#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
NOTCH2	4853	broad.mit.edu	37	1	120491184	120491184	+	Missense_Mutation	SNP	G	G	A	rs587730290		TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr1:120491184G>A	ENST00000256646.2	-	17	2824	c.2605C>T	c.(2605-2607)Cgg>Tgg	p.R869W		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	869	EGF-like 22. {ECO:0000255|PROSITE- ProRule:PRU00076}.				apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|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)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		ATGGTACACCGCTGACCTAGG	0.512			"""N, F, Mis"""		"""marginal zone lymphoma, DLBCL"""				Alagille Syndrome		OREG0013733	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1	0.000199681	0.0	0.0	5008	,	,		21478	0.0		0.001	False		,,,				2504	0.0					ENST00000256646.2				Dom	yes		1	1p13-p11	4853	"""N, F, Mis"""	Notch homolog 2			L			"""marginal zone lymphoma, DLBCL"""		0				breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158						c.(2605-2607)Cgg>Tgg		notch 2							121.0	99.0	107.0					1																	120491184		2203	4300	6503	SO:0001583	missense	4853	Alagille Syndrome	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity	g.chr1:120491184G>A	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"""Ankyrin repeat domain containing"""	7882	protein-coding gene	gene with protein product		600275	"""Notch (Drosophila) homolog 2"", ""Notch homolog 2 (Drosophila)"""			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.2605C>T	1.37:g.120491184G>A	ENSP00000256646:p.Arg869Trp		OREG0013733	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1504		p.R869W	NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)	17	2824	-	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)	869			EGF-like 22.		Q5T3X7|Q99734|Q9H240	Missense_Mutation	SNP	ENST00000256646.2	37	c.2605C>T	CCDS908.1	.	.	.	.	.	.	.	.	.	.	G	12.42	1.933963	0.34096	.	.	ENSG00000134250	ENST00000256646	T	0.11604	2.76	5.71	3.82	0.43975	EGF (1);Epidermal growth factor-like (1);EGF-like region, conserved site (2);Epidermal growth factor-like, type 3 (1);	0.233214	0.21963	U	0.066574	T	0.15912	0.0383	M	0.72576	2.205	0.20926	N	0.999828	D;D	0.71674	0.998;0.995	D;P	0.63192	0.912;0.745	T	0.09314	-1.0680	10	0.37606	T	0.19	.	15.4479	0.75248	0.0:0.0:0.5541:0.4459	.	869;869	Q6IQ50;Q04721	.;NOTC2_HUMAN	W	869	ENSP00000256646:R869W	ENSP00000256646:R869W	R	-	1	2	NOTCH2	120292707	0.008000	0.16893	0.979000	0.43373	0.240000	0.25518	0.786000	0.26844	0.433000	0.26313	-0.824000	0.03097	CGG		0.512	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408		29	32	0	0	0	1	0	29	32				
COL5A2	1290	broad.mit.edu	37	2	189898826	189898826	+	Silent	SNP	G	G	A	rs142895373	byFrequency	TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr2:189898826G>A	ENST00000374866.3	-	54	4744	c.4470C>T	c.(4468-4470)ggC>ggT	p.G1490G		NM_000393.3	NP_000384.2	P05997	CO5A2_HUMAN	collagen, type V, alpha 2	1490	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				axon guidance (GO:0007411)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|negative regulation of endodermal cell differentiation (GO:1903225)|skeletal system development (GO:0001501)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)	p.G1490G(1)		NS(3)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(53)|ovary(3)|prostate(2)|skin(6)|urinary_tract(3)	95			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			CAATTTCAACGCCGAATTCCT	0.473																																						ENST00000374866.3																			1	Substitution - coding silent(1)	p.G1490G(1)	large_intestine(1)	NS(3)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(53)|ovary(3)|prostate(2)|skin(6)|urinary_tract(3)	95						c.(4468-4470)ggC>ggT		collagen, type V, alpha 2		G		1,4405	2.1+/-5.4	0,1,2202	154.0	125.0	135.0		4470	2.4	0.4	2	dbSNP_134	135	0,8600		0,0,4300	no	coding-synonymous	COL5A2	NM_000393.3		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		1490/1500	189898826	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	1290				axon guidance|collagen fibril organization|eye morphogenesis|skin development	collagen type V	extracellular matrix structural constituent	g.chr2:189898826G>A	Y14690	CCDS33350.1	2q14-q32	2014-09-17			ENSG00000204262	ENSG00000204262		"""Collagens"""	2210	protein-coding gene	gene with protein product	"""AB collagen"""	120190				1572660	Standard	NM_000393		Approved		uc002uqk.3	P05997	OTTHUMG00000149842	ENST00000374866.3:c.4470C>T	2.37:g.189898826G>A							p.G1490G	NM_000393.3	NP_000384.2	P05997	CO5A2_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)		54	4744	-			1490			Fibrillar collagen NC1.		P78440|Q13908|Q53WR4|Q59GR4|Q6LDJ5|Q7KZ55|Q86XF6|Q96QB0|Q96QB3	Silent	SNP	ENST00000374866.3	37	c.4470C>T	CCDS33350.1																																																																																				0.473	COL5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313523.1	NM_000393		24	54	0	0	0	1	0	24	54				
TSSC2	650368	broad.mit.edu	37	11	3427759	3427759	+	RNA	SNP	C	C	T			TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr11:3427759C>T	ENST00000529482.1	+	0	876									tumor suppressing subtransferable candidate 2 pseudogene																		TGTCTGCACACGTCCTGCAGT	0.612																																						ENST00000529482.1																			0																																																			0							g.chr11:3427759C>T			11p15.4	2014-06-05	2008-06-30		ENSG00000223756	ENSG00000223756			12384	pseudogene	pseudogene	"""tumor-supressing STF cDNA 2"", ""asparagine-linked glycosylation 1 homolog (yeast, beta-1,4-mannosyltransferase) (ALG1) pseudogene"""	608999	"""tumor suppressing subtransferable candidate 2"""			9403053	Standard	NR_024248		Approved				OTTHUMG00000011705		11.37:g.3427759C>T														0	876	+									RNA	SNP	ENST00000529482.1	37																																																																																						0.612	TSSC2-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000392020.1			4	77	0	0	0	1	0	4	77				
ANKRD30B	374860	broad.mit.edu	37	18	14843023	14843023	+	Splice_Site	SNP	C	C	G	rs180690700		TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr18:14843023C>G	ENST00000358984.4	+	33	2932	c.2752C>G	c.(2752-2754)Cct>Gct	p.P918A		NM_001145029.1	NP_001138501.1	Q9BXX2	AN30B_HUMAN	ankyrin repeat domain 30B	918										breast(3)|endometrium(4)|kidney(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	22						ACCCGTTTAGCCTGCCACTGA	0.289																																						ENST00000358984.4																			0				breast(3)|endometrium(4)|kidney(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	22						c.e33-1		ankyrin repeat domain 30B							15.0	14.0	14.0					18																	14843023		689	1567	2256	SO:0001630	splice_region_variant	374860							g.chr18:14843023C>G	BC028407	CCDS54182.1	18p11.21	2013-01-10			ENSG00000180777	ENSG00000180777		"""Ankyrin repeat domain containing"""	24165	protein-coding gene	gene with protein product						11280766	Standard	NM_001145029		Approved	NY-BR-1.1	uc010dlo.2	Q9BXX2		ENST00000358984.4:c.2752-1C>G	18.37:g.14843023C>G							p.P918_splice	NM_001145029.1	NP_001138501.1	Q9BXX2	AN30B_HUMAN			33	2932	+			1003					B4DGP1|F8WAG3|Q4G175	Splice_Site	SNP	ENST00000358984.4	37	c.2751_splice	CCDS54182.1	14	0.00641025641025641	0	0.0	4	0.011049723756906077	0	0.0	10	0.013192612137203167	c	9.262	1.043562	0.19748	.	.	ENSG00000180777	ENST00000358984;ENST00000320584;ENST00000277669	T	0.08458	3.09	2.31	1.41	0.22369	.	.	.	.	.	T	0.09642	0.0237	L	0.32530	0.975	0.09310	N	1	D;P	0.63880	0.993;0.877	D;P	0.68192	0.956;0.728	T	0.18745	-1.0327	8	.	.	.	.	4.9234	0.13882	0.0:0.8119:0.0:0.1881	.	1003;918	Q9BXX2;F8WAG3	AN30B_HUMAN;.	A	918;312;338	ENSP00000351875:P918A	.	P	+	1	0	ANKRD30B	14833023	0.021000	0.18746	0.038000	0.18304	0.005000	0.04900	-0.426000	0.07008	0.308000	0.22923	0.453000	0.30009	CCT		0.289	ANKRD30B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443557.1	NM_001145029	Missense_Mutation	3	9	0	0	0	1	0	3	9				
TUBB8P7	197331	broad.mit.edu	37	16	90162513	90162513	+	RNA	SNP	T	T	C			TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr16:90162513T>C	ENST00000564451.1	+	0	1866				TUBB8P7_ENST00000567960.1_RNA					tubulin, beta 8 class VIII pseudogene 7									p.N415N(2)									GCAACATGAATGACCTGGTGT	0.537																																						ENST00000567960.1																			2	Substitution - coding silent(2)	p.N415N(2)	prostate(1)|kidney(1)																																																0							g.chr16:90162513T>C			16q24.3	2013-02-18			ENSG00000261812	ENSG00000261812			42345	pseudogene	pseudogene							Standard	NG_002334		Approved				OTTHUMG00000172847		16.37:g.90162513T>C						TUBB8P7_ENST00000564451.1_RNA								0	1249	+									RNA	SNP	ENST00000564451.1	37																																																																																						0.537	TUBB8P7-004	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000420856.1	NG_002334		6	138	0	0	0	1	0	6	138				
PWWP2B	170394	broad.mit.edu	37	10	134218474	134218474	+	Missense_Mutation	SNP	G	G	A			TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr10:134218474G>A	ENST00000305233.5	+	2	529	c.470G>A	c.(469-471)cGc>cAc	p.R157H	PWWP2B_ENST00000368609.4_Missense_Mutation_p.R157H	NM_138499.3	NP_612508.3	Q6NUJ5	PWP2B_HUMAN	PWWP domain containing 2B	157										central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(5)|urinary_tract(1)	9		all_cancers(35;6.69e-12)|all_epithelial(44;1.55e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.109)|Melanoma(40;0.123)|Glioma(114;0.203)|all_hematologic(284;0.224)		OV - Ovarian serous cystadenocarcinoma(35;7.49e-05)|Epithelial(32;0.00016)|all cancers(32;0.000186)		CGTCTGTCCCGCAACCGCGAC	0.726																																						ENST00000305233.5																			0				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(5)|urinary_tract(1)	9						c.(469-471)cGc>cAc		PWWP domain containing 2B							6.0	6.0	6.0					10																	134218474		1896	3775	5671	SO:0001583	missense	170394							g.chr10:134218474G>A	AK128663	CCDS7667.2	10q26.3	2009-06-03	2007-10-22	2007-10-22	ENSG00000171813	ENSG00000171813			25150	protein-coding gene	gene with protein product			"""PWWP domain containing 2"""	PWWP2			Standard	NM_001098637		Approved	bA432J24.1, FLJ46823	uc001lll.4	Q6NUJ5	OTTHUMG00000019286	ENST00000305233.5:c.470G>A	10.37:g.134218474G>A	ENSP00000306324:p.Arg157His					PWWP2B_ENST00000368609.4_Missense_Mutation_p.R157H	p.R157H	NM_138499.3	NP_612508.3	Q6NUJ5	PWP2B_HUMAN		OV - Ovarian serous cystadenocarcinoma(35;7.49e-05)|Epithelial(32;0.00016)|all cancers(32;0.000186)	2	529	+		all_cancers(35;6.69e-12)|all_epithelial(44;1.55e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.109)|Melanoma(40;0.123)|Glioma(114;0.203)|all_hematologic(284;0.224)	157					A6NM90|B5MDQ1|H9KV61|Q5SZI0|Q6ZQX5|Q96F43	Missense_Mutation	SNP	ENST00000305233.5	37	c.470G>A	CCDS7667.2	.	.	.	.	.	.	.	.	.	.	G	32	5.130804	0.94473	.	.	ENSG00000171813	ENST00000305233;ENST00000368609	T;T	0.27890	1.64;1.64	3.92	3.92	0.45320	.	0.000000	0.38381	U	0.001710	T	0.50446	0.1616	L	0.55990	1.75	0.58432	D	0.999998	D	0.89917	1.0	D	0.91635	0.999	T	0.55023	-0.8205	10	0.72032	D	0.01	-12.6993	15.4817	0.75534	0.0:0.0:1.0:0.0	.	157	Q6NUJ5	PWP2B_HUMAN	H	157	ENSP00000306324:R157H;ENSP00000357598:R157H	ENSP00000306324:R157H	R	+	2	0	PWWP2B	134068464	0.986000	0.35501	0.976000	0.42696	0.882000	0.50991	2.368000	0.44222	2.189000	0.69895	0.455000	0.32223	CGC		0.726	PWWP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051075.3	NM_138499		14	23	0	0	0	1	0	14	23				
PCLO	27445	broad.mit.edu	37	7	82578793	82578793	+	Splice_Site	SNP	G	G	A	rs530909855		TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr7:82578793G>A	ENST00000333891.9	-	6	11448	c.11111C>T	c.(11110-11112)aCg>aTg	p.T3704M	PCLO_ENST00000437081.1_Splice_Site_p.T424M|PCLO_ENST00000423517.2_Splice_Site_p.T3704M	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											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						CACTCTTACCGTATAGCCCTC	0.463													G|||	1	0.000199681	0.0	0.0	5008	,	,		18581	0.0		0.0	False		,,,				2504	0.001					ENST00000423517.2																			0				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						c.e6+1		piccolo presynaptic cytomatrix protein							145.0	139.0	141.0					7																	82578793		1897	4135	6032	SO:0001630	splice_region_variant	27445				cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity	g.chr7:82578793G>A	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.11112+1C>T	7.37:g.82578793G>A						PCLO_ENST00000333891.8_Splice_Site_p.T3704_splice|PCLO_ENST00000437081.1_Splice_Site_p.T424_splice	p.T3704_splice	NM_014510.2	NP_055325.2	Q9Y6V0	PCLO_HUMAN			6	11448	-			3635						Splice_Site	SNP	ENST00000333891.9	37	c.11112_splice	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	G	15.78	2.933593	0.52866	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517;ENST00000437081	T;T	0.15952	2.38;2.38	5.92	4.94	0.65067	.	.	.	.	.	T	0.07638	0.0192	N	0.16478	0.41	0.33221	D	0.55472	B;P;B	0.38167	0.11;0.621;0.414	B;B;B	0.24155	0.004;0.051;0.034	T	0.07673	-1.0760	9	0.87932	D	0	.	3.931	0.09285	0.3173:0.0:0.6827:0.0	.	3635;3704;3704	Q9Y6V0;Q9Y6V0-5;Q9Y6V0-6	PCLO_HUMAN;.;.	M	3635;3704;3704;424	ENSP00000334319:T3704M;ENSP00000388393:T3704M	ENSP00000334319:T3704M	T	-	2	0	PCLO	82416729	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.008000	0.70739	2.801000	0.96364	0.650000	0.86243	ACG		0.463	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	Missense_Mutation	66	165	0	0	0	1	0	66	165				
