#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_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	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_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	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_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	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_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	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_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
FBXO8	26269	broad.mit.edu	37	4	175183979	175183979	+	Missense_Mutation	SNP	T	T	C			TCGA-WB-A81K-01A-11D-A35I-08	TCGA-WB-A81K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c745e12-f34a-43b4-907f-25f18f3092ff	47fd631e-685a-4b72-8555-f76929369287	g.chr4:175183979T>C	ENST00000393674.2	-	2	1127	c.265A>G	c.(265-267)Act>Gct	p.T89A	FBXO8_ENST00000503293.1_Intron	NM_012180.2	NP_036312.2	Q9NRD0	FBX8_HUMAN	F-box protein 8	89	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell junction (GO:0030054)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			breast(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|prostate(1)|urinary_tract(1)	14		Prostate(90;0.00201)|Melanoma(52;0.012)|Renal(120;0.0183)|all_neural(102;0.0887)|all_hematologic(60;0.107)		all cancers(43;7.29e-18)|Epithelial(43;1.85e-15)|OV - Ovarian serous cystadenocarcinoma(60;5.62e-09)|GBM - Glioblastoma multiforme(59;0.00115)|STAD - Stomach adenocarcinoma(60;0.00299)|LUSC - Lung squamous cell carcinoma(193;0.1)		CAAAGGTCAGTTGCATTCAGG	0.423																																						ENST00000393674.2																			0				breast(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|prostate(1)|urinary_tract(1)	14						c.(265-267)Act>Gct		F-box protein 8							143.0	123.0	129.0					4																	175183979		2203	4300	6503	SO:0001583	missense	26269				regulation of ARF protein signal transduction|ubiquitin-dependent protein catabolic process	cytoplasm|ubiquitin ligase complex	ARF guanyl-nucleotide exchange factor activity	g.chr4:175183979T>C	AF174596	CCDS3820.1	4q34.1	2008-02-05	2004-06-15			ENSG00000164117		"""F-boxes /  ""other"""""	13587	protein-coding gene	gene with protein product		605649	"""F-box only protein 8"""			10531035, 10531037	Standard	NM_012180		Approved	FBX8, FBS	uc003itp.3	Q9NRD0		ENST00000393674.2:c.265A>G	4.37:g.175183979T>C	ENSP00000377280:p.Thr89Ala					FBXO8_ENST00000503293.1_Intron	p.T89A	NM_012180.2	NP_036312.2	Q9NRD0	FBX8_HUMAN		all cancers(43;7.29e-18)|Epithelial(43;1.85e-15)|OV - Ovarian serous cystadenocarcinoma(60;5.62e-09)|GBM - Glioblastoma multiforme(59;0.00115)|STAD - Stomach adenocarcinoma(60;0.00299)|LUSC - Lung squamous cell carcinoma(193;0.1)	2	1127	-		Prostate(90;0.00201)|Melanoma(52;0.012)|Renal(120;0.0183)|all_neural(102;0.0887)|all_hematologic(60;0.107)	89			F-box.		B2RB40|D3DP41|G5E9Z0|Q6UWN4|Q8IWE1|Q9NRP5|Q9UKC4	Missense_Mutation	SNP	ENST00000393674.2	37	c.265A>G	CCDS3820.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.311757	0.81358	.	.	ENSG00000164117	ENST00000393674;ENST00000513696	T;T	0.41758	0.99;0.99	5.67	5.67	0.87782	F-box domain, cyclin-like (1);F-box domain, Skp2-like (1);	0.000000	0.85682	D	0.000000	T	0.56746	0.2006	L	0.39566	1.225	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.59327	-0.7475	10	0.72032	D	0.01	.	15.9168	0.79524	0.0:0.0:0.0:1.0	.	89	Q9NRD0	FBX8_HUMAN	A	89	ENSP00000377280:T89A;ENSP00000427506:T89A	ENSP00000377280:T89A	T	-	1	0	FBXO8	175420554	1.000000	0.71417	0.997000	0.53966	0.994000	0.84299	7.396000	0.79891	2.166000	0.68216	0.383000	0.25322	ACT		0.423	FBXO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362085.2	NM_012180		9	50	0	0	0	1	0	9	50				
PRTG	283659	broad.mit.edu	37	15	55965852	55965852	+	Silent	SNP	A	A	G			TCGA-WB-A81K-01A-11D-A35I-08	TCGA-WB-A81K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c745e12-f34a-43b4-907f-25f18f3092ff	47fd631e-685a-4b72-8555-f76929369287	g.chr15:55965852A>G	ENST00000389286.4	-	10	1616	c.1569T>C	c.(1567-1569)atT>atC	p.I523I		NM_173814.4	NP_776175.2			protogenin											breast(1)|endometrium(6)|kidney(4)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	41				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)		TTGTCAAACTAATTTCAGGAG	0.443																																						ENST00000389286.4																			0				breast(1)|endometrium(6)|kidney(4)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	41						c.(1567-1569)atT>atC		protogenin							76.0	78.0	77.0					15																	55965852		1853	4091	5944	SO:0001819	synonymous_variant	283659				multicellular organismal development	integral to membrane		g.chr15:55965852A>G	AK098622	CCDS42040.1	15q21.3	2013-02-11	2010-06-24		ENSG00000166450	ENSG00000166450		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	26373	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 5"""	613261	"""protogenin homolog (Gallus gallus)"""				Standard	NM_173814		Approved	FLJ25756, IGDCC5	uc002adg.3	Q2VWP7		ENST00000389286.4:c.1569T>C	15.37:g.55965852A>G							p.I523I	NM_173814.4	NP_776175.2	Q2VWP7	PRTG_HUMAN		all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)	10	1616	-			523			Fibronectin type-III 2.			Silent	SNP	ENST00000389286.4	37	c.1569T>C	CCDS42040.1																																																																																				0.443	PRTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419357.1	NM_173814		8	55	0	0	0	1	0	8	55				
