#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_IsAdjacentToRepeatRegion	i_IsMicroSat	i_MUTSIG_Published_Results	i_Mutation_Status	i_NumberOfSatRepeats	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	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_is_in_m2pon	i_refseq_mrna_id	i_secondary_variant_classification	i_site
CSTF2T	23283	broad.mit.edu	37	10	53457704	53457733	+	In_Frame_Del	DEL	CTCCTTGTATGCCTGCCCCCTGCATCCCTC	CTCCTTGTATGCCTGCCCCCTGCATCCCTC	-	rs563071162		TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	CTCCTTGTATGCCTGCCCCCTGCATCCCTC	CTCCTTGTATGCCTGCCCCCTGCATCCCTC	-	-	CTCCTTGTATGCCTGCCCCCTGCATCCCTC	CTCCTTGTATGCCTGCCCCCTGCATCCCTC	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr10:53457704_53457733delCTCCTTGTATGCCTGCCCCCTGCATCCCTC	ENST00000331173.4	-	1	1622_1651	c.1577_1606delGAGGGATGCAGGGGGCAGGCATACAAGGAG	c.(1576-1608)ggagggatgcagggggcaggcatacaaggagtc>gtc	p.GGMQGAGIQG526del	PRKG1_ENST00000401604.2_Intron|PRKG1_ENST00000373980.4_Intron|PRKG1_ENST00000373985.1_Intron	NM_015235.2	NP_056050.1	Q9H0L4	CSTFT_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant	526	9 X 5 AA tandem repeats of G-[AT]-G-[MI]- Q.|Gly-rich.				mRNA processing (GO:0006397)	intracellular (GO:0005622)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.G532D(1)		NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	30				COAD - Colon adenocarcinoma(2;0.00736)|Colorectal(2;0.00898)|all cancers(4;0.0188)|GBM - Glioblastoma multiforme(4;0.0778)|Epithelial(53;0.122)		tgtatactgactccttgtatgcctgccccctgcatccctcctccttgtat	0.561																																						ENST00000331173.4		NA																	1	Substitution - Missense(1)	p.G532D(1)	large_intestine(1)	NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						c.(1576-1608)ggagggatgcagggggcaggcatacaaggagtc>gtc		cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant																																				SO:0001651	inframe_deletion	23283				mRNA processing	nucleus	nucleotide binding|RNA binding	g.chr10:53457704_53457733delCTCCTTGTATGCCTGCCCCCTGCATCCCTC	AB014589	CCDS7245.1	10q11	2013-02-12			ENSG00000177613	ENSG00000177613		"""RNA binding motif (RRM) containing"""	17086	protein-coding gene	gene with protein product		611968				12408968, 11113135	Standard	NM_015235		Approved	DKFZp434C1013, KIAA0689, CstF-64T	uc001jjp.3	Q9H0L4	OTTHUMG00000018246	ENST00000331173.4:c.1577_1606delGAGGGATGCAGGGGGCAGGCATACAAGGAG	10.37:g.53457704_53457733delCTCCTTGTATGCCTGCCCCCTGCATCCCTC	ENSP00000332444:p.Gly526_Gly535del	True	False		Somatic	1				PRKG1_ENST00000373985.1_Intron|PRKG1_ENST00000401604.2_Intron|PRKG1_ENST00000373980.4_Intron	p.GGMQGAGIQG526del	NM_015235.2	NP_056050.1	WXS	Illumina HiSeq	Phase_I	Q9H0L4	CSTFT_HUMAN		COAD - Colon adenocarcinoma(2;0.00736)|Colorectal(2;0.00898)|all cancers(4;0.0188)|GBM - Glioblastoma multiforme(4;0.0778)|Epithelial(53;0.122)	1	1622_1651	-			526			9 X 5 AA tandem repeats of G-[AT]-G-[MI]- Q.|Gly-rich.		B2RAR9|O75174|Q53HK6|Q7LGE8|Q8N6T1	In_Frame_Del	DEL	ENST00000331173.4	37	c.1577_1606delGAGGGATGCAGGGGGCAGGCATACAAGGAG	CCDS7245.1																																																																																				0.561	CSTF2T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048097.1	0	NM_015235		10:53457704
