			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	879					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)	p.R879*(1)		NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(16)|lung(43)|ovary(5)|pancreas(1)|prostate(1)|skin(11)|stomach(2)|upper_aerodigestive_tract(1)	97						AAAGGCAGTCGAAACATAAAG	0.383																																																	1	Substitution - Nonsense(1)	kidney(1)											83.0	81.0	82.0					1																	196254849		2203	4300	6503	SO:0001587	stop_gained	343450			BX647852, AY359444, AK127807	CCDS1384.1, CCDS72994.1, CCDS72995.1	1q31.3	2012-07-05			ENSG00000162687	ENSG00000162687		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	18866	protein-coding gene	gene with protein product	"""sodium and chloride activated ATP sensitive potassium channel"""	610044				16382103	Standard	NM_198503		Approved	KCa4.2, SLICK, SLO2.1	uc001gtd.1	Q6UVM3	OTTHUMG00000035611	ENST00000294725.9:c.2635C>T	1.37:g.196254849G>A	ENSP00000294725:p.Arg879*		Q3SY59|Q5VTN1|Q6ZMT3	Nonsense_Mutation	SNP	ENST00000294725.9	37	CCDS1384.1	.	.	.	.	.	.	.	.	.	.	G	40	8.396762	0.98794	.	.	ENSG00000162687	ENST00000367433;ENST00000367431;ENST00000294725	.	.	.	5.57	5.57	0.84162	.	0.000000	0.52532	D	0.000076	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.3986	13.6193	0.62128	0.0:0.0:0.8447:0.1553	.	.	.	.	X	855;805;879	.	ENSP00000294725:R879X	R	-	1	2	KCNT2	194521472	1.000000	0.71417	0.989000	0.46669	0.988000	0.76386	9.099000	0.94207	2.779000	0.95612	0.591000	0.81541	CGA		0.383	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086418.2		NM_198503	
KIF14	9928	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	200555334	200555334	+	Missense_Mutation	SNP	G	G	C			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr1:200555334G>C	ENST00000367350.4	-	19	3574	c.3136C>G	c.(3136-3138)Cgc>Ggc	p.R1046G		NM_014875.2	NP_055690.1	Q15058	KIF14_HUMAN	kinesin family member 14	1046	Required for CIT-binding.				ATP catabolic process (GO:0006200)|cytoskeleton-dependent intracellular transport (GO:0030705)|establishment of protein localization (GO:0045184)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of integrin activation (GO:0033624)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of Rap protein signal transduction (GO:0032487)|substrate adhesion-dependent cell spreading (GO:0034446)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|PDZ domain binding (GO:0030165)	p.R1046G(1)		NS(1)|breast(5)|central_nervous_system(2)|endometrium(8)|kidney(8)|large_intestine(15)|lung(13)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	61						CTTGCATGGCGGATGCTATGG	0.353																																																	1	Substitution - Missense(1)	kidney(1)											118.0	122.0	120.0					1																	200555334		2203	4298	6501	SO:0001583	missense	9928			D26361	CCDS30963.1	1q32.1	2008-03-03			ENSG00000118193	ENSG00000118193		"""Kinesins"""	19181	protein-coding gene	gene with protein product		611279				7584044	Standard	NM_014875		Approved	KIAA0042	uc010ppk.1	Q15058	OTTHUMG00000035723	ENST00000367350.4:c.3136C>G	1.37:g.200555334G>C	ENSP00000356319:p.Arg1046Gly		Q14CI8|Q4G0A5|Q5T1W3	Missense_Mutation	SNP	ENST00000367350.4	37	CCDS30963.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.114410	0.77210	.	.	ENSG00000118193	ENST00000367350	T	0.18174	2.23	4.97	4.97	0.65823	.	0.130103	0.51477	D	0.000081	T	0.40322	0.1112	M	0.72894	2.215	0.52501	D	0.999958	D	0.71674	0.998	D	0.63703	0.917	T	0.12372	-1.0550	10	0.37606	T	0.19	.	18.582	0.91174	0.0:0.0:1.0:0.0	.	1046	Q15058	KIF14_HUMAN	G	1046	ENSP00000356319:R1046G	ENSP00000356319:R1046G	R	-	1	0	KIF14	198821957	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.067000	0.71193	2.442000	0.82660	0.491000	0.48974	CGC		0.353	KIF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086878.1		NM_014875	
KIF1A	547	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	241686667	241686667	+	Nonsense_Mutation	SNP	G	G	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr2:241686667G>A	ENST00000320389.7	-	27	2904	c.2746C>T	c.(2746-2748)Cag>Tag	p.Q916*	KIF1A_ENST00000498729.2_Nonsense_Mutation_p.Q1017*	NM_004321.6	NP_004312.2	Q12756	KIF1A_HUMAN	kinesin family member 1A	916					anterograde axon cargo transport (GO:0008089)|ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)	p.Q916*(1)		NS(1)|central_nervous_system(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(25)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	66		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		TCAAAATGCTGGTCATCAAAG	0.552																																																	1	Substitution - Nonsense(1)	kidney(1)											64.0	70.0	68.0					2																	241686667		1951	4153	6104	SO:0001587	stop_gained	547			AF004425	CCDS46561.1, CCDS58757.1	2q37.2	2014-09-17	2004-01-09	2004-01-14	ENSG00000130294	ENSG00000130294		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	888	protein-coding gene	gene with protein product		601255	"""axonal transport of synaptic vesicles"", ""chromosome 2 open reading frame 20"", ""spastic paraplegia 30 (autosomal recessive)"""	ATSV, C2orf20, SPG30		7539720, 10323250, 22258533	Standard	NM_001244008		Approved	UNC104	uc010fzk.3	Q12756	OTTHUMG00000151940	ENST00000320389.7:c.2746C>T	2.37:g.241686667G>A	ENSP00000322791:p.Gln916*		B0I1S5|F5H045|O95068|Q13355|Q14752|Q2NKJ6|Q4LE42|Q53T78|Q59GH1|Q63Z40|Q6P1R9|Q7KZ57	Nonsense_Mutation	SNP	ENST00000320389.7	37	CCDS46561.1	.	.	.	.	.	.	.	.	.	.	G	44	10.622107	0.99439	.	.	ENSG00000130294	ENST00000320389;ENST00000498729;ENST00000373308;ENST00000404283	.	.	.	4.61	2.68	0.31781	.	0.062457	0.64402	U	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10111	T	0.7	.	13.0981	0.59204	0.0:0.3097:0.6903:0.0	.	.	.	.	X	916;1017;1017;1017	.	ENSP00000322791:Q916X	Q	-	1	0	KIF1A	241335340	0.999000	0.42202	0.993000	0.49108	0.864000	0.49448	2.002000	0.40835	0.320000	0.23234	0.467000	0.42956	CAG		0.552	KIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324536.3		NM_138483	
LCP2	3937	broad.mit.edu;hgsc.bcm.edu	37	5	169694070	169694070	+	Missense_Mutation	SNP	G	G	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr5:169694070G>A	ENST00000046794.5	-	9	1246	c.631C>T	c.(631-633)Cca>Tca	p.P211S	LCP2_ENST00000521416.1_Missense_Mutation_p.P6S	NM_005565.3	NP_005556.1	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2 (SH2 domain containing leukocyte protein of 76kDa)	211					blood coagulation (GO:0007596)|cytokine secretion (GO:0050663)|Fc-epsilon receptor signaling pathway (GO:0038095)|immune response (GO:0006955)|innate immune response (GO:0045087)|mast cell activation (GO:0045576)|platelet activation (GO:0030168)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)		p.P211S(2)		cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	23	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.247)		GTCTGGGGTGGGGGCAGTGGC	0.537																																																	2	Substitution - Missense(2)	kidney(2)											140.0	152.0	148.0					5																	169694070		1975	4159	6134	SO:0001583	missense	3937				CCDS47339.1	5q35.1	2013-02-14	2002-08-29		ENSG00000043462	ENSG00000043462		"""SH2 domain containing"""	6529	protein-coding gene	gene with protein product	"""76 kDa tyrosine phosphoprotein"", ""SH2 domain-containing leukocyte protein of 76kD"""	601603	"""lymphocyte cytosolic protein 2 (SH2 domain-containing leukocyte protein of 76kD)"""	SLP76		7706237	Standard	NM_005565		Approved	SLP-76	uc003man.1	Q13094	OTTHUMG00000163121	ENST00000046794.5:c.631C>T	5.37:g.169694070G>A	ENSP00000046794:p.Pro211Ser		A8KA25|Q53XV4	Missense_Mutation	SNP	ENST00000046794.5	37	CCDS47339.1	.	.	.	.	.	.	.	.	.	.	G	7.158	0.585150	0.13749	.	.	ENSG00000043462	ENST00000046794;ENST00000521416;ENST00000520344	T;T	0.43688	0.96;0.94	5.18	3.33	0.38152	.	0.436636	0.23870	N	0.043755	T	0.33789	0.0875	L	0.43152	1.355	0.09310	N	0.999999	B;B;B	0.30793	0.295;0.027;0.033	B;B;B	0.32211	0.142;0.009;0.021	T	0.14980	-1.0453	9	.	.	.	-0.3784	10.5029	0.44817	0.0:0.0:0.6473:0.3527	.	6;211;211	E7ESF6;A8KA25;Q13094	.;.;LCP2_HUMAN	S	211;6;6	ENSP00000046794:P211S;ENSP00000428871:P6S	.	P	-	1	0	LCP2	169626648	0.847000	0.29606	0.036000	0.18154	0.123000	0.20343	1.681000	0.37618	0.526000	0.28541	0.561000	0.74099	CCA		0.537	LCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371727.1		NM_005565	