SLC36A2	153201	broad.mit.edu	37	5	150722489	150722489	+	Missense_Mutation	SNP	T	T	A			TCGA-WB-A81K-01A-11D-A35I-08	TCGA-WB-A81K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c745e12-f34a-43b4-907f-25f18f3092ff	47fd631e-685a-4b72-8555-f76929369287	g.chr5:150722489T>A	ENST00000335244.4	-	4	529	c.400A>T	c.(400-402)Aac>Tac	p.N134Y	SLC36A2_ENST00000521967.1_Missense_Mutation_p.N134Y	NM_181776.2	NP_861441.2	Q495M3	S36A2_HUMAN	solute carrier family 36 (proton/amino acid symporter), member 2	134					amino acid transport (GO:0006865)|ion transport (GO:0006811)|proline transmembrane transport (GO:0035524)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine transmembrane transporter activity (GO:0015187)|hydrogen:amino acid symporter activity (GO:0005280)|L-alanine transmembrane transporter activity (GO:0015180)|L-proline transmembrane transporter activity (GO:0015193)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(14)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Cycloserine(DB00260)	GCGTTGGGGTTGGCTTCTAGT	0.517																																						ENST00000335244.4																			0				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(14)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	33						c.(400-402)Aac>Tac		solute carrier family 36 (proton/amino acid symporter), member 2							179.0	143.0	155.0					5																	150722489		2203	4300	6503	SO:0001583	missense	153201				cellular nitrogen compound metabolic process	cytoplasm|integral to membrane|plasma membrane	glycine transmembrane transporter activity	g.chr5:150722489T>A	AY162214	CCDS4315.1	5q33.1	2013-05-22			ENSG00000186335	ENSG00000186335		"""Solute carriers"""	18762	protein-coding gene	gene with protein product		608331				11959859	Standard	NM_181776		Approved	PAT2, tramdorin, TRAMD1	uc003lty.3	Q495M3	OTTHUMG00000130129	ENST00000335244.4:c.400A>T	5.37:g.150722489T>A	ENSP00000334223:p.Asn134Tyr					SLC36A2_ENST00000521967.1_Missense_Mutation_p.N134Y	p.N134Y	NM_181776.2	NP_861441.2	Q495M3	S36A2_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		4	529	-		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	134					Q495M4|Q495M6|Q6ZWK5|Q7Z6B5	Missense_Mutation	SNP	ENST00000335244.4	37	c.400A>T	CCDS4315.1	.	.	.	.	.	.	.	.	.	.	T	11.94	1.788889	0.31685	.	.	ENSG00000186335	ENST00000335244;ENST00000521967	T;T	0.09445	3.81;2.98	4.87	2.51	0.30379	.	0.519730	0.22688	N	0.056855	T	0.06462	0.0166	N	0.14661	0.345	0.80722	D	1	B;B;B	0.19331	0.035;0.004;0.001	B;B;B	0.17722	0.019;0.016;0.003	T	0.26780	-1.0093	10	0.66056	D	0.02	-9.5167	8.1702	0.31249	0.0:0.2361:0.0:0.7639	.	134;134;134	B4DMY0;E5RJJ5;Q495M3	.;.;S36A2_HUMAN	Y	134	ENSP00000334223:N134Y;ENSP00000430535:N134Y	ENSP00000334223:N134Y	N	-	1	0	SLC36A2	150702682	0.019000	0.18553	0.969000	0.41365	0.654000	0.38779	0.627000	0.24506	0.456000	0.26937	0.533000	0.62120	AAC		0.517	SLC36A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252437.1			5	68	0	0	0	1	0	5	68				
HAO2	51179	broad.mit.edu	37	1	119934877	119934877	+	Missense_Mutation	SNP	G	G	A			TCGA-WB-A81K-01A-11D-A35I-08	TCGA-WB-A81K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c745e12-f34a-43b4-907f-25f18f3092ff	47fd631e-685a-4b72-8555-f76929369287	g.chr1:119934877G>A	ENST00000325945.3	+	6	989	c.916G>A	c.(916-918)Ggc>Agc	p.G306S	HAO2_ENST00000361035.4_Missense_Mutation_p.G319S	NM_001005783.1|NM_016527.2	NP_001005783.1|NP_057611.1	Q9NYQ3	HAOX2_HUMAN	hydroxyacid oxidase 2 (long chain)	306	FMN hydroxy acid dehydrogenase. {ECO:0000255|PROSITE-ProRule:PRU00683}.				fatty acid oxidation (GO:0019395)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)	(S)-2-hydroxy-acid oxidase activity (GO:0003973)|FMN binding (GO:0010181)|long-chain-(S)-2-hydroxy-long-chain-acid oxidase activity (GO:0052853)|medium-chain-(S)-2-hydroxy-acid oxidase activity (GO:0052854)|receptor binding (GO:0005102)|very-long-chain-(S)-2-hydroxy-acid oxidase activity (GO:0052852)			breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(10)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	30	all_neural(166;0.187)	all_lung(203;1.06e-06)|Lung NSC(69;7.5e-06)|all_epithelial(167;0.000284)		Lung(183;0.0155)|LUSC - Lung squamous cell carcinoma(189;0.0856)		AATCCTATGGGGCCTTGCCTG	0.498																																						ENST00000361035.4																			0				breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(10)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	30						c.(955-957)Ggc>Agc		hydroxyacid oxidase 2 (long chain)							112.0	105.0	107.0					1																	119934877		2203	4300	6503	SO:0001583	missense	51179				fatty acid alpha-oxidation	peroxisome	(S)-2-hydroxy-acid oxidase activity	g.chr1:119934877G>A	AF231917	CCDS901.1	1p13.3-p13.1	2008-07-18			ENSG00000116882	ENSG00000116882	1.1.3.15		4810	protein-coding gene	gene with protein product	"""(S)-2-hydroxy-acid oxidase"", ""glycolate oxidase"", ""long-chain L-2-hydroxy acid oxidase"", ""growth-inhibiting protein 16"""	605176				10777549	Standard	XM_005270913		Approved	HAOX2, GIG16	uc001ehr.1	Q9NYQ3	OTTHUMG00000012410	ENST00000325945.3:c.916G>A	1.37:g.119934877G>A	ENSP00000316339:p.Gly306Ser					HAO2_ENST00000325945.3_Missense_Mutation_p.G306S	p.G319S	NM_001005783.1	NP_001005783.1	Q9NYQ3	HAOX2_HUMAN		Lung(183;0.0155)|LUSC - Lung squamous cell carcinoma(189;0.0856)	7	1238	+	all_neural(166;0.187)	all_lung(203;1.06e-06)|Lung NSC(69;7.5e-06)|all_epithelial(167;0.000284)	306			FMN hydroxy acid dehydrogenase.		Q2TU86|Q5QP00|Q9UJS6	Missense_Mutation	SNP	ENST00000325945.3	37	c.955G>A	CCDS901.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.170008	0.78452	.	.	ENSG00000116882	ENST00000361035;ENST00000325945	T;T	0.42900	0.96;0.96	6.07	6.07	0.98685	Aldolase-type TIM barrel (1);FMN-dependent dehydrogenase (1);	0.045710	0.85682	D	0.000000	T	0.63153	0.2487	M	0.78285	2.405	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.59931	-0.7361	9	.	.	.	-21.514	20.6593	0.99626	0.0:0.0:1.0:0.0	.	306	Q9NYQ3	HAOX2_HUMAN	S	319;306	ENSP00000354314:G319S;ENSP00000316339:G306S	.	G	+	1	0	HAO2	119736400	1.000000	0.71417	1.000000	0.80357	0.462000	0.32619	9.331000	0.96430	2.885000	0.99019	0.655000	0.94253	GGC		0.498	HAO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034984.1	NM_001005783		3	25	0	0	0	1	0	3	25				
BAGE2	85319	broad.mit.edu	37	21	11058353	11058353	+	RNA	SNP	T	T	C	rs79433933		TCGA-WB-A81K-01A-11D-A35I-08	TCGA-WB-A81K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c745e12-f34a-43b4-907f-25f18f3092ff	47fd631e-685a-4b72-8555-f76929369287	g.chr21:11058353T>C	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		GAAATCTCTTTATAAAACCTT	0.343																																						ENST00000470054.1																			0													B melanoma antigen family, member 2							20.0	18.0	19.0					21																	11058353		692	1589	2281			85319							g.chr21:11058353T>C	AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"""cancer/testis antigen family 2, member 2"""					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		21.37:g.11058353T>C												Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)	0	324	-								A8K925|Q08ER0	RNA	SNP	ENST00000470054.1	37																																																																																						0.343	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482		6	103	0	0	0	1	0	6	103				
