#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
BMS1P20	96610	broad.mit.edu	37	22	22663271	22663271	+	RNA	SNP	A	A	G	rs200792818		TCGA-QR-A6H5-01A-11D-A35D-08	TCGA-QR-A6H5-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03b4fb36-83b8-4482-9847-313f5b25fe61	61abdecd-d8a4-4784-a6e9-c4ff8e355a37	g.chr22:22663271A>G	ENST00000426066.1	+	0	623					NR_027293.1				BMS1 pseudogene 20																		TGGGCCTCATATTTTTAGAAA	0.259																																						ENST00000426066.1																			0																																																			96610							g.chr22:22663271A>G			22q11.22	2013-09-20			ENSG00000236850	ENSG00000236850			49153	pseudogene	pseudogene							Standard	XR_430414		Approved				OTTHUMG00000151046		22.37:g.22663271A>G								NR_027293.1						0	623	+									RNA	SNP	ENST00000426066.1	37																																																																																						0.259	BMS1P20-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000473090.1			3	11	0	0	0	1	0	3	11				
SPANXN2	494119	broad.mit.edu	37	X	142795397	142795397	+	Missense_Mutation	SNP	C	C	A			TCGA-QR-A6H5-01A-11D-A35D-08	TCGA-QR-A6H5-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03b4fb36-83b8-4482-9847-313f5b25fe61	61abdecd-d8a4-4784-a6e9-c4ff8e355a37	g.chrX:142795397C>A	ENST00000370498.1	-	2	1034	c.281G>T	c.(280-282)gGa>gTa	p.G94V		NM_001009615.1	NP_001009615.1	Q5MJ10	SPXN2_HUMAN	SPANX family, member N2	94								p.G94V(1)|p.I76I(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27	Acute lymphoblastic leukemia(192;6.56e-05)					CTGTGAAGATCCTTCAGCTGA	0.502																																						ENST00000370498.1																			2	Substitution - Missense(1)|Substitution - coding silent(1)	p.G94V(1)|p.I76I(1)	lung(2)	NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27						c.(280-282)gGa>gTa		SPANX family, member N2							328.0	296.0	307.0					X																	142795397		2203	4300	6503	SO:0001583	missense	494119							g.chrX:142795397C>A		CCDS35419.1	Xq27.3	2012-06-12			ENSG00000203924	ENSG00000268988			33175	protein-coding gene	gene with protein product	"""cancer/testis antigen family 11, member 7"""	300665				14973187, 17012309	Standard	NM_001009615		Approved	SPANX-N2, CT11.7	uc004fbz.3	Q5MJ10	OTTHUMG00000022583	ENST00000370498.1:c.281G>T	X.37:g.142795397C>A	ENSP00000359529:p.Gly94Val						p.G94V	NM_001009615.1	NP_001009615.1	Q5MJ10	SPXN2_HUMAN			2	1034	-	Acute lymphoblastic leukemia(192;6.56e-05)		94					Q0ZNM2	Missense_Mutation	SNP	ENST00000370498.1	37	c.281G>T	CCDS35419.1	.	.	.	.	.	.	.	.	.	.	C	0.004	-2.261648	0.00262	.	.	ENSG00000203924	ENST00000370498	T	0.07021	3.23	0.628	-1.26	0.09376	.	.	.	.	.	T	0.03783	0.0107	L	0.36672	1.1	0.09310	N	1	P	0.42456	0.78	B	0.33454	0.164	T	0.39563	-0.9608	8	0.11182	T	0.66	.	.	.	.	.	94	Q5MJ10	SPXN2_HUMAN	V	94	ENSP00000359529:G94V	ENSP00000359529:G94V	G	-	2	0	SPANXN2	142623063	0.993000	0.37304	0.000000	0.03702	0.000000	0.00434	1.462000	0.35266	-2.912000	0.00307	-3.171000	0.00057	GGA		0.502	SPANXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058621.2	NM_001009615		7	471	1	0	5.18039e-06	1	5.75599e-06	7	471				
ALMS1	7840	broad.mit.edu	37	2	73675507	73675507	+	Missense_Mutation	SNP	C	C	T			TCGA-QR-A6H5-01A-11D-A35D-08	TCGA-QR-A6H5-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03b4fb36-83b8-4482-9847-313f5b25fe61	61abdecd-d8a4-4784-a6e9-c4ff8e355a37	g.chr2:73675507C>T	ENST00000264448.6	+	8	1961	c.1850C>T	c.(1849-1851)aCc>aTc	p.T617I	ALMS1_ENST00000377715.1_Missense_Mutation_p.T617I|ALMS1_ENST00000409009.1_Missense_Mutation_p.T575I	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	617	34 X 47 AA approximate tandem repeat.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						TCAACTCTAACCTCTACTTCC	0.463																																						ENST00000264448.6																			0				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						c.(1849-1851)aCc>aTc		Alstrom syndrome 1							117.0	119.0	118.0					2																	73675507		1891	4109	6000	SO:0001583	missense	7840				G2/M transition of mitotic cell cycle	centrosome|cilium|cytosol|microtubule basal body|spindle pole		g.chr2:73675507C>T	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.1850C>T	2.37:g.73675507C>T	ENSP00000264448:p.Thr617Ile					ALMS1_ENST00000409009.1_Missense_Mutation_p.T575I|ALMS1_ENST00000377715.1_Missense_Mutation_p.T617I	p.T617I	NM_015120.4	NP_055935.4	Q8TCU4	ALMS1_HUMAN			8	1961	+			617			34 X 47 AA approximate tandem repeat.		Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	c.1850C>T	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	C	5.684	0.310791	0.10733	.	.	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.16597	3.21;3.21;2.33	3.93	-0.295	0.12828	.	1.990460	0.02273	N	0.068611	T	0.10637	0.0260	N	0.22421	0.69	0.09310	N	1	P;P;P	0.37038	0.579;0.579;0.579	B;B;B	0.34093	0.175;0.175;0.175	T	0.13764	-1.0497	10	0.32370	T	0.25	.	3.0348	0.06118	0.3618:0.4136:0.0:0.2246	.	617;575;617	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	I	575;617;617	ENSP00000386627:T575I;ENSP00000264448:T617I;ENSP00000366944:T617I	ENSP00000264448:T617I	T	+	2	0	ALMS1	73529015	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	0.436000	0.21526	-0.070000	0.12908	0.655000	0.94253	ACC		0.463	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		28	117	0	0	0	1	0	28	117				