SPTY2D1	144108	broad.mit.edu	37	11	18633969	18633971	+	In_Frame_Del	DEL	TCG	TCG	-	rs11605097	byFrequency	TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	TCG	TCG	-	-	TCG	TCG	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr11:18633969_18633971delTCG	ENST00000336349.5	-	4	2011_2013	c.1776_1778delCGA	c.(1774-1779)gacgat>gat	p.592_593DD>D	SPTY2D1-AS1_ENST00000501599.2_RNA	NM_194285.2	NP_919261.2	Q68D10	SPT2_HUMAN	SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae)	592	Poly-Asp.									breast(4)|cervix(3)|endometrium(2)|kidney(3)|large_intestine(7)|lung(9)|skin(1)|stomach(1)	30						TTCATCATCATCGTCATCTTCCT	0.365																																						ENST00000336349.5		NA																	0				breast(4)|cervix(3)|endometrium(2)|kidney(3)|large_intestine(7)|lung(9)|skin(1)|stomach(1)	30						c.(1774-1779)gacgat>gat		SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae)																																				SO:0001651	inframe_deletion	144108							g.chr11:18633969_18633971delTCG	BX647798	CCDS31441.1	11p15.1	2005-10-28			ENSG00000179119	ENSG00000179119			26818	protein-coding gene	gene with protein product							Standard	NM_194285		Approved	FLJ39441, DKFZp686I068	uc001moy.3	Q68D10	OTTHUMG00000167733	ENST00000336349.5:c.1776_1778delCGA	11.37:g.18633969_18633971delTCG	ENSP00000337991:p.Asp595del	True	False		Somatic	1					p.592_593DD>D	NM_194285.2	NP_919261.2	WXS	Illumina HiSeq	Phase_I	Q68D10	SPT2_HUMAN			4	2011_2013	-			592			Poly-Asp.		Q6AWA5|Q6MZI5|Q7Z390|Q7Z470|Q86VG8|Q8N3E7|Q8N417|Q8N8I3	In_Frame_Del	DEL	ENST00000336349.5	37	c.1776_1778delCGA	CCDS31441.1																																																																																				0.365	SPTY2D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395941.1	0	NM_194285		11:18633969
OR5D18	219438	broad.mit.edu	37	11	55587770	55587772	+	In_Frame_Del	DEL	TTG	TTG	-			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	TTG	TTG	-	-	TTG	TTG	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr11:55587770_55587772delTTG	ENST00000333976.4	+	1	685_687	c.665_667delTTG	c.(664-669)attgtt>att	p.V224del		NM_001001952.1	NP_001001952.1	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D, member 18	224						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(1)|endometrium(3)|large_intestine(6)|lung(33)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		all_epithelial(135;0.208)				TATGCGTTCATTGTTGTAACCAT	0.483																																						ENST00000333976.4		NA																	0				NS(2)|breast(1)|endometrium(3)|large_intestine(6)|lung(33)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						c.(664-669)attgtt>att		olfactory receptor, family 5, subfamily D, member 18																																				SO:0001651	inframe_deletion	219438				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:55587770_55587772delTTG	AB065781	CCDS31510.1	11q11	2012-08-09			ENSG00000186119	ENSG00000186119		"""GPCR / Class A : Olfactory receptors"""	15285	protein-coding gene	gene with protein product							Standard	NM_001001952		Approved		uc010rin.2	Q8NGL1	OTTHUMG00000166811	ENST00000333976.4:c.665_667delTTG	11.37:g.55587773_55587775delTTG	ENSP00000335025:p.Val224del	False	False		Somatic	2					p.V224del	NM_001001952.1	NP_001001952.1	WXS	Illumina HiSeq	Phase_I	Q8NGL1	OR5DI_HUMAN			1	685_687	+		all_epithelial(135;0.208)	224					Q6IF67|Q6IFD3|Q96RB3	In_Frame_Del	DEL	ENST00000333976.4	37	c.665_667delTTG	CCDS31510.1																																																																																				0.483	OR5D18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391515.1	0	NM_001001952		11:55587770
RBM4	5936	broad.mit.edu	37	11	66411364	66411384	+	In_Frame_Del	DEL	GCTGCTGCTGCAGCAGCAGCC	GCTGCTGCTGCAGCAGCAGCC	-			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	GCTGCTGCTGCAGCAGCAGCC	GCTGCTGCTGCAGCAGCAGCC	-	-	GCTGCTGCTGCAGCAGCAGCC	GCTGCTGCTGCAGCAGCAGCC	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr11:66411364_66411384delGCTGCTGCTGCAGCAGCAGCC	ENST00000409406.1	+	2	1633_1653	c.856_876delGCTGCTGCTGCAGCAGCAGCC	c.