#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
EPHB2	2048	broad.mit.edu	37	1	23235625	23235625	+	Silent	SNP	C	C	T			TCGA-QR-A6GZ-01A-11D-A35D-08	TCGA-QR-A6GZ-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba3bfaaf-b42e-4279-a234-da6b29fffb5f	dc831897-5afc-4187-860f-4ac7b570871d	g.chr1:23235625C>T	ENST00000400191.3	+	13	2481	c.2463C>T	c.(2461-2463)tcC>tcT	p.S821S	EPHB2_ENST00000374632.3_Silent_p.S822S|EPHB2_ENST00000374627.1_Silent_p.S816S|EPHB2_ENST00000374630.3_Silent_p.S821S	NM_004442.6|NM_017449.3	NP_004433.2|NP_059145.2	P29323	EPHB2_HUMAN	EPH receptor B2	821	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|camera-type eye morphogenesis (GO:0048593)|central nervous system projection neuron axonogenesis (GO:0021952)|commissural neuron axon guidance (GO:0071679)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|ephrin receptor signaling pathway (GO:0048013)|inner ear morphogenesis (GO:0042472)|learning (GO:0007612)|negative regulation of axonogenesis (GO:0050771)|nervous system development (GO:0007399)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse assembly (GO:0051965)|regulation of body fluid levels (GO:0050878)|retinal ganglion cell axon guidance (GO:0031290)|urogenital system development (GO:0001655)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|protein tyrosine kinase activity (GO:0004713)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(8)|stomach(1)|urinary_tract(1)	56		Colorectal(325;3.46e-05)|Lung NSC(340;3.7e-05)|all_lung(284;5.45e-05)|Renal(390;0.000228)|Breast(348;0.0027)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0258)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0348)|OV - Ovarian serous cystadenocarcinoma(117;3.67e-26)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|GBM - Glioblastoma multiforme(114;2.93e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000606)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.126)|Lung(427;0.153)		AGGTGATGTCCTATGGGGAGC	0.597																																						ENST00000400191.3																			0				NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(8)|stomach(1)|urinary_tract(1)	56						c.(2461-2463)tcC>tcT		EPH receptor B2							131.0	116.0	121.0					1																	23235625		2203	4300	6503	SO:0001819	synonymous_variant	2048				axon guidance	integral to plasma membrane	ATP binding|transmembrane-ephrin receptor activity	g.chr1:23235625C>T	AF025304	CCDS229.2, CCDS230.1	1p36.1-p35	2014-09-17	2004-10-28		ENSG00000133216	ENSG00000133216	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3393	protein-coding gene	gene with protein product		600997	"""EphB2"""	DRT, ERK, EPHT3		1648701	Standard	NM_017449		Approved	Hek5, Tyro5	uc001bge.3	P29323	OTTHUMG00000002881	ENST00000400191.3:c.2463C>T	1.37:g.23235625C>T						EPHB2_ENST00000374630.3_Silent_p.S821S|EPHB2_ENST00000374627.1_Silent_p.S816S|EPHB2_ENST00000374632.3_Silent_p.S822S	p.S821S	NM_004442.6|NM_017449.3	NP_004433.2|NP_059145.2	P29323	EPHB2_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0348)|OV - Ovarian serous cystadenocarcinoma(117;3.67e-26)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|GBM - Glioblastoma multiforme(114;2.93e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000606)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.126)|Lung(427;0.153)	13	2481	+		Colorectal(325;3.46e-05)|Lung NSC(340;3.7e-05)|all_lung(284;5.45e-05)|Renal(390;0.000228)|Breast(348;0.0027)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0258)	821			Protein kinase.		O43477|Q5T0U6|Q5T0U7|Q5T0U8	Silent	SNP	ENST00000400191.3	37	c.2463C>T																																																																																					0.597	EPHB2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000008060.2	NM_017449		13	37	0	0	0	1	0	13	37				
THEMIS	387357	broad.mit.edu	37	6	128134119	128134119	+	Missense_Mutation	SNP	C	C	T			TCGA-QR-A6GZ-01A-11D-A35D-08	TCGA-QR-A6GZ-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba3bfaaf-b42e-4279-a234-da6b29fffb5f	dc831897-5afc-4187-860f-4ac7b570871d	g.chr6:128134119C>T	ENST00000368248.2	-	4	1815	c.1667G>A	c.(1666-1668)cGc>cAc	p.R556H	THEMIS_ENST00000543064.1_Missense_Mutation_p.R556H|THEMIS_ENST00000368250.1_Missense_Mutation_p.R477H|THEMIS_ENST00000537166.1_Missense_Mutation_p.R521H	NM_001010923.2	NP_001010923.1	Q8N1K5	THMS1_HUMAN	thymocyte selection associated	556					negative T cell selection (GO:0043383)|positive T cell selection (GO:0043368)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(3)	60						TTTCGGAGGGCGAGGTGGGGG	0.493																																						ENST00000368250.1																			0				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(3)	60						c.(1429-1431)cGc>cAc		thymocyte selection associated							111.0	114.0	113.0					6																	128134119		2203	4300	6503	SO:0001583	missense	387357				negative T cell selection|positive T cell selection|T cell receptor signaling pathway	cytoplasm|nucleus		g.chr6:128134119C>T	AK094863	CCDS34534.1, CCDS55055.1	6q22.33	2012-02-08	2009-06-25	2009-06-25	ENSG00000172673	ENSG00000172673			21569	protein-coding gene	gene with protein product	"""thymocyte expressed molecule involved in selection"""	613607	"""chromosome 6 open reading frame 207"", ""chromosome 6 open reading frame 190"", ""thymocyte selection pathway associated"""	C6orf207, C6orf190, TSEPA		19597499, 19597498, 19597497	Standard	NM_001010923		Approved	bA325O24.4, FLJ40584, bA325O24.3	uc011ebt.2	Q8N1K5	OTTHUMG00000015534	ENST00000368248.2:c.1667G>A	6.37:g.128134119C>T	ENSP00000357231:p.Arg556His					THEMIS_ENST00000543064.1_Missense_Mutation_p.R556H|THEMIS_ENST00000537166.1_Missense_Mutation_p.R521H|THEMIS_ENST00000368248.2_Missense_Mutation_p.R556H	p.R477H			Q8N1K5	THMS1_HUMAN			5	1928	-			556			CABIT 2.		A1L4F0|A8K7N1|B3KT31|B3KW32|B3KY07|F5H1J9|Q5T3C4|Q5T3C5|Q6MZT7	Missense_Mutation	SNP	ENST00000368248.2	37	c.1430G>A	CCDS34534.1	.	.	.	.	.	.	.	.	.	.	C	17.07	3.294707	0.60086	.	.	ENSG00000172673	ENST00000368250;ENST00000543064;ENST00000368248;ENST00000537166	T;T;T;T	0.32988	1.43;1.58;1.48;1.44	5.83	2.91	0.33838	.	0.258158	0.36482	N	0.002576	T	0.38904	0.1058	M	0.65498	2.005	0.36638	D	0.876665	D;D	0.89917	1.0;0.999	D;P	0.63597	0.916;0.763	T	0.46261	-0.9204	10	0.72032	D	0.01	-0.4145	14.6116	0.68519	0.3819:0.6181:0.0:0.0	.	556;556	F5H1J9;Q8N1K5	.;THMS1_HUMAN	H	477;556;556;521	ENSP00000357233:R477H;ENSP00000439594:R556H;ENSP00000357231:R556H;ENSP00000439863:R521H	ENSP00000357231:R556H	R	-	2	0	THEMIS	128175812	0.985000	0.35326	0.907000	0.35723	0.898000	0.52572	2.713000	0.47194	0.293000	0.22520	0.563000	0.77884	CGC		0.493	THEMIS-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_001010923		4	106	0	0	0	1	0	4	106				