COL11A2	1302	broad.mit.edu	37	6	33147561	33147561	+	Missense_Mutation	SNP	C	C	G			TCGA-QR-A6H5-01A-11D-A35D-08	TCGA-QR-A6H5-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03b4fb36-83b8-4482-9847-313f5b25fe61	61abdecd-d8a4-4784-a6e9-c4ff8e355a37	g.chr6:33147561C>G	ENST00000374708.4	-	11	1381	c.1123G>C	c.(1123-1125)Ggt>Cgt	p.G375R	COL11A2_ENST00000374712.1_Missense_Mutation_p.G380R|COL11A2_ENST00000477772.1_5'Flank|COL11A2_ENST00000357486.1_Missense_Mutation_p.G440R|COL11A2_ENST00000341947.2_Missense_Mutation_p.G461R|COL11A2_ENST00000374713.1_Missense_Mutation_p.G414R|COL11A2_ENST00000361917.1_Missense_Mutation_p.G354R|COL11A2_ENST00000395197.1_Missense_Mutation_p.G401R|COL11A2_ENST00000374714.1_Missense_Mutation_p.G435R	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	461	Nonhelical region.				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						CCCTTGTCACCCCCACCACTG	0.637																																					Melanoma(1;90 116 3946 5341 17093)	ENST00000341947.2																			0				biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						c.(1381-1383)Ggt>Cgt		collagen, type XI, alpha 2							46.0	55.0	52.0					6																	33147561		2203	4300	6503	SO:0001583	missense	1302				cartilage development|cell adhesion|collagen fibril organization|sensory perception of sound|soft palate development	collagen type XI	extracellular matrix structural constituent conferring tensile strength|protein binding, bridging	g.chr6:33147561C>G	U32169	CCDS43452.1, CCDS54992.1	6p21.3	2013-01-16			ENSG00000204248	ENSG00000204248		"""Collagens"""	2187	protein-coding gene	gene with protein product		120290		DFNA13, DFNB53		7559422, 10581026	Standard	NM_080679		Approved	HKE5	uc003ocx.1	P13942	OTTHUMG00000031036	ENST00000374708.4:c.1123G>C	6.37:g.33147561C>G	ENSP00000363840:p.Gly375Arg					COL11A2_ENST00000374712.1_Missense_Mutation_p.G380R|COL11A2_ENST00000374708.4_Missense_Mutation_p.G375R|COL11A2_ENST00000361917.1_Missense_Mutation_p.G354R|COL11A2_ENST00000395197.1_Missense_Mutation_p.G401R|COL11A2_ENST00000374713.1_Missense_Mutation_p.G414R|COL11A2_ENST00000374714.1_Missense_Mutation_p.G435R|COL11A2_ENST00000357486.1_Missense_Mutation_p.G440R	p.G461R	NM_080680.2	NP_542411.2	P13942	COBA2_HUMAN			13	1608	-			461			Nonhelical region.		A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Missense_Mutation	SNP	ENST00000374708.4	37	c.1381G>C	CCDS43452.1	.	.	.	.	.	.	.	.	.	.	c	21.2	4.120245	0.77323	.	.	ENSG00000204248	ENST00000374708;ENST00000341947;ENST00000357486;ENST00000374714;ENST00000374713;ENST00000395197;ENST00000374712;ENST00000361917;ENST00000457788	D;D;D;D;D;D;D;D;D	0.91295	-2.41;-2.33;-2.36;-2.37;-2.36;-2.37;-2.46;-2.38;-2.82	4.54	3.67	0.42095	.	0.000000	0.85682	D	0.000000	D	0.92277	0.7550	M	0.75447	2.3	0.50467	D	0.999878	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.994;0.994;1.0	D	0.92172	0.5744	10	0.62326	D	0.03	.	8.3072	0.32049	0.0:0.8924:0.0:0.1076	.	354;375;461	P13942-8;P13942-6;P13942	.;.;COBA2_HUMAN	R	375;461;440;435;414;401;380;354;461	ENSP00000363840:G375R;ENSP00000339915:G461R;ENSP00000350079:G440R;ENSP00000363846:G435R;ENSP00000363845:G414R;ENSP00000378623:G401R;ENSP00000363844:G380R;ENSP00000355123:G354R;ENSP00000405520:G461R	ENSP00000339915:G461R	G	-	1	0	COL11A2	33255539	1.000000	0.71417	0.991000	0.47740	0.994000	0.84299	5.604000	0.67626	1.137000	0.42214	0.543000	0.68304	GGT		0.637	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2			3	43	0	0	0	1	0	3	43				
SIK1	150094	broad.mit.edu	37	21	44837473	44837473	+	Silent	SNP	G	G	A			TCGA-QR-A6H5-01A-11D-A35D-08	TCGA-QR-A6H5-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03b4fb36-83b8-4482-9847-313f5b25fe61	61abdecd-d8a4-4784-a6e9-c4ff8e355a37	g.chr21:44837473G>A	ENST00000270162.6	-	13	2058	c.1926C>T	c.(1924-1926)gcC>gcT	p.A642A		NM_173354.3	NP_775490.2	P57059	SIK1_HUMAN	salt-inducible kinase 1	642					cardiac muscle cell differentiation (GO:0055007)|cell cycle (GO:0007049)|entrainment of circadian clock by photoperiod (GO:0043153)|intracellular signal transduction (GO:0035556)|negative regulation of CREB transcription factor activity (GO:0032792)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of triglyceride biosynthetic process (GO:0010868)|positive regulation of anoikis (GO:2000210)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell differentiation (GO:0045595)|regulation of mitotic cell cycle (GO:0007346)|regulation of myotube differentiation (GO:0010830)|regulation of sodium ion transport (GO:0002028)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|cAMP response element binding protein binding (GO:0008140)|magnesium ion binding (GO:0000287)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|testis(2)|urinary_tract(1)	21					Dabrafenib(DB08912)	CCCGGCTGCCGGCTGCGCCGC	0.756																																						ENST00000270162.6																			0				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|testis(2)|urinary_tract(1)	21						c.(1924-1926)gcC>gcT		salt-inducible kinase 1							7.0	10.0	9.0					21																	44837473		2089	4063	6152	SO:0001819	synonymous_variant	150094				anoikis|cell cycle|cell differentiation|intracellular protein kinase cascade|multicellular organismal development|regulation of cell differentiation|regulation of mitotic cell cycle	nucleus	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity	g.chr21:44837473G>A	BC038504	CCDS33575.1	21q22.3	2008-12-23	2008-12-23	2008-12-23	ENSG00000142178	ENSG00000142178			11142	protein-coding gene	gene with protein product	"""myocardial SNF1-like kinase"""	605705	"""SNF1-like kinase"""	SNF1LK		7893599	Standard	NM_173354		Approved	msk	uc002zdf.2	P57059	OTTHUMG00000086874	ENST00000270162.6:c.1926C>T	21.37:g.44837473G>A							p.A642A	NM_173354.3	NP_775490.2	P57059	SIK1_HUMAN			13	2058	-			642					A6NC84|Q5R2V5|Q6ZNL8|Q86YJ2	Silent	SNP	ENST00000270162.6	37	c.1926C>T	CCDS33575.1																																																																																				0.756	SIK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195654.1	NM_173354		4	7	0	0	0	1	0	4	7				