RP11-156P1.3	0	broad.mit.edu	37	17	45128742	45128742	+	RNA	SNP	T	T	G	rs34655963	byFrequency	TCGA-WB-A81K-01A-11D-A35I-08	TCGA-WB-A81K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c745e12-f34a-43b4-907f-25f18f3092ff	47fd631e-685a-4b72-8555-f76929369287	g.chr17:45128742T>G	ENST00000575173.1	-	0	418				LRRC37A17P_ENST00000570478.1_RNA																							TAATGATTTTTATTATACTTT	0.328													g|||	2160	0.43131	0.3593	0.4986	5008	,	,		16551	0.3482		0.4861	False		,,,				2504	0.5102					ENST00000575173.1																			0																																																			0							g.chr17:45128742T>G																													17.37:g.45128742T>G														0	418	-									RNA	SNP	ENST00000575173.1	37																																																																																						0.328	RP11-156P1.3-009	KNOWN	basic	lincRNA	processed_transcript	OTTHUMT00000440924.1			4	93	0	0	0	1	0	4	93				
FAT4	79633	broad.mit.edu	37	4	126408600	126408600	+	Missense_Mutation	SNP	C	C	G			TCGA-WB-A81K-01A-11D-A35I-08	TCGA-WB-A81K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c745e12-f34a-43b4-907f-25f18f3092ff	47fd631e-685a-4b72-8555-f76929369287	g.chr4:126408600C>G	ENST00000394329.3	+	16	12930	c.12917C>G	c.(12916-12918)aCt>aGt	p.T4306S	FAT4_ENST00000335110.5_Missense_Mutation_p.T2547S	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	4306	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						CACTGGCACACTTTTCTAATT	0.398																																						ENST00000394329.3																			0				NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						c.(12916-12918)aCt>aGt		FAT atypical cadherin 4							80.0	82.0	82.0					4																	126408600		2203	4300	6503	SO:0001583	missense	79633				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	g.chr4:126408600C>G	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.12917C>G	4.37:g.126408600C>G	ENSP00000377862:p.Thr4306Ser					FAT4_ENST00000335110.5_Missense_Mutation_p.T2547S	p.T4306S	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN			16	12930	+			4306			Laminin G-like 2.		A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	c.12917C>G	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	C	10.72	1.431081	0.25726	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.79141	-1.15;-1.24	5.06	4.21	0.49690	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.248964	0.20502	U	0.091070	T	0.62146	0.2404	N	0.17764	0.52	0.36175	D	0.849033	B;B;B	0.09022	0.002;0.001;0.0	B;B;B	0.12837	0.005;0.008;0.005	T	0.58239	-0.7671	10	0.09084	T	0.74	.	13.8681	0.63600	0.1538:0.8462:0.0:0.0	.	2547;4306;4306	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	S	4306;2547	ENSP00000377862:T4306S;ENSP00000335169:T2547S	ENSP00000335169:T2547S	T	+	2	0	FAT4	126628050	0.998000	0.40836	0.942000	0.38095	0.719000	0.41307	4.146000	0.58072	1.102000	0.41551	0.650000	0.86243	ACT		0.398	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		5	62	0	0	0	1	0	5	62				
TBP	6908	broad.mit.edu	37	6	170871052	170871052	+	Silent	SNP	G	G	A	rs112083427|rs369312237	byFrequency	TCGA-WB-A81K-01A-11D-A35I-08	TCGA-WB-A81K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c745e12-f34a-43b4-907f-25f18f3092ff	47fd631e-685a-4b72-8555-f76929369287	g.chr6:170871052G>A	ENST00000392092.2	+	3	507	c.228G>A	c.(226-228)caG>caA	p.Q76Q	TBP_ENST00000540980.1_Silent_p.Q56Q|TBP_ENST00000230354.6_Silent_p.Q76Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	76	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.Q76Q(4)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		agcaacagcagcagcagcagc	0.572																																						ENST00000392092.2																			4	Substitution - coding silent(4)	p.Q76Q(4)	lung(3)|prostate(1)	breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26						c.(226-228)caG>caA		TATA box binding protein							14.0	19.0	17.0					6																	170871052		1952	3842	5794	SO:0001819	synonymous_variant	6908				cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction	transcription factor TFIIA complex|transcription factor TFIID complex	repressing transcription factor binding|transcription regulatory region DNA binding	g.chr6:170871052G>A	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"""General transcription factors"""	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.228G>A	6.37:g.170871052G>A						TBP_ENST00000540980.1_Silent_p.Q56Q|TBP_ENST00000230354.6_Silent_p.Q76Q	p.Q76Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)	3	507	+		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)	76			Poly-Gln.		B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	37	c.228G>A	CCDS5315.1																																																																																				0.572	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194		3	30	0	0	0	1	0	3	30				