(856-876)gctgctgctgcagcagcagccdel	p.AAAAAAA286del	RBM4_ENST00000398692.4_Intron|RBM4_ENST00000310092.7_In_Frame_Del_p.AAAAAAA286del|RBM4_ENST00000396053.4_Intron|RBM4_ENST00000578778.1_Intron|RBM4_ENST00000506523.2_Intron|RBM4_ENST00000515838.2_3'UTR|RBM4_ENST00000514361.3_In_Frame_Del_p.AAAAAAA261del|RBM14-RBM4_ENST00000412278.2_In_Frame_Del_p.AAAAAAA261del|RBM14-RBM4_ENST00000500635.2_Intron|RBM4_ENST00000530235.1_Intron|RBM4_ENST00000503028.2_In_Frame_Del_p.AAAAAAA286del|RBM4_ENST00000408993.2_In_Frame_Del_p.AAAAAAA286del			Q9BWF3	RBM4_HUMAN	RNA binding motif protein 4	286	Interaction with TNPO3.|Poly-Ala.				cap-independent translational initiation (GO:0002190)|cell differentiation (GO:0030154)|circadian regulation of translation (GO:0097167)|entrainment of circadian clock by photoperiod (GO:0043153)|IRES-dependent translational initiation (GO:0002192)|mRNA processing (GO:0006397)|negative regulation of translation (GO:0017148)|negative regulation of translation in response to stress (GO:0032055)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|negative regulation of translational initiation (GO:0045947)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of nucleocytoplasmic transport (GO:0046822)|response to arsenic-containing substance (GO:0046685)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|stress-activated MAPK cascade (GO:0051403)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	miRNA binding (GO:0035198)|mRNA 3'-UTR binding (GO:0003730)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA intronic binding (GO:0097157)|pre-mRNA intronic pyrimidine-rich binding (GO:0097158)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(4)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13				Lung(977;0.0112)|LUSC - Lung squamous cell carcinoma(976;0.0266)		tgctgccacagctgctgctgcagcagcagccgctgctgctg	0.615																																						ENST00000412278.2		NA																	0					NA						c.(781-801)gctgctgctgcagcagcagccdel																																						SO:0001651	inframe_deletion	0							g.chr11:66411364_66411384delGCTGCTGCTGCAGCAGCAGCC	U89505	CCDS41676.1, CCDS55776.1, CCDS55777.1	11q13	2013-02-12			ENSG00000173933	ENSG00000173933		"""Zinc fingers, CCHC domain containing"", ""RNA binding motif (RRM) containing"""	9901	protein-coding gene	gene with protein product		602571				9169144, 16260624	Standard	NM_002896		Approved	LARK, RBM4A, ZCRB3A, ZCCHC21		Q9BWF3	OTTHUMG00000154171	ENST00000409406.1:c.856_876delGCTGCTGCTGCAGCAGCAGCC	11.37:g.66411364_66411384delGCTGCTGCTGCAGCAGCAGCC	ENSP00000386894:p.Ala286_Ala292del	True	False		Somatic	1				RBM4_ENST00000396053.4_Intron|RBM4_ENST00000310092.7_In_Frame_Del_p.AAAAAAA286del|RBM4_ENST00000515838.2_3'UTR|RBM4_ENST00000409406.1_In_Frame_Del_p.AAAAAAA286del|RBM4_ENST00000408993.2_In_Frame_Del_p.AAAAAAA286del|RBM4_ENST00000578778.1_Intron|RBM4_ENST00000530235.1_Intron|RBM4_ENST00000506523.2_Intron|RBM4_ENST00000503028.2_In_Frame_Del_p.AAAAAAA286del|RBM4_ENST00000514361.3_In_Frame_Del_p.AAAAAAA261del|RBM4_ENST00000398692.4_Intron|RBM14-RBM4_ENST00000500635.2_Intron	p.AAAAAAA261del	NM_001198845.1	NP_001185774.1	WXS	Illumina HiSeq	Phase_I					2	876_896	+			NA					B3KUN0|B4E1U0|E7EQS3|O02916|Q4VC48|Q6P1P2|Q8WU85	In_Frame_Del	DEL	ENST00000409406.1	37	c.781_801delGCTGCTGCTGCAGCAGCAGCC	CCDS41676.1																																																																																				0.615	RBM4-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334212.1	0	NM_002896		11:66411364