FEM1B	10116	broad.mit.edu	37	15	68581943	68581943	+	Splice_Site	SNP	A	A	G	rs111343207		TCGA-QR-A6H5-01A-11D-A35D-08	TCGA-QR-A6H5-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03b4fb36-83b8-4482-9847-313f5b25fe61	61abdecd-d8a4-4784-a6e9-c4ff8e355a37	g.chr15:68581943A>G	ENST00000306917.4	+	2	863		c.e2-1			NM_015322.4	NP_056137.1	Q9UK73	FEM1B_HUMAN	fem-1 homolog b (C. elegans)						apoptotic process (GO:0006915)|branching involved in prostate gland morphogenesis (GO:0060442)|epithelial cell maturation involved in prostate gland development (GO:0060743)|regulation of DNA damage checkpoint (GO:2000001)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|regulation of ubiquitin-protein transferase activity (GO:0051438)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	death receptor binding (GO:0005123)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(1)	9						TTTCATGTGTAGGTATGTCAT	0.453																																						ENST00000306917.4																			0				endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(1)	9						c.e2-1		fem-1 homolog b (C. elegans)							55.0	50.0	52.0					15																	68581943		2199	4298	6497	SO:0001630	splice_region_variant	10116				apoptosis|induction of apoptosis|regulation of DNA damage checkpoint|regulation of ubiquitin-protein ligase activity	cytoplasm|nucleus	death receptor binding|ubiquitin-protein ligase activity	g.chr15:68581943A>G		CCDS10228.1	15q22	2013-02-19	2001-11-28		ENSG00000169018	ENSG00000169018		"""Ankyrin repeat domain containing"""	3649	protein-coding gene	gene with protein product		613539	"""FEM-1 (C. elegans) homolog b"""			10623617	Standard	NM_015322		Approved		uc002arg.3	Q9UK73	OTTHUMG00000133285	ENST00000306917.4:c.249-1A>G	15.37:g.68581943A>G								NM_015322.3	NP_056137.1	Q9UK73	FEM1B_HUMAN			2	863	+								O43146	Splice_Site	SNP	ENST00000306917.4	37		CCDS10228.1	.	.	.	.	.	.	.	.	.	.	A	15.23	2.772734	0.49680	.	.	ENSG00000169018	ENST00000306917	.	.	.	5.67	5.67	0.87782	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0888	0.72177	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FEM1B	66368997	1.000000	0.71417	0.956000	0.39512	0.984000	0.73092	8.864000	0.92294	2.149000	0.67028	0.454000	0.30748	.		0.453	FEM1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257065.1		Intron	7	25	0	0	0	1	0	7	25				
CXADR	1525	broad.mit.edu	37	21	18937753	18937753	+	Missense_Mutation	SNP	G	G	A			TCGA-QR-A6H5-01A-11D-A35D-08	TCGA-QR-A6H5-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03b4fb36-83b8-4482-9847-313f5b25fe61	61abdecd-d8a4-4784-a6e9-c4ff8e355a37	g.chr21:18937753G>A	ENST00000284878.7	+	7	1589	c.841G>A	c.(841-843)Gtg>Atg	p.V281M	CXADR_ENST00000400165.1_Missense_Mutation_p.M141I|CXADR_ENST00000356275.6_Missense_Mutation_p.C73Y|CXADR_ENST00000400166.1_Missense_Mutation_p.M193I|CXADR_ENST00000400169.1_Missense_Mutation_p.V281M|CXADR_ENST00000306618.10_Missense_Mutation_p.V240M	NM_001338.4	NP_001329.1	P78310	CXAR_HUMAN	coxsackie virus and adenovirus receptor	281					actin cytoskeleton reorganization (GO:0031532)|AV node cell to bundle of His cell communication (GO:0086067)|blood coagulation (GO:0007596)|cardiac muscle fiber development (GO:0048739)|cell-cell junction organization (GO:0045216)|defense response to virus (GO:0051607)|epithelial structure maintenance (GO:0010669)|gamma-delta T cell activation (GO:0046629)|germ cell migration (GO:0008354)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|homotypic cell-cell adhesion (GO:0034109)|leukocyte migration (GO:0050900)|mitochondrion organization (GO:0007005)|neutrophil chemotaxis (GO:0030593)|regulation of immune response (GO:0050776)|transepithelial transport (GO:0070633)|viral process (GO:0016032)	acrosomal vesicle (GO:0001669)|adherens junction (GO:0005912)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|cell body (GO:0044297)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|filopodium (GO:0030175)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|cell adhesion molecule binding (GO:0050839)|connexin binding (GO:0071253)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|PDZ domain binding (GO:0030165)|receptor binding (GO:0005102)|virus receptor activity (GO:0001618)			endometrium(2)|large_intestine(5)|lung(1)|ovary(1)|prostate(2)	11				Epithelial(23;0.000206)|all cancers(11;0.000302)|OV - Ovarian serous cystadenocarcinoma(11;0.0194)|Lung(58;0.0233)|COAD - Colon adenocarcinoma(22;0.0389)|Colorectal(24;0.0483)|LUSC - Lung squamous cell carcinoma(23;0.0782)		CAGGGAAGATGTGCCACCTCC	0.438																																						ENST00000284878.7																			0				endometrium(2)|large_intestine(5)|lung(1)|ovary(1)|prostate(2)	11						c.