MID1IP1	58526	broad.mit.edu	37	X	38664318	38664318	+	Missense_Mutation	SNP	A	A	T			TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chrX:38664318A>T	ENST00000336949.6	+	2	1064	c.119A>T	c.(118-120)gAc>gTc	p.D40V	MID1IP1-AS1_ENST00000436893.1_RNA|MID1IP1_ENST00000457894.1_Missense_Mutation_p.D40V|MID1IP1_ENST00000378474.3_Missense_Mutation_p.D40V	NM_021242.4	NP_067065.1	Q9NPA3	M1IP1_HUMAN	MID1 interacting protein 1	40					lipid metabolic process (GO:0006629)|negative regulation of microtubule depolymerization (GO:0007026)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of ligase activity (GO:0051351)|protein polymerization (GO:0051258)|regulation of lipid biosynthetic process (GO:0046890)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)				kidney(1)|large_intestine(3)|lung(2)|prostate(1)	7						TTGCTGCGCGACGTGCCCCTG	0.632																																						ENST00000336949.6																			0				kidney(1)|large_intestine(3)|lung(2)|prostate(1)	7						c.(118-120)gAc>gTc		MID1 interacting protein 1							80.0	55.0	64.0					X																	38664318		2202	4300	6502	SO:0001583	missense	58526				lipid biosynthetic process|negative regulation of microtubule depolymerization|positive regulation of fatty acid biosynthetic process|positive regulation of ligase activity|protein polymerization	cytosol|microtubule|nucleus		g.chrX:38664318A>T		CCDS14249.1	Xp11.4	2012-02-23	2012-02-23		ENSG00000165175	ENSG00000165175			20715	protein-coding gene	gene with protein product	"""gastrulation specific G12 homolog (zebrafish)"""		"""MID1 interacting protein 1 (gastrulation specific G12-like (zebrafish))"""				Standard	NM_001098790		Approved	STRAIT11499, FLJ10386, MIG12, THRSPL, G12-like	uc010ngz.3	Q9NPA3	OTTHUMG00000024092	ENST00000336949.6:c.119A>T	X.37:g.38664318A>T	ENSP00000338706:p.Asp40Val					MID1IP1_ENST00000378474.3_Missense_Mutation_p.D40V|MID1IP1_ENST00000457894.1_Missense_Mutation_p.D40V	p.D40V	NM_021242.4	NP_067065.1	Q9NPA3	M1IP1_HUMAN			2	1064	+			40					D3DWB2	Missense_Mutation	SNP	ENST00000336949.6	37	c.119A>T	CCDS14249.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.157335	0.78114	.	.	ENSG00000165175	ENST00000457894;ENST00000378474;ENST00000336949	.	.	.	4.84	4.84	0.62591	.	0.000000	0.85682	D	0.000000	T	0.80380	0.4612	M	0.85373	2.75	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.83894	0.0286	9	0.87932	D	0	-11.9323	13.3172	0.60413	1.0:0.0:0.0:0.0	.	40	Q9NPA3	M1IP1_HUMAN	V	40	.	ENSP00000338706:D40V	D	+	2	0	MID1IP1	38549262	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.564000	0.90726	1.796000	0.52611	0.430000	0.28490	GAC		0.632	MID1IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060655.1			31	48	0	0	0	1	0	31	48				
CHEK2	11200	broad.mit.edu	37	22	29091840	29091840	+	Missense_Mutation	SNP	T	T	C	rs142470496	byFrequency	TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr22:29091840T>C	ENST00000405598.1	-	12	1308	c.1117A>G	c.(1117-1119)Aag>Gag	p.K373E	CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000464581.1_5'Flank|CHEK2_ENST00000382578.1_Missense_Mutation_p.K282E|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000403642.1_Missense_Mutation_p.K282E|CHEK2_ENST00000348295.3_Missense_Mutation_p.K344E|CHEK2_ENST00000544772.1_Missense_Mutation_p.K152E|CHEK2_ENST00000404276.1_Missense_Mutation_p.K373E|CHEK2_ENST00000328354.6_Missense_Mutation_p.K373E|CHEK2_ENST00000402731.1_Missense_Mutation_p.K344E|CHEK2_ENST00000382580.2_Missense_Mutation_p.K416E			O96017	CHK2_HUMAN	checkpoint kinase 2	373	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|T-loop/activation segment.				cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)	p.K373E(9)		central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						CCCAAAATCTTGGAGTGCCCA	0.418			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																														ENST00000544772.1			yes	Rec		familial breast cancer	22	22q12.1	11200	F	CHK2 checkpoint homolog (S. pombe)			E		breast			9	Substitution - Missense(9)	p.K373E(9)	kidney(4)|prostate(2)|endometrium(1)|stomach(1)|central_nervous_system(1)	central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						c.(454-456)Aag>Gag	Direct reversal of damage;Other conserved DNA damage response genes	checkpoint kinase 2																																				SO:0001583	missense	11200				cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity	g.chr22:29091840T>C	AF086904	CCDS13843.1, CCDS13844.1, CCDS33629.1	22q12.1	2014-09-17	2011-11-11	2001-09-27	ENSG00000183765	ENSG00000183765			16627	protein-coding gene	gene with protein product		604373	"""CHK2 (checkpoint, S.pombe) homolog"", ""CHK2 checkpoint homolog (S. pombe)"""	RAD53		9836640, 10097108	Standard	NM_001257387		Approved	CDS1, CHK2, HuCds1, PP1425, bA444G7	uc003adt.1	O96017	OTTHUMG00000151023	ENST00000405598.1:c.1117A>G	22.37:g.29091840T>C	ENSP00000386087:p.Lys373Glu					CHEK2_ENST00000405598.1_Missense_Mutation_p.K373E|CHEK2_ENST00000348295.3_Missense_Mutation_p.K344E|CHEK2_ENST00000403642.1_Missense_Mutation_p.K282E|CHEK2_ENST00000402731.1_Missense_Mutation_p.K344E|CHEK2_ENST00000382580.2_Missense_Mutation_p.K416E|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000404276.1_Missense_Mutation_p.K373E|CHEK2_ENST00000328354.6_Missense_Mutation_p.K373E|CHEK2_ENST00000382578.1_Missense_Mutation_p.K282E	p.K152E	NM_001257387.1	NP_001244316.1	O96017	CHK2_HUMAN			12	1890	-			373			FHA.		A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Missense_Mutation	SNP	ENST00000405598.1	37	c.454A>G	CCDS13843.1	.	.	.	.	.	.	.	.	.	.	T	19.06	3.754336	0.69648	.	.	ENSG00000183765	ENST00000348295;ENST00000382578;ENST00000544772;ENST00000328354;ENST00000404276;ENST00000405598;ENST00000382580;ENST00000403642;ENST00000402731	T;T;T;T;T;T;T;T;T	0.54071	0.9;0.59;0.59;0.59;0.59;0.59;0.59;0.59;0.9	5.89	5.89	0.94794	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.043710	0.85682	D	0.000000	T	0.56292	0.1975	N	0.11756	0.17	0.80722	D	1	D;D;D;D;D;D	0.76494	0.996;0.999;0.998;0.998;0.993;0.991	P;D;D;D;D;P	0.74674	0.905;0.984;0.943;0.969;0.923;0.896	T	0.64769	-0.6329	10	0.87932	D	0	-1.7726	15.4726	0.75453	0.0:0.0:0.0:1.0	.	282;152;373;344;373;416	O96017-4;Q9HBS5;A8JZZ5;O96017-12;O96017;O96017-9	.;.;.;.;CHK2_HUMAN;.	E	344;282;152;373;373;373;416;282;344	ENSP00000329012:K344E;ENSP00000372021:K282E;ENSP00000442458:K152E;ENSP00000329178:K373E;ENSP00000385747:K373E;ENSP00000386087:K373E;ENSP00000372023:K416E;ENSP00000384919:K282E;ENSP00000384835:K344E	ENSP00000329178:K373E	K	-	1	0	CHEK2	27421840	1.000000	0.71417	1.000000	0.80357	0.479000	0.33129	4.270000	0.58896	2.248000	0.74166	0.528000	0.53228	AAG		0.418	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1	NM_001005735		5	86	0	0	0	1	0	5	86				
RP11-423O2.5	0	broad.mit.edu	37	1	142803543	142803543	+	lincRNA	SNP	C	C	T			TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	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	160	0	0	0	1	0	6	160				
AXIN2	8313	broad.mit.edu	37	17	63533498	63533498	+	Silent	SNP	G	G	A			TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr17:63533498G>A	ENST00000375702.5	-	5	1764	c.1656C>T	c.(1654-1656)taC>taT	p.Y552Y	AXIN2_ENST00000307078.5_Silent_p.Y552Y			Q9Y2T1	AXIN2_HUMAN	axin 2	552					bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to organic cyclic compound (GO:0071407)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|dorsal/ventral axis specification (GO:0009950)|intramembranous ossification (GO:0001957)|maintenance of DNA repeat elements (GO:0043570)|mRNA stabilization (GO:0048255)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell proliferation (GO:0008285)|negative regulation of osteoblast differentiation (GO:0045668)|odontogenesis (GO:0042476)|positive regulation of cell death (GO:0010942)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein phosphorylation (GO:0001934)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of chondrocyte development (GO:0061181)|regulation of mismatch repair (GO:0032423)|secondary heart field specification (GO:0003139)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)			NS(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	34						TGCATTTCGAGTAGCAGTAAT	0.627									Oligodontia, Ectodermal Dysplasia and Colorectal Polyp syndrome																													ENST00000307078.5																			0				NS(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	34						c.(1654-1656)taC>taT		axin 2							123.0	114.0	117.0					17																	63533498		2203	4300	6503	SO:0001819	synonymous_variant	8313	Oligodontia, Ectodermal Dysplasia and Colorectal Polyp syndrome	Familial Cancer Database	Oligodontia-Colorectal Cancer syndrome, Tooth Agenesis-Colorectal Cancer Syndrome	cellular protein localization|cellular response to organic cyclic compound|dorsal/ventral axis specification|intramembranous ossification|maintenance of DNA repeat elements|mRNA stabilization|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of cell proliferation|negative regulation of osteoblast differentiation|odontogenesis|positive regulation of cell death|positive regulation of epithelial to mesenchymal transition|positive regulation of protein phosphorylation|regulation of centromeric sister chromatid cohesion|regulation of mismatch repair|Wnt receptor signaling pathway involved in somitogenesis	Axin-APC-beta-catenin-GSK3B complex|cell cortex|centrosome|cytoplasmic membrane-bounded vesicle|cytoplasmic microtubule|nucleus|plasma membrane|postsynaptic density	armadillo repeat domain binding|beta-catenin binding|GTPase activator activity|protein kinase binding|signal transducer activity|ubiquitin protein ligase binding	g.chr17:63533498G>A	AF078165	CCDS11662.1	17q24.1	2014-09-17	2008-08-01		ENSG00000168646				904	protein-coding gene	gene with protein product	"""conductin"", ""axil"""	604025				10049590	Standard	NM_004655		Approved	MGC126582, DKFZp781B0869	uc002jfi.3	Q9Y2T1	OTTHUMG00000179353	ENST00000375702.5:c.1656C>T	17.37:g.63533498G>A						AXIN2_ENST00000375702.5_Silent_p.Y552Y	p.Y552Y	NM_004655.3	NP_004646.3	Q9Y2T1	AXIN2_HUMAN			6	1969	-			552					Q3MJ88|Q9H3M6|Q9UH84	Silent	SNP	ENST00000375702.5	37	c.1656C>T																																																																																					0.627	AXIN2-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000445901.1	NM_004655		4	138	0	0	0	1	0	4	138				
ZC3H15	55854	broad.mit.edu	37	2	187371527	187371527	+	Missense_Mutation	SNP	C	C	G			TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr2:187371527C>G	ENST00000337859.6	+	9	1281	c.1054C>G	c.(1054-1056)Ctt>Gtt	p.L352V		NM_018471.2	NP_060941.2	Q8WU90	ZC3HF_HUMAN	zinc finger CCCH-type containing 15	352					cytokine-mediated signaling pathway (GO:0019221)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|skin(1)	15			OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Epithelial(96;0.0922)|all cancers(119;0.233)			TGTAGCCAGTCTTGAAAGATT	0.348																																						ENST00000337859.6																			0				breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|skin(1)	15						c.(1054-1056)Ctt>Gtt		zinc finger CCCH-type containing 15							131.0	121.0	124.0					2																	187371527		1847	4094	5941	SO:0001583	missense	55854					cytoplasm|nucleolus|plasma membrane	nucleic acid binding|zinc ion binding	g.chr2:187371527C>G		CCDS42791.1	2q32.1	2012-07-05			ENSG00000065548	ENSG00000065548		"""Zinc fingers, CCCH-type domain containing"""	29528	protein-coding gene	gene with protein product	"""likely ortholog of mouse immediate early response, erythropoietin 4"""					10880228	Standard	NM_018471		Approved	LEREPO4	uc002upo.3	Q8WU90	OTTHUMG00000154251	ENST00000337859.6:c.1054C>G	2.37:g.187371527C>G	ENSP00000338788:p.Leu352Val						p.L352V	NM_018471.2	NP_060941.2	Q8WU90	ZC3HF_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Epithelial(96;0.0922)|all cancers(119;0.233)		9	1281	+			352					B4DMW2|D3DPG7|Q5QTQ4|Q8WZ06|Q9NUZ3|Q9NZ37|Q9P079	Missense_Mutation	SNP	ENST00000337859.6	37	c.1054C>G	CCDS42791.1	.	.	.	.	.	.	.	.	.	.	C	14.87	2.663119	0.47572	.	.	ENSG00000065548	ENST00000337859;ENST00000536434;ENST00000445547	T;T	0.49432	1.54;0.78	6.03	4.21	0.49690	.	0.486738	0.24791	N	0.035562	T	0.30070	0.0753	N	0.17474	0.49	0.80722	D	1	B	0.11235	0.004	B	0.08055	0.003	T	0.04870	-1.0921	10	0.27082	T	0.32	-2.5915	10.5697	0.45194	0.0:0.6823:0.2523:0.0654	.	352	Q8WU90	ZC3HF_HUMAN	V	352;352;30	ENSP00000338788:L352V;ENSP00000415788:L30V	ENSP00000338788:L352V	L	+	1	0	ZC3H15	187079772	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	2.792000	0.47837	0.853000	0.35312	-0.315000	0.08773	CTT		0.348	ZC3H15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334547.2	NM_018471		23	61	0	0	0	1	0	23	61				
CHEK2	11200	broad.mit.edu	37	22	29091841	29091841	+	Silent	SNP	G	G	A	rs146546850	byFrequency	TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr22:29091841G>A	ENST00000405598.1	-	12	1307	c.1116C>T	c.(1114-1116)tcC>tcT	p.S372S	CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000464581.1_5'Flank|CHEK2_ENST00000382578.1_Silent_p.S281S|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000403642.1_Silent_p.S281S|CHEK2_ENST00000348295.3_Silent_p.S343S|CHEK2_ENST00000544772.1_Silent_p.S151S|CHEK2_ENST00000404276.1_Silent_p.S372S|CHEK2_ENST00000328354.6_Silent_p.S372S|CHEK2_ENST00000402731.1_Silent_p.S343S|CHEK2_ENST00000382580.2_Silent_p.S415S			O96017	CHK2_HUMAN	checkpoint kinase 2	372	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|T-loop/activation segment.				cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)	p.S372S(8)		central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						CCAAAATCTTGGAGTGCCCAA	0.413			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																														ENST00000544772.1			yes	Rec		familial breast cancer	22	22q12.1	11200	F	CHK2 checkpoint homolog (S. pombe)			E		breast			8	Substitution - coding silent(8)	p.S372S(8)	kidney(4)|prostate(2)|endometrium(1)|central_nervous_system(1)	central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						c.(451-453)tcC>tcT	Direct reversal of damage;Other conserved DNA damage response genes	checkpoint kinase 2							43.0	44.0	44.0					22																	29091841		2203	4300	6503	SO:0001819	synonymous_variant	11200				cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity	g.chr22:29091841G>A	AF086904	CCDS13843.1, CCDS13844.1, CCDS33629.1	22q12.1	2014-09-17	2011-11-11	2001-09-27	ENSG00000183765	ENSG00000183765			16627	protein-coding gene	gene with protein product		604373	"""CHK2 (checkpoint, S.pombe) homolog"", ""CHK2 checkpoint homolog (S. pombe)"""	RAD53		9836640, 10097108	Standard	NM_001257387		Approved	CDS1, CHK2, HuCds1, PP1425, bA444G7	uc003adt.1	O96017	OTTHUMG00000151023	ENST00000405598.1:c.1116C>T	22.37:g.29091841G>A						CHEK2_ENST00000405598.1_Silent_p.S372S|CHEK2_ENST00000348295.3_Silent_p.S343S|CHEK2_ENST00000403642.1_Silent_p.S281S|CHEK2_ENST00000402731.1_Silent_p.S343S|CHEK2_ENST00000382580.2_Silent_p.S415S|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000404276.1_Silent_p.S372S|CHEK2_ENST00000328354.6_Silent_p.S372S|CHEK2_ENST00000382578.1_Silent_p.S281S	p.S151S	NM_001257387.1	NP_001244316.1	O96017	CHK2_HUMAN			12	1889	-			372			FHA.		A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Silent	SNP	ENST00000405598.1	37	c.453C>T	CCDS13843.1	.	.	.	.	.	.	.	.	.	.	G	5.792	0.330417	0.10956	.	.	ENSG00000183765	ENST00000434810	.	.	.	5.89	-2.11	0.07187	.	.	.	.	.	T	0.42154	0.1190	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33854	-0.9852	4	.	.	.	-7.6356	3.2532	0.06822	0.327:0.1103:0.4613:0.1014	.	.	.	.	L	116	.	.	P	-	2	0	CHEK2	27421841	0.997000	0.39634	0.996000	0.52242	0.470000	0.32858	0.318000	0.19504	-0.075000	0.12798	-0.907000	0.02831	CCA		0.413	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1	NM_001005735		5	87	0	0	0	1	0	5	87				