NBPF15	284565	broad.mit.edu	37	1	148753330	148753330	+	Frame_Shift_Del	DEL	T	T	-			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	T	T	-	-	T	T	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr1:148753330delT	ENST00000417839.1	+	12	1537	c.1347delT	c.(1345-1347)gatfs	p.D449fs		NM_001102663.1	NP_001096133	Q5SXJ2	NBPFG_HUMAN		449	NBPF 4. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)				breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4	all_hematologic(923;0.032)					CTCCTTCAGATTATCTTGAAC	0.493																																						ENST00000417839.1		NA																	0				breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4						c.(1345-1347)gatfs		neuroblastoma breakpoint family, member 16							1.0	1.0	1.0					1																	148753330		531	579	1110	SO:0001589	frameshift_variant	728936							g.chr1:148753330delT																												ENST00000417839.1:c.1347delT	1.37:g.148753330delT	ENSP00000395369:p.Asp449fs	False	False		Somatic	2					p.D449fs	NM_001102663.1	NP_001096133.1	WXS	Illumina HiSeq	Phase_I					12	1537	+	all_hematologic(923;0.032)		NA					A8MPT6	Frame_Shift_Del	DEL	ENST00000417839.1	37	c.1347delT	CCDS41384.1																																																																																				0.493	NBPF16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097693.1	0			1:148753330
HERC2P2	400322	broad.mit.edu	37	15	23311793	23311794	+	RNA	INS	-	-	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr15:23311793_23311794insA	ENST00000560464.1	-	0	3310_3311									hect domain and RLD 2 pseudogene 2																		GTGGGTGGCAGTCAGCGAGGCC	0.634																																						ENST00000560464.1		NA																	0					NA																																														0							g.chr15:23311793_23311794insA	AF041080		15q11.2	2014-03-18			ENSG00000140181				4870	pseudogene	pseudogene						9730612	Standard	NR_002824		Approved	D15F37S3	uc001yvq.2		OTTHUMG00000171926		15.37:g.23311793_23311794insA		False	False		Somatic	0								WXS	Illumina HiSeq	Phase_I					0	3310_3311	-			NA						RNA	INS	ENST00000560464.1	37																																																																																						0.634	HERC2P2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000415936.1	0			15:23311793
AXDND1	126859	broad.mit.edu	37	1	179504035	179504040	+	In_Frame_Del	DEL	AAGAAC	AAGAAC	-	rs200097954|rs368406759|rs79330752|rs6425573	byFrequency	TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	AAGAAC	AAGAAC	-	-	AAGAAC	AAGAAC	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr1:179504035_179504040delAAGAAC	ENST00000367618.3	+	25	3356_3361	c.2969_2974delAAGAAC	c.(2968-2976)gaagaacaa>gaa	p.EQ991del		NM_144696.4	NP_653297.3	Q5T1B0	AXDN1_HUMAN	axonemal dynein light chain domain containing 1	991	Glu-rich.		E -> Q (in dbSNP:rs6425573).					p.E991_Q992delEQ(1)		NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(27)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	59						aaagaagaagaagaacaacaagaaga	0.316																																						ENST00000367618.3		NA																	1	Deletion - In frame(1)	p.E991_Q992delEQ(1)	haematopoietic_and_lymphoid_tissue(1)	NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(27)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	59						c.(2968-2976)gaagaacaa>gaa		axonemal dynein light chain domain containing 1				750,3386		64,622,1382						-7.3	0.0		dbSNP_131	50	2737,5481		321,2095,1693	no	coding	AXDND1	NM_144696.4		385,2717,3075	A1A1,A1R,RR		33.3049,18.1335,28.2257				3487,8867				SO:0001651	inframe_deletion	126859							g.chr1:179504035_179504040delAAGAAC	BX647935	CCDS30948.1	1q25.2	2011-02-18	2011-02-18	2011-02-18	ENSG00000162779	ENSG00000162779			26564	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 125"""	C1orf125		14702039	Standard	NM_144696		Approved	FLJ32940	uc001gmo.3	Q5T1B0	OTTHUMG00000035266	ENST00000367618.3:c.2969_2974delAAGAAC	1.37:g.179504035_179504040delAAGAAC	ENSP00000356590:p.Glu991_Gln992del	True	False		Somatic	1					p.EQ991del	NM_144696.4	NP_653297.3	WXS	Illumina HiSeq	Phase_I	Q5T1B0	AXDN1_HUMAN			25	3356_3361	+			991		E -> Q (in dbSNP:rs6425573).	Glu-rich.		Q6AWB2|Q96LJ3|Q96M01	In_Frame_Del	DEL	ENST00000367618.3	37	c.2969_2974delAAGAAC	CCDS30948.1																																																																																				0.316	AXDND1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085312.1	0	NM_144696		1:179504035