(841-843)Gtg>Atg		coxsackie virus and adenovirus receptor							75.0	79.0	78.0					21																	18937753		2203	4300	6503	SO:0001583	missense	1525				blood coagulation|cell adhesion|interspecies interaction between organisms|leukocyte migration|regulation of immune response	adherens junction|basolateral plasma membrane|extracellular region|integral to plasma membrane|nucleus|tight junction	receptor activity	g.chr21:18937753G>A	Y07593	CCDS33519.1, CCDS56204.1, CCDS56205.1, CCDS56206.1, CCDS56207.1	21q21.1	2013-01-29			ENSG00000154639	ENSG00000154639		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	2559	protein-coding gene	gene with protein product		602621				9036860, 9096397	Standard	NM_001338		Approved	CAR	uc002yki.3	P78310	OTTHUMG00000074508	ENST00000284878.7:c.841G>A	21.37:g.18937753G>A	ENSP00000284878:p.Val281Met					CXADR_ENST00000400166.1_Missense_Mutation_p.M193I|CXADR_ENST00000306618.10_Missense_Mutation_p.V240M|CXADR_ENST00000400169.1_Missense_Mutation_p.V281M|CXADR_ENST00000400165.1_Missense_Mutation_p.M141I|CXADR_ENST00000356275.6_Missense_Mutation_p.C73Y	p.V281M	NM_001338.4	NP_001329.1	P78310	CXAR_HUMAN		Epithelial(23;0.000206)|all cancers(11;0.000302)|OV - Ovarian serous cystadenocarcinoma(11;0.0194)|Lung(58;0.0233)|COAD - Colon adenocarcinoma(22;0.0389)|Colorectal(24;0.0483)|LUSC - Lung squamous cell carcinoma(23;0.0782)	7	1589	+			281					B2R8V8|B7WPI3|D3YHP0|O00694|Q8WWT6|Q8WWT7|Q8WWT8|Q9UKV4	Missense_Mutation	SNP	ENST00000284878.7	37	c.841G>A	CCDS33519.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	19.14|19.14|19.14	3.770503|3.770503|3.770503	0.69992|0.69992|0.69992	.|.|.	.|.|.	ENSG00000154639|ENSG00000154639|ENSG00000154639	ENST00000356275|ENST00000400166;ENST00000400165|ENST00000284878;ENST00000400169;ENST00000306618	.|D;D|T;T;D	.|0.90261|0.87256	.|-2.45;-2.64|-1.07;-1.19;-2.23	5.3|5.3|5.3	5.3|5.3|5.3	0.74995|0.74995|0.74995	.|.|.	.|.|0.000000	.|.|0.85682	.|.|D	.|.|0.000000	D|D|D	0.93406|0.93406|0.93406	0.7897|0.7897|0.7897	.|.|.	.|.|.	.|.|.	0.80722|0.80722|0.80722	D|D|D	1|1|1	P|B;B|D;D	0.40875|0.26845|0.89917	0.731|0.161;0.161|1.0;1.0	B|B;B|D;D	0.43478|0.24394|0.91635	0.421|0.053;0.053|0.999;0.991	D|D|D	0.92793|0.92793|0.92793	0.6250|0.6250|0.6250	7|8|9	0.72032|0.35671|0.44086	D|T|T	0.01|0.21|0.13	.|.|.	18.3313|18.3313|18.3313	0.90270|0.90270|0.90270	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.|.	73|141;193|281;281	P78310-3|P78310-4;P78310-5|B7WPI3;P78310	.|.;.|.;CXAR_HUMAN	Y|I|M	73|193;141|281;281;240	.|ENSP00000383030:M193I;ENSP00000383029:M141I|ENSP00000284878:V281M;ENSP00000383033:V281M;ENSP00000303395:V240M	ENSP00000348620:C73Y|ENSP00000383029:M141I|ENSP00000284878:V281M	C|M|V	+|+|+	2|3|1	0|0|0	CXADR|CXADR|CXADR	17859624|17859624|17859624	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.738000|0.738000|0.738000	0.30950|0.30950|0.30950	0.564000|0.564000|0.564000	0.35744|0.35744|0.35744	9.132000|9.132000|9.132000	0.94455|0.94455|0.94455	2.644000|2.644000|2.644000	0.89710|0.89710|0.89710	0.561000|0.561000|0.561000	0.74099|0.74099|0.74099	TGT|ATG|GTG		0.438	CXADR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000158209.1			13	52	0	0	0	1	0	13	52				
VHL	7428	broad.mit.edu	37	3	10191489	10191489	+	Missense_Mutation	SNP	G	G	A			TCGA-QR-A6H5-01A-11D-A35D-08	TCGA-QR-A6H5-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03b4fb36-83b8-4482-9847-313f5b25fe61	61abdecd-d8a4-4784-a6e9-c4ff8e355a37	g.chr3:10191489G>A	ENST00000256474.2	+	3	1322	c.482G>A	c.(481-483)cGa>cAa	p.R161Q	VHL_ENST00000477538.1_3'UTR|VHL_ENST00000345392.2_Missense_Mutation_p.R120Q	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	161	Interaction with Elongin BC complex.		R -> G (in VHLD; type II; dbSNP:rs5030818).|R -> P (in pheochromocytoma and VHLD; type I). {ECO:0000269|PubMed:12000816, ECO:0000269|PubMed:8956040}.|R -> Q (in pheochromocytoma and VHLD; type II). {ECO:0000269|PubMed:12000816, ECO:0000269|PubMed:9829912}.		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.R161P(4)|p.R161del(1)|p.R161fs*12(1)|p.E160fs*9(1)|p.C162fs*12(1)|p.?fs(1)|p.C162fs*9(1)|p.L158fs*6(1)|p.R161Q(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		CTGAAAGAGCGATGCCTCCAG	0.502		1	"""D, Mis, N, F, S"""		"""renal, hemangioma, pheochromocytoma"""	"""renal, hemangioma, pheochromocytoma"""			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																													ENST00000256474.2		1	yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	"""D, Mis, N, F, S"""	von Hippel-Lindau syndrome gene			"""E, M, O"""		"""renal, hemangioma, pheochromocytoma"""	"""renal, hemangioma, pheochromocytoma"""		12	Substitution - Missense(5)|Deletion - Frameshift(4)|Insertion - Frameshift(2)|Deletion - In frame(1)	p.R161P(4)|p.R161del(1)|p.R161fs*12(1)|p.E160fs*9(1)|p.C162fs*12(1)|p.?fs(1)|p.C162fs*9(1)|p.L158fs*6(1)|p.R161Q(1)	kidney(11)|adrenal_gland(1)	adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769	GRCh37	CM951290|CM961431	VHL	M		c.(481-483)cGa>cAa		von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase							94.0	85.0	88.0					3																	10191489		2203	4300	6503	SO:0001583	missense	7428	von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	g.chr3:10191489G>A	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.482G>A	3.37:g.10191489G>A	ENSP00000256474:p.Arg161Gln					VHL_ENST00000345392.2_Missense_Mutation_p.R120Q|VHL_ENST00000477538.1_3'UTR	p.R161Q	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN		Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)	3	1322	+			161		R -> G (in VHLD; type II; dbSNP:rs5030818).|R -> P (in pheochromocytoma and VHLD; type I).