EBI3	10148	broad.mit.edu	37	19	4236975	4236975	+	Missense_Mutation	SNP	C	C	T	rs182560914		TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr19:4236975C>T	ENST00000221847.5	+	5	633	c.580C>T	c.(580-582)Cgg>Tgg	p.R194W		NM_005755.2	NP_005746.2	Q14213	IL27B_HUMAN	Epstein-Barr virus induced 3	194	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|humoral immune response (GO:0006959)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|T-helper 1 type immune response (GO:0042088)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)			large_intestine(1)|lung(2)|ovary(1)|urinary_tract(1)	5		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0336)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGGGCTGTGCGGCCCCGAGC	0.607													C|||	1	0.000199681	0.0	0.0	5008	,	,		14648	0.0		0.001	False		,,,				2504	0.0					ENST00000221847.5																			0				large_intestine(1)|lung(2)|ovary(1)|urinary_tract(1)	5						c.(580-582)Cgg>Tgg		Epstein-Barr virus induced 3							58.0	57.0	57.0					19																	4236975		2203	4300	6503	SO:0001583	missense	10148				humoral immune response|positive regulation of alpha-beta T cell proliferation|positive regulation of interferon-gamma biosynthetic process|T-helper 1 type immune response	extracellular space|plasma membrane	cytokine activity|cytokine receptor activity	g.chr19:4236975C>T	L08187	CCDS12123.1	19p13	2013-02-11	2008-09-12		ENSG00000105246	ENSG00000105246		"""Fibronectin type III domain containing"""	3129	protein-coding gene	gene with protein product	"""IL27 subunit"", ""IL35 subunit"""	605816				8551575	Standard	NM_005755		Approved		uc002lzu.3	Q14213		ENST00000221847.5:c.580C>T	19.37:g.4236975C>T	ENSP00000221847:p.Arg194Trp						p.R194W	NM_005755.2	NP_005746.2	Q14213	IL27B_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0336)|STAD - Stomach adenocarcinoma(1328;0.18)	5	633	+		Hepatocellular(1079;0.137)	194			Fibronectin type-III 2.		A0N0N2|O75269	Missense_Mutation	SNP	ENST00000221847.5	37	c.580C>T	CCDS12123.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	12.49	1.954193	0.34471	.	.	ENSG00000105246	ENST00000221847	T	0.59502	0.26	5.41	-0.774	0.10991	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.861076	0.10217	N	0.701413	T	0.47544	0.1451	L	0.54323	1.7	0.09310	N	1	B	0.26147	0.143	B	0.20577	0.03	T	0.36939	-0.9727	10	0.40728	T	0.16	-21.3836	7.7652	0.28976	0.4553:0.4575:0.0:0.0872	.	194	Q14213	IL27B_HUMAN	W	194	ENSP00000221847:R194W	ENSP00000221847:R194W	R	+	1	2	EBI3	4187975	0.000000	0.05858	0.002000	0.10522	0.035000	0.12851	-0.061000	0.11693	-0.095000	0.12351	0.650000	0.86243	CGG		0.607	EBI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458005.1			4	120	0	0	0	1	0	4	120				
RUNX2	860	broad.mit.edu	37	6	45390463	45390463	+	Silent	SNP	G	G	A			TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr6:45390463G>A	ENST00000371438.1	+	2	550	c.192G>A	c.(190-192)caG>caA	p.Q64Q	RUNX2_ENST00000576263.1_Silent_p.Q64Q|RUNX2_ENST00000541979.1_Silent_p.Q132Q|RUNX2_ENST00000465038.2_Silent_p.Q64Q|RUNX2_ENST00000371432.3_Silent_p.Q50Q|RUNX2_ENST00000352853.5_Silent_p.Q132Q|RUNX2_ENST00000359524.5_Silent_p.Q50Q|RP1-244F24.1_ENST00000606796.1_RNA|RUNX2_ENST00000371436.6_Silent_p.Q64Q	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN	runt-related transcription factor 2	64	Poly-Gln.				BMP signaling pathway (GO:0030509)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|chondrocyte development (GO:0002063)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|endochondral ossification (GO:0001958)|gene expression (GO:0010467)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|osteoblast development (GO:0002076)|osteoblast differentiation (GO:0001649)|osteoblast fate commitment (GO:0002051)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|stem cell differentiation (GO:0048863)|T cell differentiation (GO:0030217)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(18)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						agcagcagcagcaacagcagc	0.736																																						ENST00000371438.1																			0				breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(18)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						c.(190-192)caG>caA		runt-related transcription factor 2							11.0	16.0	14.0					6																	45390463		1448	3096	4544	SO:0001819	synonymous_variant	860				negative regulation of transcription, DNA-dependent|osteoblast differentiation|positive regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity	g.chr6:45390463G>A	AF001450	CCDS43467.1, CCDS43468.1, CCDS43467.2, CCDS43468.2	6p21	2010-08-20			ENSG00000124813	ENSG00000124813			10472	protein-coding gene	gene with protein product		600211		CCD, CBFA1, CCD1		7835892	Standard	NM_001024630		Approved	AML3, PEBP2A1, PEBP2aA1	uc011dvx.2	Q13950	OTTHUMG00000014774	ENST00000371438.1:c.192G>A	6.37:g.45390463G>A						RUNX2_ENST00000541979.1_Silent_p.Q132Q|RUNX2_ENST00000371436.6_Silent_p.Q64Q|RUNX2_ENST00000359524.5_Silent_p.Q50Q|RUNX2_ENST00000352853.5_Silent_p.Q132Q|RUNX2_ENST00000371432.3_Silent_p.Q50Q|RUNX2_ENST00000576263.1_Silent_p.Q64Q|RUNX2_ENST00000465038.2_Silent_p.Q64Q	p.Q64Q	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN			2	550	+			64			Poly-Gln.		O14614|O14615|O95181	Silent	SNP	ENST00000371438.1	37	c.192G>A	CCDS43467.2																																																																																				0.736	RUNX2-003	KNOWN	not_organism_supported|upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040755.2	NM_004348		4	71	0	0	0	1	0	4	71				
CELF5	60680	broad.mit.edu	37	19	3251064	3251064	+	Splice_Site	SNP	G	G	T			TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr19:3251064G>T	ENST00000292672.2	+	2	378	c.341G>T	c.(340-342)gGa>gTa	p.G114V	CELF5_ENST00000541430.2_Splice_Site_p.G114V	NM_021938.3	NP_068757.2	Q8N6W0	CELF5_HUMAN	CUGBP, Elav-like family member 5	114	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			kidney(1)|large_intestine(2)|lung(7)|ovary(2)|skin(1)	13						ACCTTGCCCGGAGTGAGTCCT	0.602																																						ENST00000541430.2																			0				kidney(1)|large_intestine(2)|lung(7)|ovary(2)|skin(1)	13						c.e2+1		CUGBP, Elav-like family member 5							80.0	68.0	72.0					19																	3251064		2203	4300	6503	SO:0001630	splice_region_variant	60680				mRNA processing	cytoplasm|nucleus	nucleotide binding|RNA binding	g.chr19:3251064G>T	AF248649	CCDS12106.1, CCDS54197.1	19p13	2013-02-12	2010-02-19	2010-02-19		ENSG00000161082		"""RNA binding motif (RRM) containing"""	14058	protein-coding gene	gene with protein product		612680	"""Bruno (Drosophila) -like 5, RNA binding protein"", ""bruno-like 5, RNA binding protein (Drosophila)"""	BRUNOL5		10893231	Standard	NM_001172673		Approved		uc002lxm.3	Q8N6W0		ENST00000292672.2:c.342+1G>T	19.37:g.3251064G>T						CELF5_ENST00000292672.2_Splice_Site_p.G114_splice	p.G114_splice	NM_001172673.1	NP_001166144.1	Q8N6W0	CELF5_HUMAN			2	377	+			114			RRM 1.		D6W614|O75253|Q59GP2|Q86VW6|Q9BZC0|Q9NR86	Splice_Site	SNP	ENST00000292672.2	37	c.342_splice	CCDS12106.1	.	.	.	.	.	.	.	.	.	.	G	14.83	2.654022	0.47362	.	.	ENSG00000161082	ENST00000292672;ENST00000541430	T;T	0.56103	0.48;1.33	2.81	2.81	0.32909	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.000000	0.85682	U	0.000000	T	0.74030	0.3663	M	0.91249	3.19	0.80722	D	1	D;D	0.71674	0.998;0.989	D;P	0.66497	0.944;0.805	T	0.80630	-0.1297	10	0.87932	D	0	.	11.7992	0.52118	0.0:0.0:1.0:0.0	.	114;114	Q8N6W0-2;Q8N6W0	.;CELF5_HUMAN	V	114	ENSP00000292672:G114V;ENSP00000443498:G114V	ENSP00000292672:G114V	G	+	2	0	CELF5	3202064	1.000000	0.71417	1.000000	0.80357	0.192000	0.23643	8.600000	0.90860	1.894000	0.54839	0.416000	0.27883	GGA		0.602	CELF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452574.1	NM_021938	Missense_Mutation	4	81	1	0	0.00909568	1	0.0092378	4	81				
IDH1	3417	broad.mit.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000446179.1_Missense_Mutation_p.R132H|IDH1_ENST00000345146.2_Missense_Mutation_p.R132H	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)	ENST00000415913.1				Dom	yes		2	2q33.3	3417	Mis	"""isocitrate dehydrogenase 1 (NADP+), soluble"""			O			gliobastoma		2835	Substitution - Missense(2834)|Complex - compound substitution(1)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)	central_nervous_system(2579)|haematopoietic_and_lymphoid_tissue(205)|bone(43)|prostate(4)|biliary_tract(2)|urinary_tract(1)|skin(1)	NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887						c.(394-396)cGt>cAt		isocitrate dehydrogenase 1 (NADP+), soluble							79.0	73.0	75.0					2																	209113112		2203	4300	6503	SO:0001583	missense	3417				2-oxoglutarate metabolic process|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle	cytosol|peroxisomal matrix	isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity	g.chr2:209113112C>T		CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.395G>A	2.37:g.209113112C>T	ENSP00000390265:p.Arg132His					IDH1_ENST00000345146.2_Missense_Mutation_p.R132H|IDH1_ENST00000446179.1_Missense_Mutation_p.R132H	p.R132H			O75874	IDHC_HUMAN		Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)	4	776	-			132		R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate).|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation).|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).			Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	c.395G>A	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657324	0.88154	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.57	4.69	0.59074	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.93145	0.7817	H	0.99379	4.54	0.80722	D	1	B	0.25486	0.127	B	0.25405	0.06	D	0.92324	0.5868	10	0.87932	D	0	-20.0399	14.3783	0.66895	0.0:0.9288:0.0:0.0712	.	132	O75874	IDHC_HUMAN	H	132	ENSP00000260985:R132H;ENSP00000410513:R132H;ENSP00000390265:R132H;ENSP00000391075:R132H	ENSP00000260985:R132H	R	-	2	0	IDH1	208821357	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	6.088000	0.71371	1.356000	0.45884	0.555000	0.69702	CGT		0.393	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			21	41	0	0	0	1	0	21	41				
UNC13D	201294	broad.mit.edu	37	17	73826535	73826535	+	Missense_Mutation	SNP	G	G	A			TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr17:73826535G>A	ENST00000207549.4	-	29	3117	c.2738C>T	c.(2737-2739)gCt>gTt	p.A913V	UNC13D_ENST00000412096.2_Missense_Mutation_p.A913V	NM_199242.2	NP_954712.1	Q70J99	UN13D_HUMAN	unc-13 homolog D (C. elegans)	913	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				defense response to virus (GO:0051607)|germinal center formation (GO:0002467)|granuloma formation (GO:0002432)|natural killer cell degranulation (GO:0043320)|phagocytosis (GO:0006909)|positive regulation of exocytosis (GO:0045921)|regulation of mast cell degranulation (GO:0043304)	endosome (GO:0005768)|exocytic vesicle (GO:0070382)|lysosome (GO:0005764)|membrane (GO:0016020)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29			all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)			GACTGTCACAGCCCCCAGCTC	0.682									Familial Hemophagocytic Lymphohistiocytosis		OREG0024741	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000207549.4																			0				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						c.(2737-2739)gCt>gTt		unc-13 homolog D (C. elegans)							33.0	34.0	34.0					17																	73826535		2189	4296	6485	SO:0001583	missense	201294	Familial Hemophagocytic Lymphohistiocytosis	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	positive regulation of exocytosis|regulation of mast cell degranulation	exocytic vesicle|late endosome|lysosome|membrane|recycling endosome	protein binding	g.chr17:73826535G>A	AK024474	CCDS11730.1	17q25.3	2014-09-17				ENSG00000092929			23147	protein-coding gene	gene with protein product		608897					Standard	NM_199242		Approved	Munc13-4	uc002jpp.3	Q70J99		ENST00000207549.4:c.2738C>T	17.37:g.73826535G>A	ENSP00000207549:p.Ala913Val		OREG0024741	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1148	UNC13D_ENST00000412096.2_Missense_Mutation_p.A913V	p.A913V	NM_199242.2	NP_954712.1	Q70J99	UN13D_HUMAN	all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)		29	3117	-			913			C2 2.		B4DWG9|Q9H7K5	Missense_Mutation	SNP	ENST00000207549.4	37	c.2738C>T	CCDS11730.1	.	.	.	.	.	.	.	.	.	.	G	13.76	2.333107	0.41297	.	.	ENSG00000092929	ENST00000207549;ENST00000412096	T;T	0.78481	-1.18;-1.18	4.71	3.71	0.42584	C2 calcium/lipid-binding domain, CaLB (1);	0.143577	0.46442	N	0.000296	T	0.66703	0.2816	L	0.38953	1.18	0.80722	D	1	B	0.12013	0.005	B	0.15870	0.014	T	0.60326	-0.7285	10	0.29301	T	0.29	-0.2295	11.0361	0.47802	0.0968:0.0:0.9031:0.0	.	913	Q70J99	UN13D_HUMAN	V	913	ENSP00000207549:A913V;ENSP00000388093:A913V	ENSP00000207549:A913V	A	-	2	0	UNC13D	71338130	1.000000	0.71417	0.462000	0.27118	0.511000	0.34104	5.132000	0.64758	1.105000	0.41606	0.462000	0.41574	GCT		0.682	UNC13D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448847.2	XM_113950		5	10	0	0	0	1	0	5	10				
CNTD2	79935	broad.mit.edu	37	19	40730639	40730639	+	Missense_Mutation	SNP	A	A	C	rs199816045		TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr19:40730639A>C	ENST00000430325.2	-	2	395	c.347T>G	c.(346-348)gTc>gGc	p.V116G	CNTD2_ENST00000513948.1_Missense_Mutation_p.V10G|CNTD2_ENST00000433940.1_Intron	NM_024877.3	NP_079153.2	Q9H8S5	CNTD2_HUMAN	cyclin N-terminal domain containing 2	116	Cyclin N-terminal.				regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)					lung(1)|prostate(1)	2						GTGCACCTGGACCAGCCAGTC	0.697																																						ENST00000430325.2																			0				lung(1)|prostate(1)	2						c.(346-348)gTc>gGc		cyclin N-terminal domain containing 2							22.0	37.0	32.0					19																	40730639		692	1591	2283	SO:0001583	missense	79935				regulation of cyclin-dependent protein kinase activity		protein kinase binding	g.chr19:40730639A>C	AK023327	CCDS12551.1, CCDS12551.2	19q13.2	2014-07-03				ENSG00000105219			25805	protein-coding gene	gene with protein product	"""cyclin P"""					11237006	Standard	NM_024877		Approved	FLJ13265, CCNP	uc010xvi.2	Q9H8S5		ENST00000430325.2:c.347T>G	19.37:g.40730639A>C	ENSP00000396755:p.Val116Gly					CNTD2_ENST00000513948.1_Missense_Mutation_p.V10G|CNTD2_ENST00000433940.1_Intron	p.V116G	NM_024877.3	NP_079153.2	B4DX65	B4DX65_HUMAN			2	395	-			116					B4DX65	Missense_Mutation	SNP	ENST00000430325.2	37	c.347T>G	CCDS12551.2	.	.	.	.	.	.	.	.	.	.	A	15.10	2.732544	0.48939	.	.	ENSG00000105219	ENST00000430325;ENST00000513948	T;T	0.13538	2.58;2.58	5.57	5.57	0.84162	.	.	.	.	.	T	0.22551	0.0544	M	0.70787	2.145	0.80722	D	1	B	0.32128	0.357	B	0.38225	0.268	T	0.01940	-1.1243	9	0.87932	D	0	.	13.2323	0.59951	1.0:0.0:0.0:0.0	.	116	B4DX65	.	G	116;10	ENSP00000396755:V116G;ENSP00000425529:V10G	ENSP00000396755:V116G	V	-	2	0	CNTD2	45422479	0.993000	0.37304	0.973000	0.42090	0.579000	0.36224	5.473000	0.66774	2.107000	0.64212	0.459000	0.35465	GTC		0.697	CNTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360785.1	NM_024877		4	17	0	0	0	1	0	4	17				