CROCCP2	84809	broad.mit.edu	37	1	16945409	16945409	+	lincRNA	SNP	T	T	A	rs13566	byFrequency	TCGA-QR-A6GZ-01A-11D-A35D-08	TCGA-QR-A6GZ-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba3bfaaf-b42e-4279-a234-da6b29fffb5f	dc831897-5afc-4187-860f-4ac7b570871d	g.chr1:16945409T>A	ENST00000412962.1	-	0	2110				RP5-1182A14.5_ENST00000607700.1_lincRNA			Q86T23	CROL1_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 2						centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)											GCGGGATAGCTCGGTGGAGAG	0.612													.|||	1533	0.30611	0.2254	0.3473	5008	,	,		64331	0.2113		0.3767	False		,,,				2504	0.411					ENST00000412962.1																			0																																																			84809							g.chr1:16945409T>A	AK090414		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000215908	ENSG00000215908			28170	pseudogene	pseudogene			"""ciliary rootlet coiled-coil, rootletin-like 1"""	CROCCL1		12477932	Standard	NR_026752		Approved	MGC12760	uc001azf.3	Q86T23	OTTHUMG00000037884		1.37:g.16945409T>A														0	2110	-								Q8NF65|Q96FR5|Q9BRE8	RNA	SNP	ENST00000412962.1	37																																																																																						0.612	CROCCP2-003	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000092784.1	NR_026752.1		3	33	0	0	0	1	0	3	33				
SLC33A1	9197	broad.mit.edu	37	3	155571395	155571395	+	Missense_Mutation	SNP	G	G	A			TCGA-QR-A6GZ-01A-11D-A35D-08	TCGA-QR-A6GZ-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba3bfaaf-b42e-4279-a234-da6b29fffb5f	dc831897-5afc-4187-860f-4ac7b570871d	g.chr3:155571395G>A	ENST00000392845.3	-	1	772	c.392C>T	c.(391-393)gCg>gTg	p.A131V	SLC33A1_ENST00000359479.3_Missense_Mutation_p.A131V|SLC33A1_ENST00000460729.1_5'Flank			O00400	ACATN_HUMAN	solute carrier family 33 (acetyl-CoA transporter), member 1	131					acetyl-CoA transport (GO:0015876)|cell death (GO:0008219)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	acetyl-CoA transporter activity (GO:0008521)			endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	22			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			AACGTAGACCGCATCAACCAA	0.438																																						ENST00000392845.2																			0				endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	22						c.(391-393)gCg>gTg		solute carrier family 33 (acetyl-CoA transporter), member 1							62.0	67.0	65.0					3																	155571395		2203	4300	6503	SO:0001583	missense	9197				cell death|transmembrane transport	endoplasmic reticulum membrane|Golgi membrane|integral to plasma membrane|membrane fraction	acetyl-CoA transporter activity	g.chr3:155571395G>A	D88152	CCDS3173.1	3q25.31	2013-05-22		2002-12-06	ENSG00000169359	ENSG00000169359		"""Solute carriers"""	95	protein-coding gene	gene with protein product		603690	"""acetyl-Coenzyme A transporter"", ""spastic paraplegia 42 (autosomal dominant)"""	ACATN, SPG42		9096318, 19061983	Standard	NM_004733		Approved	AT-1, AT1	uc003fao.2	O00400	OTTHUMG00000158481	ENST00000392845.3:c.392C>T	3.37:g.155571395G>A	ENSP00000376587:p.Ala131Val					SLC33A1_ENST00000359479.3_Missense_Mutation_p.A131V	p.A131V	NM_004733.3	NP_004724.1	O00400	ACATN_HUMAN	Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)		1	772	-			131					B2R5Q2|D3DNK4	Missense_Mutation	SNP	ENST00000392845.3	37	c.392C>T	CCDS3173.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.283162	0.80803	.	.	ENSG00000169359	ENST00000392845;ENST00000359479	T;T	0.80566	-1.39;-1.39	5.42	5.42	0.78866	Major facilitator superfamily domain, general substrate transporter (1);	0.111009	0.64402	D	0.000006	T	0.78966	0.4367	L	0.55213	1.73	0.53688	D	0.999976	P	0.38020	0.615	B	0.36186	0.219	T	0.79636	-0.1721	10	0.49607	T	0.09	-12.5777	19.6435	0.95767	0.0:0.0:1.0:0.0	.	131	O00400	ACATN_HUMAN	V	131	ENSP00000376587:A131V;ENSP00000352456:A131V	ENSP00000352456:A131V	A	-	2	0	SLC33A1	157054089	1.000000	0.71417	0.351000	0.25721	0.847000	0.48162	9.529000	0.98049	2.712000	0.92718	0.650000	0.86243	GCG		0.438	SLC33A1-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351130.3	NM_004733		3	36	0	0	0	1	0	3	36				
TPCN1	53373	broad.mit.edu	37	12	113714812	113714812	+	Missense_Mutation	SNP	A	A	G			TCGA-QR-A6GZ-01A-11D-A35D-08	TCGA-QR-A6GZ-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba3bfaaf-b42e-4279-a234-da6b29fffb5f	dc831897-5afc-4187-860f-4ac7b570871d	g.chr12:113714812A>G	ENST00000335509.6	+	11	1345	c.1031A>G	c.(1030-1032)cAt>cGt	p.H344R	TPCN1_ENST00000550785.1_Missense_Mutation_p.H416R|TPCN1_ENST00000392569.4_Missense_Mutation_p.H276R|TPCN1_ENST00000541517.1_Missense_Mutation_p.H416R	NM_017901.4	NP_060371.2	Q9ULQ1	TPC1_HUMAN	two pore segment channel 1	344					calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|NAADP-sensitive calcium-release channel activity (GO:0072345)|voltage-gated calcium channel activity (GO:0005245)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(2)|prostate(3)|skin(3)|urinary_tract(1)	40						GCTATCCAGCATGCCTACCGC	0.567																																						ENST00000550785.1																			0				cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(2)|prostate(3)|skin(3)|urinary_tract(1)	40						c.