RP13-60M5.2	0	broad.mit.edu;ucsc.edu	37	9	91262512	91262512	+	lincRNA	SNP	G	G	C			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr9:91262512G>C	ENST00000418343.2	-	0	239																											CAGTGAGTAAGGGGTTGGATT	0.393																																																	0													154.0	145.0	147.0					9																	91262512		1940	4134	6074			286238																															9.37:g.91262512G>C				Missense_Mutation	SNP	ENST00000418343.2	37																																																																																					0.393	RP13-60M5.2-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000052976.2			
LRP12	29967	hgsc.bcm.edu;ucsc.edu	37	8	105503470	105503470	+	Missense_Mutation	SNP	C	C	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr8:105503470C>T	ENST00000276654.5	-	7	2119	c.2011G>A	c.(2011-2013)Gtt>Att	p.V671I	LRP12_ENST00000424843.2_Missense_Mutation_p.V652I|LRP12_ENST00000518375.1_5'UTR	NM_013437.4	NP_038465.1	Q9Y561	LRP12_HUMAN	low density lipoprotein receptor-related protein 12	671					endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48			OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)			GGAGCTGCAACCCCACCAGAT	0.488																																																	0													78.0	75.0	76.0					8																	105503470		2203	4300	6503	SO:0001583	missense	29967			AF166350	CCDS6303.1, CCDS47907.1	8q22.2	2013-02-27	2010-01-26		ENSG00000147650	ENSG00000147650		"""Low density lipoprotein receptors"""	31708	protein-coding gene	gene with protein product						12809483, 14676824	Standard	NM_013437		Approved	ST7, FLJ12929	uc003yma.3	Q9Y561	OTTHUMG00000164892	ENST00000276654.5:c.2011G>A	8.37:g.105503470C>T	ENSP00000276654:p.Val671Ile		A8K137|B4DRQ2	Missense_Mutation	SNP	ENST00000276654.5	37	CCDS6303.1	.	.	.	.	.	.	.	.	.	.	C	14.44	2.536511	0.45176	.	.	ENSG00000147650	ENST00000424843;ENST00000276654;ENST00000520873	D;D	0.83673	-1.75;-1.68	5.72	3.9	0.45041	.	0.240138	0.43110	D	0.000602	T	0.70649	0.3248	N	0.19112	0.55	0.39646	D	0.970392	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.67229	-0.5723	10	0.36615	T	0.2	-21.4697	12.0121	0.53293	0.0:0.8606:0.0:0.1394	.	652;671	Q9Y561-2;Q9Y561	.;LRP12_HUMAN	I	652;671;36	ENSP00000399148:V652I;ENSP00000276654:V671I	ENSP00000276654:V671I	V	-	1	0	LRP12	105572646	0.961000	0.32948	1.000000	0.80357	0.997000	0.91878	1.955000	0.40372	1.554000	0.49487	0.650000	0.86243	GTT		0.488	LRP12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380821.1		NM_013437	
MAGEC1	9947	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	140993373	140993373	+	Silent	SNP	G	G	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chrX:140993373G>A	ENST00000285879.4	+	4	469	c.183G>A	c.(181-183)gaG>gaA	p.E61E	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	61								p.E61D(1)|p.E61E(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127	Acute lymphoblastic leukemia(192;6.56e-05)					CTGAGGGGGAGGACTCCTCGG	0.602										HNSCC(15;0.026)																																							2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|kidney(1)											79.0	80.0	80.0					X																	140993373		2203	4300	6503	SO:0001819	synonymous_variant	9947			AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 1"""	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.183G>A	X.37:g.140993373G>A			A0PK03|O75451|Q8TCV4	Silent	SNP	ENST00000285879.4	37	CCDS35417.1																																																																																				0.602	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1		NM_005462	
MEGF6	1953	broad.mit.edu	37	1	3519151	3519152	+	Frame_Shift_Del	DEL	CA	CA	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr1:3519151_3519152delCA	ENST00000356575.4	-	2	370_371	c.144_145delTG	c.(142-147)tgtgctfs	p.A49fs		NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	49	EMI. {ECO:0000255|PROSITE- ProRule:PRU00384}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			cervix(2)|endometrium(3)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_cancers(77;0.00681)|all_epithelial(69;0.00301)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.105)	all_epithelial(116;7.41e-22)|all_lung(118;8.3e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.78e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.86e-22)|GBM - Glioblastoma multiforme(42;1.96e-12)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000448)|BRCA - Breast invasive adenocarcinoma(365;0.000779)|KIRC - Kidney renal clear cell carcinoma(229;0.00645)|STAD - Stomach adenocarcinoma(132;0.00669)|Lung(427;0.213)		TCCTGCTCAGCACACACGTGGG	0.708																																					Ovarian(73;978 3658)												0																																										SO:0001589	frameshift_variant	1953			AB011539	CCDS41237.1	1p36.3	2008-02-05	2006-03-31	2006-03-31	ENSG00000162591	ENSG00000162591			3232	protein-coding gene	gene with protein product		604266	"""EGF-like-domain, multiple 3"""	EGFL3		9693030	Standard	NM_001409		Approved		uc001akl.3	O75095	OTTHUMG00000000611	ENST00000356575.4:c.144_145delTG	1.37:g.3519155_3519156delCA	ENSP00000348982:p.Ala49fs		Q4AC86|Q5VV39	Frame_Shift_Del	DEL	ENST00000356575.4	37	CCDS41237.1																																																																																				0.708	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1		NM_001409	
PLEKHA3	65977	hgsc.bcm.edu;ucsc.edu	37	2	179350870	179350870	+	Intron	SNP	G	G	C			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr2:179350870G>C	ENST00000234453.5	+	2	559				PLEKHA3_ENST00000461474.1_Intron	NM_019091.3	NP_061964.3	Q9HB20	PKHA3_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 3							Golgi apparatus (GO:0005794)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phospholipid binding (GO:0005543)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	11			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.0266)|all cancers(119;0.0865)			AGCTCTGTAGGGTTTTGATAA	0.368																																																	0													223.0	199.0	206.0					2																	179350870		692	1591	2283	SO:0001627	intron_variant	100302152			AF286162	CCDS33336.1	2q31.2	2013-01-10	2002-01-14		ENSG00000116095	ENSG00000116095		"""Pleckstrin homology (PH) domain containing"""	14338	protein-coding gene	gene with protein product	"""four-phosphate-adaptor protein 1"""	607774	"""pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3"""			11001876, 15107860	Standard	NM_019091		Approved	FAPP1	uc002umn.3	Q9HB20	OTTHUMG00000154446	ENST00000234453.5:c.157+386G>C	2.37:g.179350870G>C			Q4ZG69|Q86TQ1|Q9NXT3	RNA	SNP	ENST00000234453.5	37	CCDS33336.1																																																																																				0.368	PLEKHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335241.2		NM_019091	