NSUN2	54888	broad.mit.edu	37	5	6600272	6600272	+	Missense_Mutation	SNP	G	G	T			TCGA-WB-A81K-01A-11D-A35I-08	TCGA-WB-A81K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c745e12-f34a-43b4-907f-25f18f3092ff	47fd631e-685a-4b72-8555-f76929369287	g.chr5:6600272G>T	ENST00000264670.6	-	19	2382	c.2071C>A	c.(2071-2073)Ccc>Acc	p.P691T	NSUN2_ENST00000539938.1_Missense_Mutation_p.P455T|NSUN2_ENST00000506139.1_Missense_Mutation_p.P656T	NM_017755.5	NP_060225.4	Q08J23	NSUN2_HUMAN	NOP2/Sun RNA methyltransferase family, member 2	691					mitotic nuclear division (GO:0007067)|tRNA methylation (GO:0030488)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|tRNA (cytosine-5-)-methyltransferase activity (GO:0016428)|tRNA binding (GO:0000049)			breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(23)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	41						TCATTCTTGGGCACAAAAGTT	0.498																																						ENST00000264670.6																			0				breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(23)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	41						c.(2071-2073)Ccc>Acc		NOP2/Sun RNA methyltransferase family, member 2							83.0	84.0	84.0					5																	6600272		2203	4300	6503	SO:0001583	missense	54888					cytoplasm|nucleolus	tRNA (cytosine-5-)-methyltransferase activity|tRNA binding	g.chr5:6600272G>T	AK000310	CCDS3869.1, CCDS54832.1	5p15.32	2014-01-31	2012-06-12		ENSG00000037474	ENSG00000037474		"""NOP2/Sun domain containing"""	25994	protein-coding gene	gene with protein product	"""tRNA methyltransferase 4 homolog (S. cerevisiae)"", ""Myc-induced SUN-domain-containing protein"""	610916	"""NOL1/NOP2/Sun domain family, member 2"", ""NOP2/Sun domain family, member 2"", ""mental retardation, non-syndromic, autosomal recessive, 5"""	MRT5		17071714, 22541559	Standard	NM_017755		Approved	FLJ20303, TRM4, Misu	uc003jdu.3	Q08J23	OTTHUMG00000090455	ENST00000264670.6:c.2071C>A	5.37:g.6600272G>T	ENSP00000264670:p.Pro691Thr					NSUN2_ENST00000506139.1_Missense_Mutation_p.P656T|NSUN2_ENST00000539938.1_Missense_Mutation_p.P455T	p.P691T	NM_017755.5	NP_060225.4	Q08J23	NSUN2_HUMAN			19	2382	-			691					A8K529|B2RNR4|B3KP09|B4DQW2|G3V1R4|Q9BVN4|Q9H858|Q9NXD9	Missense_Mutation	SNP	ENST00000264670.6	37	c.2071C>A	CCDS3869.1	.	.	.	.	.	.	.	.	.	.	G	18.81	3.704114	0.68615	.	.	ENSG00000037474	ENST00000264670;ENST00000539938;ENST00000506139	T;T;T	0.69040	-0.37;-0.37;-0.37	5.43	5.43	0.79202	.	0.048610	0.85682	D	0.000000	T	0.75852	0.3906	M	0.78049	2.395	0.58432	D	0.999995	D;B;B	0.54397	0.966;0.444;0.262	P;B;B	0.51016	0.656;0.206;0.206	T	0.73814	-0.3864	10	0.23891	T	0.37	-25.1087	19.2497	0.93919	0.0:0.0:1.0:0.0	.	656;691;691	B4DQW2;Q08J23;A8K529	.;NSUN2_HUMAN;.	T	691;455;656	ENSP00000264670:P691T;ENSP00000444338:P455T;ENSP00000420957:P656T	ENSP00000264670:P691T	P	-	1	0	NSUN2	6653272	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.633000	0.67825	2.532000	0.85374	0.563000	0.77884	CCC		0.498	NSUN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206902.1	NM_017755		3	41	1	0	0.115264	1	0.115264	3	41				
RP11-423O2.5	0	broad.mit.edu	37	1	142803543	142803543	+	lincRNA	SNP	C	C	T			TCGA-WB-A81K-01A-11D-A35I-08	TCGA-WB-A81K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c745e12-f34a-43b4-907f-25f18f3092ff	47fd631e-685a-4b72-8555-f76929369287	g.chr1:142803543C>T	ENST00000423385.1	-	0	1422																											TGTTGGAATTCCTGATGAATC	0.269																																						ENST00000423385.1																			0																																																			0							g.chr1:142803543C>T																													1.37:g.142803543C>T														0	1422	-									RNA	SNP	ENST00000423385.1	37																																																																																						0.269	RP11-423O2.5-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000193203.1			6	139	0	0	0	1	0	6	139				
CD244	51744	broad.mit.edu	37	1	160801173	160801173	+	Silent	SNP	G	G	A			TCGA-WB-A81K-01A-11D-A35I-08	TCGA-WB-A81K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c745e12-f34a-43b4-907f-25f18f3092ff	47fd631e-685a-4b72-8555-f76929369287	g.chr1:160801173G>A	ENST00000368033.3	-	9	1159	c.1077C>T	c.(1075-1077)agC>agT	p.S359S	CD244_ENST00000322302.7_Silent_p.S262S|CD244_ENST00000481677.1_5'Flank|CD244_ENST00000368034.4_Silent_p.S354S			Q9BZW8	CD244_HUMAN	CD244 molecule, natural killer cell receptor 2B4	359					blood coagulation (GO:0007596)|leukocyte migration (GO:0050900)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			central_nervous_system(1)|large_intestine(3)|lung(12)|ovary(1)|urinary_tract(1)	18	all_cancers(52;2.72e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)			GCTCTTTGCGGCTCAATCGAG	0.458																																						ENST00000368034.4																			0				central_nervous_system(1)|large_intestine(3)|lung(12)|ovary(1)|urinary_tract(1)	18						c.(1060-1062)agC>agT		CD244 molecule, natural killer cell receptor 2B4							151.0	145.0	147.0					1																	160801173		2203	4300	6503	SO:0001819	synonymous_variant	51744				blood coagulation|leukocyte migration	integral to membrane|plasma membrane	protein binding|receptor activity	g.chr1:160801173G>A	AF105261	CCDS1210.1, CCDS53398.1, CCDS53399.1	1q23.1	2013-01-11	2006-03-29		ENSG00000122223	ENSG00000122223		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18171	protein-coding gene	gene with protein product		605554	"""natural killer cell receptor 2B4"", ""CD244 natural killer cell receptor 2B4"""			3772297, 10458320	Standard	NM_016382		Approved	2B4, NAIL, NKR2B4, Nmrk, SLAMF4	uc009wtq.3	Q9BZW8	OTTHUMG00000028606	ENST00000368033.3:c.1077C>T	1.37:g.160801173G>A						CD244_ENST00000368033.3_Silent_p.S359S|CD244_ENST00000322302.7_Silent_p.S262S	p.S354S	NM_001166663.1|NM_001166664.1|NM_016382.3	NP_001160135.1|NP_001160136.1|NP_057466.1	Q9BZW8	CD244_HUMAN	BRCA - Breast invasive adenocarcinoma(70;0.00737)		9	1239	-	all_cancers(52;2.72e-17)|all_hematologic(112;0.093)		359					Q5VYI2|Q5VYI6|Q5VYI7|Q96T47|Q9NQD2|Q9NQD3|Q9Y288	Silent	SNP	ENST00000368033.3	37	c.1062C>T	CCDS53399.1																																																																																				0.458	CD244-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071469.1	NM_016382		4	110	0	0	0	1	0	4	110				