(1246-1248)cAt>cGt		two pore segment channel 1							197.0	195.0	196.0					12																	113714812		2203	4300	6503	SO:0001583	missense	53373					endosome membrane|integral to membrane|lysosomal membrane	NAADP-sensitive calcium-release channel activity|voltage-gated ion channel activity	g.chr12:113714812A>G	AB032995	CCDS31908.1, CCDS44985.1	12q24.21	2011-07-05			ENSG00000186815	ENSG00000186815		"""Voltage-gated ion channels / Two-pore channels"""	18182	protein-coding gene	gene with protein product		609666				10574461, 10753632, 16382101	Standard	XM_005253905		Approved	KIAA1169, FLJ20612, TPC1	uc001tux.3	Q9ULQ1	OTTHUMG00000169625	ENST00000335509.6:c.1031A>G	12.37:g.113714812A>G	ENSP00000335300:p.His344Arg					TPCN1_ENST00000392569.4_Missense_Mutation_p.H276R|TPCN1_ENST00000541517.1_Missense_Mutation_p.H416R|TPCN1_ENST00000335509.6_Missense_Mutation_p.H344R	p.H416R	NM_001143819.1	NP_001137291.1	Q9ULQ1	TPC1_HUMAN			12	1416	+			344					A7E258|Q86XS9|Q8NC20	Missense_Mutation	SNP	ENST00000335509.6	37	c.1247A>G	CCDS31908.1	.	.	.	.	.	.	.	.	.	.	A	8.548	0.874813	0.17395	.	.	ENSG00000186815	ENST00000335509;ENST00000550785;ENST00000541517;ENST00000392569	D;D;D;D	0.96491	-3.93;-4.03;-4.03;-3.99	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	D	0.92642	0.7662	L	0.38531	1.155	0.58432	D	0.999993	B;P;B	0.39352	0.126;0.669;0.185	B;B;B	0.38020	0.027;0.263;0.057	D	0.91657	0.5339	10	0.10111	T	0.7	-28.1955	15.4089	0.74902	1.0:0.0:0.0:0.0	.	344;416;344	A5PKY2;Q9ULQ1-3;Q9ULQ1	.;.;TPC1_HUMAN	R	344;416;416;276	ENSP00000335300:H344R;ENSP00000448083:H416R;ENSP00000438125:H416R;ENSP00000376350:H276R	ENSP00000335300:H344R	H	+	2	0	TPCN1	112199195	1.000000	0.71417	0.977000	0.42913	0.363000	0.29612	8.333000	0.90026	2.117000	0.64856	0.496000	0.49642	CAT		0.567	TPCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405156.3	NM_017901		63	159	0	0	0	1	0	63	159				
NDUFAF2	91942	broad.mit.edu	37	5	60241050	60241050	+	De_novo_Start_OutOfFrame	SNP	G	G	A	rs200299226	byFrequency	TCGA-QR-A6GZ-01A-11D-A35D-08	TCGA-QR-A6GZ-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba3bfaaf-b42e-4279-a234-da6b29fffb5f	dc831897-5afc-4187-860f-4ac7b570871d	g.chr5:60241050G>A	ENST00000296597.5	+	0	95				ERCC8_ENST00000426742.2_5'Flank|NDUFAF2_ENST00000511107.1_De_novo_Start_OutOfFrame|ERCC8_ENST00000543101.1_5'Flank|ERCC8_ENST00000265038.5_5'Flank	NM_174889.4	NP_777549.1	Q8N183	MIMIT_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 2						negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|reactive oxygen species metabolic process (GO:0072593)|respiratory electron transport chain (GO:0022904)	mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|ovary(1)	6		Lung NSC(810;3.36e-05)|Prostate(74;0.0225)|Ovarian(174;0.17)|Breast(144;0.237)				TGCGGGTCCCGCTGCTGGCAG	0.632																																						ENST00000296597.5																			0				central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|ovary(1)	6								NADH dehydrogenase (ubiquinone) complex I, assembly factor 2							29.0	29.0	29.0					5																	60241050		2203	4300	6503			91942					membrane|mitochondrion	electron carrier activity|NADH dehydrogenase (ubiquinone) activity	g.chr5:60241050G>A	AB183433	CCDS3979.1	5q12.1	2012-10-12	2012-05-08	2008-02-15	ENSG00000164182	ENSG00000164182		"""Mitochondrial respiratory chain complex assembly factors"""	28086	protein-coding gene	gene with protein product	"""Myc-induced mitochondrial protein"""	609653	"""NDUFA12-like"", ""NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 2"""	NDUFA12L		15774466, 16200211, 17383918	Standard	NM_174889		Approved	B17.2L, MMTN, mimitin	uc003jsp.4	Q8N183	OTTHUMG00000131221	ENST00000296597.5:c.-33G>A	5.37:g.60241050G>A						NDUFAF2_ENST00000511107.1_De_novo_Start_OutOfFrame		NM_174889.4	NP_777549.1	Q8N183	MIMIT_HUMAN			0	95	+		Lung NSC(810;3.36e-05)|Prostate(74;0.0225)|Ovarian(174;0.17)|Breast(144;0.237)						A8K5I1	Translation_Start_Site	SNP	ENST00000296597.5	37		CCDS3979.1																																																																																				0.632	NDUFAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253965.1	NM_174889		3	19	0	0	0	1	0	3	19				
LINC00969	440993	broad.mit.edu	37	3	195400799	195400799	+	lincRNA	SNP	G	G	A	rs7635172		TCGA-QR-A6GZ-01A-11D-A35D-08	TCGA-QR-A6GZ-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba3bfaaf-b42e-4279-a234-da6b29fffb5f	dc831897-5afc-4187-860f-4ac7b570871d	g.chr3:195400799G>A	ENST00000445430.1	+	0	1395									long intergenic non-protein coding RNA 969																		CAAACTCGCTGTTGGACCTGG	0.597																																						ENST00000445430.1																			0																																																			440993							g.chr3:195400799G>A	AK128346		3q29	2013-06-07			ENSG00000242086	ENSG00000242086		"""Long non-coding RNAs"""	48729	non-coding RNA	RNA, long non-coding							Standard	XR_427455		Approved				OTTHUMG00000155834		3.37:g.195400799G>A														0	1395	+									RNA	SNP	ENST00000445430.1	37																																																																																						0.597	LINC00969-038	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000341951.1			4	9	0	0	0	1	0	4	9				