MSR1	4481	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	16035394	16035394	+	Splice_Site	SNP	C	C	T	rs150131889	byFrequency	TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr8:16035394C>T	ENST00000262101.5	-	2	225		c.e2+1		MSR1_ENST00000536385.1_Splice_Site|MSR1_ENST00000350896.3_Splice_Site|MSR1_ENST00000355282.2_Splice_Site|MSR1_ENST00000445506.2_Splice_Site|MSR1_ENST00000381998.4_Splice_Site			P21757	MSRE_HUMAN	macrophage scavenger receptor 1						cholesterol transport (GO:0030301)|lipoprotein transport (GO:0042953)|plasma lipoprotein particle clearance (GO:0034381)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|receptor-mediated endocytosis (GO:0006898)	collagen trimer (GO:0005581)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|plasma membrane (GO:0005886)	low-density lipoprotein particle binding (GO:0030169)|scavenger receptor activity (GO:0005044)	p.?(2)		haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(7)|lung(14)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	37				Colorectal(111;0.00475)|COAD - Colon adenocarcinoma(73;0.0164)		CCTCTACTTACTCGGAGGAAG	0.428																																																	2	Unknown(2)	kidney(2)											72.0	67.0	69.0					8																	16035394		2203	4300	6503	SO:0001630	splice_region_variant	4481			D13263	CCDS5995.1, CCDS5996.1, CCDS5997.1	8p22	2006-02-22			ENSG00000038945	ENSG00000038945		"""CD molecules"""	7376	protein-coding gene	gene with protein product		153622				2251254	Standard	NM_138715		Approved	SCARA1, CD204	uc003wwz.3	P21757	OTTHUMG00000094809	ENST00000262101.5:c.103+1G>A	8.37:g.16035394C>T			D3DSP3|O60505|P21759|Q45F10	Splice_Site	SNP	ENST00000262101.5	37	CCDS5995.1	.	.	.	.	.	.	.	.	.	.	C	9.336	1.061785	0.19987	.	.	ENSG00000038945	ENST00000350896;ENST00000262101;ENST00000445506;ENST00000355282;ENST00000381998;ENST00000518960;ENST00000518026	.	.	.	5.36	5.36	0.76844	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.016	0.71584	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MSR1	16079765	0.994000	0.37717	0.980000	0.43619	0.027000	0.11550	3.498000	0.53302	2.703000	0.92315	0.543000	0.68304	.		0.428	MSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211627.2			Intron
MTMR11	10903	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	149908474	149908474	+	Splice_Site	SNP	C	C	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr1:149908474C>T	ENST00000439741.2	-	1	317		c.e1+1		MTMR11_ENST00000492824.1_Splice_Site|MTMR11_ENST00000406732.3_Splice_Site|MTMR11_ENST00000369140.3_5'Flank|MTMR11_ENST00000361405.6_Splice_Site	NM_001145862.1	NP_001139334.1	A4FU01	MTMRB_HUMAN	myotubularin related protein 11								phosphatase activity (GO:0016791)	p.?(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(13)|prostate(2)|stomach(1)|urinary_tract(4)	34	Breast(34;0.0009)|Ovarian(49;0.0377)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)			cttctccttacccccatctct	0.592																																																	1	Unknown(1)	kidney(1)											118.0	112.0	114.0					1																	149908474		692	1591	2283	SO:0001630	splice_region_variant	10903			AK097000	CCDS72901.1, CCDS72902.1	1q12-q21	2011-06-09			ENSG00000014914	ENSG00000014914		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	24307	protein-coding gene	gene with protein product	"""cisplatin resistance associated"""					12495846	Standard	NM_181873		Approved	CRA	uc001etl.4	A4FU01	OTTHUMG00000012207	ENST00000439741.2:c.66+1G>A	1.37:g.149908474C>T			B3KUE4|B4DJI6|B4DQF5|B4E3Q6|Q3ZCP7|Q5SZ62|Q6P2Q8|Q99752|Q99753	Splice_Site	SNP	ENST00000439741.2	37	CCDS53360.1																																																																																				0.592	MTMR11-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			NM_181873	Intron
NDP	4693	broad.mit.edu;ucsc.edu	37	X	43809267	43809267	+	Silent	SNP	C	C	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chrX:43809267C>A	ENST00000378062.5	-	3	587	c.180G>T	c.(178-180)gtG>gtT	p.V60V	NDP_ENST00000470584.1_5'UTR|NDP-AS1_ENST00000435093.1_RNA	NM_000266.3	NP_000257.1	Q00604	NDP_HUMAN	Norrie disease (pseudoglioma)	60	CTCK. {ECO:0000255|PROSITE- ProRule:PRU00039}.		V -> E (in ND; reduction of protein amount in the extracellular matrix). {ECO:0000269|PubMed:1303264}.		canonical Wnt signaling pathway (GO:0060070)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|extracellular matrix-cell signaling (GO:0035426)|nervous system development (GO:0007399)|placenta development (GO:0001890)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|vacuole organization (GO:0007033)|visual perception (GO:0007601)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)	frizzled binding (GO:0005109)|growth factor activity (GO:0008083)|protein homodimerization activity (GO:0042803)	p.V60V(1)		kidney(1)|lung(2)	3						TGGCCAGGAGCACCATCTGGG	0.567											OREG0019744	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					1	Substitution - coding silent(1)	kidney(1)											31.0	25.0	27.0					X																	43809267		2198	4297	6495	SO:0001819	synonymous_variant	4693			X65882	CCDS14262.1	Xp11.4-p11.3	2013-02-26			ENSG00000124479	ENSG00000124479		"""Endogenous ligands"""	7678	protein-coding gene	gene with protein product		300658	"""exudative vitreoretinopathy 2 (X-linked)"""	EVR2		8252044	Standard	NM_000266		Approved	norrin	uc004dga.3	Q00604	OTTHUMG00000021391	ENST00000378062.5:c.180G>T	X.37:g.43809267C>A		919	B2R8K6|Q5JYH5	Silent	SNP	ENST00000378062.5	37	CCDS14262.1																																																																																				0.567	NDP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056309.1		NM_000266	
NFKBIZ	64332	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	101573504	101573504	+	Missense_Mutation	SNP	G	G	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr3:101573504G>T	ENST00000326172.5	+	6	1535	c.1420G>T	c.(1420-1422)Gat>Tat	p.D474Y	NFKBIZ_ENST00000326151.5_Missense_Mutation_p.D352Y|NFKBIZ_ENST00000394054.2_Missense_Mutation_p.D374Y	NM_031419.3	NP_113607.1	Q9BYH8	IKBZ_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, zeta	474	Interaction with NFKB1/p50. {ECO:0000250}.				inflammatory response (GO:0006954)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.D474Y(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24						TCACATGCTGGATATTAAAGA	0.463																																																	1	Substitution - Missense(1)	kidney(1)											118.0	104.0	109.0					3																	101573504		2203	4300	6503	SO:0001583	missense	64332			AF548362	CCDS2946.1, CCDS43123.1	3p12-q12	2013-01-10			ENSG00000144802	ENSG00000144802		"""Ankyrin repeat domain containing"""	29805	protein-coding gene	gene with protein product	"""IL-1 inducible nuclear ankyrin-repeat protein"""	608004				12565889, 16513645	Standard	NM_031419		Approved	MAIL, FLJ34463, INAP	uc003dvp.3	Q9BYH8	OTTHUMG00000159194	ENST00000326172.5:c.1420G>T	3.37:g.101573504G>T	ENSP00000325663:p.Asp474Tyr		B3KNR2|D3DN54|Q8IUL4|Q8NAZ8	Missense_Mutation	SNP	ENST00000326172.5	37	CCDS2946.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.486554	0.84854	.	.	ENSG00000144802	ENST00000483180;ENST00000394054;ENST00000326151;ENST00000326172	T;T;T;T	0.39056	1.1;1.1;1.1;1.1	5.68	5.68	0.88126	Ankyrin repeat-containing domain (4);	0.064033	0.64402	D	0.000005	T	0.73187	0.3555	M	0.89658	3.05	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.77640	-0.2512	10	0.72032	D	0.01	-5.8635	20.148	0.98083	0.0:0.0:1.0:0.0	.	352;474	Q9BYH8-3;Q9BYH8	.;IKBZ_HUMAN	Y	374;374;352;474	ENSP00000419800:D374Y;ENSP00000377618:D374Y;ENSP00000325593:D352Y;ENSP00000325663:D474Y	ENSP00000325593:D352Y	D	+	1	0	NFKBIZ	103056194	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.192000	0.77771	2.834000	0.97654	0.655000	0.94253	GAT		0.463	NFKBIZ-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353793.1		NM_031419	
OR4N3P	390539	broad.mit.edu	37	15	22414024	22414024	+	IGR	SNP	C	C	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr15:22414024C>T								RP11-69H14.6 (30216 upstream) : RP11-2F9.4 (19865 downstream)																							ATCAAGCTGGCTTGCACCGAC	0.507																																																	0																																										SO:0001628	intergenic_variant	390539																															15.37:g.22414024C>T				Missense_Mutation	SNP		37																																																																																				0	0.507									