SLC38A10	124565	broad.mit.edu	37	17	79219501	79219503	+	In_Frame_Del	DEL	ATG	ATG	-	rs10569617|rs3833102|rs201518560	byFrequency	TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	ATG	ATG	-	-	ATG	ATG	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr17:79219501_79219503delATG	ENST00000374759.3	-	16	3596_3598	c.3213_3215delCAT	c.(3211-3216)atcatt>att	p.1071_1072II>I		NM_001037984.1	NP_001033073.1	Q9HBR0	S38AA_HUMAN	solute carrier family 38, member 10	1071				Missing (in Ref. 5; AAG17235). {ECO:0000305}.	amino acid transport (GO:0006865)|bone development (GO:0060348)|sodium ion transport (GO:0006814)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			GTTAAGGCCAATGATGACCCCAT	0.685														2114	0.422125	0.025	0.4712	5008	,	,		16375	0.6776		0.4364	False		,,,				2504	0.6462					ENST00000374759.3		NA																	0				NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						c.(3211-3216)atcatt>att		solute carrier family 38, member 10				353,3595		37,279,1658						-2.8	0.0		dbSNP_119	35	3598,4380		853,1892,1244	no	coding	SLC38A10	NM_001037984.1		890,2171,2902	A1A1,A1R,RR		45.099,8.9412,33.1293				3951,7975				SO:0001651	inframe_deletion	124565				amino acid transport|sodium ion transport	integral to membrane		g.chr17:79219501_79219503delATG	BC014642	CCDS11780.1, CCDS42397.1	17q25.3	2013-05-22			ENSG00000157637	ENSG00000157637		"""Solute carriers"""	28237	protein-coding gene	gene with protein product							Standard	XM_005257019		Approved	MGC15523, PP1744	uc002jzz.1	Q9HBR0	OTTHUMG00000168049	ENST00000374759.3:c.3213_3215delCAT	17.37:g.79219504_79219506delATG	ENSP00000363891:p.Ile1072del	False	False		Somatic	2					p.1071_1072II>I	NM_001037984.1	NP_001033073.1	WXS	Illumina HiSeq	Phase_I	Q9HBR0	S38AA_HUMAN	BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)		16	3596_3598	-	all_neural(118;0.0804)|Melanoma(429;0.242)		1071	Missing (in Ref. 5; AAG17235).				Q6ZRC5|Q8NA99|Q96C66	In_Frame_Del	DEL	ENST00000374759.3	37	c.3213_3215delCAT	CCDS42397.1																																																																																				0.685	SLC38A10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397747.1	0	NM_138570		17:79219501
ANKRD12	23253	broad.mit.edu	37	18	9263840	9263850	+	Frame_Shift_Del	DEL	AGGAAGTTGTA	AGGAAGTTGTA	-	rs556228007		TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	AGGAAGTTGTA	AGGAAGTTGTA	-	-	AGGAAGTTGTA	AGGAAGTTGTA	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr18:9263840_9263850delAGGAAGTTGTA	ENST00000262126.4	+	10	5957_5967	c.5717_5727delAGGAAGTTGTA	c.(5716-5727)caggaagttgtafs	p.QEVV1906fs	ANKRD12_ENST00000400020.3_Frame_Shift_Del_p.QEVV1883fs|ANKRD12_ENST00000383440.2_Frame_Shift_Del_p.QEVV1883fs	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	1906						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.V1908A(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						TTTCGACAACAGGAAGTTGTAAGGATGAAAC	0.284																																						ENST00000383440.2		NA																	1	Substitution - Missense(1)	p.V1908A(1)	skin(1)	NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						c.