MMP19	4327	broad.mit.edu	37	12	56230872	56230872	+	Missense_Mutation	SNP	C	C	T			TCGA-QR-A6GZ-01A-11D-A35D-08	TCGA-QR-A6GZ-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba3bfaaf-b42e-4279-a234-da6b29fffb5f	dc831897-5afc-4187-860f-4ac7b570871d	g.chr12:56230872C>T	ENST00000322569.4	-	9	1566	c.1475G>A	c.(1474-1476)gGc>gAc	p.G492D	MMP19_ENST00000548629.1_Missense_Mutation_p.G469D|TMEM198B_ENST00000478241.1_RNA|MMP19_ENST00000409200.3_3'UTR|MMP19_ENST00000394182.1_Missense_Mutation_p.G206D	NM_002429.4	NP_002420.1	Q99542	MMP19_HUMAN	matrix metallopeptidase 19	492					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|luteolysis (GO:0001554)|ovarian follicle development (GO:0001541)|ovulation from ovarian follicle (GO:0001542)|proteolysis (GO:0006508)|response to cAMP (GO:0051591)|response to hormone (GO:0009725)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(2)|skin(2)	26					Marimastat(DB00786)	CAAGGTTATGCCCGTACCTGA	0.507																																						ENST00000394182.1																			0				endometrium(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(2)|skin(2)	26						c.(616-618)gGc>gAc		matrix metallopeptidase 19							254.0	240.0	245.0					12																	56230872		2203	4300	6503	SO:0001583	missense	4327				angiogenesis|cell differentiation|collagen catabolic process|proteolysis	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding	g.chr12:56230872C>T	X92521	CCDS8895.1, CCDS61146.1	12q14	2005-08-08	2005-08-08			ENSG00000123342			7165	protein-coding gene	gene with protein product		601807	"""matrix metalloproteinase 19"""	MMP18		9232430	Standard	NM_002429		Approved	RASI-1	uc001sib.4	Q99542	OTTHUMG00000170216	ENST00000322569.4:c.1475G>A	12.37:g.56230872C>T	ENSP00000313437:p.Gly492Asp					MMP19_ENST00000548629.1_Missense_Mutation_p.G469D|MMP19_ENST00000322569.4_Missense_Mutation_p.G492D|MMP19_ENST00000409200.3_3'UTR	p.G206D			Q99542	MMP19_HUMAN			4	616	-			492					B4E030|O15278|O95606|Q99580	Missense_Mutation	SNP	ENST00000322569.4	37	c.617G>A	CCDS8895.1	.	.	.	.	.	.	.	.	.	.	C	10.58	1.388699	0.25118	.	.	ENSG00000123342	ENST00000394182;ENST00000322569;ENST00000548629	T;T;T	0.16196	4.61;2.52;2.36	5.08	-1.03	0.10102	.	380.668000	0.00166	N	0.000000	T	0.09905	0.0243	N	0.14661	0.345	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.08055	0.001;0.003	T	0.27262	-1.0079	10	0.08381	T	0.77	.	8.2874	0.31937	0.0:0.4412:0.0:0.5588	.	492;206	Q99542;Q99542-3	MMP19_HUMAN;.	D	206;492;469	ENSP00000377736:G206D;ENSP00000313437:G492D;ENSP00000446979:G469D	ENSP00000313437:G492D	G	-	2	0	MMP19	54517139	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	-1.224000	0.02959	-0.161000	0.10983	-0.291000	0.09656	GGC		0.507	MMP19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408023.1	NM_002429		4	156	0	0	0	1	0	4	156				
GULP1	51454	broad.mit.edu	37	2	189342446	189342446	+	Missense_Mutation	SNP	G	G	A			TCGA-QR-A6GZ-01A-11D-A35D-08	TCGA-QR-A6GZ-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba3bfaaf-b42e-4279-a234-da6b29fffb5f	dc831897-5afc-4187-860f-4ac7b570871d	g.chr2:189342446G>A	ENST00000409580.1	+	4	731	c.17G>A	c.(16-18)aGc>aAc	p.S6N	GULP1_ENST00000410051.1_Missense_Mutation_p.S6N|GULP1_ENST00000479019.1_3'UTR|GULP1_ENST00000409830.1_Missense_Mutation_p.S6N|GULP1_ENST00000409843.1_Missense_Mutation_p.S6N|GULP1_ENST00000409805.1_Missense_Mutation_p.S6N|GULP1_ENST00000409637.3_Missense_Mutation_p.S6N|GULP1_ENST00000409609.1_Missense_Mutation_p.S6N|GULP1_ENST00000359135.3_Missense_Mutation_p.S6N			Q9UBP9	GULP1_HUMAN	GULP, engulfment adaptor PTB domain containing 1	6					apoptotic process (GO:0006915)|lipid transport (GO:0006869)|phagocytosis, engulfment (GO:0006911)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	signal transducer activity (GO:0004871)			endometrium(3)|large_intestine(2)|lung(5)|ovary(1)|skin(2)	13			OV - Ovarian serous cystadenocarcinoma(117;0.0423)|Epithelial(96;0.158)			CGTGCTTTTAGCAGGAAGAAA	0.348																																					Pancreas(178;563 2065 20199 42378 52815)	ENST00000409580.1																			0				endometrium(3)|large_intestine(2)|lung(5)|ovary(1)|skin(2)	13						c.(16-18)aGc>aAc		GULP, engulfment adaptor PTB domain containing 1							165.0	160.0	162.0					2																	189342446		2203	4299	6502	SO:0001583	missense	51454				apoptosis|lipid transport|phagocytosis, engulfment	cytoplasm|intracellular membrane-bounded organelle	signal transducer activity	g.chr2:189342446G>A	AF191771	CCDS2295.1, CCDS58742.1, CCDS58743.1	2q32.3-q33	2008-02-05			ENSG00000144366	ENSG00000144366			18649	protein-coding gene	gene with protein product		608165				11729193	Standard	NM_001252668		Approved	CED6, CED-6, GULP	uc010fru.3	Q9UBP9	OTTHUMG00000132647	ENST00000409580.1:c.17G>A	2.37:g.189342446G>A	ENSP00000386289:p.Ser6Asn					GULP1_ENST00000409637.3_Missense_Mutation_p.S6N|GULP1_ENST00000410051.1_Missense_Mutation_p.S6N|GULP1_ENST00000409843.1_Missense_Mutation_p.S6N|GULP1_ENST00000409830.1_Missense_Mutation_p.S6N|GULP1_ENST00000409609.1_Missense_Mutation_p.S6N|GULP1_ENST00000359135.3_Missense_Mutation_p.S6N|GULP1_ENST00000479019.1_3'UTR|GULP1_ENST00000409805.1_Missense_Mutation_p.S6N	p.S6N			Q9UBP9	GULP1_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.0423)|Epithelial(96;0.158)		4	731	+			6					B2RB51|B4DQ40|B8ZZ72|D3DPH1|E9PB86|Q53PC1|Q53RF3|Q9BVL3	Missense_Mutation	SNP	ENST00000409580.1	37	c.17G>A	CCDS2295.1	.	.	.	.	.	.	.	.	.	.	G	12.74	2.030001	0.35797	.	.	ENSG00000144366	ENST00000409843;ENST00000409830;ENST00000410051;ENST00000409927;ENST00000409805;ENST00000359135;ENST00000409580;ENST00000409637;ENST00000409609	T;T;T;T;T;T;T;T	0.42900	0.96;0.97;2.56;2.56;0.97;0.97;2.56;0.97	4.6	3.7	0.42460	.	0.236286	0.41001	D	0.000963	T	0.12347	0.0300	N	0.00707	-1.245	0.27771	N	0.943481	B;B;B;B	0.09022	0.0;0.0;0.0;0.002	B;B;B;B	0.11329	0.004;0.0;0.001;0.006	T	0.18524	-1.0334	10	0.18276	T	0.48	-0.0176	7.9345	0.29923	0.1131:0.0:0.8869:0.0	.	6;6;6;6	E9PB86;Q9UBP9;B8ZZ72;Q9UBP9-2	.;GULP1_HUMAN;.;.	N	6	ENSP00000387144:S6N;ENSP00000386732:S6N;ENSP00000387013:S6N;ENSP00000386809:S6N;ENSP00000352047:S6N;ENSP00000386289:S6N;ENSP00000386402:S6N;ENSP00000386867:S6N	ENSP00000352047:S6N	S	+	2	0	GULP1	189050691	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.650000	0.37292	2.257000	0.74773	0.655000	0.94253	AGC		0.348	GULP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335722.1	NM_016315		4	74	0	0	0	1	0	4	74				