OR6V1	346517	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	142749937	142749937	+	Missense_Mutation	SNP	G	G	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr7:142749937G>A	ENST00000418316.1	+	1	521	c.500G>A	c.(499-501)tGc>tAc	p.C167Y		NM_001001667.1	NP_001001667.1	Q8N148	OR6V1_HUMAN	olfactory receptor, family 6, subfamily V, member 1	167						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.C167Y(2)		endometrium(2)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|upper_aerodigestive_tract(1)	20	Melanoma(164;0.059)					CTTGATTACTGCCATGGCGAC	0.547																																																	2	Substitution - Missense(2)	kidney(2)											117.0	125.0	123.0					7																	142749937		2116	4257	6373	SO:0001583	missense	346517				CCDS47728.1	7q34	2014-05-06			ENSG00000225781	ENSG00000225781		"""GPCR / Class A : Olfactory receptors"""	15090	protein-coding gene	gene with protein product						12732197	Standard	NM_001001667		Approved	GPR138	uc011ksv.2	Q8N148	OTTHUMG00000158385	ENST00000418316.1:c.500G>A	7.37:g.142749937G>A	ENSP00000396085:p.Cys167Tyr		A4D2I0|B9EH48|Q6IF70	Missense_Mutation	SNP	ENST00000418316.1	37	CCDS47728.1	.	.	.	.	.	.	.	.	.	.	G	11.33	1.608363	0.28623	.	.	ENSG00000225781	ENST00000418316	T	0.00245	8.45	4.72	3.81	0.43845	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00724	0.0024	M	0.91249	3.19	0.24389	N	0.994756	D	0.89917	1.0	D	0.97110	1.0	T	0.24512	-1.0158	9	0.87932	D	0	.	12.439	0.55614	0.0:0.1705:0.8295:0.0	.	167	Q8N148	OR6V1_HUMAN	Y	167	ENSP00000396085:C167Y	ENSP00000396085:C167Y	C	+	2	0	OR6V1	142460059	0.997000	0.39634	0.582000	0.28627	0.091000	0.18340	1.588000	0.36633	1.170000	0.42753	0.655000	0.94253	TGC		0.547	OR6V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350860.1			
PBRM1	55193	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	52610659	52610659	+	Frame_Shift_Del	DEL	T	T	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr3:52610659delT	ENST00000296302.7	-	22	3590	c.3589delA	c.(3589-3591)attfs	p.I1197fs	PBRM1_ENST00000394830.3_Frame_Shift_Del_p.I1172fs|PBRM1_ENST00000409114.3_Frame_Shift_Del_p.I1212fs|PBRM1_ENST00000409057.1_Frame_Shift_Del_p.I1197fs|PBRM1_ENST00000409767.1_Frame_Shift_Del_p.I1212fs|PBRM1_ENST00000410007.1_Frame_Shift_Del_p.I1172fs|PBRM1_ENST00000337303.4_Frame_Shift_Del_p.I1197fs|SMIM4_ENST00000476842.1_Intron|PBRM1_ENST00000356770.4_Frame_Shift_Del_p.I1165fs			Q86U86	PB1_HUMAN	polybromo 1	1197	BAH 2. {ECO:0000255|PROSITE- ProRule:PRU00370}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TCTGGGTGAATGAAGATGGGG	0.363			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																			Rec	yes		3	3p21	55193	polybromo 1		E	0													117.0	113.0	115.0					3																	52610659		2203	4300	6503	SO:0001589	frameshift_variant	55193			BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.3589delA	3.37:g.52610659delT	ENSP00000296302:p.Ile1197fs		A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Frame_Shift_Del	DEL	ENST00000296302.7	37																																																																																					0.363	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1		NM_018165	
PCDH12	51294	broad.mit.edu	37	5	141337114	141337114	+	Missense_Mutation	SNP	C	C	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr5:141337114C>A	ENST00000231484.3	-	1	1513	c.303G>T	c.(301-303)tgG>tgT	p.W101C	PCDH12_ENST00000512221.1_5'Flank	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	101	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.W101C(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGCAGGGATCCCACTGTCGGC	0.587																																																	1	Substitution - Missense(1)	kidney(1)											70.0	74.0	73.0					5																	141337114		2203	4300	6503	SO:0001583	missense	51294			AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"""Cadherins / Protocadherins : Non-clustered"""	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.303G>T	5.37:g.141337114C>A	ENSP00000231484:p.Trp101Cys		Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Missense_Mutation	SNP	ENST00000231484.3	37	CCDS4269.1	.	.	.	.	.	.	.	.	.	.	C	11.74	1.728627	0.30593	.	.	ENSG00000113555	ENST00000231484	T	0.26957	1.7	4.81	2.36	0.29203	Cadherin, N-terminal (1);Cadherin (3);	1.422770	0.03830	N	0.268906	T	0.17323	0.0416	N	0.08118	0	0.34435	D	0.69896	P	0.41784	0.762	B	0.41440	0.357	T	0.15752	-1.0426	10	0.66056	D	0.02	.	7.1945	0.25845	0.0:0.6966:0.0:0.3034	.	101	Q9NPG4	PCD12_HUMAN	C	101	ENSP00000231484:W101C	ENSP00000231484:W101C	W	-	3	0	PCDH12	141317298	0.000000	0.05858	0.926000	0.36857	0.994000	0.84299	-1.041000	0.03542	0.918000	0.36919	0.563000	0.77884	TGG		0.587	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1		NM_016580	
PCLO	27445	hgsc.bcm.edu	37	7	82784434	82784463	+	In_Frame_Del	DEL	TTTGTTGAGCCAGGCTGTTGAGATGGGGGC	TTTGTTGAGCCAGGCTGTTGAGATGGGGGC	-	rs6972461|rs375483530|rs369207658	byFrequency	TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	TTTGTTGAGCCAGGCTGTTGAGATGGGGGC	TTTGTTGAGCCAGGCTGTTGAGATGGGGGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr7:82784434_82784463delTTTGTTGAGCCAGGCTGTTGAGATGGGGGC	ENST00000333891.9	-	2	1831_1860	c.1494_1523delGCCCCCATCTCAACAGCCTGGCTCAACAAA	c.(1492-1524)aagcccccatctcaacagcctggctcaacaaaa>aaa	p.498_508KPPSQQPGSTK>K	PCLO_ENST00000423517.2_In_Frame_Del_p.498_508KPPSQQPGSTK>K	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.P500Q(2)|p.P446Q(1)		breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						AGGTGGGGGTTTTGTTGAGCCAGGCTGTTGAGATGGGGGCTTTGCTGAGC	0.6																																																	3	Substitution - Missense(3)	lung(3)																																								SO:0001651	inframe_deletion	27445			AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.1494_1523delGCCCCCATCTCAACAGCCTGGCTCAACAAA	7.37:g.82784434_82784463delTTTGTTGAGCCAGGCTGTTGAGATGGGGGC	ENSP00000334319:p.Lys498_Thr507del			In_Frame_Del	DEL	ENST00000333891.9	37	CCDS47630.1																																																																																				0.600	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5		NM_014510	
PLEKHO2	80301	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	65157277	65157277	+	Silent	SNP	G	G	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr15:65157277G>A	ENST00000323544.4	+	6	791	c.663G>A	c.(661-663)agG>agA	p.R221R	AC069368.3_ENST00000437723.1_Intron	NM_001195059.1|NM_025201.4	NP_001181988.1|NP_079477.2	Q8TD55	PKHO2_HUMAN	pleckstrin homology domain containing, family O member 2	221	Pro-rich.							p.R221R(1)		NS(1)|breast(1)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	25						CTGGTGACAGGGTGGAGACCC	0.627																																																	1	Substitution - coding silent(1)	kidney(1)											65.0	73.0	70.0					15																	65157277		2202	4299	6501	SO:0001819	synonymous_variant	80301			AF318373	CCDS10196.1, CCDS73739.1	15q22.31	2013-01-10	2007-12-14	2007-12-14	ENSG00000241839	ENSG00000241839		"""Pleckstrin homology (PH) domain containing"""	30026	protein-coding gene	gene with protein product			"""pleckstrin homology domain containing, family Q member 1"""	PLEKHQ1		12477932	Standard	NM_025201		Approved	DKFZp761K2312, PP1628, pp9099	uc002anv.3	Q8TD55	OTTHUMG00000133050	ENST00000323544.4:c.663G>A	15.37:g.65157277G>A			Q7L4H4|Q8WYS8	Silent	SNP	ENST00000323544.4	37	CCDS10196.1																																																																																				0.627	PLEKHO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256659.1		NM_025201	