ECD	11319	broad.mit.edu	37	10	74899424	74899424	+	Missense_Mutation	SNP	A	A	T	rs374769397		TCGA-WB-A81K-01A-11D-A35I-08	TCGA-WB-A81K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c745e12-f34a-43b4-907f-25f18f3092ff	47fd631e-685a-4b72-8555-f76929369287	g.chr10:74899424A>T	ENST00000372979.4	-	10	1405	c.1199T>A	c.(1198-1200)cTt>cAt	p.L400H	ECD_ENST00000454759.2_Missense_Mutation_p.L357H|ECD_ENST00000430082.2_Missense_Mutation_p.L433H	NM_007265.2	NP_009196.1	O95905	SGT1_HUMAN	ecdysoneless homolog (Drosophila)	400					cell proliferation (GO:0008283)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of glycolytic process (GO:0006110)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Prostate(51;0.0119)					TTCTTTCTTAAGGTCTTCTAT	0.348																																						ENST00000372979.4																			0				breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						c.(1198-1200)cTt>cAt		ecdysoneless homolog (Drosophila)							261.0	282.0	275.0					10																	74899424		2203	4300	6503	SO:0001583	missense	11319				regulation of glycolysis|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleus	transcription coactivator activity	g.chr10:74899424A>T	BC000721	CCDS7321.1, CCDS44433.1, CCDS44434.1	10q22.3	2006-02-07				ENSG00000122882			17029	protein-coding gene	gene with protein product						9928932, 15128659	Standard	NM_007265		Approved	hSGT1, GCR2	uc001jtn.3	O95905		ENST00000372979.4:c.1199T>A	10.37:g.74899424A>T	ENSP00000362070:p.Leu400His					ECD_ENST00000454759.1_Missense_Mutation_p.L357H|ECD_ENST00000430082.1_Missense_Mutation_p.L433H	p.L400H	NM_007265.2	NP_009196.1	O95905	SGT1_HUMAN			10	1405	-	Prostate(51;0.0119)		400					C9JX46|E9PAW8	Missense_Mutation	SNP	ENST00000372979.4	37	c.1199T>A	CCDS7321.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.048048	0.75846	.	.	ENSG00000122882	ENST00000372979;ENST00000430082;ENST00000454759	T;T;T	0.19669	2.13;2.13;2.13	4.78	4.78	0.61160	.	0.124899	0.56097	D	0.000036	T	0.42653	0.1212	M	0.76574	2.34	0.53688	D	0.999972	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.74674	0.965;0.984;0.975	T	0.26189	-1.0110	10	0.23891	T	0.37	1.8398	12.2881	0.54803	1.0:0.0:0.0:0.0	.	357;433;400	E9PAW8;C9JX46;O95905	.;.;SGT1_HUMAN	H	400;433;357	ENSP00000362070:L400H;ENSP00000401566:L433H;ENSP00000395786:L357H	ENSP00000362070:L400H	L	-	2	0	ECD	74569430	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	6.877000	0.75562	1.985000	0.57927	0.533000	0.62120	CTT		0.348	ECD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048606.1	NM_007265		17	220	0	0	0	1	0	17	220				
NDNL2	56160	broad.mit.edu	37	15	29561154	29561154	+	Silent	SNP	C	C	T			TCGA-WB-A81K-01A-11D-A35I-08	TCGA-WB-A81K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c745e12-f34a-43b4-907f-25f18f3092ff	47fd631e-685a-4b72-8555-f76929369287	g.chr15:29561154C>T	ENST00000332303.4	-	1	879	c.756G>A	c.(754-756)ccG>ccA	p.P252P	FAM189A1_ENST00000261275.4_Intron	NM_138704.3	NP_619649.1	Q96MG7	MAGG1_HUMAN	necdin-like 2	252	Interaction with NSMCE1.|MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				DNA recombination (GO:0006310)|DNA repair (GO:0006281)|positive regulation of protein ubiquitination (GO:0031398)|regulation of growth (GO:0040008)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Smc5-Smc6 complex (GO:0030915)				breast(3)|large_intestine(2)|lung(3)	8		all_lung(180;4.69e-11)|Breast(32;0.0013)		all cancers(64;8.37e-11)|Epithelial(43;9.29e-10)|BRCA - Breast invasive adenocarcinoma(123;0.00736)|GBM - Glioblastoma multiforme(186;0.018)|Lung(196;0.153)		GGTTGGTTCGCGGGCCCCACT	0.532																																						ENST00000332303.4																			0				breast(3)|large_intestine(2)|lung(3)	8						c.(754-756)ccG>ccA		necdin-like 2							83.0	90.0	88.0					15																	29561154		2203	4300	6503	SO:0001819	synonymous_variant	56160				regulation of growth	cytoplasm|nucleus		g.chr15:29561154C>T	AF490510	CCDS10023.1	15q13.1	2008-02-01			ENSG00000185115	ENSG00000185115			7677	protein-coding gene	gene with protein product		608243				18086888	Standard	NM_138704		Approved	HCA4, MAGEG1, MAGEL3, NSE3, NSMCE3	uc001zco.3	Q96MG7	OTTHUMG00000129261	ENST00000332303.4:c.756G>A	15.37:g.29561154C>T						FAM189A1_ENST00000261275.4_Intron	p.P252P	NM_138704.3	NP_619649.1	Q96MG7	MAGG1_HUMAN		all cancers(64;8.37e-11)|Epithelial(43;9.29e-10)|BRCA - Breast invasive adenocarcinoma(123;0.00736)|GBM - Glioblastoma multiforme(186;0.018)|Lung(196;0.153)	1	879	-		all_lung(180;4.69e-11)|Breast(32;0.0013)	252			MAGE.		Q8IW16|Q8TEI6|Q9H214	Silent	SNP	ENST00000332303.4	37	c.756G>A	CCDS10023.1																																																																																				0.532	NDNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251370.1	NM_138704		4	150	0	0	0	1	0	4	150				
INPP5B	3633	broad.mit.edu	37	1	38397417	38397417	+	Silent	SNP	G	G	T	rs201779932		TCGA-WB-A81K-01A-11D-A35I-08	TCGA-WB-A81K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c745e12-f34a-43b4-907f-25f18f3092ff	47fd631e-685a-4b72-8555-f76929369287	g.chr1:38397417G>T	ENST00000373026.1	-	6	700	c.700C>A	c.(700-702)Cgg>Agg	p.R234R	INPP5B_ENST00000373027.1_5'UTR|INPP5B_ENST00000373023.2_Silent_p.R234R|INPP5B_ENST00000373024.3_Intron|INPP5B_ENST00000373021.1_Silent_p.R234R			P32019	I5P2_HUMAN	inositol polyphosphate-5-phosphatase, 75kDa	234					in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol dephosphorylation (GO:0046856)|regulation of protein processing (GO:0070613)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|metal ion binding (GO:0046872)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)			breast(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(9)|urinary_tract(1)	15	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				TCCTCATCCCGCCGCCCGTCC	0.692																																						ENST00000373023.2																			0				breast(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(9)|urinary_tract(1)	15						c.(700-702)Cgg>Agg		inositol polyphosphate-5-phosphatase, 75kDa																																				SO:0001819	synonymous_variant	3633				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|integral to membrane|microtubule cytoskeleton	GTPase activator activity|inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|protein binding	g.chr1:38397417G>T	M74161	CCDS41306.1, CCDS72760.1	1p34	2008-02-05	2002-08-29		ENSG00000204084	ENSG00000204084	3.1.3.56		6077	protein-coding gene	gene with protein product		147264	"""inositol polyphosphate-5-phosphatase, 75kD"""			1718960	Standard	NM_005540		Approved		uc001ccg.1	P32019	OTTHUMG00000004436	ENST00000373026.1:c.700C>A	1.37:g.38397417G>T						INPP5B_ENST00000373024.3_Intron|INPP5B_ENST00000373021.1_Silent_p.R234R|INPP5B_ENST00000373027.1_5'UTR|INPP5B_ENST00000373026.1_Silent_p.R234R	p.R234R	NM_005540.2	NP_005531.2	P32019	I5P2_HUMAN			7	793	-	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)	234					C9J6U5|Q5VSG9|Q5VSH0|Q5VSH1|Q658Q5|Q6P6D4|Q6PD53|Q86YE1	Silent	SNP	ENST00000373026.1	37	c.700C>A																																																																																					0.692	INPP5B-003	KNOWN	non_canonical_conserved|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000012968.1	NM_005540		3	19	1	0	0.004672	1	0.0051392	3	19				