TSSC2	650368	broad.mit.edu	37	11	3427765	3427765	+	RNA	SNP	G	G	C			TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr11:3427765G>C	ENST00000529482.1	+	0	882									tumor suppressing subtransferable candidate 2 pseudogene																		CACACGTCCTGCAGTGGCCTG	0.602																																						ENST00000529482.1																			0																																																			0							g.chr11:3427765G>C			11p15.4	2014-06-05	2008-06-30		ENSG00000223756	ENSG00000223756			12384	pseudogene	pseudogene	"""tumor-supressing STF cDNA 2"", ""asparagine-linked glycosylation 1 homolog (yeast, beta-1,4-mannosyltransferase) (ALG1) pseudogene"""	608999	"""tumor suppressing subtransferable candidate 2"""			9403053	Standard	NR_024248		Approved				OTTHUMG00000011705		11.37:g.3427765G>C														0	882	+									RNA	SNP	ENST00000529482.1	37																																																																																						0.602	TSSC2-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000392020.1			4	80	0	0	0	1	0	4	80				
KCNAB2	8514	broad.mit.edu	37	1	6155592	6155592	+	Missense_Mutation	SNP	G	G	T			TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr1:6155592G>T	ENST00000164247.1	+	13	1276	c.712G>T	c.(712-714)Gtg>Ttg	p.V238L	KCNAB2_ENST00000378083.3_Missense_Mutation_p.V286L|KCNAB2_ENST00000352527.1_Missense_Mutation_p.V224L|KCNAB2_ENST00000378097.1_Missense_Mutation_p.V238L|KCNAB2_ENST00000341524.1_Missense_Mutation_p.V238L|KCNAB2_ENST00000458166.2_Missense_Mutation_p.V171L|KCNAB2_ENST00000378092.1_Missense_Mutation_p.V224L|KCNAB2_ENST00000378111.1_Intron|KCNAB2_ENST00000602612.1_Missense_Mutation_p.V238L|KCNAB2_ENST00000378087.3_Intron	NM_001199860.1	NP_001186789.1	Q13303	KCAB2_HUMAN	potassium voltage-gated channel, shaker-related subfamily, beta member 2	238					hematopoietic progenitor cell differentiation (GO:0002244)|protein heterooligomerization (GO:0051291)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|plasma membrane (GO:0005886)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)	p.V238L(1)		large_intestine(1)|lung(4)|skin(3)	8	Ovarian(185;0.0634)	all_cancers(23;5.85e-39)|all_epithelial(116;4.88e-22)|all_lung(118;4.21e-08)|Lung NSC(185;9.77e-07)|all_hematologic(16;2.78e-06)|all_neural(13;3.18e-06)|Acute lymphoblastic leukemia(12;0.000272)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00106)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0393)|Medulloblastoma(700;0.211)		Epithelial(90;6.9e-37)|GBM - Glioblastoma multiforme(13;8.8e-31)|OV - Ovarian serous cystadenocarcinoma(86;1.45e-19)|Colorectal(212;2.46e-07)|COAD - Colon adenocarcinoma(227;2.07e-05)|Kidney(185;7.88e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00131)|BRCA - Breast invasive adenocarcinoma(365;0.00133)|STAD - Stomach adenocarcinoma(132;0.00391)|READ - Rectum adenocarcinoma(331;0.0649)		CTCTTCAGGAGTGGGCGCCAT	0.632																																						ENST00000164247.1																			1	Substitution - Missense(1)	p.V238L(1)	lung(1)	large_intestine(1)|lung(4)|skin(3)	8						c.(712-714)Gtg>Ttg		potassium voltage-gated channel, shaker-related subfamily, beta member 2							86.0	85.0	85.0					1																	6155592		2203	4299	6502	SO:0001583	missense	8514					cytoplasm|integral to membrane|juxtaparanode region of axon	oxidoreductase activity|potassium channel regulator activity|voltage-gated potassium channel activity	g.chr1:6155592G>T	U33429	CCDS55.1, CCDS56.1, CCDS55570.1, CCDS55571.1	1p36.3	2008-02-05			ENSG00000069424	ENSG00000069424		"""Potassium channels"", ""Aldo-keto reductases"""	6229	protein-coding gene	gene with protein product		601142				8838324	Standard	NM_003636		Approved	AKR6A5, KCNA2B, HKvbeta2.1, HKvbeta2.2	uc001aly.2	Q13303	OTTHUMG00000000795	ENST00000164247.1:c.712G>T	1.37:g.6155592G>T	ENSP00000164247:p.Val238Leu					KCNAB2_ENST00000378083.3_Missense_Mutation_p.V286L|KCNAB2_ENST00000378097.1_Missense_Mutation_p.V238L|KCNAB2_ENST00000378111.1_Intron|KCNAB2_ENST00000352527.1_Missense_Mutation_p.V224L|KCNAB2_ENST00000341524.1_Missense_Mutation_p.V238L|KCNAB2_ENST00000602612.1_Missense_Mutation_p.V238L|KCNAB2_ENST00000458166.2_Missense_Mutation_p.V171L|KCNAB2_ENST00000378087.3_Intron|KCNAB2_ENST00000378092.1_Missense_Mutation_p.V224L	p.V238L	NM_001199860.1	NP_001186789.1	Q13303	KCAB2_HUMAN		Epithelial(90;6.9e-37)|GBM - Glioblastoma multiforme(13;8.8e-31)|OV - Ovarian serous cystadenocarcinoma(86;1.45e-19)|Colorectal(212;2.46e-07)|COAD - Colon adenocarcinoma(227;2.07e-05)|Kidney(185;7.88e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00131)|BRCA - Breast invasive adenocarcinoma(365;0.00133)|STAD - Stomach adenocarcinoma(132;0.00391)|READ - Rectum adenocarcinoma(331;0.0649)	13	1276	+	Ovarian(185;0.0634)	all_cancers(23;5.85e-39)|all_epithelial(116;4.88e-22)|all_lung(118;4.21e-08)|Lung NSC(185;9.77e-07)|all_hematologic(16;2.78e-06)|all_neural(13;3.18e-06)|Acute lymphoblastic leukemia(12;0.000272)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00106)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0393)|Medulloblastoma(700;0.211)	238					A0AVM9|A8K1A4|B0AZR7|O43659|Q5TG82|Q5TG83|Q6ZNE4|Q99411	Missense_Mutation	SNP	ENST00000164247.1	37	c.712G>T	CCDS55.1	.	.	.	.	.	.	.	.	.	.	G	14.63	2.591699	0.46214	.	.	ENSG00000069424	ENST00000378097;ENST00000378092;ENST00000428161;ENST00000389632;ENST00000341524;ENST00000352527;ENST00000164247;ENST00000378083;ENST00000458166	T;T;T;T;T;T;T;T;T	0.31510	1.49;1.49;1.49;1.49;1.49;1.49;1.49;1.49;1.49	4.75	4.75	0.60458	NADP-dependent oxidoreductase domain (3);	0.000000	0.85682	D	0.000000	T	0.23249	0.0562	N	0.24115	0.695	0.80722	D	1	B;B;B;B	0.31054	0.306;0.042;0.052;0.003	B;B;B;B	0.37091	0.241;0.052;0.054;0.012	T	0.02766	-1.1113	10	0.07325	T	0.83	-19.8608	16.3108	0.82869	0.0:0.0:1.0:0.0	.	286;224;238;238	Q13303-3;Q13303-2;Q13303;Q2YD85	.;.;KCAB2_HUMAN;.	L	238;224;224;238;238;224;238;286;171	ENSP00000367337:V238L;ENSP00000367332:V224L;ENSP00000400285:V224L;ENSP00000374283:V238L;ENSP00000340824:V238L;ENSP00000318772:V224L;ENSP00000164247:V238L;ENSP00000367323:V286L;ENSP00000396167:V171L	ENSP00000164247:V238L	V	+	1	0	KCNAB2	6078179	1.000000	0.71417	1.000000	0.80357	0.834000	0.47266	9.736000	0.98828	2.187000	0.69744	0.561000	0.74099	GTG		0.632	KCNAB2-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000002114.3	NM_172130		45	41	1	0	1.76056e-25	1	1.9396e-25	45	41				
LOC220729	220729	broad.mit.edu	37	3	197348674	197348674	+	RNA	SNP	A	A	G	rs376114863		TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr3:197348674A>G	ENST00000418868.1	-	0	585					NR_003266.2																						GGCTCTGTCCACCAAATGCAC	0.478																																						ENST00000418868.1																			0																																																			0							g.chr3:197348674A>G																													3.37:g.197348674A>G								NR_003266.2						0	585	-									RNA	SNP	ENST00000418868.1	37																																																																																						0.478	AC024560.3-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000340283.1			6	126	0	0	0	1	0	6	126				
PSME3	10197	broad.mit.edu	37	17	40990763	40990763	+	Nonsense_Mutation	SNP	C	C	T			TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr17:40990763C>T	ENST00000590720.1	+	7	654	c.421C>T	c.(421-423)Cag>Tag	p.Q141*	PSME3_ENST00000592169.1_Nonsense_Mutation_p.Q85*|PSME3_ENST00000293362.3_Nonsense_Mutation_p.Q154*|PSME3_ENST00000541124.1_3'UTR|PSME3_ENST00000545225.1_Nonsense_Mutation_p.Q80*|PSME3_ENST00000441946.2_Nonsense_Mutation_p.Q152*			P61289	PSME3_HUMAN	proteasome (prosome, macropain) activator subunit 3 (PA28 gamma; Ki)	141					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of endopeptidase activity (GO:0010950)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome activator complex (GO:0008537)|proteasome complex (GO:0000502)	endopeptidase activator activity (GO:0061133)|MDM2/MDM4 family protein binding (GO:0097371)|p53 binding (GO:0002039)			NS(1)|cervix(1)|large_intestine(3)|lung(1)	6		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)		AATGTGGGTACAGCTCCTGAT	0.463																																						ENST00000293362.3																			0				NS(1)|cervix(1)|large_intestine(3)|lung(1)	6						c.(460-462)Cag>Tag		proteasome (prosome, macropain) activator subunit 3 (PA28 gamma; Ki)							91.0	94.0	93.0					17																	40990763		2203	4300	6503	SO:0001587	stop_gained	10197				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|regulation of proteasomal protein catabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome activator complex	endopeptidase activator activity|identical protein binding|MDM2 binding|p53 binding	g.chr17:40990763C>T	U11292	CCDS11442.1, CCDS45689.1, CCDS59290.1	17q12-q21	2004-02-17				ENSG00000131467		"""Proteasome (prosome, macropain) subunits"""	9570	protein-coding gene	gene with protein product		605129				7951316	Standard	NM_005789		Approved	Ki, PA28-gamma, REG-GAMMA, PA28G	uc002ibq.4	P61289		ENST00000590720.1:c.421C>T	17.37:g.40990763C>T	ENSP00000466794:p.Gln141*					PSME3_ENST00000590720.1_Nonsense_Mutation_p.Q141*|PSME3_ENST00000592169.1_Nonsense_Mutation_p.Q85*|PSME3_ENST00000545225.1_Nonsense_Mutation_p.Q80*|PSME3_ENST00000441946.2_Nonsense_Mutation_p.Q152*|PSME3_ENST00000541124.1_3'UTR	p.Q154*	NM_005789.3|NM_176863.2	NP_005780.2|NP_789839.1	P61289	PSME3_HUMAN		BRCA - Breast invasive adenocarcinoma(366;0.156)	7	621	+		Breast(137;0.000143)	141					A8K9A3|O35563|P97373|Q12920|Q13172|Q9BQD9	Nonsense_Mutation	SNP	ENST00000590720.1	37	c.460C>T	CCDS45689.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	37|37	6.441427|6.441427	0.97568|0.97568	.|.	.|.	ENSG00000131467|ENSG00000131467	ENST00000545225;ENST00000293362;ENST00000441946|ENST00000543428	.|T	.|0.39406	.|1.08	5.65|5.65	4.68|4.68	0.58851|0.58851	.|.	0.107289|.	0.64402|.	D|.	0.000003|.	.|T	.|0.49949	.|0.1587	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.42498	.|-0.9448	.|6	0.34782|0.28530	T|T	0.22|0.3	-3.6003|-3.6003	14.6852|14.6852	0.69044|0.69044	0.0:0.9312:0.0:0.0688|0.0:0.9312:0.0:0.0688	.|.	.|.	.|.	.|.	X|I	80;154;141|103	.|ENSP00000437924:T103I	ENSP00000293362:Q154X|ENSP00000437924:T103I	Q|T	+|+	1|2	0|0	PSME3|PSME3	38244289|38244289	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.418000|7.418000	0.80167|0.80167	1.635000|1.635000	0.50512|0.50512	0.655000|0.655000	0.94253|0.94253	CAG|ACA		0.463	PSME3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452430.1	NM_176863		29	51	0	0	0	1	0	29	51				
TRPV6	55503	broad.mit.edu	37	7	142571891	142571891	+	Missense_Mutation	SNP	A	A	G			TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr7:142571891A>G	ENST00000359396.3	-	12	1702	c.1457T>C	c.(1456-1458)aTt>aCt	p.I486T	RP11-114L10.2_ENST00000438839.1_RNA	NM_018646.3	NP_061116	Q9H1D0	TRPV6_HUMAN	transient receptor potential cation channel, subfamily V, member 6	486					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|regulation of calcium ion-dependent exocytosis (GO:0017158)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)			breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	42	Melanoma(164;0.059)					GTCGCCAAAAATCATCTAGAA	0.547																																						ENST00000359396.3																			0				breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	42						c.(1456-1458)aTt>aCt		transient receptor potential cation channel, subfamily V, member 6							68.0	51.0	57.0					7																	142571891		2203	4300	6503	SO:0001583	missense	55503				regulation of calcium ion-dependent exocytosis	integral to plasma membrane	calcium channel activity|calmodulin binding	g.chr7:142571891A>G	AJ277909	CCDS5874.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000165125	ENSG00000165125		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	14006	protein-coding gene	gene with protein product		606680	"""epithelial calcium channel 2"""	ECAC2		11097838, 11549322, 16382100, 16717058	Standard	NM_018646		Approved	CaT1	uc003wbx.2	Q9H1D0	OTTHUMG00000157158	ENST00000359396.3:c.1457T>C	7.37:g.142571891A>G	ENSP00000352358:p.Ile486Thr						p.I486T	NM_018646.3	NP_061116.2	Q9H1D0	TRPV6_HUMAN			12	1702	-	Melanoma(164;0.059)		486					A4D2I8|Q8TDL3|Q8WXR8|Q96LC5|Q9H1D1|Q9H296	Missense_Mutation	SNP	ENST00000359396.3	37	c.1457T>C	CCDS5874.1	.	.	.	.	.	.	.	.	.	.	A	16.18	3.051601	0.55218	.	.	ENSG00000165125	ENST00000359396;ENST00000311470;ENST00000436401	D;D	0.98381	-4.9;-2.68	5.0	5.0	0.66597	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98792	0.9593	M	0.83118	2.625	0.80722	D	1	D	0.57257	0.979	D	0.66979	0.948	D	0.99744	1.1016	10	0.87932	D	0	-16.0181	14.171	0.65510	1.0:0.0:0.0:0.0	.	486	Q9H1D0	TRPV6_HUMAN	T	486;318;109	ENSP00000352358:I486T;ENSP00000411100:I109T	ENSP00000310825:I318T	I	-	2	0	TRPV6	142282013	1.000000	0.71417	1.000000	0.80357	0.254000	0.26022	8.102000	0.89548	1.996000	0.58369	0.533000	0.62120	ATT		0.547	TRPV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347662.1	NM_014274		5	35	0	0	0	1	0	5	35				
ZC3H13	23091	broad.mit.edu	37	13	46619598	46619598	+	Silent	SNP	A	A	G			TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr13:46619598A>G	ENST00000242848.4	-	2	393	c.45T>C	c.(43-45)acT>acC	p.T15T	ZC3H13_ENST00000282007.3_Silent_p.T15T			Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	15							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|lung(25)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	79		Lung NSC(96;7.26e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;4.18e-05)		TATCAGATATAGTCTTGGTAT	0.413																																					Esophageal Squamous(187;747 2077 11056 31291 44172)	ENST00000242848.4																			0				cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|lung(25)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	79						c.(43-45)acT>acC		zinc finger CCCH-type containing 13							216.0	221.0	220.0					13																	46619598		2203	4300	6503	SO:0001819	synonymous_variant	23091						nucleic acid binding|zinc ion binding	g.chr13:46619598A>G	AB020660	CCDS9400.1	13q14.11	2012-07-05	2006-05-15	2006-05-15	ENSG00000123200	ENSG00000123200		"""Zinc fingers, CCCH-type domain containing"""	20368	protein-coding gene	gene with protein product			"""KIAA0853"""	KIAA0853		10048485	Standard	XM_005266301		Approved	DKFZp434D1812	uc001vas.1	Q5T200	OTTHUMG00000016863	ENST00000242848.4:c.45T>C	13.37:g.46619598A>G						ZC3H13_ENST00000282007.3_Silent_p.T15T	p.T15T			Q5T200	ZC3HD_HUMAN	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;4.18e-05)	2	393	-		Lung NSC(96;7.26e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	15					A2A323|O94936|Q5T1Z9|Q7Z7J3|Q8NDT6|Q9H0L6	Silent	SNP	ENST00000242848.4	37	c.45T>C																																																																																					0.413	ZC3H13-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000044789.1	NM_015070		52	105	0	0	0	1	0	52	105				