PROS1	5627	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	93598122	93598122	+	Frame_Shift_Del	DEL	A	A	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr3:93598122delA	ENST00000394236.3	-	13	1845	c.1529delT	c.(1528-1530)gtgfs	p.V510fs	PROS1_ENST00000407433.1_Frame_Shift_Del_p.V379fs	NM_000313.3	NP_000304.2	P07225	PROS_HUMAN	protein S (alpha)	510	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|leukocyte migration (GO:0050900)|negative regulation of endopeptidase activity (GO:0010951)|peptidyl-glutamic acid carboxylation (GO:0017187)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|Golgi membrane (GO:0000139)|platelet alpha granule lumen (GO:0031093)	calcium ion binding (GO:0005509)|endopeptidase inhibitor activity (GO:0004866)			endometrium(3)|kidney(5)|large_intestine(8)|lung(26)|ovary(1)|skin(2)|urinary_tract(1)	46					Drotrecogin alfa(DB00055)|Menadione(DB00170)|Sodium Tetradecyl Sulfate(DB00464)	ATTCAAGGTCACATTTACATG	0.433																																																	0													153.0	132.0	139.0					3																	93598122		2203	4300	6503	SO:0001589	frameshift_variant	5627				CCDS2923.1	3q11.1	2013-06-03			ENSG00000184500	ENSG00000184500			9456	protein-coding gene	gene with protein product		176880		PROS		214811, 1833851	Standard	NM_000313		Approved		uc003drb.4	P07225	OTTHUMG00000150354	ENST00000394236.3:c.1529delT	3.37:g.93598122delA	ENSP00000377783:p.Val510fs		A8KAC9|D3DN28|Q15518|Q7Z715|Q9UCZ8	Frame_Shift_Del	DEL	ENST00000394236.3	37	CCDS2923.1																																																																																				0.433	PROS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317762.1		NM_000313	
GBA2	57704	broad.mit.edu;hgsc.bcm.edu	37	9	35751400	35751400	+	5'Flank	SNP	C	C	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr9:35751400C>T	ENST00000378103.3	-	0	0				MSMP_ENST00000414286.1_5'Flank|GBA2_ENST00000545786.1_5'Flank|RGP1_ENST00000456972.2_Missense_Mutation_p.R249C|RGP1_ENST00000378078.4_Missense_Mutation_p.R209C|GBA2_ENST00000378094.4_5'Flank	NM_020944.2	NP_065995.1	Q9HCG7	GBA2_HUMAN	glucosidase, beta (bile acid) 2						bile acid metabolic process (GO:0008206)|cell death (GO:0008219)|central nervous system neuron development (GO:0021954)|glucosylceramide catabolic process (GO:0006680)|glycoside catabolic process (GO:0016139)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)	beta-glucosidase activity (GO:0008422)|glucosylceramidase activity (GO:0004348)	p.R249C(1)|p.R209C(1)		NS(1)|kidney(3)|large_intestine(5)|lung(5)|ovary(4)|skin(3)	21	all_epithelial(49;0.167)		Lung(28;0.00416)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			CACATCCTGCCGCAGCCTCCG	0.527																																																	2	Substitution - Missense(2)	kidney(2)											47.0	54.0	52.0					9																	35751400		2043	4206	6249	SO:0001631	upstream_gene_variant	9827			AJ309567	CCDS6589.1	9p13.2	2013-09-11			ENSG00000070610	ENSG00000070610			18986	protein-coding gene	gene with protein product	"""bile acid beta-glucosidase"", ""non-lysosomal glucosylceramidase"""	609471	"""spastic paraplegia 46 (autosomal recessive)"""	SPG46		11489889, 23332916, 23332917	Standard	NM_020944		Approved	KIAA1605, AD035, DKFZp762K054	uc003zxw.3	Q9HCG7	OTTHUMG00000021024		9.37:g.35751400C>T	Exception_encountered		D3DRP2|Q5TCV6|Q96A51|Q96LY1|Q96SJ2|Q9H2L8	Missense_Mutation	SNP	ENST00000378103.3	37	CCDS6589.1	.	.	.	.	.	.	.	.	.	.	C	19.42	3.824879	0.71143	.	.	ENSG00000107185	ENST00000456972;ENST00000378078	.	.	.	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.76884	0.4050	M	0.81112	2.525	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.67548	0.952;0.952	T	0.79388	-0.1824	9	0.87932	D	0	-14.8918	9.6342	0.39798	0.1433:0.783:0.0:0.0737	.	209;209	Q92546;A8K0K1	RGP1_HUMAN;.	C	249;209	.	ENSP00000367318:R209C	R	+	1	0	RGP1	35741400	0.992000	0.36948	1.000000	0.80357	0.987000	0.75469	6.659000	0.74412	2.756000	0.94617	0.561000	0.74099	CGC		0.527	GBA2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055456.1		NM_020944	
RNF144A	9781	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	7164573	7164573	+	Missense_Mutation	SNP	G	G	C			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr2:7164573G>C	ENST00000320892.6	+	7	1025	c.583G>C	c.(583-585)Gac>Cac	p.D195H	RNF144A_ENST00000467276.1_3'UTR	NM_014746.3	NP_055561.2	P50876	R144A_HUMAN	ring finger protein 144A	195					protein ubiquitination (GO:0016567)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.D195H(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(15)|ovary(1)|prostate(1)	25	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;0.226)		OV - Ovarian serous cystadenocarcinoma(76;0.195)		CATCGAGCGAGACGAAGGCTG	0.557																																																	1	Substitution - Missense(1)	kidney(1)											108.0	91.0	97.0					2																	7164573		2203	4300	6503	SO:0001583	missense	9781			D79983	CCDS1657.1	2p25.2	2008-02-05	2007-08-20	2007-08-20	ENSG00000151692	ENSG00000151692		"""RING-type (C3HC4) zinc fingers"""	20457	protein-coding gene	gene with protein product			"""ring finger protein 144"""	RNF144		8724849, 10431818	Standard	NM_014746		Approved	UBCE7IP4, KIAA0161	uc002qys.3	P50876	OTTHUMG00000090353	ENST00000320892.6:c.583G>C	2.37:g.7164573G>C	ENSP00000321330:p.Asp195His		D6W4Y6|Q585H5	Missense_Mutation	SNP	ENST00000320892.6	37	CCDS1657.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.83|16.83	3.230189|3.230189	0.58777|0.58777	.|.	.|.	ENSG00000151692|ENSG00000151692	ENST00000320892|ENST00000432850	T|.	0.81163|.	-1.46|.	5.87|5.87	5.87|5.87	0.94306|0.94306	Zinc finger, C6HC-type (2);Zinc finger, RING-type (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.76069|0.76069	0.3936|0.3936	M|M	0.69248|0.69248	2.105|2.105	0.80722|0.80722	D|D	1|1	D|.	0.71674|.	0.998|.	D|.	0.72338|.	0.977|.	T|T	0.72763|0.72763	-0.4195|-0.4195	10|5	0.54805|.	T|.	0.06|.	.|.	20.2181|20.2181	0.98305|0.98305	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	195|.	P50876|.	R144A_HUMAN|.	H|D	195|190	ENSP00000321330:D195H|.	ENSP00000321330:D195H|.	D|E	+|+	1|3	0|2	RNF144A|RNF144A	7082024|7082024	1.000000|1.000000	0.71417|0.71417	0.638000|0.638000	0.29380|0.29380	0.056000|0.056000	0.15407|0.15407	7.949000|7.949000	0.87791|0.87791	2.785000|2.785000	0.95823|0.95823	0.655000|0.655000	0.94253|0.94253	GAC|GAG		0.557	RNF144A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206725.2		NM_014746	
SETD2	29072	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	47163209	47163209	+	Nonsense_Mutation	SNP	T	T	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr3:47163209T>A	ENST00000409792.3	-	3	2959	c.2917A>T	c.(2917-2919)Aga>Tga	p.R973*		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	973					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)	p.R973*(1)|p.R470*(1)		breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		CTTCCTCTTCTTTCAGGCAAT	0.408			"""N, F, S, Mis"""		clear cell renal carcinoma																																			Rec	yes		3	3p21.31	29072	SET domain containing 2		E	2	Substitution - Nonsense(2)	kidney(2)											93.0	93.0	93.0					3																	47163209		2203	4300	6503	SO:0001587	stop_gained	29072			AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"""Chromatin-modifying enzymes / K-methyltransferases"""	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.2917A>T	3.37:g.47163209T>A	ENSP00000386759:p.Arg973*		O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Nonsense_Mutation	SNP	ENST00000409792.3	37	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	T	38	6.882653	0.97908	.	.	ENSG00000181555	ENST00000451092;ENST00000543224;ENST00000409792;ENST00000412450	.	.	.	5.16	3.99	0.46301	.	0.291027	0.29846	N	0.011051	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.2577	0.06837	0.0:0.1436:0.2478:0.6086	.	.	.	.	X	973;973;973;929	.	.	R	-	1	2	SETD2	47138213	0.035000	0.19736	0.997000	0.53966	0.977000	0.68977	0.334000	0.19787	2.154000	0.67381	0.528000	0.53228	AGA		0.408	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2		NM_014159	