FAM86B3P	286042	broad.mit.edu	37	8	8095990	8095990	+	RNA	SNP	C	C	G			TCGA-QR-A6GZ-01A-11D-A35D-08	TCGA-QR-A6GZ-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba3bfaaf-b42e-4279-a234-da6b29fffb5f	dc831897-5afc-4187-860f-4ac7b570871d	g.chr8:8095990C>G	ENST00000310542.3	+	0	0				ALG1L13P_ENST00000523017.1_RNA					family with sequence similarity 86, member B3, pseudogene																		CCAGGAGCCCCGAGACCTGCA	0.647																																						ENST00000523017.1																			0																																																			286042							g.chr8:8095990C>G			8p23.1	2013-06-10			ENSG00000173295	ENSG00000173295			44371	pseudogene	pseudogene							Standard	NR_024361		Approved		uc011kwt.2		OTTHUMG00000163669		8.37:g.8095990C>G														0	608	-									RNA	SNP	ENST00000310542.3	37																																																																																						0.647	FAM86B3P-005	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000448496.1			2	1	0	0	0	1	0	2	1				
AQP12A	375318	broad.mit.edu	37	2	241631584	241631584	+	Missense_Mutation	SNP	G	G	T	rs199880904		TCGA-QR-A6GZ-01A-11D-A35D-08	TCGA-QR-A6GZ-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba3bfaaf-b42e-4279-a234-da6b29fffb5f	dc831897-5afc-4187-860f-4ac7b570871d	g.chr2:241631584G>T	ENST00000337801.4	+	2	286	c.217G>T	c.(217-219)Gtc>Ttc	p.V73F	AQP12A_ENST00000429564.1_Missense_Mutation_p.V85F|AC011298.2_ENST00000407635.2_lincRNA	NM_198998.2	NP_945349.1	Q8IXF9	AQ12A_HUMAN	aquaporin 12A	73						integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			endometrium(2)|kidney(3)|large_intestine(2)|lung(7)	14		all_epithelial(40;7.49e-12)|Breast(86;0.000148)|Renal(207;0.00571)|Ovarian(221;0.104)|all_neural(83;0.107)|all_hematologic(139;0.182)|all_lung(227;0.186)|Melanoma(123;0.238)		Epithelial(32;2.2e-31)|all cancers(36;1.08e-28)|OV - Ovarian serous cystadenocarcinoma(60;2.13e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.52e-06)|Lung(119;0.00163)|LUSC - Lung squamous cell carcinoma(224;0.008)|Colorectal(34;0.0124)|COAD - Colon adenocarcinoma(134;0.0757)		GGCGCACGGGGTCACCTTGGA	0.667																																						ENST00000429564.1																			0				endometrium(2)|kidney(3)|large_intestine(2)|lung(7)	14						c.(253-255)Gtc>Ttc		aquaporin 12A							30.0	45.0	40.0					2																	241631584		2151	4265	6416	SO:0001583	missense	375318					integral to membrane	transporter activity	g.chr2:241631584G>T	AB040748		2q37.3	2013-06-03	2005-05-26	2005-05-26	ENSG00000184945	ENSG00000184945		"""Ion channels / Aquaporins"""	19941	protein-coding gene	gene with protein product		609789	"""aquaporin 12"""	AQP12			Standard	NM_198998		Approved		uc002vzu.3	Q8IXF9	OTTHUMG00000183906	ENST00000337801.4:c.217G>T	2.37:g.241631584G>T	ENSP00000337144:p.Val73Phe					AQP12A_ENST00000337801.4_Missense_Mutation_p.V73F	p.V85F			Q8IXF9	AQ12A_HUMAN		Epithelial(32;2.2e-31)|all cancers(36;1.08e-28)|OV - Ovarian serous cystadenocarcinoma(60;2.13e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.52e-06)|Lung(119;0.00163)|LUSC - Lung squamous cell carcinoma(224;0.008)|Colorectal(34;0.0124)|COAD - Colon adenocarcinoma(134;0.0757)	2	316	+		all_epithelial(40;7.49e-12)|Breast(86;0.000148)|Renal(207;0.00571)|Ovarian(221;0.104)|all_neural(83;0.107)|all_hematologic(139;0.182)|all_lung(227;0.186)|Melanoma(123;0.238)	73						Missense_Mutation	SNP	ENST00000337801.4	37	c.253G>T		.	.	.	.	.	.	.	.	.	.	.	1.073	-0.669235	0.03403	.	.	ENSG00000184945	ENST00000337801;ENST00000429564;ENST00000420599	T;T	0.11277	2.79;2.79	2.58	2.58	0.30949	Aquaporin-like (2);	0.350897	0.29198	N	0.012848	T	0.03434	0.0099	N	0.02916	-0.46	0.09310	N	0.999998	B	0.11235	0.004	B	0.12837	0.008	T	0.45600	-0.9250	10	0.09843	T	0.71	.	6.7793	0.23636	0.0:0.0:0.7211:0.2789	.	73	Q8IXF9	AQ12A_HUMAN	F	73;85;58	ENSP00000337144:V73F;ENSP00000405899:V85F	ENSP00000337144:V73F	V	+	1	0	AQP12A	241280257	0.003000	0.15002	0.643000	0.29450	0.067000	0.16453	1.019000	0.30014	1.474000	0.48178	0.186000	0.17326	GTC		0.667	AQP12A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000257185.2	NM_198998		4	66	1	0	0.00307968	1	0.00307968	4	66				
SALL1	6299	broad.mit.edu	37	16	51173041	51173041	+	Missense_Mutation	SNP	C	C	T			TCGA-QR-A6GZ-01A-11D-A35D-08	TCGA-QR-A6GZ-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba3bfaaf-b42e-4279-a234-da6b29fffb5f	dc831897-5afc-4187-860f-4ac7b570871d	g.chr16:51173041C>T	ENST00000251020.4	-	2	3125	c.3092G>A	c.(3091-3093)tGc>tAc	p.C1031Y	SALL1_ENST00000566102.1_Intron|SALL1_ENST00000440970.1_Missense_Mutation_p.C934Y|SALL1_ENST00000541611.1_Intron	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	1031					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			GCAAACTGTGCAAATAAATGG	0.423																																					GBM(103;1352 1446 1855 4775 8890)	ENST00000440970.1																			0				NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126						c.(2800-2802)tGc>tAc		spalt-like transcription factor 1							86.0	84.0	85.0					16																	51173041		2198	4300	6498	SO:0001583	missense	6299				adrenal gland development|branching involved in ureteric bud morphogenesis|embryonic digestive tract development|embryonic digit morphogenesis|gonad development|histone deacetylation|inductive cell-cell signaling|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of transcription from RNA polymerase II promoter|olfactory bulb interneuron differentiation|olfactory bulb mitral cell layer development|olfactory nerve development|outer ear morphogenesis|pituitary gland development|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway|ureteric bud invasion|ventricular septum development	chromocenter|cytoplasm|heterochromatin|nucleus	beta-catenin binding|DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr16:51173041C>T	X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"""Zinc fingers, C2H2-type"""	10524	protein-coding gene	gene with protein product		602218	"""sal (Drosophila)-like 1"", ""sal-like 1 (Drosophila)"""	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.3092G>A	16.37:g.51173041C>T	ENSP00000251020:p.Cys1031Tyr					SALL1_ENST00000566102.1_Intron|SALL1_ENST00000541611.1_Intron|SALL1_ENST00000251020.4_Missense_Mutation_p.C1031Y	p.C934Y	NM_001127892.1	NP_001121364.1	Q9NSC2	SALL1_HUMAN	COAD - Colon adenocarcinoma(2;0.24)		2	3232	-		all_cancers(37;0.0322)	1031					Q99881|Q9NSC3|Q9P1R0	Missense_Mutation	SNP	ENST00000251020.4	37	c.2801G>A	CCDS10747.1	.	.	.	.	.	.	.	.	.	.	C	13.35	2.210209	0.39003	.	.	ENSG00000103449	ENST00000251020;ENST00000440970;ENST00000457559	D;D	0.85088	-1.94;-1.94	5.83	5.83	0.93111	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.94437	0.8210	M	0.91920	3.255	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94776	0.7949	10	0.72032	D	0.01	.	20.1337	0.98010	0.0:1.0:0.0:0.0	.	1031	Q9NSC2	SALL1_HUMAN	Y	1031;934;995	ENSP00000251020:C1031Y;ENSP00000407914:C934Y	ENSP00000251020:C1031Y	C	-	2	0	SALL1	49730542	1.000000	0.71417	1.000000	0.80357	0.098000	0.18820	7.818000	0.86416	2.753000	0.94483	0.650000	0.86243	TGC		0.423	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968		8	36	0	0	0	1	0	8	36				