|R -> Q (in pheochromocytoma and VHLD; type II).	Interaction with Elongin BC complex.		B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	c.482G>A	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.898538	0.91962	.	.	ENSG00000134086	ENST00000256474;ENST00000345392;ENST00000450183	D;D	0.99826	-6.98;-6.98	4.86	4.86	0.63082	von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);von Hippel-Lindau disease tumor suppressor, alpha domain (1);	0.000000	0.85682	D	0.000000	D	0.99684	0.9881	L	0.60455	1.87	0.46823	D	0.999215	D;D	0.89917	1.0;1.0	D;D	0.91635	0.996;0.999	D	0.97408	1.0000	10	0.42905	T	0.14	-3.8766	15.8663	0.79067	0.0:0.0:1.0:0.0	.	120;161	P40337-2;P40337	.;VHL_HUMAN	Q	161;120;79	ENSP00000256474:R161Q;ENSP00000344757:R120Q	ENSP00000256474:R161Q	R	+	2	0	VHL	10166489	1.000000	0.71417	0.914000	0.36105	0.805000	0.45488	7.062000	0.76706	2.676000	0.91093	0.655000	0.94253	CGA		0.502	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1	NM_000551		10	19	0	0	0	1	0	10	19				
ANKRD20A8P	729171	broad.mit.edu	37	2	95522815	95522815	+	RNA	SNP	A	A	G	rs372261324		TCGA-QR-A6H5-01A-11D-A35D-08	TCGA-QR-A6H5-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03b4fb36-83b8-4482-9847-313f5b25fe61	61abdecd-d8a4-4784-a6e9-c4ff8e355a37	g.chr2:95522815A>G	ENST00000432432.2	-	0	212					NR_040113.1		Q5CZ79	AN20B_HUMAN	ankyrin repeat domain 20 family, member A8, pseudogene																		ATCTTCTGCAATTCGGAGTCC	0.652																																						ENST00000432432.2																			0																																																			729171							g.chr2:95522815A>G			2q11.1	2011-09-16	2010-12-15	2010-12-15	ENSG00000229089	ENSG00000229089			23666	pseudogene	pseudogene			"""ankyrin repeat domain 20B"""	ANKRD20B			Standard	NR_003366		Approved		uc010fhq.2	Q5CZ79	OTTHUMG00000155138		2.37:g.95522815A>G								NR_040113.1						0	212	-								A6NC18	RNA	SNP	ENST00000432432.2	37																																																																																						0.652	ANKRD20A8P-002	KNOWN	not_best_in_genome_evidence|basic	processed_transcript	pseudogene	OTTHUMT00000451404.1			5	47	0	0	0	1	0	5	47				
UBB	7314	broad.mit.edu	37	17	16285491	16285491	+	Silent	SNP	C	C	T	rs16962973		TCGA-QR-A6H5-01A-11D-A35D-08	TCGA-QR-A6H5-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03b4fb36-83b8-4482-9847-313f5b25fe61	61abdecd-d8a4-4784-a6e9-c4ff8e355a37	g.chr17:16285491C>T	ENST00000395837.1	+	2	451	c.270C>T	c.(268-270)acC>acT	p.T90T	UBB_ENST00000395839.1_Silent_p.T90T|UBB_ENST00000535788.1_Intron|RP11-138I1.4_ENST00000583934.1_RNA|UBB_ENST00000578649.1_Intron|UBB_ENST00000302182.3_Silent_p.T90T	NM_001281718.1|NM_001281720.1	NP_001268647.1|NP_001268649.1	P0CG47	UBB_HUMAN	ubiquitin B	90	Ubiquitin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00214}.		GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFV KTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFA GKQLEDGRTLSDYNIQKESTLHLVLRLRGGC -> YADLRE DPDRQDHHPGSGAQ (in UBB(+1); loss of polyubiquitination; impairs the ubiquitin-proteasome pathway; refractory to disassembly by DUBs; slow degradation by UCHL3).		activation of MAPK activity (GO:0000187)|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)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|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 transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)		AGACCATCACCCTGGAAGTGG	0.552																																					Melanoma(163;1126 3406 34901)	ENST00000302182.3																			0				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						c.(268-270)acC>acT		ubiquitin B							75.0	76.0	75.0					17																	16285491		2203	4297	6500	SO:0001819	synonymous_variant	7314				activation of MAPK activity|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|anti-apoptosis|apoptosis|cellular membrane organization|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA repair|endosome transport|epidermal growth factor receptor signaling pathway|G1/S transition of mitotic cell cycle|I-kappaB kinase/NF-kappaB cascade|induction of apoptosis by extracellular signals|innate immune response|JNK cascade|M/G1 transition of mitotic cell cycle|mRNA metabolic process|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of type I interferon production|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|S phase of mitotic cell cycle|stress-activated MAPK cascade|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|viral reproduction	cytosol|endocytic vesicle membrane|endosome membrane|nucleoplasm|plasma membrane	protein binding	g.chr17:16285491C>T		CCDS11177.1	17p12-p11.2	2010-11-25			ENSG00000170315	ENSG00000170315			12463	protein-coding gene	gene with protein product	"""polyubiquitin B"""	191339				2154095	Standard	NM_018955		Approved	MGC8385, FLJ25987	uc002gpx.3	P0CG47	OTTHUMG00000058987	ENST00000395837.1:c.270C>T	17.37:g.16285491C>T						UBB_ENST00000395837.1_Silent_p.T90T|UBB_ENST00000395839.1_Silent_p.T90T|UBB_ENST00000578649.1_Intron|UBB_ENST00000535788.1_Intron|RP11-138I1.4_ENST00000583934.1_RNA	p.T90T	NM_018955.2	NP_061828.1	P0CG47	UBB_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)	2	662	+			90			Ubiquitin-like 2.		P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Silent	SNP	ENST00000395837.1	37	c.270C>T	CCDS11177.1																																																																																				0.552	UBB-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000130459.1	NM_018955		6	117	0	0	0	1	0	6	117				