SLC2A8	29988	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	130169437	130169437	+	Missense_Mutation	SNP	G	G	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr9:130169437G>A	ENST00000373371.3	+	10	1432	c.1343G>A	c.(1342-1344)tGc>tAc	p.C448Y	SLC2A8_ENST00000373360.3_Silent_p.L399L|SLC2A8_ENST00000373352.1_Missense_Mutation_p.C185Y	NM_001271712.1|NM_014580.3	NP_001258641.1|NP_055395.2	Q9NY64	GTR8_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 8	448					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|insulin receptor signaling pathway (GO:0008286)|male meiosis I (GO:0007141)|response to hypoxia (GO:0001666)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	glucose binding (GO:0005536)|glucose transmembrane transporter activity (GO:0005355)	p.C448Y(1)		cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)	11						TCCGCTTTCTGCATCTTCAGT	0.542																																																	1	Substitution - Missense(1)	kidney(1)											148.0	129.0	136.0					9																	130169437		2203	4300	6503	SO:0001583	missense	29988			AJ245937	CCDS6870.1, CCDS65138.1, CCDS75903.1	9q33.3	2013-05-22	2008-09-02		ENSG00000136856	ENSG00000136856		"""Solute carriers"""	13812	protein-coding gene	gene with protein product		605245	"""solute carrier family 2 (facilitated glucose transporter) member 8"""			10671487, 10821868	Standard	NM_014580		Approved	GLUTX1, GLUT8	uc004bqu.4	Q9NY64	OTTHUMG00000020702	ENST00000373371.3:c.1343G>A	9.37:g.130169437G>A	ENSP00000362469:p.Cys448Tyr		Q8WUZ9|Q9NSC4	Missense_Mutation	SNP	ENST00000373371.3	37	CCDS6870.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.112202	0.77210	.	.	ENSG00000136856	ENST00000373371;ENST00000373352	T;T	0.80824	0.32;-1.42	4.94	4.94	0.65067	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.92090	0.7493	M	0.93150	3.385	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93767	0.7071	10	0.62326	D	0.03	.	16.0489	0.80740	0.0:0.0:1.0:0.0	.	448	Q9NY64	GTR8_HUMAN	Y	448;185	ENSP00000362469:C448Y;ENSP00000362450:C185Y	ENSP00000362450:C185Y	C	+	2	0	SLC2A8	129209258	1.000000	0.71417	0.957000	0.39632	0.794000	0.44872	9.167000	0.94773	2.445000	0.82738	0.655000	0.94253	TGC		0.542	SLC2A8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054177.1		NM_014580	
TRO	7216	hgsc.bcm.edu	37	X	54949288	54949289	+	Frame_Shift_Ins	INS	-	-	C			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chrX:54949288_54949289insC	ENST00000173898.7	+	3	435_436	c.323_324insC	c.(322-327)aacctgfs	p.L109fs	TRO_ENST00000375041.2_Intron|TRO_ENST00000420798.2_Intron|TRO_ENST00000319167.8_Frame_Shift_Ins_p.L109fs|TRO_ENST00000399736.1_Intron|TRO_ENST00000375022.4_Frame_Shift_Ins_p.L109fs|TRO_ENST00000484031.1_Intron	NM_001039705.2	NP_001034794.1	Q12816	TROP_HUMAN	trophinin	109					embryo implantation (GO:0007566)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|skin(2)|urinary_tract(1)	37						CAGGCTTTAAACCTGCCAGTCA	0.49																																																	0																																										SO:0001589	frameshift_variant	7216			U04811	CCDS43958.1, CCDS43959.1, CCDS59527.1, CCDS59528.1, CCDS59529.1	Xp11.22-p11.21	2008-02-05			ENSG00000067445	ENSG00000067445			12326	protein-coding gene	gene with protein product		300132				9533028, 11454705	Standard	NM_001039705		Approved	MAGE-D3, KIAA1114, MAGED3	uc004dtq.4	Q12816	OTTHUMG00000021640	ENST00000173898.7:c.325dupC	X.37:g.54949290_54949290dupC	ENSP00000173898:p.Leu109fs		B1AKE9|B1AKF1|F5GY27|Q96SX2|Q9NU89|Q9UPN8	Frame_Shift_Ins	INS	ENST00000173898.7	37	CCDS43959.1																																																																																				0.490	TRO-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056837.3		NM_016157	
TAF1	6872	broad.mit.edu	37	X	70607246	70607246	+	Missense_Mutation	SNP	C	C	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chrX:70607246C>T	ENST00000373790.4	+	15	2410	c.2359C>T	c.(2359-2361)Ccc>Tcc	p.P787S	TAF1_ENST00000276072.3_Missense_Mutation_p.P808S|TAF1_ENST00000423759.1_Missense_Mutation_p.P808S|TAF1_ENST00000449580.1_Missense_Mutation_p.P787S	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	787	Histone acetyltransferase (HAT).				cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.P808S(1)|p.P787S(1)		breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				CCAGCAGTGTCCCTTGTTTGA	0.443																																																	2	Substitution - Missense(2)	kidney(2)											130.0	118.0	122.0					X																	70607246		2203	4300	6503	SO:0001583	missense	6872				CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"""Chromatin-modifying enzymes / K-acetyltransferases"""	11535	protein-coding gene	gene with protein product		313650	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD"", ""dystonia 3 (with Parkinsonism)"""	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.2359C>T	X.37:g.70607246C>T	ENSP00000362895:p.Pro787Ser		A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Missense_Mutation	SNP	ENST00000373790.4	37	CCDS35325.1	.	.	.	.	.	.	.	.	.	.	.	14.79	2.640167	0.47153	.	.	ENSG00000147133	ENST00000373790;ENST00000449580;ENST00000423759;ENST00000276072	T;T;T;T	0.22743	1.94;1.94;1.94;1.94	4.7	4.7	0.59300	Transcription initiation factor TFIID subunit 1, domain of unknown function (1);	0.153774	0.64402	D	0.000013	T	0.46328	0.1387	H	0.95402	3.665	0.58432	D	0.999996	P;B	0.42941	0.794;0.384	P;B	0.48227	0.571;0.426	T	0.60291	-0.7292	10	0.72032	D	0.01	.	11.688	0.51499	0.0:0.9112:0.0:0.0888	.	787;808	P21675;P21675-2	TAF1_HUMAN;.	S	787;787;808;808	ENSP00000362895:P787S;ENSP00000389000:P787S;ENSP00000406549:P808S;ENSP00000276072:P808S	ENSP00000276072:P808S	P	+	1	0	TAF1	70523971	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	4.618000	0.61211	2.070000	0.61991	0.458000	0.33432	CCC		0.443	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2		NM_004606	
TRRAP	8295	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	98507681	98507681	+	Silent	SNP	T	T	C			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr7:98507681T>C	ENST00000359863.4	+	15	1562	c.1353T>C	c.(1351-1353)gtT>gtC	p.V451V	TRRAP_ENST00000446306.3_Silent_p.V451V|TRRAP_ENST00000355540.3_Silent_p.V451V	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	451					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)	p.V451V(2)		NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			CCCGTTAGGTTTTCGTTCTCA	0.443																																																	2	Substitution - coding silent(2)	kidney(2)											108.0	116.0	113.0					7																	98507681		2203	4300	6503	SO:0001819	synonymous_variant	8295			AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.1353T>C	7.37:g.98507681T>C			A4D265|O75218|Q9Y631|Q9Y6H4	Silent	SNP	ENST00000359863.4	37	CCDS59066.1	.	.	.	.	.	.	.	.	.	.	T	4.365	0.067332	0.08388	.	.	ENSG00000196367	ENST00000456197	.	.	.	4.85	-5.27	0.02763	.	.	.	.	.	T	0.37758	0.1015	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.34625	-0.9821	4	.	.	.	.	2.3318	0.04238	0.2823:0.1401:0.4135:0.1641	.	.	.	.	S	166	.	.	F	+	2	0	TRRAP	98345617	0.979000	0.34478	0.920000	0.36463	0.660000	0.38997	0.054000	0.14205	-1.369000	0.02147	-0.501000	0.04562	TTT		0.443	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1		NM_003496	