CDH20	28316	broad.mit.edu	37	18	59221533	59221533	+	Missense_Mutation	SNP	G	G	A			TCGA-QR-A6GZ-01A-11D-A35D-08	TCGA-QR-A6GZ-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba3bfaaf-b42e-4279-a234-da6b29fffb5f	dc831897-5afc-4187-860f-4ac7b570871d	g.chr18:59221533G>A	ENST00000262717.4	+	12	2409	c.2011G>A	c.(2011-2013)Ggc>Agc	p.G671S	CDH20_ENST00000536675.2_Missense_Mutation_p.G671S|CDH20_ENST00000538374.1_Missense_Mutation_p.G671S			Q9HBT6	CAD20_HUMAN	cadherin 20, type 2	671					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|skin(3)	61		Colorectal(73;0.186)				CGAGGGCGGCGGCGAGGAGGA	0.652																																						ENST00000262717.4																			0				breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|skin(3)	61						c.(2011-2013)Ggc>Agc		cadherin 20, type 2							102.0	102.0	102.0					18																	59221533		2203	4300	6503	SO:0001583	missense	28316				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	g.chr18:59221533G>A	AF217289	CCDS11977.1	18q21.33	2010-01-26			ENSG00000101542	ENSG00000101542		"""Cadherins / Major cadherins"""	1760	protein-coding gene	gene with protein product		605807				10995570	Standard	NM_031891		Approved	CDH7L3, Cdh7	uc010dps.1	Q9HBT6	OTTHUMG00000132768	ENST00000262717.4:c.2011G>A	18.37:g.59221533G>A	ENSP00000262717:p.Gly671Ser					CDH20_ENST00000536675.2_Missense_Mutation_p.G671S|CDH20_ENST00000538374.1_Missense_Mutation_p.G671S	p.G671S			Q9HBT6	CAD20_HUMAN			12	2409	+		Colorectal(73;0.186)	671					Q495S3	Missense_Mutation	SNP	ENST00000262717.4	37	c.2011G>A	CCDS11977.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.047846	0.93740	.	.	ENSG00000101542	ENST00000536675;ENST00000538374;ENST00000262717	D;D;D	0.98701	-5.08;-5.08;-5.08	5.39	4.46	0.54185	Cadherin, cytoplasmic domain (1);	0.000000	0.85682	D	0.000000	D	0.99257	0.9741	M	0.91612	3.225	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.98720	1.0708	10	0.87932	D	0	.	15.8931	0.79315	0.0:0.1353:0.8647:0.0	.	671	Q9HBT6	CAD20_HUMAN	S	671	ENSP00000444767:G671S;ENSP00000442226:G671S;ENSP00000262717:G671S	ENSP00000262717:G671S	G	+	1	0	CDH20	57372513	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.943000	0.87716	2.699000	0.92147	0.655000	0.94253	GGC		0.652	CDH20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256141.2	NM_031891		29	96	0	0	0	1	0	29	96				
OR10A5	144124	broad.mit.edu	37	11	6867636	6867636	+	Silent	SNP	G	G	A			TCGA-QR-A6GZ-01A-11D-A35D-08	TCGA-QR-A6GZ-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba3bfaaf-b42e-4279-a234-da6b29fffb5f	dc831897-5afc-4187-860f-4ac7b570871d	g.chr11:6867636G>A	ENST00000299454.4	+	1	754	c.723G>A	c.(721-723)acG>acA	p.T241T	OR10A5_ENST00000379831.2_Silent_p.T245T			Q9H207	O10A5_HUMAN	olfactory receptor, family 10, subfamily A, member 5	241					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(1)|skin(2)|urinary_tract(2)	21		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.68e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		CCTTCTCTACGTGCTCCTCAC	0.443																																					Pancreas(44;21 1072 25662 28041 45559)	ENST00000299454.4																			0				endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(1)|skin(2)|urinary_tract(2)	21						c.(721-723)acG>acA		olfactory receptor, family 10, subfamily A, member 5							259.0	227.0	238.0					11																	6867636		2201	4296	6497	SO:0001819	synonymous_variant	144124				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:6867636G>A	AF324499	CCDS7773.1	11p15.4	2012-08-09			ENSG00000166363	ENSG00000166363		"""GPCR / Class A : Olfactory receptors"""	15131	protein-coding gene	gene with protein product		608493		OR10A1			Standard	NM_178168		Approved	OR11-403, JCG6	uc001met.1	Q9H207	OTTHUMG00000165738	ENST00000299454.4:c.723G>A	11.37:g.6867636G>A						OR10A5_ENST00000379831.2_Silent_p.T245T	p.T241T			Q9H207	O10A5_HUMAN		Epithelial(150;4.68e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)	1	754	+		Medulloblastoma(188;0.0523)|all_neural(188;0.236)	241					O95223|Q52M66|Q96R21|Q96R22	Silent	SNP	ENST00000299454.4	37	c.723G>A	CCDS7773.1																																																																																				0.443	OR10A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385983.1	NM_178168		4	107	0	0	0	1	0	4	107				
STAG3L2	442582	broad.mit.edu	37	7	74300557	74300564	+	RNA	DEL	AGAGCTCC	AGAGCTCC	-	rs367732188		TCGA-QR-A6GZ-01A-11D-A35D-08	TCGA-QR-A6GZ-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba3bfaaf-b42e-4279-a234-da6b29fffb5f	dc831897-5afc-4187-860f-4ac7b570871d	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						442582					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		3	5						3	5	---	---	---	---