CD40	958	broad.mit.edu	37	20	44751286	44751286	+	Silent	SNP	A	A	G			TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr20:44751286A>G	ENST00000372285.3	+	4	366	c.294A>G	c.(292-294)gaA>gaG	p.E98E	CD40_ENST00000489304.1_3'UTR|CD40_ENST00000372276.3_Silent_p.E98E	NM_001250.4	NP_001241.1	P25942	TNR5_HUMAN	CD40 molecule, TNF receptor superfamily member 5	98					B cell proliferation (GO:0042100)|cellular calcium ion homeostasis (GO:0006874)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|immune response-regulating cell surface receptor signaling pathway (GO:0002768)|inflammatory response (GO:0006954)|platelet activation (GO:0030168)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|protein complex assembly (GO:0006461)|regulation of immune response (GO:0050776)|regulation of immunoglobulin secretion (GO:0051023)	CD40 receptor complex (GO:0035631)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|enzyme binding (GO:0019899)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10		Myeloproliferative disorder(115;0.0122)				GCACCTCAGAAACAGACACCA	0.607									Immune Deficiency with Hyper-IgM																													ENST00000372285.3																			0				endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10						c.(292-294)gaA>gaG		CD40 molecule, TNF receptor superfamily member 5	Simvastatin(DB00641)						115.0	101.0	106.0					20																	44751286		2203	4300	6503	SO:0001819	synonymous_variant	958	Immune Deficiency with Hyper-IgM	Familial Cancer Database	Hypogammaglobulinemia with Hyper-IgM, HIGM type I-V, XLHIGM	B cell proliferation|cellular response to mechanical stimulus|inflammatory response|platelet activation|positive regulation of endothelial cell apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein complex assembly	CD40 receptor complex|extracellular region	enzyme binding|receptor activity	g.chr20:44751286A>G	X60592	CCDS13393.1, CCDS13394.1	20q12-q13.2	2014-09-17	2006-03-28	2005-01-14	ENSG00000101017	ENSG00000101017		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11919	protein-coding gene	gene with protein product		109535	"""tumor necrosis factor receptor superfamily, member 5"""	TNFRSF5		7687385, 2998589	Standard	XM_005260617		Approved	p50, Bp50	uc002xrg.1	P25942	OTTHUMG00000033053	ENST00000372285.3:c.294A>G	20.37:g.44751286A>G						CD40_ENST00000489304.1_3'UTR|CD40_ENST00000372276.3_Silent_p.E98E	p.E98E	NM_001250.4	NP_001241.1	P25942	TNR5_HUMAN			4	366	+		Myeloproliferative disorder(115;0.0122)	98					E1P5S9|Q53GN5|Q5JY15|Q5U007|Q7M4Q8|Q86YK5|Q9BYU0	Silent	SNP	ENST00000372285.3	37	c.294A>G	CCDS13393.1																																																																																				0.607	CD40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080376.1	NM_001250		38	81	0	0	0	1	0	38	81				
SUMF2	25870	broad.mit.edu	37	7	56142409	56142409	+	Missense_Mutation	SNP	C	C	T			TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr7:56142409C>T	ENST00000413756.1	+	5	538	c.515C>T	c.(514-516)gCc>gTc	p.A172V	SUMF2_ENST00000434526.2_Missense_Mutation_p.A191V|SUMF2_ENST00000275607.9_Missense_Mutation_p.A84V|SUMF2_ENST00000342190.6_Missense_Mutation_p.A191V|SUMF2_ENST00000437307.2_Intron|SUMF2_ENST00000395436.2_Missense_Mutation_p.A176V|SUMF2_ENST00000395435.2_Intron			Q8NBJ7	SUMF2_HUMAN	sulfatase modifying factor 2	172					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)	endoplasmic reticulum lumen (GO:0005788)	metal ion binding (GO:0046872)			breast(2)|endometrium(2)|large_intestine(1)|lung(6)|ovary(2)|skin(1)	14	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			TGGGAGTTTGCCGCCCGAGGG	0.567											OREG0018081	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000434526.2																			0				breast(2)|endometrium(2)|large_intestine(1)|lung(6)|ovary(2)|skin(1)	14						c.(571-573)gCc>gTc		sulfatase modifying factor 2							80.0	82.0	81.0					7																	56142409		2203	4300	6503	SO:0001583	missense	25870					endoplasmic reticulum lumen	metal ion binding	g.chr7:56142409C>T	AK075477	CCDS5524.2, CCDS43588.2, CCDS43589.2, CCDS47589.1, CCDS55111.1	7q11.1	2004-04-30			ENSG00000129103	ENSG00000129103			20415	protein-coding gene	gene with protein product		607940				12757706	Standard	NM_015411		Approved	DKFZp566I1024	uc003trv.3	Q8NBJ7	OTTHUMG00000129373	ENST00000413756.1:c.515C>T	7.37:g.56142409C>T	ENSP00000406445:p.Ala172Val		OREG0018081	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1013	SUMF2_ENST00000437307.2_Intron|SUMF2_ENST00000413756.1_Missense_Mutation_p.A172V|SUMF2_ENST00000395435.2_Intron|SUMF2_ENST00000342190.6_Missense_Mutation_p.A191V|SUMF2_ENST00000275607.9_Missense_Mutation_p.A84V|SUMF2_ENST00000395436.2_Missense_Mutation_p.A176V	p.A191V	NM_001042469.1|NM_015411.2	NP_001035934.2|NP_056226.2	Q8NBJ7	SUMF2_HUMAN	Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)		5	603	+	Breast(14;0.214)		172					B4DU41|B4DWQ0|Q14DW5|Q53ZE3|Q96BH2|Q9BRN3|Q9BWI1|Q9Y405	Missense_Mutation	SNP	ENST00000413756.1	37	c.572C>T		.	.	.	.	.	.	.	.	.	.	C	36	5.686691	0.96784	.	.	ENSG00000129103	ENST00000395436;ENST00000434526;ENST00000275607;ENST00000413952;ENST00000342190;ENST00000413756;ENST00000451338	D;D;D;D;D;D;D	0.98968	-5.28;-5.28;-5.28;-5.28;-5.28;-5.28;-5.28	5.53	5.53	0.82687	C-type lectin fold (1);Formylglycine-generating sulphatase enzyme domain (2);	0.000000	0.85682	D	0.000000	D	0.99309	0.9758	M	0.90198	3.095	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.951	D	0.99226	1.0880	10	0.87932	D	0	-11.665	18.8414	0.92186	0.0:1.0:0.0:0.0	.	176;172;191	A8MXB9;Q8NBJ7;F8WA42	.;SUMF2_HUMAN;.	V	176;191;84;194;191;172;189	ENSP00000378824:A176V;ENSP00000400922:A191V;ENSP00000275607:A84V;ENSP00000414434:A194V;ENSP00000341938:A191V;ENSP00000406445:A172V;ENSP00000410796:A189V	ENSP00000275607:A84V	A	+	2	0	SUMF2	56109903	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.607000	0.82883	2.777000	0.95525	0.591000	0.81541	GCC		0.567	SUMF2-013	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000341457.2	NM_015411		5	172	0	0	0	1	0	5	172				
C15orf43	145645	broad.mit.edu	37	15	45248953	45248953	+	Missense_Mutation	SNP	G	G	A	rs369672721		TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr15:45248953G>A	ENST00000340827.3	+	1	54	c.37G>A	c.(37-39)Gtt>Att	p.V13I		NM_152448.2	NP_689661.1	Q8NHR7	CO043_HUMAN	chromosome 15 open reading frame 43	13										NS(1)|breast(2)|large_intestine(1)|lung(2)|skin(2)	8		all_cancers(109;3.68e-08)|all_epithelial(112;1.05e-06)|Lung NSC(122;1.42e-05)|all_lung(180;0.000112)|Melanoma(134;0.0192)		all cancers(107;7.64e-17)|GBM - Glioblastoma multiforme(94;2.03e-06)		TTGCGGCAGCGTTAGCCAGGA	0.582																																						ENST00000340827.3																			0				NS(1)|breast(2)|large_intestine(1)|lung(2)|skin(2)	8						c.(37-39)Gtt>Att		chromosome 15 open reading frame 43		G	ILE/VAL	0,4396		0,0,2198	102.0	92.0	95.0		37	4.8	1.0	15		95	2,8594		0,2,4296	no	missense	C15orf43	NM_152448.1	29	0,2,6494	AA,AG,GG		0.0233,0.0,0.0154	possibly-damaging	13/221	45248953	2,12990	2198	4298	6496	SO:0001583	missense	145645							g.chr15:45248953G>A	BC029537	CCDS10115.1	15q21.1	2006-02-03			ENSG00000167014	ENSG00000167014			28520	protein-coding gene	gene with protein product							Standard	NM_152448		Approved	MGC33951	uc001zuk.4	Q8NHR7	OTTHUMG00000131264	ENST00000340827.3:c.37G>A	15.37:g.45248953G>A	ENSP00000340644:p.Val13Ile						p.V13I	NM_152448.2	NP_689661.1	Q8NHR7	CO043_HUMAN		all cancers(107;7.64e-17)|GBM - Glioblastoma multiforme(94;2.03e-06)	1	54	+		all_cancers(109;3.68e-08)|all_epithelial(112;1.05e-06)|Lung NSC(122;1.42e-05)|all_lung(180;0.000112)|Melanoma(134;0.0192)	13						Missense_Mutation	SNP	ENST00000340827.3	37	c.37G>A	CCDS10115.1	.	.	.	.	.	.	.	.	.	.	-	9.277	1.047108	0.19827	0.0	2.33E-4	ENSG00000167014	ENST00000340827	T	0.55588	0.51	4.83	4.83	0.62350	.	0.000000	0.51477	D	0.000083	T	0.61350	0.2340	L	0.32530	0.975	0.33155	D	0.546262	D	0.71674	0.998	D	0.75484	0.986	T	0.70479	-0.4860	10	0.87932	D	0	.	13.6092	0.62065	0.0:0.0:1.0:0.0	.	13	Q8NHR7	CO043_HUMAN	I	13	ENSP00000340644:V13I	ENSP00000340644:V13I	V	+	1	0	C15orf43	43036245	1.000000	0.71417	0.995000	0.50966	0.033000	0.12548	4.391000	0.59652	2.666000	0.90696	0.643000	0.83706	GTT		0.582	C15orf43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254032.1	NM_152448		26	78	0	0	0	1	0	26	78				
PRR14	78994	broad.mit.edu	37	16	30664041	30664041	+	Splice_Site	SNP	G	G	A	rs147414936		TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr16:30664041G>A	ENST00000542965.2	+	3	648		c.e3-1		PRR14_ENST00000300835.4_Splice_Site			Q9BWN1	PRR14_HUMAN	proline rich 14											breast(3)|endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|skin(1)	18			Colorectal(24;0.103)			TTCTCTTCCAGGTCCCCGTGG	0.587																																						ENST00000542965.2																			0				breast(3)|endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|skin(1)	18						c.e3-1		proline rich 14							100.0	90.0	94.0					16																	30664041		2197	4300	6497	SO:0001630	splice_region_variant	78994							g.chr16:30664041G>A	AK074783	CCDS10687.1	16p11.2	2008-02-05			ENSG00000156858	ENSG00000156858			28458	protein-coding gene	gene with protein product						12477932	Standard	NM_024031		Approved	MGC3121	uc002dyy.3	Q9BWN1	OTTHUMG00000132414	ENST00000542965.2:c.193-1G>A	16.37:g.30664041G>A						PRR14_ENST00000300835.4_Splice_Site				Q9BWN1	PRR14_HUMAN	Colorectal(24;0.103)		3	648	+								Q8WTX2	Splice_Site	SNP	ENST00000542965.2	37		CCDS10687.1	.	.	.	.	.	.	.	.	.	.	G	14.89	2.671608	0.47781	.	.	ENSG00000156858	ENST00000300835;ENST00000542965	.	.	.	5.5	5.5	0.81552	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8984	0.70659	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PRR14	30571542	0.995000	0.38212	0.388000	0.26195	0.214000	0.24535	4.350000	0.59392	2.584000	0.87258	0.585000	0.79938	.		0.587	PRR14-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434433.1	NM_024031	Intron	4	107	0	0	0	1	0	4	107				
HYLS1	219844	broad.mit.edu	37	11	125770123	125770123	+	Missense_Mutation	SNP	T	T	C			TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr11:125770123T>C	ENST00000425380.2	+	3	1641	c.860T>C	c.(859-861)gTc>gCc	p.V287A	PUS3_ENST00000227474.3_Intron|HYLS1_ENST00000526028.1_Missense_Mutation_p.V287A|HYLS1_ENST00000356438.3_Missense_Mutation_p.V287A	NM_001134793.1	NP_001128265.1	Q96M11	HYLS1_HUMAN	hydrolethalus syndrome 1	287						centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|large_intestine(3)|skin(3)|upper_aerodigestive_tract(1)	9	all_hematologic(175;0.177)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.131)|all_lung(97;0.139)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0446)		GCAAATGGTGTCATACCCAGG	0.403																																					Esophageal Squamous(172;2590 2636 8884 10471)	ENST00000425380.2																			0				breast(1)|endometrium(1)|large_intestine(3)|skin(3)|upper_aerodigestive_tract(1)	9						c.(859-861)gTc>gCc		hydrolethalus syndrome 1							100.0	97.0	98.0					11																	125770123		2201	4299	6500	SO:0001583	missense	219844					centrosome|nucleus		g.chr11:125770123T>C	AK057477	CCDS8467.1	11q24	2014-06-18				ENSG00000198331			26558	protein-coding gene	gene with protein product		610693				15843405	Standard	NM_145014		Approved	FLJ32915	uc009zbv.3	Q96M11		ENST00000425380.2:c.860T>C	11.37:g.125770123T>C	ENSP00000414884:p.Val287Ala					PUS3_ENST00000227474.3_Intron|HYLS1_ENST00000356438.3_Missense_Mutation_p.V287A|HYLS1_ENST00000526028.1_Missense_Mutation_p.V287A	p.V287A	NM_001134793.1	NP_001128265.1	Q96M11	HYLS1_HUMAN		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0446)	3	1641	+	all_hematologic(175;0.177)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.131)|all_lung(97;0.139)|all_neural(223;0.224)	287					B3KXI8|Q96BX9	Missense_Mutation	SNP	ENST00000425380.2	37	c.860T>C	CCDS8467.1	.	.	.	.	.	.	.	.	.	.	T	14.05	2.420342	0.42918	.	.	ENSG00000198331	ENST00000356438;ENST00000425380;ENST00000526028	T;T;T	0.64991	-0.13;-0.13;-0.13	6.02	3.68	0.42216	.	0.648498	0.13652	N	0.372207	T	0.53351	0.1791	L	0.51422	1.61	0.54753	D	0.999981	B	0.06786	0.001	B	0.08055	0.003	T	0.45600	-0.9250	10	0.46703	T	0.11	.	6.8412	0.23963	0.2351:0.0643:0.0:0.7006	.	287	Q96M11	HYLS1_HUMAN	A	287	ENSP00000348815:V287A;ENSP00000414884:V287A;ENSP00000436833:V287A	ENSP00000348815:V287A	V	+	2	0	HYLS1	125275333	0.624000	0.27102	0.982000	0.44146	0.982000	0.71751	1.345000	0.33953	0.507000	0.28148	0.533000	0.62120	GTC		0.403	HYLS1-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386733.1	NM_145014		27	44	0	0	0	1	0	27	44				