UBXN11	91544	broad.mit.edu	37	1	26608878	26608883	+	In_Frame_Del	DEL	CCGGGA	CCGGGA	-	rs1134580|rs1134581|rs140364749	byFrequency	TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	CCGGGA	CCGGGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr1:26608878_26608883delCCGGGA	ENST00000374222.1	-	16	1934_1939	c.1470_1475delTCCCGG	c.(1468-1476)ggtcccggc>ggc	p.490_492GPG>G	UBXN11_ENST00000374223.1_In_Frame_Del_p.247_249GPG>G|UBXN11_ENST00000314675.7_In_Frame_Del_p.370_372GPG>G|UBXN11_ENST00000374217.2_In_Frame_Del_p.457_459GPG>G|UBXN11_ENST00000357089.4_In_Frame_Del_p.457_459GPG>G|UBXN11_ENST00000374221.3_In_Frame_Del_p.490_492GPG>G			Q5T124	UBX11_HUMAN	UBX domain protein 11	490	3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|Pro-rich.		Missing.|Missing. {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.2}.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.G490_P515delGPGPSPGPGPGPSPGPGPGPSPCPGP(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						gggactggggccgggaccgggaccgg	0.718																																																	1	Deletion - In frame(1)	ovary(1)																																								SO:0001651	inframe_deletion	91544			AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"""UBX domain containing"""	30600	protein-coding gene	gene with protein product	"""socius"""	609151	"""UBX domain containing 5"""	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.1470_1475delTCCCGG	1.37:g.26608884_26608889delCCGGGA	ENSP00000363339:p.Gly492_Pro493del		D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	In_Frame_Del	DEL	ENST00000374222.1	37	CCDS41288.1																																																																																				0.718	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1		NM_145345	
TP53TG3D	729264	broad.mit.edu	37	16	32266881	32266881	+	IGR	DEL	T	T	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr16:32266881delT	ENST00000354614.3	+	0	412				RP11-56L13.7_ENST00000562604.1_RNA|TP53TG3D_ENST00000398664.3_3'UTR			Q9ULZ0	T53G3_HUMAN	TP53 target 3D							cytoplasm (GO:0005737)|nucleus (GO:0005634)											ttctttaaacttttttttttc	0.299																																																	0																																										SO:0001628	intergenic_variant	0				CCDS58456.1	16p11.2	2012-12-11			ENSG00000205456	ENSG00000205456			44657	protein-coding gene	gene with protein product							Standard	NM_001243722		Approved		uc021tgy.1	Q9ULZ0	OTTHUMG00000132469		16.37:g.32266881delT			B2R5K6|Q4KN31|Q9ULY9	RNA	DEL	ENST00000354614.3	37																																																																																					0.299	TP53TG3D-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding			NM_001243722	
MIR4477B	100616194	broad.mit.edu	37	9	68414259	68414259	+	RNA	SNP	C	C	T	rs368099104		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr9:68414259C>T	ENST00000581659.1	+	0	0					NR_039688.1|NR_039689.1				microRNA 4477b																		ccacagtggcctcaaagaact	0.483																																																	0																																												0					9	2011-09-12						"""ncRNAs / Micro RNAs"""	41898	non-coding RNA	RNA, micro							Standard	NR_039689		Approved	hsa-mir-4477b					9.37:g.68414259C>T				RNA	SNP	ENST00000581659.1	37																																																																																					0.483	MIR4477B-201	KNOWN	basic	miRNA	miRNA			NR_039689	
Unknown	0	broad.mit.edu	37	9	70182346	70182346	+	IGR	DEL	G	G	-	rs202095854|rs201125425|rs200827494	byFrequency	TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr9:70182346delG								FOXD4L5 (3531 upstream) : FOXD4L4 (244276 downstream)																							TCTGTGTATTGTTTTTTTTTT	0.239													G|G|-|deletion	3377	0.674321	0.6747	0.6671	5008	,	,		11982	0.5556		0.6928	False		,,,				2504	0.7822																0																																										SO:0001628	intergenic_variant	0																															9.37:g.70182346delG				RNA	DEL		37																																																																																				0	0.239									
RP1-241P17.4	0	broad.mit.edu	37	X	114953432	114953432	+	Missense_Mutation	SNP	G	G	T			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chrX:114953432G>T	ENST00000449327.1	-	1	237	c.118C>A	c.(118-120)Ctt>Att	p.L40I															p.L40I(1)									AGTTTACTAAGTGGTGTATGC	0.448																																																	1	Substitution - Missense(1)	kidney(1)																																								SO:0001583	missense	0																														ENST00000449327.1:c.118C>A	X.37:g.114953432G>T	ENSP00000391266:p.Leu40Ile			RNA	SNP	ENST00000449327.1	37		.	.	.	.	.	.	.	.	.	.	G	14.69	2.611032	0.46631	.	.	ENSG00000228532	ENST00000449327	T	0.27720	1.65	1.61	1.61	0.23674	.	0.000000	0.49916	U	0.000122	T	0.37210	0.0995	.	.	.	.	.	.	.	.	.	.	.	.	T	0.54022	-0.8355	6	0.66056	D	0.02	.	8.89	0.35427	0.0:0.0:1.0:0.0	.	.	.	.	I	40	ENSP00000391266:L40I	ENSP00000391266:L40I	L	-	1	0	RP1-241P17.4	114859688	1.000000	0.71417	0.999000	0.59377	0.876000	0.50452	3.497000	0.53295	1.158000	0.42547	0.456000	0.33151	CTT		0.448	RP1-241P17.4-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000057980.1			
USF1	7391	hgsc.bcm.edu;ucsc.edu	37	1	161011524	161011524	+	Frame_Shift_Del	DEL	C	C	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr1:161011524delC	ENST00000368021.3	-	6	593	c.389delG	c.(388-390)ggtfs	p.G130fs	USF1_ENST00000368020.1_Frame_Shift_Del_p.G130fs|F11R_ENST00000289779.3_5'Flank|TSTD1_ENST00000368023.3_5'Flank|TSTD1_ENST00000368024.1_5'Flank|TSTD1_ENST00000423014.2_5'Flank|USF1_ENST00000435396.1_Frame_Shift_Del_p.G71fs|TSTD1_ENST00000318289.10_5'Flank|USF1_ENST00000368019.1_Splice_Site	NM_007122.3	NP_009053.1	P22415	USF1_HUMAN	upstream transcription factor 1	130					carbon catabolite regulation of transcription (GO:0045990)|cellular response to insulin stimulus (GO:0032869)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|late viral transcription (GO:0019086)|lipid homeostasis (GO:0055088)|negative regulation of fibrinolysis (GO:0051918)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by glucose (GO:0000432)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter by glucose (GO:0000430)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)	p.G130fs*33(1)		central_nervous_system(1)|large_intestine(3)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9	all_cancers(52;6.73e-18)|Breast(13;0.012)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			CGATGTGGTACCCCCTGCCCC	0.592											OREG0013936	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					1	Deletion - Frameshift(1)	large_intestine(1)											87.0	82.0	84.0					1																	161011524		2203	4300	6503	SO:0001589	frameshift_variant	7391			BC035505	CCDS1214.1	1q22-q23	2013-05-21			ENSG00000158773	ENSG00000158773		"""Basic helix-loop-helix proteins"""	12593	protein-coding gene	gene with protein product		191523				8486371	Standard	NM_007122		Approved	UEF, MLTFI, bHLHb11	uc031pqv.1	P22415	OTTHUMG00000031472	ENST00000368021.3:c.389delG	1.37:g.161011524delC	ENSP00000357000:p.Gly130fs	1813	B2RBZ4|Q5SY46|Q7Z5Y1	Frame_Shift_Del	DEL	ENST00000368021.3	37	CCDS1214.1																																																																																				0.592	USF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077050.1		NM_007122	