FOXP2	93986	broad.mit.edu	37	7	114270000	114270000	+	Silent	SNP	G	G	A			TCGA-QR-A6GZ-01A-11D-A35D-08	TCGA-QR-A6GZ-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba3bfaaf-b42e-4279-a234-da6b29fffb5f	dc831897-5afc-4187-860f-4ac7b570871d	g.chr7:114270000G>A	ENST00000393494.2	+	5	816	c.537G>A	c.(535-537)caG>caA	p.Q179Q	FOXP2_ENST00000393489.3_Silent_p.Q87Q|FOXP2_ENST00000360232.4_Silent_p.Q179Q|AC020606.1_ENST00000580664.1_RNA|FOXP2_ENST00000350908.4_Silent_p.Q179Q|FOXP2_ENST00000378237.3_Silent_p.Q179Q|FOXP2_ENST00000390668.3_Silent_p.Q203Q|FOXP2_ENST00000393498.2_Silent_p.Q159Q|FOXP2_ENST00000393491.3_Silent_p.Q87Q|FOXP2_ENST00000408937.3_Silent_p.Q204Q|FOXP2_ENST00000393500.3_Silent_p.Q104Q|FOXP2_ENST00000403559.4_Silent_p.Q196Q			O15409	FOXP2_HUMAN	forkhead box P2	179	Gln-rich.				camera-type eye development (GO:0043010)|caudate nucleus development (GO:0021757)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|growth (GO:0040007)|lung alveolus development (GO:0048286)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of mesenchymal cell proliferation (GO:0002053)|post-embryonic development (GO:0009791)|putamen development (GO:0021758)|righting reflex (GO:0060013)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|vocal learning (GO:0042297)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q204Q(1)		breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	52						agcaacaacagcagcagcagc	0.498																																						ENST00000393500.3																			1	Substitution - coding silent(1)	p.Q204Q(1)	lung(1)	breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	52						c.(310-312)caG>caA		forkhead box P2							41.0	38.0	39.0					7																	114270000		2199	4282	6481	SO:0001819	synonymous_variant	93986				camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of transcription, DNA-dependent|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding	g.chr7:114270000G>A	U80741	CCDS5760.1, CCDS5761.1, CCDS43635.1, CCDS5761.2, CCDS55154.1	7q31	2008-07-18			ENSG00000128573	ENSG00000128573		"""Forkhead boxes"""	13875	protein-coding gene	gene with protein product	"""trinucleotide repeat containing 10"", ""forkhead/winged-helix transcription factor"", ""speech and language disorder 1"", ""CAG repeat protein 44"""	605317		TNRC10, SPCH1		11586359, 9225980	Standard	NM_014491		Approved	CAGH44	uc003vgz.3	O15409	OTTHUMG00000023131	ENST00000393494.2:c.537G>A	7.37:g.114270000G>A						FOXP2_ENST00000393494.2_Silent_p.Q179Q|FOXP2_ENST00000350908.4_Silent_p.Q179Q|FOXP2_ENST00000393498.2_Silent_p.Q159Q|FOXP2_ENST00000403559.4_Silent_p.Q196Q|AC020606.1_ENST00000580664.1_RNA|FOXP2_ENST00000408937.3_Silent_p.Q204Q|FOXP2_ENST00000378237.3_Silent_p.Q179Q|FOXP2_ENST00000393489.3_Silent_p.Q87Q|FOXP2_ENST00000393491.3_Silent_p.Q87Q|FOXP2_ENST00000390668.3_Silent_p.Q203Q|FOXP2_ENST00000360232.4_Silent_p.Q179Q	p.Q104Q			O15409	FOXP2_HUMAN			11	1132	+			179			Gln-rich.		A0AUV6|A4D0U8|A6NNW4|B4DLD9|Q6ZND1|Q75MJ3|Q8IZE0|Q8N0W2|Q8N6B7|Q8N6B8|Q8NFQ1|Q8NFQ2|Q8NFQ3|Q8NFQ4|Q8TD74	Silent	SNP	ENST00000393494.2	37	c.312G>A	CCDS5760.1																																																																																				0.498	FOXP2-014	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317366.1	NM_014491		4	53	0	0	0	1	0	4	53				
WNK2	65268	broad.mit.edu	37	9	96002081	96002081	+	Frame_Shift_Del	DEL	G	G	-			TCGA-QR-A6GZ-01A-11D-A35D-08	TCGA-QR-A6GZ-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba3bfaaf-b42e-4279-a234-da6b29fffb5f	dc831897-5afc-4187-860f-4ac7b570871d	g.chr9:96002081delG	ENST00000297954.4	+	6	1365	c.1365delG	c.(1363-1365)gagfs	p.E455fs	WNK2_ENST00000427277.2_Frame_Shift_Del_p.E67fs|WNK2_ENST00000356055.3_5'UTR|WNK2_ENST00000395477.2_Frame_Shift_Del_p.E455fs|WNK2_ENST00000349097.3_Frame_Shift_Del_p.E67fs|WNK2_ENST00000395475.2_Frame_Shift_Del_p.E441fs	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	455					intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						TCTTCGCAGAGGACACAGGCG	0.647																																						ENST00000297954.4																			0				breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						c.(1363-1365)gafs		WNK lysine deficient protein kinase 2							33.0	24.0	27.0					9																	96002081		2197	4282	6479	SO:0001589	frameshift_variant	65268				intracellular protein kinase cascade		ATP binding|protein binding|protein serine/threonine kinase activity	g.chr9:96002081delG	AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"""serologically defined colon cancer antigen 43"""	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.1365delG	9.37:g.96002081delG	ENSP00000297954:p.Glu455fs					WNK2_ENST00000427277.2_Frame_Shift_Del_p.E67fs|WNK2_ENST00000349097.3_Frame_Shift_Del_p.E67fs|WNK2_ENST00000395475.2_Frame_Shift_Del_p.E441fs|WNK2_ENST00000395477.2_Frame_Shift_Del_p.E455fs|WNK2_ENST00000356055.3_5'UTR	p.E455fs			Q9Y3S1	WNK2_HUMAN			6	1365	+			455					Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Frame_Shift_Del	DEL	ENST00000297954.4	37	c.1365delG																																																																																					0.647	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648		2	4						2	4	---	---	---	---
DNAJC4	3338	broad.mit.edu	37	11	63997583	63997584	+	5'Flank	INS	-	-	C			TCGA-QR-A6GZ-01A-11D-A35D-08	TCGA-QR-A6GZ-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba3bfaaf-b42e-4279-a234-da6b29fffb5f	dc831897-5afc-4187-860f-4ac7b570871d	g.chr11:63997583_63997584insC	ENST00000321685.3	+	0	0				DNAJC4_ENST00000321460.5_5'Flank|DNAJC4_ENST00000355040.4_5'Flank|RP11-783K16.14_ENST00000534988.1_RNA|RP11-783K16.14_ENST00000539963.1_RNA	NM_005528.3	NP_005519.2	Q9NNZ3	DNJC4_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 4						protein folding (GO:0006457)|response to unfolded protein (GO:0006986)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)	unfolded protein binding (GO:0051082)			endometrium(1)|lung(1)|prostate(1)	3						AAAAAAAAAAACCCGCCCAGCC	0.53																																						ENST00000534988.1																			0																																																	SO:0001631	upstream_gene_variant	84304							g.chr11:63997583_63997584insC	AF012106	CCDS41666.1	11q13	2011-09-02			ENSG00000110011	ENSG00000110011		"""Heat shock proteins / DNAJ (HSP40)"""	5271	protein-coding gene	gene with protein product		604189		HSPF2		9473517, 11147971	Standard	NM_005528		Approved	MCG18	uc001nys.3	Q9NNZ3	OTTHUMG00000167792		11.37:g.63997586_63997586dupC	Exception_encountered													0	99	-								O14716	RNA	INS	ENST00000321685.3	37		CCDS41666.1																																																																																				0.530	DNAJC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396305.1			6	1						6	1	---	---	---	---