POM121L9P	29774	broad.mit.edu	37	22	24659734	24659734	+	RNA	SNP	T	T	C			TCGA-QR-A6H5-01A-11D-A35D-08	TCGA-QR-A6H5-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03b4fb36-83b8-4482-9847-313f5b25fe61	61abdecd-d8a4-4784-a6e9-c4ff8e355a37	g.chr22:24659734T>C	ENST00000414583.2	+	0	3259					NR_003714.1				POM121 transmembrane nucleoporin-like 9, pseudogene																		CTCTCTCCTGTGGGAGGGGGG	0.632																																						ENST00000414583.2																			0																																																			29774							g.chr22:24659734T>C	AL040062, AL117401		22q11.22	2012-03-13	2012-03-13		ENSG00000128262	ENSG00000128262			30080	pseudogene	pseudogene			"""POM121 membrane glycoprotein-like 9, pseudogene"""				Standard	NR_003714		Approved				OTTHUMG00000150763		22.37:g.24659734T>C								NR_003714.1						0	3259	+									RNA	SNP	ENST00000414583.2	37																																																																																						0.632	POM121L9P-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000319991.1	NM_014549		3	14	0	0	0	1	0	3	14				
SMARCC2	6601	broad.mit.edu	37	12	56578857	56578857	+	Missense_Mutation	SNP	C	C	T			TCGA-QR-A6H5-01A-11D-A35D-08	TCGA-QR-A6H5-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03b4fb36-83b8-4482-9847-313f5b25fe61	61abdecd-d8a4-4784-a6e9-c4ff8e355a37	g.chr12:56578857C>T	ENST00000267064.4	-	4	442	c.356G>A	c.(355-357)cGc>cAc	p.R119H	SMARCC2_ENST00000347471.4_Missense_Mutation_p.R119H|SMARCC2_ENST00000550859.1_5'UTR|SMARCC2_ENST00000550164.1_Missense_Mutation_p.R119H|SMARCC2_ENST00000394023.3_Missense_Mutation_p.R119H|RP11-977G19.5_ENST00000553176.1_RNA	NM_003075.3	NP_003066.2	Q8TAQ2	SMRC2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	119					ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome disassembly (GO:0006337)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment (GO:0021882)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(3)|lung(20)|ovary(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	41			OV - Ovarian serous cystadenocarcinoma(18;0.123)			TTCCACATTGCGGTCCATGCG	0.468																																						ENST00000394023.3																			0				breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(3)|lung(20)|ovary(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	41						c.(355-357)cGc>cAc		SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2							137.0	118.0	124.0					12																	56578857		2203	4300	6503	SO:0001583	missense	6601				chromatin remodeling|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity	g.chr12:56578857C>T	U66616	CCDS8907.1, CCDS8908.1, CCDS55835.1	12q13.2	2008-05-14				ENSG00000139613			11105	protein-coding gene	gene with protein product		601734				8804307, 9693044	Standard	NM_001130420		Approved	BAF170, Rsc8, CRACC2	uc001skb.3	Q8TAQ2	OTTHUMG00000170288	ENST00000267064.4:c.356G>A	12.37:g.56578857C>T	ENSP00000267064:p.Arg119His					SMARCC2_ENST00000550164.1_Missense_Mutation_p.R119H|SMARCC2_ENST00000550859.1_5'UTR|SMARCC2_ENST00000347471.4_Missense_Mutation_p.R119H|RP11-977G19.5_ENST00000553176.1_RNA|SMARCC2_ENST00000267064.4_Missense_Mutation_p.R119H	p.R119H	NM_001130420.1	NP_001123892.1	Q8TAQ2	SMRC2_HUMAN	OV - Ovarian serous cystadenocarcinoma(18;0.123)		4	461	-			119					F8VTJ5|Q59GV3|Q92923|Q96E12|Q96GY4	Missense_Mutation	SNP	ENST00000267064.4	37	c.356G>A	CCDS8907.1	.	.	.	.	.	.	.	.	.	.	C	36	5.687984	0.96784	.	.	ENSG00000139613	ENST00000394023;ENST00000550164;ENST00000347471;ENST00000267064	T;T;T;T	0.24151	1.87;1.87;1.87;1.87	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.52158	0.1717	M	0.72353	2.195	0.53688	D	0.999978	D;D;D;D;D	0.76494	0.999;0.999;0.999;0.999;0.999	D;D;D;D;D	0.80764	0.987;0.994;0.987;0.987;0.994	T	0.50355	-0.8838	10	0.66056	D	0.02	-10.6913	18.3142	0.90213	0.0:1.0:0.0:0.0	.	8;119;124;119;119	B4DF22;F8VTJ5;Q59G16;Q8TAQ2;Q8TAQ2-2	.;.;.;SMRC2_HUMAN;.	H	119	ENSP00000377591:R119H;ENSP00000449396:R119H;ENSP00000302919:R119H;ENSP00000267064:R119H	ENSP00000267064:R119H	R	-	2	0	SMARCC2	54865124	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.317000	0.79018	2.941000	0.99782	0.655000	0.94253	CGC		0.468	SMARCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408370.1			4	143	0	0	0	1	0	4	143				
BMS1P20	96610	broad.mit.edu	37	22	22663260	22663260	+	RNA	SNP	A	A	G	rs199801066		TCGA-QR-A6H5-01A-11D-A35D-08	TCGA-QR-A6H5-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03b4fb36-83b8-4482-9847-313f5b25fe61	61abdecd-d8a4-4784-a6e9-c4ff8e355a37	g.chr22:22663260A>G	ENST00000426066.1	+	0	623					NR_027293.1				BMS1 pseudogene 20																		CCTCTAAAATATGGGCCTCAT	0.249																																						ENST00000426066.1																			0																																																			96610							g.chr22:22663260A>G			22q11.22	2013-09-20			ENSG00000236850	ENSG00000236850			49153	pseudogene	pseudogene							Standard	XR_430414		Approved				OTTHUMG00000151046		22.37:g.22663260A>G								NR_027293.1						0	623	+									RNA	SNP	ENST00000426066.1	37																																																																																						0.249	BMS1P20-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000473090.1			3	14	0	0	0	1	0	3	14				