(5647-5658)caggaagttgtafs		ankyrin repeat domain 12																																				SO:0001589	frameshift_variant	23253					nucleus		g.chr18:9263840_9263850delAGGAAGTTGTA	AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"""Ankyrin repeat domain containing"""	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.5717_5727delAGGAAGTTGTA	18.37:g.9263840_9263850delAGGAAGTTGTA	ENSP00000262126:p.Gln1906fs	False	False		Somatic	1				ANKRD12_ENST00000262126.3_Frame_Shift_Del_p.QEVV1906fs|ANKRD12_ENST00000400020.3_Frame_Shift_Del_p.QEVV1883fs	p.QEVV1883fs	NM_001083625.2	NP_001077094.1	WXS	Illumina HiSeq	Phase_I	Q6UB98	ANR12_HUMAN			9	5905_5915	+			1906					O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Frame_Shift_Del	DEL	ENST00000262126.4	37	c.5648_5658delAGGAAGTTGTA	CCDS11843.1																																																																																				0.284	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	0	NM_015208		18:9263840
SLC14A2	8170	broad.mit.edu	37	18	43221254	43221267	+	Frame_Shift_Del	DEL	GGAGGCATGTTCTA	GGAGGCATGTTCTA	-	rs143740023		TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	GGAGGCATGTTCTA	GGAGGCATGTTCTA	-	-	GGAGGCATGTTCTA	GGAGGCATGTTCTA	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr18:43221254_43221267delGGAGGCATGTTCTA	ENST00000255226.6	+	8	1888_1901	c.1072_1085delGGAGGCATGTTCTA	c.(1072-1086)ggaggcatgttctatfs	p.GGMFY358fs	SLC14A2_ENST00000586448.1_Frame_Shift_Del_p.GGMFY358fs	NM_007163.3	NP_009094.3	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter), member 2	358					transmembrane transport (GO:0055085)|urea transport (GO:0015840)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|urea transmembrane transporter activity (GO:0015204)			NS(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(35)|ovary(1)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						CATCGCCATCGGAGGCATGTTCTATGCCCTCACC	0.551																																						ENST00000255226.6		NA																	0				NS(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(35)|ovary(1)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						c.(1072-1086)ggaggcatgttctatfs		solute carrier family 14 (urea transporter), member 2																																				SO:0001589	frameshift_variant	8170					apical plasma membrane|integral to membrane|membrane fraction	protein binding|urea transmembrane transporter activity	g.chr18:43221254_43221267delGGAGGCATGTTCTA	X96969	CCDS11924.1	18q12.1-q21.1	2013-05-22			ENSG00000132874	ENSG00000132874		"""Solute carriers"""	10919	protein-coding gene	gene with protein product		601611				8647271	Standard	NM_007163		Approved	HUT2, UT2	uc010dnj.3	Q15849	OTTHUMG00000132616	ENST00000255226.6:c.1072_1085delGGAGGCATGTTCTA	18.37:g.43221254_43221267delGGAGGCATGTTCTA	ENSP00000255226:p.Gly358fs	False	False		Somatic	1				SLC14A2_ENST00000586448.1_Frame_Shift_Del_p.GGMFY358fs	p.GGMFY358fs	NM_007163.3	NP_009094.3	WXS	Illumina HiSeq	Phase_I	Q15849	UT2_HUMAN			8	1888_1901	+			358					A8K8Q7|Q2TBD6|Q96PH5	Frame_Shift_Del	DEL	ENST00000255226.6	37	c.1072_1085delGGAGGCATGTTCTA	CCDS11924.1																																																																																				0.551	SLC14A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255858.1	0			18:43221254
TMEM91	641649	broad.mit.edu	37	19	41888851	41888861	+	Intron	DEL	GGGGACTGGGC	GGGGACTGGGC	-	rs138731997|rs369679620	byFrequency	TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	GGGGACTGGGC	GGGGACTGGGC	-	-	GGGGACTGGGC	GGGGACTGGGC	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr19:41888851_41888861delGGGGACTGGGC	ENST00000392002.2	+	3	1020				TMEM91_ENST00000542945.1_Frame_Shift_Del_p.GDWA129fs|TMEM91_ENST00000413014.2_Intron|TMEM91_ENST00000356385.4_Intron|CTC-435M10.3_ENST00000540732.1_Intron|TMEM91_ENST00000604123.1_Intron|TMEM91_ENST00000544232.1_Intron|CTC-435M10.3_ENST00000604424.1_Intron|BCKDHA_ENST00000595085.1_Intron|TMEM91_ENST00000539627.1_Frame_Shift_Del_p.GDWA129fs|TMEM91_ENST00000447302.2_Intron|TMEM91_ENST00000436170.2_Intron	NM_001098821.1	NP_001092291.1	Q6ZNR0	TMM91_HUMAN	transmembrane protein 91						hematopoietic progenitor cell differentiation (GO:0002244)|response to biotic stimulus (GO:0009607)	integral component of membrane (GO:0016021)				lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	5						GGGACTTGGAGGGGACTGGGCATAAAAGAGA	0.531														414	0.0826677	0.028	0.0793	5008	,	,		20818	0.0466		0.1312	False		,,,				2504	0.1462					ENST00000539627.1		NA																	0				lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	5						c.