TAOK1	57551	broad.mit.edu	37	17	27834971	27834971	+	Missense_Mutation	SNP	G	G	T			TCGA-WB-A81K-01A-11D-A35I-08	TCGA-WB-A81K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c745e12-f34a-43b4-907f-25f18f3092ff	47fd631e-685a-4b72-8555-f76929369287	g.chr17:27834971G>T	ENST00000261716.3	+	14	1915	c.1396G>T	c.(1396-1398)Ggc>Tgc	p.G466C	TAOK1_ENST00000536202.1_Missense_Mutation_p.G466C	NM_020791.2	NP_065842.1	Q7L7X3	TAOK1_HUMAN	TAO kinase 1	466					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|execution phase of apoptosis (GO:0097194)|G2 DNA damage checkpoint (GO:0031572)|mitotic cell cycle (GO:0000278)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein phosphorylation (GO:0006468)|regulation of cytoskeleton organization (GO:0051493)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transferase activity (GO:0016740)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(14)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	28			Colorectal(6;0.198)			ACAAATGTCTGGCTATAAGCG	0.393																																						ENST00000261716.3																			0				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(14)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	28						c.(1396-1398)Ggc>Tgc		TAO kinase 1							75.0	66.0	69.0					17																	27834971		2203	4300	6503	SO:0001583	missense	57551				mitotic prometaphase	cytosol|intracellular membrane-bounded organelle	ATP binding|protein serine/threonine kinase activity	g.chr17:27834971G>T	AB037782	CCDS32601.1, CCDS56024.1	17q11.2	2014-01-28				ENSG00000160551			29259	protein-coding gene	gene with protein product		610266				10718198, 14517247	Standard	NM_020791		Approved	KIAA1361, MARKK, PSK2, MAP3K16, FLJ14314, TAO1	uc002hdz.2	Q7L7X3		ENST00000261716.3:c.1396G>T	17.37:g.27834971G>T	ENSP00000261716:p.Gly466Cys					TAOK1_ENST00000536202.1_Missense_Mutation_p.G466C	p.G466C	NM_020791.2	NP_065842.1	Q7L7X3	TAOK1_HUMAN	Colorectal(6;0.198)		14	1915	+			466					A2RUT8|B7ZLV6|Q96L75|Q9H2K7|Q9H7S5|Q9P2I6	Missense_Mutation	SNP	ENST00000261716.3	37	c.1396G>T	CCDS32601.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.889991	0.91889	.	.	ENSG00000160551	ENST00000261716;ENST00000536202	T;T	0.34275	1.37;1.37	5.29	5.29	0.74685	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.66538	0.2799	M	0.85630	2.765	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.993;1.0;1.0	T	0.72500	-0.4274	10	0.87932	D	0	.	18.9681	0.92704	0.0:0.0:1.0:0.0	.	466;292;466	B7ZLV6;Q7L7X3-2;Q7L7X3	.;.;TAOK1_HUMAN	C	466	ENSP00000261716:G466C;ENSP00000438819:G466C	ENSP00000261716:G466C	G	+	1	0	TAOK1	24859097	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.863000	0.99569	2.489000	0.83994	0.655000	0.94253	GGC		0.393	TAOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447790.1	NM_020791		3	33	1	0	6.4e-05	1	7.41053e-05	3	33				
SRGAP2-AS1	100873165	broad.mit.edu	37	1	121137791	121137793	+	lincRNA	DEL	CCA	CCA	-	rs28552466|rs61625886|rs374710813	byFrequency	TCGA-WB-A81K-01A-11D-A35I-08	TCGA-WB-A81K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c745e12-f34a-43b4-907f-25f18f3092ff	47fd631e-685a-4b72-8555-f76929369287	g.chr1:121137791_121137793delCCA	ENST00000417218.1	+	0	0				RP11-343N15.1_ENST00000437515.1_lincRNA																							ATTTCGCCCTCCACCGCCGCCGC	0.631																																						ENST00000437515.1																			0																																																			100873165							g.chr1:121137791_121137793delCCA																													1.37:g.121137791_121137793delCCA														0	329	-									RNA	DEL	ENST00000417218.1	37																																																																																						0.631	AL592494.5-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000036739.1			5	4						5	4	---	---	---	---
SPEG	10290	broad.mit.edu	37	2	220348147	220348147	+	Frame_Shift_Del	DEL	A	A	-			TCGA-WB-A81K-01A-11D-A35I-08	TCGA-WB-A81K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c745e12-f34a-43b4-907f-25f18f3092ff	47fd631e-685a-4b72-8555-f76929369287	g.chr2:220348147delA	ENST00000312358.7	+	30	6094	c.5962delA	c.(5962-5964)agcfs	p.S1988fs	AC053503.11_ENST00000429882.1_RNA|SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	1988					cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		GGAGGCTCCCAGCCCAGAGGC	0.731																																						ENST00000312358.7																			0				breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100						c.(5962-5964)gcfs		SPEG complex locus							5.0	6.0	6.0					2																	220348147		1707	3881	5588	SO:0001589	frameshift_variant	10290				muscle organ development|negative regulation of cell proliferation	nucleus	ATP binding|protein serine/threonine kinase activity	g.chr2:220348147delA	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"""Immunoglobulin superfamily / I-set domain containing"""	16901	protein-coding gene	gene with protein product		615950	"""aortic preferentially expressed gene 1"""	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.5962delA	2.37:g.220348147delA	ENSP00000311684:p.Ser1988fs					AC053503.11_ENST00000429882.1_RNA|SPEG_ENST00000485813.1_3'UTR	p.S1988fs	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)	30	6094	+		Renal(207;0.0183)	1988					A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Frame_Shift_Del	DEL	ENST00000312358.7	37	c.5962delA	CCDS42824.1																																																																																				0.731	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		2	4						2	4	---	---	---	---