C20orf85	128602	broad.mit.edu	37	20	56730543	56730543	+	Missense_Mutation	SNP	A	A	G	rs532382153		TCGA-QR-A6H5-01A-11D-A35D-08	TCGA-QR-A6H5-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03b4fb36-83b8-4482-9847-313f5b25fe61	61abdecd-d8a4-4784-a6e9-c4ff8e355a37	g.chr20:56730543A>G	ENST00000371168.3	+	3	231	c.170A>G	c.(169-171)gAt>gGt	p.D57G		NM_178456.2	NP_848551.1	Q9H1P6	CT085_HUMAN	chromosome 20 open reading frame 85	57										kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	13	all_epithelial(3;5.99e-14)|Lung NSC(12;0.000152)|all_lung(29;0.000518)|Melanoma(10;0.118)		BRCA - Breast invasive adenocarcinoma(13;5.53e-12)|Epithelial(14;7.42e-08)|all cancers(14;7.19e-07)			TGTGAAGAAGATCTCCCCACC	0.493																																						ENST00000371168.3																			0				kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	13						c.(169-171)gAt>gGt		chromosome 20 open reading frame 85							90.0	86.0	88.0					20																	56730543		2203	4300	6503	SO:0001583	missense	128602							g.chr20:56730543A>G	AL354776	CCDS13465.1	20q13.32	2012-10-29			ENSG00000124237	ENSG00000124237			16216	protein-coding gene	gene with protein product	"""Low in Lung Cancer 1"""						Standard	NM_178456		Approved	bA196N14.1, LLC1	uc002xyv.3	Q9H1P6	OTTHUMG00000032836	ENST00000371168.3:c.170A>G	20.37:g.56730543A>G	ENSP00000360210:p.Asp57Gly						p.D57G	NM_178456.2	NP_848551.1	Q9H1P6	CT085_HUMAN	BRCA - Breast invasive adenocarcinoma(13;5.53e-12)|Epithelial(14;7.42e-08)|all cancers(14;7.19e-07)		3	231	+	all_epithelial(3;5.99e-14)|Lung NSC(12;0.000152)|all_lung(29;0.000518)|Melanoma(10;0.118)		57						Missense_Mutation	SNP	ENST00000371168.3	37	c.170A>G	CCDS13465.1	.	.	.	.	.	.	.	.	.	.	A	11.18	1.562790	0.27915	.	.	ENSG00000124237	ENST00000371168	T	0.21543	2.0	4.4	0.655	0.17839	.	0.436673	0.20125	N	0.098707	T	0.09598	0.0236	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30966	-0.9960	10	0.23891	T	0.37	-2.5366	5.8338	0.18594	0.5901:0.323:0.0869:0.0	.	57	Q9H1P6	CT085_HUMAN	G	57	ENSP00000360210:D57G	ENSP00000360210:D57G	D	+	2	0	C20orf85	56163949	0.017000	0.18338	0.002000	0.10522	0.607000	0.37147	1.829000	0.39121	-0.177000	0.10690	0.460000	0.39030	GAT		0.493	C20orf85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079866.2	NM_178456		8	44	0	0	0	1	0	8	44				
SLC35G3	146861	broad.mit.edu	37	17	33520392	33520392	+	Missense_Mutation	SNP	G	G	C	rs375936006		TCGA-QR-A6H5-01A-11D-A35D-08	TCGA-QR-A6H5-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03b4fb36-83b8-4482-9847-313f5b25fe61	61abdecd-d8a4-4784-a6e9-c4ff8e355a37	g.chr17:33520392G>C	ENST00000297307.5	-	1	1020	c.935C>G	c.(934-936)gCg>gGg	p.A312G	RP11-799D4.2_ENST00000590144.1_RNA	NM_152462.2	NP_689675.1	Q8N808	S35G3_HUMAN	solute carrier family 35, member G3	312	EamA 2.					integral component of membrane (GO:0016021)		p.A312G(4)									AACCCCTGCCGCCACGATGTC	0.567																																						ENST00000297307.5																			4	Substitution - Missense(4)	p.A312G(4)	kidney(4)								c.(934-936)gCg>gGg		solute carrier family 35, member G3							142.0	127.0	132.0					17																	33520392		2203	4300	6503	SO:0001583	missense	146861					integral to membrane		g.chr17:33520392G>C	AK097473	CCDS11293.1	17q21.1	2013-05-22	2011-08-03	2011-08-03	ENSG00000164729	ENSG00000164729		"""Solute carriers"""	26848	protein-coding gene	gene with protein product			"""transmembrane protein 21A"", ""acyl-malonyl condensing enzyme 1"""	TMEM21A, AMAC1			Standard	NM_152462		Approved	FLJ40154	uc002hjd.2	Q8N808	OTTHUMG00000132929	ENST00000297307.5:c.935C>G	17.37:g.33520392G>C	ENSP00000297307:p.Ala312Gly						p.A312G	NM_152462.2	NP_689675.1	Q8N808	AMAC1_HUMAN			1	1020	-			312			DUF6 2.		B9EGE9	Missense_Mutation	SNP	ENST00000297307.5	37	c.935C>G	CCDS11293.1	.	.	.	.	.	.	.	.	.	.	C	0.009	-1.804722	0.00611	.	.	ENSG00000164729	ENST00000297307	T	0.57273	0.41	.	.	.	.	0.000000	0.45126	N	0.000398	T	0.11067	0.0270	N	0.01048	-1.04	0.18873	N	0.999989	B	0.02656	0.0	B	0.01281	0.0	T	0.30475	-0.9977	8	0.02654	T	1	-1.3046	.	.	.	.	312	Q8N808	S35G3_HUMAN	G	312	ENSP00000297307:A312G	ENSP00000297307:A312G	A	-	2	0	SLC35G3	30544505	1.000000	0.71417	0.032000	0.17829	0.032000	0.12392	1.924000	0.40065	-2.418000	0.00566	-2.366000	0.00237	GCG		0.567	SLC35G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256445.2	NM_152462		4	126	0	0	0	1	0	4	126				
AC023347.1	0	broad.mit.edu	37	2	127069389	127069389	+	lincRNA	DEL	A	A	-			TCGA-QR-A6H5-01A-11D-A35D-08	TCGA-QR-A6H5-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03b4fb36-83b8-4482-9847-313f5b25fe61	61abdecd-d8a4-4784-a6e9-c4ff8e355a37	g.chr2:127069389delA	ENST00000435352.1	+	0	136																											CTGTTCCATTATCATTTTTAT	0.343																																						ENST00000435352.1																			0																																																			0							g.chr2:127069389delA																													2.37:g.127069389delA														0	136	+									RNA	DEL	ENST00000435352.1	37																																																																																						0.343	AC023347.1-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000330930.2			2	4						2	4	---	---	---	---