VHL	7428	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	10188200	10188200	+	Missense_Mutation	SNP	C	C	A	rs5030812|rs5030811		TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr3:10188200C>A	ENST00000256474.2	+	2	1183	c.343C>A	c.(343-345)Cac>Aac	p.H115N	VHL_ENST00000477538.1_3'UTR|VHL_ENST00000345392.2_Intron	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	115	Involved in binding to CCT complex.		H -> Q (in VHLD; type II). {ECO:0000269|PubMed:9829912}.|H -> R (in VHLD; type II; dbSNP:rs5030812).|H -> Y (in VHLD; type I; dbSNP:rs5030811). {ECO:0000269|PubMed:8956040}.		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.H115N(7)|p.H115Y(5)|p.?(3)|p.H115fs*15(1)|p.H115D(1)|p.H115fs*41(1)|p.H115fs*42(1)|p.H115fs*44(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		CCCGATAGGTCACCTTTGGCT	0.532		1	"""D, Mis, N, F, S"""		"""renal, hemangioma, pheochromocytoma"""	"""renal, hemangioma, pheochromocytoma"""			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																														yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"""E, M, O"""	20	Substitution - Missense(13)|Deletion - Frameshift(4)|Unknown(3)	kidney(19)|pancreas(1)	GRCh37	CM961423|CM982005	VHL	M	rs5030811						167.0	155.0	159.0					3																	10188200		2203	4300	6503	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.343C>A	3.37:g.10188200C>A	ENSP00000256474:p.His115Asn		B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	C	16.81	3.226834	0.58668	.	.	ENSG00000134086	ENST00000256474;ENST00000450183	D	0.99963	-9.61	5.07	5.07	0.68467	von Hippel-Lindau disease tumor suppressor,  beta domain (1);von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);	0.000000	0.85682	D	0.000000	D	0.99966	0.9987	M	0.84511	2.7	0.80722	D	1	D	0.64830	0.994	D	0.67548	0.952	D	0.94877	0.8035	10	0.72032	D	0.01	0.1733	16.3181	0.82935	0.0:1.0:0.0:0.0	.	115	P40337	VHL_HUMAN	N	115;33	ENSP00000256474:H115N	ENSP00000256474:H115N	H	+	1	0	VHL	10163200	1.000000	0.71417	1.000000	0.80357	0.141000	0.21300	5.806000	0.69150	2.530000	0.85305	0.563000	0.77884	CAC		0.532	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
WNK1	65125	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	977348	977348	+	Intron	SNP	A	A	G			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr12:977348A>G	ENST00000315939.6	+	9	2782				WNK1_ENST00000340908.4_Intron|WNK1_ENST00000574564.1_Missense_Mutation_p.H118R|WNK1_ENST00000535572.1_Intron|WNK1_ENST00000530271.2_Missense_Mutation_p.H904R|WNK1_ENST00000537687.1_Missense_Mutation_p.H819R	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1						intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)	p.H819R(1)		breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			ATACAGGTCCATCCTATGTTT	0.458																																					Colon(19;451 567 6672 12618 28860)												1	Substitution - Missense(1)	kidney(1)											66.0	65.0	66.0					12																	977348		1930	4133	6063	SO:0001627	intron_variant	65125			AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 167"""	605232	"""protein kinase, lysine deficient 1"", ""hereditary sensory neuropathy, type II"""	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.2140-3083A>G	12.37:g.977348A>G			A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	37	CCDS8506.1	.	.	.	.	.	.	.	.	.	.	A	0.191	-1.052956	0.01965	.	.	ENSG00000060237	ENST00000537687;ENST00000530271	T;T	0.43294	0.95;0.95	5.03	2.54	0.30619	.	.	.	.	.	T	0.31009	0.0783	.	.	.	0.18873	N	0.999981	B	0.18968	0.032	B	0.15870	0.014	T	0.22906	-1.0203	8	0.54805	T	0.06	.	8.2725	0.31853	0.7248:0.1489:0.0:0.1263	.	904	F5H2M7	.	R	819;904	ENSP00000444465:H819R;ENSP00000433548:H904R	ENSP00000433548:H904R	H	+	2	0	WNK1	847609	1.000000	0.71417	0.265000	0.24526	0.497000	0.33675	1.962000	0.40442	0.324000	0.23333	0.383000	0.25322	CAT		0.458	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1		NM_018979	
ZNF385A	25946	hgsc.bcm.edu;ucsc.edu	37	12	54764794	54764794	+	Frame_Shift_Del	DEL	C	C	-			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr12:54764794delC	ENST00000338010.5	-	6	804	c.751delG	c.(751-753)gaafs	p.E251fs	ZNF385A_ENST00000552382.1_5'UTR|ZNF385A_ENST00000551771.1_Frame_Shift_Del_p.E150fs|ZNF385A_ENST00000551109.1_Frame_Shift_Del_p.E231fs|ZNF385A_ENST00000352268.6_Frame_Shift_Del_p.E170fs|RP11-753H16.5_ENST00000552785.1_RNA|RP11-753H16.3_ENST00000550474.1_RNA|ZNF385A_ENST00000394313.2_Frame_Shift_Del_p.E231fs|ZNF385A_ENST00000546970.1_Frame_Shift_Del_p.E231fs	NM_001130967.1	NP_001124439.1	Q96PM9	Z385A_HUMAN	zinc finger protein 385A	251	Necessary for binding to ITPR1, CEBPA and p53/TP53 mRNAs. {ECO:0000250}.				apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|hemostasis (GO:0007599)|learning or memory (GO:0007611)|locomotory behavior (GO:0007626)|megakaryocyte development (GO:0035855)|mRNA localization resulting in posttranscriptional regulation of gene expression (GO:0010609)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)|positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:1902164)|positive regulation of fat cell differentiation (GO:0045600)|regulation of cytoplasmic translation (GO:2000765)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	DNA binding (GO:0003677)|mRNA 3'-UTR binding (GO:0003730)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|urinary_tract(1)	15						GCCTCTGGTTCCCCCGGGGTG	0.592																																																	0													77.0	87.0	83.0					12																	54764794		2203	4300	6503	SO:0001589	frameshift_variant	25946			AF304052	CCDS8879.1, CCDS44910.1, CCDS44911.1	12q13.13	2012-10-05	2007-12-06	2007-12-06		ENSG00000161642			17521	protein-coding gene	gene with protein product		609124	"""zinc finger protein 385"""	ZNF385			Standard	XM_005268785		Approved	DKFZp586G1122, Hzf, ZFP385	uc001sfy.3	Q96PM9	OTTHUMG00000169840	ENST00000338010.5:c.751delG	12.37:g.54764794delC	ENSP00000338927:p.Glu251fs		B2RDN5|B4DKH2|F1T0F1|J3KNS3|Q5VH53|Q9H7R6|Q9UFU3	Frame_Shift_Del	DEL	ENST00000338010.5	37	CCDS44911.1																																																																																				0.592	ZNF385A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406162.1		NM_015481	
ZNF655	79027	broad.mit.edu;hgsc.bcm.edu	37	7	99169358	99169358	+	Intron	SNP	C	C	A			TCGA-CZ-5470-01A-01D-1501-10	TCGA-CZ-5470-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	c9a7ca9e-c36e-46c1-926f-4a57a0584cb0	d0636c20-cd70-4fdf-b273-4756d9effbf1	g.chr7:99169358C>A	ENST00000394163.2	+	3	319				GS1-259H13.10_ENST00000455905.1_Intron|GS1-259H13.10_ENST00000486324.1_Intron|ZNF655_ENST00000424881.1_Missense_Mutation_p.L62I|ZNF655_ENST00000493277.1_Missense_Mutation_p.L62I|ZNF655_ENST00000252713.4_Intron|ZNF655_ENST00000419215.2_3'UTR|ZNF655_ENST00000425063.1_Silent_p.I90I|ZNF655_ENST00000454654.1_Silent_p.I90I	NM_001009960.1|NM_138494.2	NP_001009960.1|NP_612503.1	Q8N720	ZN655_HUMAN	zinc finger protein 655						negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.L62I(1)		NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	16	all_epithelial(64;3.19e-09)|Lung NSC(181;0.0066)|all_lung(186;0.011)|Esophageal squamous(72;0.0166)					GGAACAGGATCTACAGGTCTT	0.443																																																	1	Substitution - Missense(1)	kidney(1)											55.0	51.0	52.0					7																	99169358		1840	4096	5936	SO:0001627	intron_variant	79027			AY099353	CCDS5669.1, CCDS5670.1, CCDS34695.1, CCDS47655.1	7q22.1	2013-01-08			ENSG00000197343	ENSG00000197343		"""Zinc fingers, C2H2-type"", ""-"""	30899	protein-coding gene	gene with protein product						11179890, 15558030	Standard	NM_001083956		Approved	VIK-1, VIK	uc010lgc.3	Q8N720	OTTHUMG00000156637	ENST00000394163.2:c.137-510C>A	7.37:g.99169358C>A			A4D291|A6NGD3|B4E3M4|B7Z9Q9|D6W5T4|Q8IV00|Q8TA89|Q96EZ3|Q9BQ85	Missense_Mutation	SNP	ENST00000394163.2	37	CCDS5669.1	.	.	.	.	.	.	.	.	.	.	C	15.26	2.781542	0.49891	.	.	ENSG00000197343	ENST00000493277;ENST00000422164;ENST00000422647;ENST00000427931;ENST00000424881	T;T;T;T;T	0.32515	3.42;1.49;1.45;1.46;3.42	5.17	3.36	0.38483	.	.	.	.	.	T	0.22975	0.0555	L	0.44542	1.39	0.80722	D	1	B	0.33612	0.419	B	0.30782	0.12	T	0.04664	-1.0935	9	0.52906	T	0.07	.	7.0384	0.25006	0.0:0.7187:0.1884:0.093	.	62	Q8N720-3	.	I	62	ENSP00000419135:L62I;ENSP00000389260:L62I;ENSP00000393750:L62I;ENSP00000392244:L62I;ENSP00000393876:L62I	ENSP00000389260:L62I	L	+	1	2	ZNF655	99007294	0.636000	0.27207	1.000000	0.80357	0.963000	0.63663	0.641000	0.24720	0.874000	0.35823	0.655000	0.94253	CTA		0.443	ZNF655-009	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000344929.1		NM_138494	