PVRL1	5818	broad.mit.edu	37	11	119535678	119535680	+	In_Frame_Del	DEL	CCT	CCT	-	rs539461545|rs375181781|rs369523216		TCGA-WB-A81K-01A-11D-A35I-08	TCGA-WB-A81K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c745e12-f34a-43b4-907f-25f18f3092ff	47fd631e-685a-4b72-8555-f76929369287	g.chr11:119535678_119535680delCCT	ENST00000264025.3	-	6	1861_1863	c.1331_1333delAGG	c.(1330-1335)gagggc>ggc	p.E444del	PVRL1_ENST00000341398.2_Intron	NM_002855.4	NP_002846.3	Q15223	PVRL1_HUMAN	poliovirus receptor-related 1 (herpesvirus entry mediator C)	444	Poly-Glu.				adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|desmosome organization (GO:0002934)|enamel mineralization (GO:0070166)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|immune response (GO:0006955)|iron ion transport (GO:0006826)|lens morphogenesis in camera-type eye (GO:0002089)|regulation of synapse assembly (GO:0051963)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|viral entry into host cell (GO:0046718)	adherens junction (GO:0005912)|axon (GO:0030424)|cell-cell adherens junction (GO:0005913)|extracellular region (GO:0005576)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|coreceptor activity (GO:0015026)|protein homodimerization activity (GO:0042803)|virion binding (GO:0046790)|virus receptor activity (GO:0001618)	p.E444fs*>73(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Breast(348;0.037)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.29e-05)		CCTCCACCGCcctcctcctcctc	0.66																																						ENST00000264025.3																			1	Deletion - Frameshift(1)	p.E444fs*>73(1)	kidney(1)	breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						c.(1330-1335)ggc>g		poliovirus receptor-related 1 (herpesvirus entry mediator C)																																				SO:0001651	inframe_deletion	5818				adherens junction organization|cell junction assembly|entry of virus into host cell|heterophilic cell-cell adhesion|homophilic cell adhesion|immune response	cell-cell adherens junction|extracellular region|integral to membrane	cell adhesion molecule binding|coreceptor activity|protein homodimerization activity	g.chr11:119535678_119535680delCCT	X76400	CCDS8425.1, CCDS8426.1, CCDS8427.1	11q23-q24	2013-01-29	2007-06-07		ENSG00000110400	ENSG00000110400		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9706	protein-coding gene	gene with protein product	"""nectin"""	600644		HVEC, ED4		7721102, 9616127	Standard	NM_203285		Approved	PRR, PRR1, PVRR1, SK-12, HIgR, CLPED1, CD111, OFC7	uc001pwv.3	Q15223	OTTHUMG00000166177	ENST00000264025.3:c.1331_1333delAGG	11.37:g.119535687_119535689delCCT	ENSP00000264025:p.Glu444del					PVRL1_ENST00000341398.2_Intron	p.EG444del	NM_002855.4	NP_002846.3	Q15223	PVRL1_HUMAN		BRCA - Breast invasive adenocarcinoma(274;4.29e-05)	6	1861_1863	-		Breast(348;0.037)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)	444			Poly-Glu.		O75465|Q2M3D3|Q9HBE6|Q9HBW2	In_Frame_Del	DEL	ENST00000264025.3	37	c.1331_1333delAGG	CCDS8426.1																																																																																				0.660	PVRL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388231.1			7	33						7	33	---	---	---	---
FAM155A	728215	broad.mit.edu	37	13	108518687	108518689	+	In_Frame_Del	DEL	CTG	CTG	-			TCGA-WB-A81K-01A-11D-A35I-08	TCGA-WB-A81K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c745e12-f34a-43b4-907f-25f18f3092ff	47fd631e-685a-4b72-8555-f76929369287	g.chr13:108518687_108518689delCTG	ENST00000375915.2	-	1	394_396	c.256_258delCAG	c.(256-258)cagdel	p.Q86del		NM_001080396.2	NP_001073865.1	B1AL88	F155A_HUMAN	family with sequence similarity 155, member A	86	Poly-Gln.					integral component of membrane (GO:0016021)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33						gccgctgcctctgctgctgctgc	0.719																																						ENST00000375915.2																			0				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33						c.(256-258)del		family with sequence similarity 155, member A																																				SO:0001651	inframe_deletion	728215					integral to membrane	binding	g.chr13:108518687_108518689delCTG	L10374	CCDS32006.1	13q33.3	2008-04-15			ENSG00000204442	ENSG00000204442			33877	protein-coding gene	gene with protein product							Standard	NM_001080396		Approved		uc001vql.3	B1AL88	OTTHUMG00000017326	ENST00000375915.2:c.256_258delCAG	13.37:g.108518696_108518698delCTG	ENSP00000365080:p.Gln86del						p.Q86del	NM_001080396.2	NP_001073865.1	B1AL88	F155A_HUMAN			1	394_396	-			86			Poly-Gln.		B2RUV1|B7Z334	In_Frame_Del	DEL	ENST00000375915.2	37	c.256_258delCAG	CCDS32006.1																																																																																				0.719	FAM155A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045736.2	NM_001080396		7	42						7	42	---	---	---	---
RRN3P1	730092	broad.mit.edu	37	16	21817398	21817399	+	RNA	INS	-	-	A	rs371932459|rs144931984|rs149686515		TCGA-WB-A81K-01A-11D-A35I-08	TCGA-WB-A81K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c745e12-f34a-43b4-907f-25f18f3092ff	47fd631e-685a-4b72-8555-f76929369287	g.chr16:21817398_21817399insA	ENST00000546471.1	-	0	1607							Q2M238	RN3P1_HUMAN	RNA polymerase I transcription factor homolog (S. cerevisiae) pseudogene 1																		TAAATGaaaataaaaaaataaa	0.302																																						ENST00000546471.1																			0																																																			730092							g.chr16:21817398_21817399insA			16p12.2	2012-10-16			ENSG00000248124	ENSG00000248124			30548	pseudogene	pseudogene						12477932	Standard	NR_003370		Approved		uc010vbl.1	Q2M238	OTTHUMG00000170417		16.37:g.21817405_21817405dupA														0	1607	-								A8K6T4|B3KWX9|O75704	RNA	INS	ENST00000546471.1	37																																																																																						0.302	RRN3P1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000409035.1	NR_003370		5	5						5	5	---	---	---	---