SND1	27044	broad.mit.edu	37	7	127631024	127631024	+	Missense_Mutation	SNP	G	G	A			TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr7:127631024G>A	ENST00000354725.3	+	16	1888	c.1694G>A	c.(1693-1695)cGa>cAa	p.R565Q	SND1_ENST00000467238.1_3'UTR	NM_014390.2	NP_055205.2	Q7KZF4	SND1_HUMAN	staphylococcal nuclease and tudor domain containing 1	565	TNase-like 4. {ECO:0000255|PROSITE- ProRule:PRU00272}.				gene silencing by RNA (GO:0031047)|osteoblast differentiation (GO:0001649)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|dense body (GO:0097433)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|RISC complex (GO:0016442)	nuclease activity (GO:0004518)|poly(A) RNA binding (GO:0044822)|transcription cofactor activity (GO:0003712)			central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	41						AGAGGAGCCCGAAACCTCCCA	0.542																																						ENST00000354725.3																			0				central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	41						c.(1693-1695)cGa>cAa		staphylococcal nuclease and tudor domain containing 1							77.0	66.0	70.0					7																	127631024		2203	4300	6503	SO:0001583	missense	27044				gene silencing by RNA|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	melanosome|nucleus|RNA-induced silencing complex	nuclease activity|nucleic acid binding|protein binding|transcription cofactor activity	g.chr7:127631024G>A		CCDS34747.1	7q31.3	2014-03-24			ENSG00000197157	ENSG00000197157		"""Tudor domain containing"""	30646	protein-coding gene	gene with protein product	"""p100 EBNA2 co-activator"", ""Tudor-SN"""	602181				7651391, 9003410, 12819296	Standard	NM_014390		Approved	TDRD11, p100	uc003vmi.3	Q7KZF4	OTTHUMG00000157560	ENST00000354725.3:c.1694G>A	7.37:g.127631024G>A	ENSP00000346762:p.Arg565Gln					SND1_ENST00000467238.1_3'UTR	p.R565Q	NM_014390.2	NP_055205.2	Q7KZF4	SND1_HUMAN			16	1888	+			565			TNase-like 4.		Q13122|Q96AG0	Missense_Mutation	SNP	ENST00000354725.3	37	c.1694G>A	CCDS34747.1	.	.	.	.	.	.	.	.	.	.	G	36	5.663170	0.96745	.	.	ENSG00000197157	ENST00000354725;ENST00000438400;ENST00000486037	T;T	0.27557	1.66;1.66	5.54	5.54	0.83059	Staphylococcal nuclease (SNase-like) (4);Staphylococcal nuclease (SNase-like), OB-fold (1);	0.000000	0.50627	D	0.000107	T	0.57110	0.2031	M	0.81682	2.555	0.80722	D	1	D	0.71674	0.998	D	0.65573	0.936	T	0.56661	-0.7942	10	0.44086	T	0.13	-1.2187	17.3145	0.87218	0.0:0.0:1.0:0.0	.	565	Q7KZF4	SND1_HUMAN	Q	565;555;114	ENSP00000346762:R565Q;ENSP00000419327:R114Q	ENSP00000346762:R565Q	R	+	2	0	SND1	127418260	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	7.916000	0.87491	2.754000	0.94517	0.655000	0.94253	CGA		0.542	SND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349148.1	NM_014390		12	24	0	0	0	1	0	12	24				
OR5AS1	219447	broad.mit.edu	37	11	55798589	55798589	+	Missense_Mutation	SNP	G	G	T			TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr11:55798589G>T	ENST00000313555.1	+	1	695	c.695G>T	c.(694-696)gGt>gTt	p.G232V		NM_001001921.1	NP_001001921.1	Q8N127	O5AS1_HUMAN	olfactory receptor, family 5, subfamily AS, member 1	232						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(7)|large_intestine(7)|liver(1)|lung(22)|ovary(3)|prostate(4)|skin(3)|stomach(1)	48	Esophageal squamous(21;0.00693)					AAGTCCTCAGGTGGCAGAAGC	0.453																																						ENST00000313555.1																			0				endometrium(7)|large_intestine(7)|liver(1)|lung(22)|ovary(3)|prostate(4)|skin(3)|stomach(1)	48						c.(694-696)gGt>gTt		olfactory receptor, family 5, subfamily AS, member 1							181.0	162.0	168.0					11																	55798589		2201	4296	6497	SO:0001583	missense	219447				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:55798589G>T	AB065543	CCDS31516.1	11q11	2012-08-09			ENSG00000181785	ENSG00000181785		"""GPCR / Class A : Olfactory receptors"""	15261	protein-coding gene	gene with protein product							Standard	NM_001001921		Approved		uc010riw.2	Q8N127	OTTHUMG00000166830	ENST00000313555.1:c.695G>T	11.37:g.55798589G>T	ENSP00000324111:p.Gly232Val						p.G232V	NM_001001921.1	NP_001001921.1	Q8N127	O5AS1_HUMAN			1	695	+	Esophageal squamous(21;0.00693)		232					Q6IFB8	Missense_Mutation	SNP	ENST00000313555.1	37	c.695G>T	CCDS31516.1	.	.	.	.	.	.	.	.	.	.	G	13.56	2.274919	0.40194	.	.	ENSG00000181785	ENST00000313555	T	0.00107	8.72	5.23	0.0343	0.14183	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34986	U	0.003525	T	0.00241	0.0007	L	0.39514	1.22	0.19300	N	0.999977	D	0.69078	0.997	D	0.65874	0.939	T	0.51608	-0.8684	10	0.72032	D	0.01	.	9.2765	0.37703	0.4546:0.0:0.5454:0.0	.	232	Q8N127	O5AS1_HUMAN	V	232	ENSP00000324111:G232V	ENSP00000324111:G232V	G	+	2	0	OR5AS1	55555165	0.000000	0.05858	0.015000	0.15790	0.801000	0.45260	0.424000	0.21330	0.212000	0.20703	0.643000	0.83706	GGT		0.453	OR5AS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391538.1	NM_001001921		67	112	1	0	4.13886e-29	1	4.63838e-29	67	112				
NCKAP1	10787	broad.mit.edu	37	2	183866755	183866755	+	Missense_Mutation	SNP	G	G	A			TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr2:183866755G>A	ENST00000361354.4	-	6	901	c.529C>T	c.(529-531)Cgc>Tgc	p.R177C	NCKAP1_ENST00000360982.2_Missense_Mutation_p.R183C	NM_013436.3	NP_038464.1	Q9Y2A7	NCKP1_HUMAN	NCK-associated protein 1	177					apical protein localization (GO:0045176)|apoptotic process (GO:0006915)|basal protein localization (GO:0045175)|central nervous system development (GO:0007417)|embryonic body morphogenesis (GO:0010172)|embryonic foregut morphogenesis (GO:0048617)|embryonic heart tube development (GO:0035050)|endoderm development (GO:0007492)|establishment or maintenance of actin cytoskeleton polarity (GO:0030950)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|mesodermal cell migration (GO:0008078)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|paraxial mesoderm morphogenesis (GO:0048340)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|positive regulation of lamellipodium assembly (GO:0010592)|protein stabilization (GO:0050821)|Rac protein signal transduction (GO:0016601)|regulation of protein localization (GO:0032880)|somitogenesis (GO:0001756)|zygotic determination of anterior/posterior axis, embryo (GO:0007354)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|SCAR complex (GO:0031209)	protein complex binding (GO:0032403)			breast(3)|cervix(2)|endometrium(3)|kidney(4)|large_intestine(11)|lung(16)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)			TGGCCAAGGCGTGGGTATTCT	0.363																																						ENST00000360982.2																			0				breast(3)|cervix(2)|endometrium(3)|kidney(4)|large_intestine(11)|lung(16)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	45						c.(547-549)Cgc>Tgc		NCK-associated protein 1							147.0	146.0	147.0					2																	183866755		2203	4300	6503	SO:0001583	missense	10787				apoptosis|central nervous system development	integral to membrane|lamellipodium membrane	protein binding	g.chr2:183866755G>A	AB014509	CCDS2287.1, CCDS2288.1	2q32	2009-08-14			ENSG00000061676	ENSG00000061676			7666	protein-coding gene	gene with protein product		604891				10673335, 12181570, 9344857	Standard	NM_013436		Approved	Nap1, HEM2, NAP125	uc002upb.4	Q9Y2A7	OTTHUMG00000132623	ENST00000361354.4:c.529C>T	2.37:g.183866755G>A	ENSP00000355348:p.Arg177Cys					NCKAP1_ENST00000361354.3_Missense_Mutation_p.R177C	p.R183C	NM_205842.1	NP_995314.1	Q9Y2A7	NCKP1_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)		7	1305	-			177					O60329|Q53QN5|Q53S94|Q53Y35	Missense_Mutation	SNP	ENST00000361354.4	37	c.547C>T	CCDS2287.1	.	.	.	.	.	.	.	.	.	.	G	19.04	3.749934	0.69533	.	.	ENSG00000061676	ENST00000361354;ENST00000360982	T;T	0.57752	0.38;0.38	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.77955	0.4208	M	0.86953	2.85	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.81577	-0.0869	10	0.87932	D	0	-6.8641	19.4491	0.94860	0.0:0.0:1.0:0.0	.	177;183	Q9Y2A7;Q9Y2A7-2	NCKP1_HUMAN;.	C	177;183	ENSP00000355348:R177C;ENSP00000354251:R183C	ENSP00000354251:R183C	R	-	1	0	NCKAP1	183575000	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.630000	0.61297	2.603000	0.88011	0.650000	0.86243	CGC		0.363	NCKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255867.2	NM_205842		8	77	0	0	0	1	0	8	77				
ZNF285	26974	broad.mit.edu	37	19	44892133	44892133	+	Missense_Mutation	SNP	C	C	T	rs140033872		TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr19:44892133C>T	ENST00000330997.4	-	4	338	c.274G>A	c.(274-276)Gtg>Atg	p.V92M	ZNF285_ENST00000544719.2_Missense_Mutation_p.V92M|CTC-512J12.6_ENST00000588212.1_Intron|ZNF285_ENST00000591679.1_Missense_Mutation_p.V99M	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	92					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|prostate(5)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	44						TGAAGGTTCACGATATAATCC	0.418																																						ENST00000330997.4																			0				breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|prostate(5)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	44						c.(274-276)Gtg>Atg		zinc finger protein 285							89.0	89.0	89.0					19																	44892133		2203	4300	6503	SO:0001583	missense	26974							g.chr19:44892133C>T	AK055309	CCDS12638.1, CCDS74389.1	19q13.32	2013-01-08	2010-04-14	2010-04-14		ENSG00000267508		"""Zinc fingers, C2H2-type"", ""-"""	13079	protein-coding gene	gene with protein product			"""zinc finger protein 285A"""	ZNF285A			Standard	XM_005258734		Approved			Q96NJ3	OTTHUMG00000178848	ENST00000330997.4:c.274G>A	19.37:g.44892133C>T	ENSP00000333595:p.Val92Met					ZNF285_ENST00000544719.2_Missense_Mutation_p.V92M|ZNF285_ENST00000591679.1_Missense_Mutation_p.V99M|CTC-512J12.6_ENST00000588212.1_Intron	p.V92M	NM_152354.3	NP_689567.3					4	338	-								Q17RJ3|Q6B0A8|Q6ISR5	Missense_Mutation	SNP	ENST00000330997.4	37	c.274G>A	CCDS12638.1	.	.	.	.	.	.	.	.	.	.	T	4.739	0.137438	0.09032	.	.	ENSG00000062370	ENST00000544719;ENST00000330997	T	0.07021	3.23	3.33	0.726	0.18248	.	.	.	.	.	T	0.02727	0.0082	N	0.02011	-0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46871	-0.9160	9	0.23891	T	0.37	.	4.9771	0.14146	0.0:0.1211:0.4682:0.4107	.	116;92	B7ZLR9;Q96NJ3	.;ZN285_HUMAN	M	115;92	ENSP00000333595:V92M	ENSP00000333595:V92M	V	-	1	0	ZNF285	49583973	0.000000	0.05858	0.000000	0.03702	0.049000	0.14656	-0.764000	0.04735	-0.369000	0.08028	-0.566000	0.04163	GTG		0.418	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354		4	69	0	0	0	1	0	4	69				
STAG3L4	64940	broad.mit.edu	37	7	66771046	66771046	+	RNA	SNP	T	T	G			TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr7:66771046T>G	ENST00000416602.2	+	0	338					NR_040586.1		Q8TBR4	ST3L4_HUMAN	stromal antigen 3-like 4 (pseudogene)											endometrium(2)|lung(5)	7		Lung NSC(55;0.0839)|all_lung(88;0.181)				TGTTAACTTTTTCATCTGATC	0.388																																						ENST00000416602.2																			0				endometrium(2)|lung(5)	7															170.0	175.0	173.0					7																	66771046		2203	4300	6503			0							g.chr7:66771046T>G			7q11.21	2013-06-26	2013-06-26		ENSG00000106610	ENSG00000106610			33887	pseudogene	pseudogene			"""stromal antigen 3-like 4"""				Standard	NR_040585		Approved	FLJ13195, STAG3L4P	uc010laj.3	Q8TBR4	OTTHUMG00000156920		7.37:g.66771046T>G								NR_040586.1		Q8TBR4	STG34_HUMAN			0	338	+		Lung NSC(55;0.0839)|all_lung(88;0.181)						Q9H8W0	RNA	SNP	ENST00000416602.2	37			.	.	.	.	.	.	.	.	.	.	t	9.880	1.201199	0.22121	.	.	ENSG00000106610	ENST00000416602;ENST00000437742	.	.	.	1.37	-0.658	0.11428	.	0.109131	0.41396	N	0.000898	T	0.21881	0.0527	.	.	.	0.20074	N	0.999932	B	0.32425	0.371	B	0.17433	0.018	T	0.15235	-1.0444	7	0.87932	D	0	.	4.2006	0.10464	0.3019:0.0:0.0:0.6981	.	21	Q8TBR4	STG34_HUMAN	L	21	.	ENSP00000342950:F21L	F	+	3	2	STAG3L4	66408481	1.000000	0.71417	0.938000	0.37757	0.293000	0.27360	3.740000	0.55082	0.594000	0.29761	0.113000	0.15668	TTT		0.388	STAG3L4-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000346611.1	NM_022906		52	81	0	0	0	1	0	52	81				
LONP2	83752	broad.mit.edu	37	16	48296697	48296697	+	Missense_Mutation	SNP	A	A	C			TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr16:48296697A>C	ENST00000285737.4	+	6	989	c.896A>C	c.(895-897)aAa>aCa	p.K299T	LONP2_ENST00000535754.1_Missense_Mutation_p.K255T	NM_031490.2	NP_113678.2			lon peptidase 2, peroxisomal											breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						AGACTCAAAAAAATGCCTCAG	0.348																																						ENST00000285737.4																			0				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						c.(895-897)aAa>aCa		lon peptidase 2, peroxisomal							68.0	66.0	66.0					16																	48296697		2200	4300	6500	SO:0001583	missense	83752				misfolded or incompletely synthesized protein catabolic process|protein targeting to peroxisome|signal peptide processing	nucleoid|peroxisomal matrix	ATP binding|ATP-dependent peptidase activity|enzyme binding|sequence-specific DNA binding|serine-type endopeptidase activity	g.chr16:48296697A>C	AJ548761	CCDS10734.1, CCDS73880.1	16q12.1	2010-04-21			ENSG00000102910	ENSG00000102910		"""ATPases / AAA-type"""	20598	protein-coding gene	gene with protein product						14561759	Standard	XM_005256191		Approved	MGC4840, LONP, LONPL	uc002efi.1	Q86WA8	OTTHUMG00000133144	ENST00000285737.4:c.896A>C	16.37:g.48296697A>C	ENSP00000285737:p.Lys299Thr					LONP2_ENST00000535754.1_Missense_Mutation_p.K255T	p.K299T	NM_031490.2	NP_113678.2	Q86WA8	LONP2_HUMAN			6	989	+			299						Missense_Mutation	SNP	ENST00000285737.4	37	c.896A>C	CCDS10734.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.376629	0.82682	.	.	ENSG00000102910	ENST00000285737;ENST00000544734;ENST00000535754;ENST00000416006	T;T	0.33654	1.4;1.44	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.50205	0.1602	L	0.47016	1.485	0.80722	D	1	D;D	0.71674	0.998;0.998	P;P	0.58721	0.796;0.844	T	0.45585	-0.9251	10	0.52906	T	0.07	-26.536	16.8222	0.85835	1.0:0.0:0.0:0.0	.	255;299	B7ZKL7;Q86WA8	.;LONP2_HUMAN	T	299;28;255;255	ENSP00000285737:K299T;ENSP00000445426:K255T	ENSP00000285737:K299T	K	+	2	0	LONP2	46854198	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.260000	0.95568	2.371000	0.80710	0.533000	0.62120	AAA		0.348	LONP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256839.2	NM_031490		8	18	0	0	0	1	0	8	18				
POTEC	388468	broad.mit.edu	37	18	14513675	14513675	+	Missense_Mutation	SNP	T	T	C	rs371810308	byFrequency	TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr18:14513675T>C	ENST00000358970.5	-	10	1518	c.1519A>G	c.(1519-1521)Aaa>Gaa	p.K507E		NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	507								p.K507E(2)		NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						GAATTCATTTTCTTTTCAGCC	0.284													.|||	3	0.000599042	0.0	0.0	5008	,	,		16953	0.003		0.0	False		,,,				2504	0.0					ENST00000358970.5																			2	Substitution - Missense(2)	p.K507E(2)	urinary_tract(1)|prostate(1)	NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						c.(1519-1521)Aaa>Gaa		POTE ankyrin domain family, member C							164.0	115.0	130.0					18																	14513675		692	1590	2282	SO:0001583	missense	388468							g.chr18:14513675T>C	BX649118	CCDS45835.1	18p11.21	2013-01-10	2008-11-26	2008-11-26	ENSG00000183206	ENSG00000183206		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33894	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 6"""		"""ANKRD26-like family B, member 2"""	A26B2			Standard	NM_001137671		Approved	POTE18, POTE-18, DKFZp686J0529, CT104.6	uc010dln.3	B2RU33	OTTHUMG00000162963	ENST00000358970.5:c.1519A>G	18.37:g.14513675T>C	ENSP00000351856:p.Lys507Glu						p.K507E	NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN			10	1518	-			507						Missense_Mutation	SNP	ENST00000358970.5	37	c.1519A>G	CCDS45835.1	.	.	.	.	.	.	.	.	.	.	t	0.001	-3.812128	0.00004	.	.	ENSG00000183206	ENST00000358970	T	0.32753	1.44	1.53	-3.07	0.05363	.	.	.	.	.	T	0.10165	0.0249	N	0.11427	0.14	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31752	-0.9932	9	0.02654	T	1	.	3.0168	0.06063	0.0:0.3604:0.2511:0.3885	.	507	B2RU33	POTEC_HUMAN	E	507	ENSP00000351856:K507E	ENSP00000351856:K507E	K	-	1	0	POTEC	14503675	0.024000	0.19004	0.012000	0.15200	0.024000	0.10985	-0.021000	0.12504	-1.054000	0.03214	-3.018000	0.00074	AAA		0.284	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371179.1	XM_496269		4	68	0	0	0	1	0	4	68				