PTPRCAP	5790	broad.mit.edu	37	11	67203697	67203699	+	In_Frame_Del	DEL	AGC	AGC	-			TCGA-QR-A6GZ-01A-11D-A35D-08	TCGA-QR-A6GZ-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba3bfaaf-b42e-4279-a234-da6b29fffb5f	dc831897-5afc-4187-860f-4ac7b570871d	g.chr11:67203697_67203699delAGC	ENST00000326294.3	-	2	573_575	c.126_128delGCT	c.(124-129)ctgctc>ctc	p.42_43LL>L	CORO1B_ENST00000539724.1_5'Flank|AP003419.16_ENST00000535922.1_RNA	NM_005608.2	NP_005599.1	Q14761	PTCA_HUMAN	protein tyrosine phosphatase, receptor type, C-associated protein	42					defense response (GO:0006952)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				skin(1)|upper_aerodigestive_tract(1)	2			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)			cagcagtaggagcagcagcagca	0.714																																						ENST00000326294.3																			0				skin(1)|upper_aerodigestive_tract(1)	2						c.(124-129)ctc>ct		protein tyrosine phosphatase, receptor type, C-associated protein				68,3844		14,40,1902						-9.9	0.0			6	131,7505		23,85,3710	no	coding	PTPRCAP	NM_005608.2		37,125,5612	A1A1,A1R,RR		1.7156,1.7382,1.7232				199,11349				SO:0001651	inframe_deletion	5790				defense response	integral to membrane|plasma membrane		g.chr11:67203697_67203699delAGC		CCDS8163.1	11q13.2	2011-06-09			ENSG00000213402	ENSG00000213402			9667	protein-coding gene	gene with protein product		601577					Standard	NM_005608		Approved	LPAP, CD45-AP	uc001oli.1	Q14761	OTTHUMG00000150325	ENST00000326294.3:c.126_128delGCT	11.37:g.67203706_67203708delAGC	ENSP00000325589:p.Leu46del						p.LL44del	NM_005608.2	NP_005599.1	Q14761	PTCA_HUMAN	BRCA - Breast invasive adenocarcinoma(15;3.26e-06)		2	573_575	-			44					B2R512|O00643|Q6I9S6	In_Frame_Del	DEL	ENST00000326294.3	37	c.126_128delGCT	CCDS8163.1																																																																																				0.714	PTPRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317563.1	NM_005608		2	4						2	4	---	---	---	---
FBXL3	26224	broad.mit.edu	37	13	77581683	77581683	+	Frame_Shift_Del	DEL	A	A	-			TCGA-QR-A6GZ-01A-11D-A35D-08	TCGA-QR-A6GZ-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba3bfaaf-b42e-4279-a234-da6b29fffb5f	dc831897-5afc-4187-860f-4ac7b570871d	g.chr13:77581683delA	ENST00000355619.5	-	5	1208	c.884delT	c.(883-885)ttafs	p.L295fs	FBXL3_ENST00000477982.1_Intron	NM_012158.2	NP_036290.1	Q9UKT7	FBXL3_HUMAN	F-box and leucine-rich repeat protein 3	295					entrainment of circadian clock by photoperiod (GO:0043153)|protein destabilization (GO:0031648)|protein ubiquitination (GO:0016567)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	cytosol (GO:0005829)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)	p.L295fs*3(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|urinary_tract(1)	16		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.218)		GBM - Glioblastoma multiforme(99;0.0521)		TTCTTCATATAAAAAAAAATA	0.418																																						ENST00000355619.5																			1	Insertion - Frameshift(1)	p.L295fs*3(1)	lung(1)	breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|urinary_tract(1)	16						c.(883-885)tafs		F-box and leucine-rich repeat protein 3							72.0	73.0	72.0					13																	77581683		2203	4300	6503	SO:0001589	frameshift_variant	26224				regulation of circadian rhythm|rhythmic process|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	cytoplasm|nucleus|SCF ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity	g.chr13:77581683delA	AF129532	CCDS9457.1	13q22	2011-06-09	2004-07-20	2004-07-21	ENSG00000005812	ENSG00000005812		"""F-boxes / Leucine-rich repeats"""	13599	protein-coding gene	gene with protein product		605653	"""F-box and leucine-rich repeat protein 3A"""	FBXL3A		10531035, 10828603	Standard	NM_012158		Approved	FBL3, FBL3A	uc001vkd.3	Q9UKT7	OTTHUMG00000017099	ENST00000355619.5:c.884delT	13.37:g.77581683delA	ENSP00000347834:p.Leu295fs					FBXL3_ENST00000477982.1_Intron	p.L295fs	NM_012158.2	NP_036290.1	Q9UKT7	FBXL3_HUMAN		GBM - Glioblastoma multiforme(99;0.0521)	5	1208	-		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.218)	295					B2RB04|Q9P122	Frame_Shift_Del	DEL	ENST00000355619.5	37	c.884delT	CCDS9457.1																																																																																				0.418	FBXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045312.3			7	61						7	61	---	---	---	---
LGALS16	148003	broad.mit.edu	37	19	40151057	40151057	+	Frame_Shift_Del	DEL	T	T	-	rs532870150		TCGA-QR-A6GZ-01A-11D-A35D-08	TCGA-QR-A6GZ-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ba3bfaaf-b42e-4279-a234-da6b29fffb5f	dc831897-5afc-4187-860f-4ac7b570871d	g.chr19:40151057delT	ENST00000392051.3	+	4	394	c.326delT	c.(325-327)attfs	p.I109fs		NM_001190441.1	NP_001177370.1			lectin, galactoside-binding, soluble, 16																		GGTGAATACATTTATGCCTTT	0.433																																						ENST00000392051.3																			0											c.(325-327)atfs		lectin, galactoside-binding, soluble, 16																																				SO:0001589	frameshift_variant	148003						sugar binding	g.chr19:40151057delT		CCDS54267.1	19q13.2	2011-08-04			ENSG00000249861	ENSG00000249861		"""Lectins, galactoside-binding"""	40039	protein-coding gene	gene with protein product						19497882	Standard	NM_001190441		Approved		uc021uun.1	A8MUM7		ENST00000392051.3:c.326delT	19.37:g.40151057delT	ENSP00000375904:p.Ile109fs						p.I109fs	NM_001190441.1	NP_001177370.1	A8MUM7	A8MUM7_HUMAN			4	394	+			109						Frame_Shift_Del	DEL	ENST00000392051.3	37	c.326delT	CCDS54267.1																																																																																				0.433	LGALS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465022.1			2	4						2	4	---	---	---	---