MINK1	50488	broad.mit.edu	37	17	4793935	4793937	+	In_Frame_Del	DEL	CAG	CAG	-			TCGA-WB-A81K-01A-11D-A35I-08	TCGA-WB-A81K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c745e12-f34a-43b4-907f-25f18f3092ff	47fd631e-685a-4b72-8555-f76929369287	g.chr17:4793935_4793937delCAG	ENST00000355280.6	+	14	1667_1669	c.1471_1473delCAG	c.(1471-1473)cagdel	p.Q495del	MINK1_ENST00000453408.3_In_Frame_Del_p.Q495del|MINK1_ENST00000347992.7_In_Frame_Del_p.Q495del	NM_001024937.3|NM_015716.4|NM_153827.4	NP_001020108.1|NP_056531.1|NP_722549.2			misshapen-like kinase 1											central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)|stomach(1)	6						gcttcagaaacagcagcagcagc	0.611																																						ENST00000355280.6																			0				central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)|stomach(1)	6						c.(1471-1473)del		misshapen-like kinase 1			,,,	35,3871		6,23,1924					,,,	1.4	1.0			16	75,7691		20,35,3828	no	coding,coding,coding,coding	MINK1	NM_170663.4,NM_153827.4,NM_015716.4,NM_001024937.3	,,,	26,58,5752	A1A1,A1R,RR		0.9657,0.8961,0.9424	,,,	,,,		110,11562				SO:0001651	inframe_deletion	50488				JNK cascade	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity	g.chr17:4793935_4793937delCAG	AY775058	CCDS45588.1, CCDS45589.1, CCDS45590.1	17p13.2	2011-04-14	2010-06-24		ENSG00000141503	ENSG00000141503			17565	protein-coding gene	gene with protein product	"""misshapen/NIK-related kinase"""	609426	"""misshapen-like kinase 1 (zebrafish)"""			10708748, 12087176	Standard	NM_015716		Approved	B55, MINK, ZC3, MAP4K6, YSK2	uc010vsl.2	Q8N4C8		ENST00000355280.6:c.1471_1473delCAG	17.37:g.4793944_4793946delCAG	ENSP00000347427:p.Gln495del					MINK1_ENST00000347992.7_In_Frame_Del_p.Q495del|MINK1_ENST00000453408.3_In_Frame_Del_p.Q495del	p.Q495del	NM_001024937.3|NM_015716.4|NM_153827.4	NP_001020108.1|NP_056531.1|NP_722549.2	Q8N4C8	MINK1_HUMAN			14	1667_1669	+			495						In_Frame_Del	DEL	ENST00000355280.6	37	c.1471_1473delCAG	CCDS45588.1																																																																																				0.611	MINK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439801.1	NM_015716		2	4						2	4	---	---	---	---
LRRC37A11P	342666	broad.mit.edu	37	17	37196001	37196002	+	RNA	DEL	AG	AG	-	rs34712077|rs3072622|rs202166673	byFrequency	TCGA-WB-A81K-01A-11D-A35I-08	TCGA-WB-A81K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c745e12-f34a-43b4-907f-25f18f3092ff	47fd631e-685a-4b72-8555-f76929369287	g.chr17:37196001_37196002delAG	ENST00000425901.2	+	0	2604					NR_033753.2				leucine rich repeat containing 37, member A11, pseudogene																		GAATACAGACAGAAAAGAATTT	0.327														1778	0.355032	0.3911	0.3919	5008	,	,		15719	0.2123		0.4205	False		,,,				2504	0.3599					ENST00000425901.2																			0																																																			342666							g.chr17:37196001_37196002delAG			17q12	2013-05-14			ENSG00000214553	ENSG00000214553			43815	pseudogene	pseudogene							Standard	NR_033753		Approved		uc002hrd.1		OTTHUMG00000133184		17.37:g.37196001_37196002delAG								NR_033753.2						0	2604	+									RNA	DEL	ENST00000425901.2	37																																																																																						0.327	LRRC37A11P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000444105.1	NR_033753		4	3						4	3	---	---	---	---
KAT2A	2648	broad.mit.edu	37	17	40273004	40273005	+	Frame_Shift_Del	DEL	CT	CT	-			TCGA-WB-A81K-01A-11D-A35I-08	TCGA-WB-A81K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c745e12-f34a-43b4-907f-25f18f3092ff	47fd631e-685a-4b72-8555-f76929369287	g.chr17:40273004_40273005delCT	ENST00000225916.5	-	1	371_372	c.318_319delAG	c.(316-321)ctagggfs	p.G107fs	HSPB9_ENST00000355067.3_5'Flank|CTD-2132N18.3_ENST00000592574.1_Intron	NM_021078.2	NP_066564.2	Q92830	KAT2A_HUMAN	K(lysine) acetyltransferase 2A	107					cell proliferation (GO:0008283)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|histone deubiquitination (GO:0016578)|histone H3 acetylation (GO:0043966)|histone H3-K14 acetylation (GO:0044154)|in utero embryonic development (GO:0001701)|metencephalon development (GO:0022037)|midbrain development (GO:0030901)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|positive regulation of gluconeogenesis (GO:0045722)|regulation of protein stability (GO:0031647)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|somitogenesis (GO:0001756)|telencephalon development (GO:0021537)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|extracellular space (GO:0005615)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|STAGA complex (GO:0030914)|transcription factor TFTC complex (GO:0033276)	chromatin binding (GO:0003682)|H3 histone acetyltransferase activity (GO:0010484)|histone acetyltransferase activity (GO:0004402)|histone acetyltransferase activity (H4-K12 specific) (GO:0043997)|histone deacetylase binding (GO:0042826)|transcription coactivator activity (GO:0003713)			central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						GAGAAGACCCCTAGCTTCTCAA	0.693																																						ENST00000225916.5																			0				central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						c.(316-321)ctggfs		K(lysine) acetyltransferase 2A																																				SO:0001589	frameshift_variant	2648				chromatin remodeling|histone deubiquitination|interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	Ada2/Gcn5/Ada3 transcription activator complex|STAGA complex|transcription factor TFTC complex	H3 histone acetyltransferase activity|histone deacetylase binding|protein binding|transcription coactivator activity	g.chr17:40273004_40273005delCT	AF029777	CCDS11417.1	17q12-q21	2011-07-01	2008-07-04	2008-07-04	ENSG00000108773	ENSG00000108773		"""Chromatin-modifying enzymes / K-acetyltransferases"""	4201	protein-coding gene	gene with protein product		602301	"""GCN5 general control of amino-acid synthesis 5-like 2 (yeast)"""	GCN5L2		8552087	Standard	NM_021078		Approved	GCN5, PCAF-b	uc002hyx.2	Q92830	OTTHUMG00000133504	ENST00000225916.5:c.318_319delAG	17.37:g.40273004_40273005delCT	ENSP00000225916:p.Gly107fs					CTD-2132N18.3_ENST00000592574.1_Intron	p.LG106fs	NM_021078.2	NP_066564.2	Q92830	KAT2A_HUMAN			1	371_372	-			106					Q8N1A2|Q9UCW1	Frame_Shift_Del	DEL	ENST00000225916.5	37	c.318_319delAG	CCDS11417.1																																																																																				0.693	KAT2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257458.1	NM_021078		2	4						2	4	---	---	---	---