TNC	3371	broad.mit.edu	37	9	117848575	117848575	+	Missense_Mutation	SNP	G	G	A			TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr9:117848575G>A	ENST00000350763.4	-	3	1846	c.1435C>T	c.(1435-1437)Cgc>Tgc	p.R479C	TNC_ENST00000341037.4_Missense_Mutation_p.R479C|TNC_ENST00000423613.2_Missense_Mutation_p.R479C|TNC_ENST00000346706.3_Missense_Mutation_p.R479C|TNC_ENST00000340094.3_Missense_Mutation_p.R479C|TNC_ENST00000542877.1_Missense_Mutation_p.R479C|TNC_ENST00000535648.1_Missense_Mutation_p.R479C|TNC_ENST00000537320.1_Missense_Mutation_p.R479C|TNC_ENST00000345230.3_Missense_Mutation_p.R479C	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	479	EGF-like 11. {ECO:0000255|PROSITE- ProRule:PRU00076}.				bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)			NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						TTCACACAGCGGCCGTGCTGG	0.582																																						ENST00000350763.4																			0				NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						c.(1435-1437)Cgc>Tgc		tenascin C							149.0	142.0	144.0					9																	117848575		2203	4300	6503	SO:0001583	missense	3371				cell adhesion|response to wounding|signal transduction	extracellular space	receptor binding|syndecan binding	g.chr9:117848575G>A		CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	5318	protein-coding gene	gene with protein product	"""hexabrachion (tenascin)"""	187380	"""hexabrachion (tenascin C, cytotactin)"", ""deafness, autosomal dominant 56"""	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.1435C>T	9.37:g.117848575G>A	ENSP00000265131:p.Arg479Cys					TNC_ENST00000535648.1_Missense_Mutation_p.R479C|TNC_ENST00000423613.2_Missense_Mutation_p.R479C|TNC_ENST00000340094.3_Missense_Mutation_p.R479C|TNC_ENST00000345230.3_Missense_Mutation_p.R479C|TNC_ENST00000341037.4_Missense_Mutation_p.R479C|TNC_ENST00000537320.1_Missense_Mutation_p.R479C|TNC_ENST00000542877.1_Missense_Mutation_p.R479C|TNC_ENST00000346706.3_Missense_Mutation_p.R479C	p.R479C	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN			3	1846	-			479			EGF-like 11.		C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Missense_Mutation	SNP	ENST00000350763.4	37	c.1435C>T	CCDS6811.1	.	.	.	.	.	.	.	.	.	.	G	16.55	3.154440	0.57259	.	.	ENSG00000041982	ENST00000340094;ENST00000535648;ENST00000346706;ENST00000345230;ENST00000350763;ENST00000442945;ENST00000341037;ENST00000423613;ENST00000537320;ENST00000542877	T;T;T;T;T;T;T;T;T	0.03524	3.9;3.9;3.9;3.9;3.9;3.9;3.9;3.9;3.9	5.82	5.82	0.92795	EGF, extracellular (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.332477	0.37577	N	0.002036	T	0.25975	0.0633	M	0.92026	3.265	0.58432	D	0.999999	D;D	0.89917	1.0;0.994	D;P	0.68621	0.959;0.846	T	0.03981	-1.0987	10	0.87932	D	0	.	19.0681	0.93122	0.0:0.0:1.0:0.0	.	479;479	E9PC84;P24821	.;TENA_HUMAN	C	479	ENSP00000344400:R479C;ENSP00000438152:R479C;ENSP00000344555:R479C;ENSP00000345861:R479C;ENSP00000265131:R479C;ENSP00000339553:R479C;ENSP00000411406:R479C;ENSP00000443478:R479C;ENSP00000442242:R479C	ENSP00000344400:R479C	R	-	1	0	TNC	116888396	1.000000	0.71417	1.000000	0.80357	0.725000	0.41563	4.578000	0.60929	2.753000	0.94483	0.462000	0.41574	CGC		0.582	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160		89	191	0	0	0	1	0	89	191				
CIC	23152	broad.mit.edu	37	19	42799059	42799059	+	Missense_Mutation	SNP	C	C	T			TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr19:42799059C>T	ENST00000575354.2	+	20	4583	c.4543C>T	c.(4543-4545)Cgc>Tgc	p.R1515C	CIC_ENST00000160740.3_Missense_Mutation_p.R1513C|CIC_ENST00000572681.2_Missense_Mutation_p.R2421C	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	1515					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				CCGTGAGGTGCGCCAGAAGAT	0.632			"""Mis, F, S"""		oligodendroglioma																																	ENST00000572681.2				Rec	yes		19	19q13.2	23152	"""Mis, F, S"""	capicua homolog			O			oligodendroglioma		0				autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82						c.(7261-7263)Cgc>Tgc		capicua transcriptional repressor							47.0	47.0	47.0					19																	42799059		2203	4300	6503	SO:0001583	missense	23152				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding	g.chr19:42799059C>T	AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"""capicua (Drosophila) homolog"", ""capicua homolog (Drosophila)"""			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.4543C>T	19.37:g.42799059C>T	ENSP00000458663:p.Arg1515Cys					CIC_ENST00000160740.3_Missense_Mutation_p.R1513C|CIC_ENST00000575354.2_Missense_Mutation_p.R1515C	p.R2421C			Q96RK0	CIC_HUMAN			21	7329	+		Prostate(69;0.00682)	1515					Q7LGI1|Q9UEG5|Q9Y6T1	Missense_Mutation	SNP	ENST00000575354.2	37	c.7261C>T	CCDS12601.1	.	.	.	.	.	.	.	.	.	.	C	16.57	3.159893	0.57368	.	.	ENSG00000079432	ENST00000160740	.	.	.	4.49	2.33	0.28932	.	.	.	.	.	T	0.52901	0.1763	L	0.29908	0.895	0.51233	D	0.999917	D	0.89917	1.0	D	0.76575	0.988	T	0.55811	-0.8082	8	0.87932	D	0	-10.1007	2.833	0.05506	0.1907:0.5252:0.184:0.1001	.	1515	Q96RK0	CIC_HUMAN	C	1515	.	ENSP00000160740:R1515C	R	+	1	0	CIC	47490899	0.995000	0.38212	1.000000	0.80357	0.995000	0.86356	2.109000	0.41863	1.232000	0.43678	0.491000	0.48974	CGC		0.632	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			22	50	0	0	0	1	0	22	50				
ZBED9	114821	broad.mit.edu	37	6	28540332	28540332	+	Missense_Mutation	SNP	A	A	G			TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr6:28540332A>G	ENST00000452236.2	-	4	3951	c.3334T>C	c.(3334-3336)Ttt>Ctt	p.F1112L		NM_052923.1	NP_443155.1														NS(3)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(14)|liver(1)|lung(29)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(3)	71						agatcattaaaaatactgaag	0.353																																						ENST00000452236.2																			0				NS(3)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(14)|liver(1)|lung(29)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(3)	71						c.(3334-3336)Ttt>Ctt		SCAN domain containing 3							59.0	61.0	60.0					6																	28540332		2194	4290	6484	SO:0001583	missense	114821				DNA integration|viral reproduction	nucleus	DNA binding|protein dimerization activity|sequence-specific DNA binding transcription factor activity	g.chr6:28540332A>G																												ENST00000452236.2:c.3334T>C	6.37:g.28540332A>G	ENSP00000395259:p.Phe1112Leu						p.F1112L	NM_052923.1	NP_443155.1	Q6R2W3	SCND3_HUMAN			4	3951	-			1112	F -> FF (in Ref. 3; CAD28490).					Missense_Mutation	SNP	ENST00000452236.2	37	c.3334T>C	CCDS34355.1	.	.	.	.	.	.	.	.	.	.	A	0.683	-0.797464	0.02862	.	.	ENSG00000232040	ENST00000452236	T	0.26067	1.76	2.53	2.53	0.30540	Ribonuclease H-like (1);	2.437400	0.02530	N	0.093545	T	0.05135	0.0137	N	0.00507	-1.42	0.27287	N	0.957945	P	0.46578	0.88	P	0.62184	0.899	T	0.58267	-0.7666	10	0.02654	T	1	.	6.9733	0.24660	1.0:0.0:0.0:0.0	.	1112	Q6R2W3	SCND3_HUMAN	L	1112	ENSP00000395259:F1112L	ENSP00000395259:F1112L	F	-	1	0	SCAND3	28648311	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.260000	0.43267	1.405000	0.46838	0.533000	0.62120	TTT		0.353	SCAND3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000043551.3			20	37	0	0	0	1	0	20	37				
CACNA1E	777	broad.mit.edu	37	1	181680102	181680103	+	Frame_Shift_Del	DEL	AG	AG	-	rs147596634		TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr1:181680102_181680103delAG	ENST00000367573.2	+	8	1068_1069	c.1068_1069delAG	c.(1066-1071)aaagagfs	p.E357fs	CACNA1E_ENST00000357570.5_Frame_Shift_Del_p.E308fs|CACNA1E_ENST00000360108.3_Frame_Shift_Del_p.E357fs|CACNA1E_ENST00000526775.1_Frame_Shift_Del_p.E357fs|CACNA1E_ENST00000367567.4_5'UTR|CACNA1E_ENST00000358338.5_Frame_Shift_Del_p.E308fs|CACNA1E_ENST00000367570.1_Frame_Shift_Del_p.E357fs	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	357					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						AATTTGCCAAAGAGAGAGAGAG	0.51																																						ENST00000526775.1																			0				NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						c.(1066-1071)aaagfs		calcium channel, voltage-dependent, R type, alpha 1E subunit			,,	161,3503		41,79,1712					,,	5.3	1.0		dbSNP_134	61	297,7585		52,193,3696	yes	frameshift,frameshift,frameshift	CACNA1E	NM_001205294.1,NM_001205293.1,NM_000721.3	,,	93,272,5408	A1A1,A1R,RR		3.7681,4.3941,3.9667	,,	,,		458,11088				SO:0001589	frameshift_variant	777				energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity	g.chr1:181680102_181680103delAG	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.1068_1069delAG	1.37:g.181680112_181680113delAG	ENSP00000356545:p.Glu357fs					CACNA1E_ENST00000358338.5_Frame_Shift_Del_p.KE307fs|CACNA1E_ENST00000357570.5_Frame_Shift_Del_p.KE307fs|CACNA1E_ENST00000367573.2_Frame_Shift_Del_p.KE356fs|CACNA1E_ENST00000367570.1_Frame_Shift_Del_p.KE356fs|CACNA1E_ENST00000360108.3_Frame_Shift_Del_p.KE356fs|CACNA1E_ENST00000367567.4_5'UTR	p.KE356fs	NM_001205294.1	NP_001192223.1	Q15878	CAC1E_HUMAN			8	1233_1234	+			356					B1AM12|B1AM13|B1AM14|Q14580|Q14581	Frame_Shift_Del	DEL	ENST00000367573.2	37	c.1068_1069delAG	CCDS55664.1																																																																																				0.510	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		9	180						9	180	---	---	---	---
TMEM127	55654	broad.mit.edu	37	2	96919781	96919783	+	In_Frame_Del	DEL	TGC	TGC	-			TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr2:96919781_96919783delTGC	ENST00000258439.3	-	4	736_738	c.480_482delGCA	c.(478-483)cagcat>cat	p.Q160del	TMEM127_ENST00000435268.1_In_Frame_Del_p.Q76del|TMEM127_ENST00000432959.1_In_Frame_Del_p.Q160del	NM_001193304.2|NM_017849.3	NP_001180233.1|NP_060319.1	O75204	TM127_HUMAN	transmembrane protein 127	160					negative regulation of cell proliferation (GO:0008285)|negative regulation of TOR signaling (GO:0032007)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(1)|lung(1)|prostate(1)|stomach(1)	5						GTACTTCTTATGCTGCTGCTGCT	0.557																																						ENST00000258439.2																			0				endometrium(1)|large_intestine(1)|lung(1)|prostate(1)|stomach(1)	5						c.(478-483)cat>ca		transmembrane protein 127																																				SO:0001651	inframe_deletion	55654				negative regulation of cell proliferation|negative regulation of TOR signaling cascade	cytoplasm|integral to membrane|plasma membrane		g.chr2:96919781_96919783delTGC	AK000514	CCDS2018.1	2q11.2	2014-09-17			ENSG00000135956	ENSG00000135956			26038	protein-coding gene	gene with protein product		613403				10493829	Standard	NM_017849		Approved	FLJ20507, FLJ22257	uc002svr.3	O75204	OTTHUMG00000130454	ENST00000258439.3:c.480_482delGCA	2.37:g.96919790_96919792delTGC	ENSP00000258439:p.Gln160del					TMEM127_ENST00000435268.1_In_Frame_Del_p.QH76del|TMEM127_ENST00000432959.1_In_Frame_Del_p.QH160del	p.QH160del	NM_001193304.2|NM_017849.3	NP_001180233.1|NP_060319.1	O75204	TM127_HUMAN			4	736_738	-			160					D3DXH0	In_Frame_Del	DEL	ENST00000258439.3	37	c.480_482delGCA	CCDS2018.1																																																																																				0.557	TMEM127-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252845.3	NM_017849		8	173						8	173	---	---	---	---
NDUFS1	4719	broad.mit.edu	37	2	206980715	206980715	+	3'UTR	DEL	T	T	-			TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr2:206980715delT	ENST00000233190.6	-	0	10644				AC007383.4_ENST00000453039.1_RNA	NM_005006.6	NP_004997.4	P28331	NDUS1_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 1, 75kDa (NADH-coenzyme Q reductase)						apoptotic mitochondrial changes (GO:0008637)|ATP metabolic process (GO:0046034)|cellular metabolic process (GO:0044237)|cellular respiration (GO:0045333)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|reactive oxygen species metabolic process (GO:0072593)|regulation of mitochondrial membrane potential (GO:0051881)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial respiratory chain complex I (GO:0005747)	2 iron, 2 sulfur cluster binding (GO:0051537)|4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(15)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						TTAACAGTAGTTTTTTTTTCC	0.323																																						ENST00000453039.1																			0																																																	SO:0001624	3_prime_UTR_variant	0							g.chr2:206980715delT		CCDS2366.1, CCDS56162.1, CCDS56163.1, CCDS56164.1, CCDS56165.1	2q33-q34	2011-07-04	2002-08-29		ENSG00000023228	ENSG00000023228	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7707	protein-coding gene	gene with protein product	"""complex I 75kDa subunit"", ""NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial"""	157655	"""NADH dehydrogenase (ubiquinone) Fe-S protein 1 (75kD) (NADH-coenzyme Q reductase)"""			1935949	Standard	NM_005006		Approved	CI-75k	uc010ziq.2	P28331	OTTHUMG00000132892	ENST00000233190.6:c.*8194A>-	2.37:g.206980715delT								NR_033248.1						0	445	+								B4DIN9|B4DJA0|B4DPG1|B4DUC1|E7ENF3|Q53TR8|Q8N1C4|Q8TCC9	RNA	DEL	ENST00000233190.6	37		CCDS2366.1																																																																																				0.323	NDUFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256391.4	NM_005006		2	4						2	4	---	---	---	---
BSNDP4	106481726	broad.mit.edu	37	7	57698565	57698566	+	RNA	INS	-	-	TGGG	rs367832782		TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr7:57698565_57698566insTGGG	ENST00000605139.1	-	0	416																											CACAGGAGACCTGGGCTGCAGG	0.584																																						ENST00000605139.1																			0																																																			0							g.chr7:57698565_57698566insTGGG																													7.37:g.57698566_57698569dupTGGG														0	416	-									RNA	INS	ENST00000605139.1	37																																																																																						0.584	RP11-368M16.3-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000468775.1			2	4						2	4	---	---	---	---