ZNF717	100131827	broad.mit.edu	37	3	75790810	75790811	+	Frame_Shift_Ins	INS	-	-	T	rs199577560	byFrequency	TCGA-QR-A6H5-01A-11D-A35D-08	TCGA-QR-A6H5-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03b4fb36-83b8-4482-9847-313f5b25fe61	61abdecd-d8a4-4784-a6e9-c4ff8e355a37	g.chr3:75790810_75790811insT	ENST00000477374.1	-	3	305_306	c.134_135insA	c.(133-135)accfs	p.T45fs	ZNF717_ENST00000422325.1_Frame_Shift_Ins_p.T45fs|ZNF717_ENST00000491507.1_5'UTR|ZNF717_ENST00000400845.3_Frame_Shift_Ins_p.T38fs|ZNF717_ENST00000478296.1_5'UTR			Q9BY31	ZN717_HUMAN	zinc finger protein 717	38	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						CCCTGTACAGGGTCCTCTGAGC	0.51																																						ENST00000422325.1																			0				autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						c.(133-135)actfs		zinc finger protein 717																																				SO:0001589	frameshift_variant	100131827				regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding	g.chr3:75790810_75790811insT	AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124		"""Zinc fingers, C2H2-type"", ""-"""	29448	protein-coding gene	gene with protein product			"""zinc finger protein 838"""	ZNF838			Standard	NM_001128223		Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000477374.1:c.134_135insA	3.37:g.75790810_75790811insT	ENSP00000417902:p.Thr45fs					ZNF717_ENST00000478296.1_5'UTR|ZNF717_ENST00000400845.3_Frame_Shift_Ins_p.T38fs|ZNF717_ENST00000477374.1_Frame_Shift_Ins_p.T45fs|ZNF717_ENST00000491507.1_5'UTR	p.T45fs	NM_001128223.1	NP_001121695.1	C9JSV9	C9JSV9_HUMAN			3	456_457	-			45						Frame_Shift_Ins	INS	ENST00000477374.1	37	c.134_135insA																																																																																					0.510	ZNF717-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000352767.1	NM_001128223		4	7						4	7	---	---	---	---
RP11-478C19.2	0	broad.mit.edu	37	12	110868215	110868216	+	RNA	DEL	GT	GT	-	rs113592903		TCGA-QR-A6H5-01A-11D-A35D-08	TCGA-QR-A6H5-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03b4fb36-83b8-4482-9847-313f5b25fe61	61abdecd-d8a4-4784-a6e9-c4ff8e355a37	g.chr12:110868215_110868216delGT	ENST00000550231.1	-	0	97																											CAgtgtgtgcgtgtgtgtgtgt	0.49																																						ENST00000550231.1																			0																																																			0							g.chr12:110868215_110868216delGT																													12.37:g.110868225_110868226delGT														0	97	-									RNA	DEL	ENST00000550231.1	37																																																																																						0.490	RP11-478C19.2-001	KNOWN	basic|readthrough_transcript	retained_intron	processed_transcript	OTTHUMT00000404601.1			5	4						5	4	---	---	---	---
DDHD1	80821	broad.mit.edu	37	14	53619480	53619481	+	In_Frame_Ins	INS	-	-	GCCGCC	rs140904345|rs55671452|rs200797826	byFrequency	TCGA-QR-A6H5-01A-11D-A35D-08	TCGA-QR-A6H5-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03b4fb36-83b8-4482-9847-313f5b25fe61	61abdecd-d8a4-4784-a6e9-c4ff8e355a37	g.chr14:53619480_53619481insGCCGCC	ENST00000323669.5	-	1	335_336	c.336_337insGGCGGC	c.(334-339)ggcagc>ggcGGCGGCagc	p.111_112insGG	DDHD1_ENST00000395606.1_In_Frame_Ins_p.111_112insGG|DDHD1_ENST00000357758.3_In_Frame_Ins_p.111_112insGG|RP11-547D23.1_ENST00000554235.1_RNA|AL356020.1_ENST00000584587.1_RNA	NM_001160148.1	NP_001153620.1	Q8NEL9	DDHD1_HUMAN	DDHD domain containing 1	111					cell death (GO:0008219)|lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)	25	Breast(41;0.037)					GACAAGGAGCTGCCGCCGCCGC	0.703														3933	0.785343	0.4962	0.8718	5008	,	,		9770	0.9673		0.833	False		,,,				2504	0.8783					ENST00000357758.3																			0				breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)	25						c.(334-339)gggctc>ggGGCGGCgctc		DDHD domain containing 1																																				SO:0001652	inframe_insertion	80821				lipid catabolic process	cytoplasm	hydrolase activity|metal ion binding	g.chr14:53619480_53619481insGCCGCC	AB051492	CCDS9714.1, CCDS53895.1, CCDS53896.1	14q21	2012-11-23			ENSG00000100523	ENSG00000100523			19714	protein-coding gene	gene with protein product	"""phosphatidic acid-preferring phospholipase A1"""	614603	"""spastic paraplegia 28 (autosomal recessive)"""	SPG28		11214970, 20359546	Standard	NM_030637		Approved	KIAA1705, PA-PLA1	uc001xai.3	Q8NEL9	OTTHUMG00000140305	ENST00000323669.5:c.331_336dupGGCGGC	14.37:g.53619481_53619486dupGCCGCC	ENSP00000327104:p.Gly110_Gly111dup					DDHD1_ENST00000395606.1_In_Frame_Ins_p.112_113GL>GAAL|DDHD1_ENST00000323669.5_In_Frame_Ins_p.112_113GL>GAAL	p.112_113GL>GAAL	NM_030637.2	NP_085140.2	Q8NEL9	DDHD1_HUMAN			1	519_520	-	Breast(41;0.037)		112					G5E9D1|Q8WVH3|Q96LL2|Q9C0F8	In_Frame_Ins	INS	ENST00000323669.5	37	c.336_337insGGCGGC	CCDS53895.1																																																																																				0.703	DDHD1-003	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276901.1			4	4						4	4	---	---	---	---
RP11-308D16.4	0	broad.mit.edu	37	X	136030244	136030245	+	RNA	INS	-	-	T			TCGA-QR-A6H5-01A-11D-A35D-08	TCGA-QR-A6H5-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	03b4fb36-83b8-4482-9847-313f5b25fe61	61abdecd-d8a4-4784-a6e9-c4ff8e355a37	g.chrX:136030244_136030245insT	ENST00000424306.1	+	0	2052																											TGAGAACCTGCTTTTTTTTTTT	0.441																																						ENST00000424306.1																			0																																																			0							g.chrX:136030244_136030245insT																													X.37:g.136030255_136030255dupT														0	2052	+									RNA	INS	ENST00000424306.1	37																																																																																						0.441	RP11-308D16.4-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000058514.2			3	3						3	3	---	---	---	---