STAG3L2	442582	broad.mit.edu	37	7	74300557	74300564	+	RNA	DEL	AGAGCTCC	AGAGCTCC	-	rs367732188		TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr7:74300557_74300564delAGAGCTCC	ENST00000423186.1	-	0	573_580							P0CL84	ST3L2_HUMAN	stromal antigen 3-like 2 (pseudogene)							nucleus (GO:0005634)		p.E82fs*32(2)		breast(1)|central_nervous_system(1)|large_intestine(1)|lung(1)|pancreas(1)	5						CGGCCAGTGAAGAGCTCCAGGCGTGCGG	0.572																																						ENST00000423186.1																			2	Deletion - Frameshift(2)	p.E82fs*32(2)	large_intestine(1)|central_nervous_system(1)	breast(1)|central_nervous_system(1)|large_intestine(1)|lung(1)|pancreas(1)	5												96,356		38,20,168							0.0			1	208,1036		88,32,502	no	frameshift	STAG3L2	NM_001025202.2		126,52,670	A1A1,A1R,RR		16.7203,21.2389,17.9245				304,1392						0					nucleus	binding	g.chr7:74300557_74300564delAGAGCTCC			7q11.23	2013-06-26	2013-06-26			ENSG00000277072			33886	pseudogene	pseudogene			"""stromal antigen 3-like 2"""				Standard	NR_040584		Approved	MGC131759, STAG3L2P	uc011kfj.2	P0CL84	OTTHUMG00000156216		7.37:g.74300557_74300564delAGAGCTCC										P0CL84	ST3L2_HUMAN			0	573_580	-								A6NMT8|A8K0A1|Q32NE4|Q6NXR2|Q7L5M5|Q7Z5K6	RNA	DEL	ENST00000423186.1	37																																																																																						0.572	STAG3L2-002	KNOWN	basic	retained_intron	pseudogene	OTTHUMT00000343523.2	NM_001025202		6	12						6	12	---	---	---	---
POM121C	100101267	broad.mit.edu	37	7	75045497	75045497	+	IGR	DEL	G	G	-	rs201842651	byFrequency	TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr7:75045497delG	ENST00000257665.5	-	0	5700				NSUN5P1_ENST00000393633.2_RNA			A8CG34	P121C_HUMAN	POM121 transmembrane nucleoporin C						mRNA transport (GO:0051028)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|nuclear pore (GO:0005643)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	14						GGGTCGTGGAGGGGGGGGATG	0.657													|||unknown(NO_COVERAGE)	508	0.101438	0.2995	0.0317	5008	,	,		10857	0.001		0.0398	False		,,,				2504	0.0501					ENST00000393633.2																			0				large_intestine(1)|lung(1)	2												589,1955		269,51,952	7.0	15.0	12.0			2.1	0.0	7	dbSNP_114	12	725,5999		314,97,2951	no	near-gene-3				583,148,3903	A1A1,A1R,RR		10.7823,23.1525,14.1778			75045497	1314,7954	2010	4158	6168	SO:0001628	intergenic_variant	0							g.chr7:75045497delG		CCDS47617.1	7q11.23	2012-03-13	2012-03-13		ENSG00000135213	ENSG00000272391			34005	protein-coding gene	gene with protein product		615754	"""POM121 membrane glycoprotein C"""			17900573	Standard	NM_001099415		Approved		uc003udk.4	A8CG34	OTTHUMG00000156238		7.37:g.75045497delG														0	4280	+								O75115|Q9Y2N3|Q9Y4S7	RNA	DEL	ENST00000257665.5	37																																																																																						0.657	POM121C-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000343919.2	NM_001099415		6	10						6	10	---	---	---	---
IL32	9235	broad.mit.edu	37	16	3119304	3119305	+	Frame_Shift_Ins	INS	-	-	G	rs398100042|rs2981599		TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr16:3119304_3119305insG	ENST00000534507.1	+	6	864_865	c.653_654insG	c.(652-657)gacaagfs	p.DK218fs	IL32_ENST00000525643.2_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000552936.1_Frame_Shift_Ins_p.DK196fs|IL32_ENST00000552664.1_Frame_Shift_Ins_p.DK172fs|RNU1-125P_ENST00000516752.1_RNA|IL32_ENST00000382213.3_Frame_Shift_Ins_p.DK163fs|IL32_ENST00000548476.1_Frame_Shift_Ins_p.DK218fs|IL32_ENST00000396890.2_Frame_Shift_Ins_p.DK218fs|IL32_ENST00000548246.1_Frame_Shift_Ins_p.DK132fs|IL32_ENST00000551122.1_Frame_Shift_Ins_p.DK115fs|IL32_ENST00000549213.1_Frame_Shift_Ins_p.DK115fs|IL32_ENST00000530538.2_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000530890.1_Frame_Shift_Ins_p.DK152fs|IL32_ENST00000396887.3_Frame_Shift_Ins_p.DK115fs|IL32_ENST00000529550.1_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000444393.3_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000548652.1_Frame_Shift_Ins_p.DK163fs|IL32_ENST00000008180.9_Frame_Shift_Ins_p.DK152fs|IL32_ENST00000529699.1_Frame_Shift_Ins_p.DK152fs|IL32_ENST00000528163.2_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000552356.1_Frame_Shift_Ins_p.DK152fs|IL32_ENST00000526464.2_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000551513.1_Frame_Shift_Ins_p.DK209fs|IL32_ENST00000533097.2_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000531965.1_Frame_Shift_Ins_p.DK162fs|IL32_ENST00000440815.3_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000325568.5_Frame_Shift_Ins_p.DK172fs			P24001	IL32_HUMAN	interleukin 32	218					cell adhesion (GO:0007155)|defense response (GO:0006952)|immune response (GO:0006955)	extracellular space (GO:0005615)|membrane (GO:0016020)				breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	15						CCACGGGGGGACAAGGAGGAGC	0.574																																						ENST00000525643.2																			0				breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	15						c.(514-516)gaafs		interleukin 32																																				SO:0001589	frameshift_variant	9235				cell adhesion|defense response|immune response	extracellular space	cytokine activity	g.chr16:3119304_3119305insG	M59807	CCDS32377.1, CCDS32378.1, CCDS32379.1, CCDS45394.1	16p13.3	2011-07-21			ENSG00000008517	ENSG00000008517		"""Interleukins and interleukin receptors"""	16830	protein-coding gene	gene with protein product	"""natural killer cell transcript 4"""	606001				1729377, 9653642	Standard	XM_005255686		Approved	NK4, TAIF, TAIFb, TAIFd	uc002ctn.3	P24001	OTTHUMG00000167498	Exception_encountered	16.37:g.3119304_3119305insG	ENSP00000431775:p.Asp218fs					IL32_ENST00000444393.3_Frame_Shift_Ins_p.E172fs|IL32_ENST00000396890.2_Frame_Shift_Ins_p.E218fs|IL32_ENST00000534507.1_Frame_Shift_Ins_p.E218fs|IL32_ENST00000531965.1_Frame_Shift_Ins_p.E162fs|IL32_ENST00000533097.2_Frame_Shift_Ins_p.E172fs|IL32_ENST00000528163.2_Frame_Shift_Ins_p.E172fs|IL32_ENST00000529699.1_Frame_Shift_Ins_p.E152fs|IL32_ENST00000549213.1_Frame_Shift_Ins_p.E115fs|IL32_ENST00000526464.2_Frame_Shift_Ins_p.E172fs|IL32_ENST00000325568.5_Frame_Shift_Ins_p.E172fs|IL32_ENST00000529550.1_Frame_Shift_Ins_p.E172fs|IL32_ENST00000382213.3_Frame_Shift_Ins_p.E163fs|IL32_ENST00000530890.1_Frame_Shift_Ins_p.E152fs|IL32_ENST00000008180.9_Frame_Shift_Ins_p.E152fs|IL32_ENST00000440815.3_Frame_Shift_Ins_p.E172fs|IL32_ENST00000548246.1_Frame_Shift_Ins_p.E132fs|IL32_ENST00000530538.2_Frame_Shift_Ins_p.E172fs|IL32_ENST00000396887.3_Frame_Shift_Ins_p.E115fs|IL32_ENST00000552664.1_Frame_Shift_Ins_p.E172fs|IL32_ENST00000552936.1_Frame_Shift_Ins_p.E196fs|IL32_ENST00000551513.1_Frame_Shift_Ins_p.E209fs|IL32_ENST00000551122.1_Frame_Shift_Ins_p.E115fs|IL32_ENST00000548652.1_Frame_Shift_Ins_p.E163fs|IL32_ENST00000548476.1_Frame_Shift_Ins_p.E218fs|IL32_ENST00000552356.1_Frame_Shift_Ins_p.E152fs	p.E172fs			P24001	IL32_HUMAN			7	847_848	+			218					A6NNM0|A8MPX0|B4DJM1|B8Q191|D3DUB0|D3DUB2|Q5VFH7|Q5VFH8|Q8WV38|Q96GK9	Frame_Shift_Ins	INS	ENST00000534507.1	37	c.515_516insG																																																																																					0.574	IL32-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000394812.2	NM_004221		17	320						17	320	---	---	---	---
SPG7	6687	broad.mit.edu	37	16	89613072	89613073	+	Frame_Shift_Ins	INS	-	-	G	rs111475461	byFrequency	TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr16:89613072_89613073insG	ENST00000268704.2	+	11	1471_1472	c.1456_1457insG	c.(1456-1458)cggfs	p.R486fs		NM_003119.2	NP_003110.1	Q9UQ90	SPG7_HUMAN	spastic paraplegia 7 (pure and complicated autosomal recessive)	486			R -> Q (in dbSNP:rs111475461).		anterograde axon cargo transport (GO:0008089)|cell death (GO:0008219)|mitochondrion organization (GO:0007005)|nervous system development (GO:0007399)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metalloendopeptidase activity (GO:0004222)|peptidase activity (GO:0008233)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|urinary_tract(1)	20		all_hematologic(23;0.00824)|Colorectal(91;0.102)		all cancers(4;1.39e-07)|OV - Ovarian serous cystadenocarcinoma(4;5.64e-06)|BRCA - Breast invasive adenocarcinoma(80;0.015)		GCAGGAGAGGCGGGAGATTTTT	0.594																																						ENST00000268704.2																			0				autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|urinary_tract(1)	20						c.(1456-1458)ggafs		spastic paraplegia 7 (pure and complicated autosomal recessive)																																				SO:0001589	frameshift_variant	6687				cell death|nervous system development|protein catabolic process|proteolysis	integral to membrane|mitochondrial membrane	ATP binding|metalloendopeptidase activity|nucleoside-triphosphatase activity|unfolded protein binding|zinc ion binding	g.chr16:89613072_89613073insG	Y16610	CCDS10977.1, CCDS10978.1	16q24.3	2010-04-21	2007-04-23		ENSG00000197912	ENSG00000197912		"""ATPases / AAA-type"""	11237	protein-coding gene	gene with protein product	"""paraplegin"""	602783	"""cell matrix adhesion regulator"""	CMAR		9635427, 9634528	Standard	XM_006721264		Approved	CAR, SPG5C	uc002fnj.3	Q9UQ90	OTTHUMG00000138046	ENST00000268704.2:c.1459dupG	16.37:g.89613075_89613075dupG	ENSP00000268704:p.Arg486fs						p.G486fs	NM_003119.2	NP_003110.1	Q9UQ90	SPG7_HUMAN		all cancers(4;1.39e-07)|OV - Ovarian serous cystadenocarcinoma(4;5.64e-06)|BRCA - Breast invasive adenocarcinoma(80;0.015)	11	1471_1472	+		all_hematologic(23;0.00824)|Colorectal(91;0.102)	486		R -> Q.			O75756|Q2TB70|Q58F00|Q96IB0	Frame_Shift_Ins	INS	ENST00000268704.2	37	c.1456_1457insG	CCDS10977.1																																																																																				0.594	SPG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269921.2	NM_003119		7	218						7	218	---	---	---	---
TBC1D3P2	440452	broad.mit.edu	37	17	60347260	60347260	+	IGR	DEL	T	T	-	rs548240589	byFrequency	TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr17:60347260delT	ENST00000602932.1	-	0	397				TBC1D3P2_ENST00000581291.1_RNA																							CTCTGAATGATTTTTTTTTTT	0.448													|||unknown(NO_COVERAGE)	1228	0.245208	0.1778	0.2882	5008	,	,		28738	0.1518		0.3688	False		,,,				2504	0.2751					ENST00000581291.1																			0				breast(2)|kidney(1)|lung(2)	5																																												SO:0001628	intergenic_variant	0							g.chr17:60347260delT																													17.37:g.60347260delT														0	581	-									RNA	DEL	ENST00000602932.1	37																																																																																						0.448	RP11-51L5.7-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	protein_coding	OTTHUMT00000467667.1			4	6						4	6	---	---	---	---
CXXC1	30827	broad.mit.edu	37	18	47812275	47812277	+	In_Frame_Del	DEL	CTG	CTG	-	rs527645784	byFrequency	TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chr18:47812275_47812277delCTG	ENST00000285106.6	-	5	1195_1197	c.481_483delCAG	c.(481-483)cagdel	p.Q161del	CXXC1_ENST00000589940.1_In_Frame_Del_p.Q161del|CXXC1_ENST00000587396.1_5'Flank|CXXC1_ENST00000412036.2_In_Frame_Del_p.Q161del	NM_001101654.1|NM_014593.3	NP_001095124.1|NP_055408.2	Q9P0U4	CXXC1_HUMAN	CXXC finger protein 1	161					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|histone H3-K4 methylation (GO:0051568)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	24						ACCGTTTGATctgctgctgctgc	0.557														27	0.00539137	0.0151	0.0	5008	,	,		19878	0.0		0.0	False		,,,				2504	0.0072					ENST00000285106.6																			0				autonomic_ganglia(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	24						c.(481-483)del		CXXC finger protein 1																																				SO:0001651	inframe_deletion	30827				histone H3-K4 methylation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck|Set1C/COMPASS complex	protein binding|unmethylated CpG binding|zinc ion binding	g.chr18:47812275_47812277delCTG	BC014940	CCDS11945.1, CCDS45866.1	18q12	2014-02-20	2014-02-20		ENSG00000154832	ENSG00000154832		"""Zinc fingers, PHD-type"""	24343	protein-coding gene	gene with protein product	"""CpG binding protein"", ""DNA-binding protein with PHD finger and CXXC domain"", ""zinc finger, CpG binding-type containing 1"""	609150	"""CXXC finger 1 (PHD domain)"""			10799292, 10688657	Standard	NM_014593		Approved	HsT2645, PCCX1, hCGBP, PHF18, CGBP, SPP1, CFP1, ZCGPC1	uc002ler.4	Q9P0U4	OTTHUMG00000132670	ENST00000285106.6:c.481_483delCAG	18.37:g.47812284_47812286delCTG	ENSP00000285106:p.Gln161del					CXXC1_ENST00000589940.1_In_Frame_Del_p.Q161del|CXXC1_ENST00000412036.2_In_Frame_Del_p.Q161del	p.Q161del	NM_001101654.1|NM_014593.3	NP_001095124.1|NP_055408.2	Q9P0U4	CXXC1_HUMAN			5	1195_1197	-			161					B2RC03|Q8N2W4|Q96BC8|Q9P2V7	In_Frame_Del	DEL	ENST00000285106.6	37	c.481_483delCAG	CCDS11945.1																																																																																				0.557	CXXC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255927.2	NM_014593		7	80						7	80	---	---	---	---
XG	7499	broad.mit.edu	37	X	2670333	2670333	+	Frame_Shift_Del	DEL	A	A	-			TCGA-QH-A65V-01A-11D-A29Q-08	TCGA-QH-A65V-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03328f23-41c2-42b8-8c9c-1824338aa98b	f5978804-96d3-4d66-92a0-b3075996bc9e	g.chrX:2670333delA	ENST00000381174.5	+	1	243	c.18delA	c.(16-18)ggafs	p.G6fs	XG_ENST00000419513.2_Frame_Shift_Del_p.G6fs|XG_ENST00000426774.1_Frame_Shift_Del_p.G6fs			P55808	XG_HUMAN	Xg blood group	6						integral component of plasma membrane (GO:0005887)				endometrium(1)|large_intestine(3)|lung(3)|ovary(1)	8		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				GCTGGTGGGGACTTCCCTGTC	0.532																																						ENST00000426774.1																			0				endometrium(1)|large_intestine(3)|lung(3)|ovary(1)	8						c.(16-18)ggfs		Xg blood group							105.0	108.0	107.0					X																	2670333		2203	4293	6496	SO:0001589	frameshift_variant	7499					integral to membrane|plasma membrane		g.chrX:2670333delA	AF380356	CCDS14120.1, CCDS48073.1	Xp22.32	2014-07-19	2006-01-12		ENSG00000124343	ENSG00000124343		"""Blood group antigens"", ""Pseudoautosomal regions / PAR1"""	12806	protein-coding gene	gene with protein product		300879	"""Xg blood group (pseudoautosomal boundary-divided on the X chromosome)"""	PBDX		8054981	Standard	NM_175569		Approved		uc004cqp.3	P55808	OTTHUMG00000021075	ENST00000381174.5:c.18delA	X.37:g.2670333delA	ENSP00000370566:p.Gly6fs					XG_ENST00000419513.2_Frame_Shift_Del_p.G6fs|XG_ENST00000381174.5_Frame_Shift_Del_p.G6fs	p.G6fs	NM_001141920.1|NM_175569.2	NP_001135392.1|NP_780778.1	P55808	XG_HUMAN			1	241	+		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)	6					E9PCH1|Q496N8|Q496N9|Q496P0|Q71BZ5	Frame_Shift_Del	DEL	ENST00000381174.5	37	c.18delA	CCDS14120.1																																																																																				0.532	XG-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055633.2	NM_175569		40	111						40	111	---	---	---	---