(385-396)ggggactgggcafs		transmembrane protein 91			,,,,,	128,3724		3,122,1801					,,,,,	2.4	0.6		dbSNP_134	228	1093,6889		86,921,2984	no	intron,intron,intron,intron,intron,intron	TMEM91	NM_001098825.1,NM_001098824.1,NM_001098823.1,NM_001098822.1,NM_001098821.1,NM_001042595.2	,,,,,	89,1043,4785	A1A1,A1R,RR		13.6933,3.3229,10.3177	,,,,,	,,,,,		1221,10613				SO:0001627	intron_variant	641649							g.chr19:41888851_41888861delGGGGACTGGGC	AK130820, BC063705	CCDS42571.1, CCDS42572.1, CCDS46082.1, CCDS46083.1, CCDS46084.1	19q13.2	2009-10-16							32393	protein-coding gene	gene with protein product	"""interferon induced transmembrane protein domain containing 6"""					12477932	Standard	NM_001098824		Approved	FLJ27310, IFITMD6		Q6ZNR0		ENST00000392002.2:c.360+25GGGGACTGGGC>-	19.37:g.41888851_41888861delGGGGACTGGGC		False	False		Somatic	1				TMEM91_ENST00000604123.1_Intron|BCKDHA_ENST00000595085.1_Intron|TMEM91_ENST00000447302.2_Intron|TMEM91_ENST00000436170.2_Intron|TMEM91_ENST00000356385.4_Intron|TMEM91_ENST00000544232.1_Intron|CTC-435M10.3_ENST00000540732.1_Intron|TMEM91_ENST00000542945.1_Frame_Shift_Del_p.GDWA129fs|TMEM91_ENST00000413014.2_Intron|TMEM91_ENST00000392002.2_Intron	p.GDWA129fs			WXS	Illumina HiSeq	Phase_I					3	706_716	+			NA					C9J9D1|C9JZ62|C9K046|Q6P434	Frame_Shift_Del	DEL	ENST00000392002.2	37	c.385_395delGGGGACTGGGC	CCDS42571.1																																																																																				0.531	TMEM91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398302.2	0			19:41888851
ZNF880	400713	broad.mit.edu	37	19	52888074	52888075	+	Frame_Shift_Ins	INS	-	-	AT			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr19:52888074_52888075insAT	ENST00000422689.2	+	4	1256_1257	c.1241_1242insAT	c.(1240-1245)ggcaaafs	p.K415fs		NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	415					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						AATGAATGTGGCAAAGCATTTA	0.411																																						ENST00000422689.2		NA																	0				breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						c.(1240-1245)ggcaaafs		zinc finger protein 880																																				SO:0001589	frameshift_variant	400713				regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding	g.chr19:52888074_52888075insAT	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"""Zinc fingers, C2H2-type"", ""-"""	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	Exception_encountered	19.37:g.52888074_52888075insAT	ENSP00000406318:p.Lys415fs	True	False		Somatic	0					p.K415fs	NM_001145434.1	NP_001138906.1	WXS	Illumina HiSeq	Phase_I	Q6PDB4	ZN880_HUMAN			4	1256_1257	+			415					B4DNA6	Frame_Shift_Ins	INS	ENST00000422689.2	37	c.1241_1242insAT	CCDS46164.1																																																																																				0.411	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	0	NM_001145434		19:52888074
ZNF880	400713	broad.mit.edu	37	19	52888076	52888077	+	In_Frame_Ins	INS	-	-	TGAGGTCAGGAGATCGAGACCATCCTGGCT			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr19:52888076_52888077insTGAGGTCAGGAGATCGAGACCATCCTGGCT	ENST00000422689.2	+	4	1258_1259	c.1243_1244insTGAGGTCAGGAGATCGAGACCATCCTGGCT	c.(1243-1245)aaa>aTGAGGTCAGGAGATCGAGACCATCCTGGCTaa	p.415_415K>MRSGDRDHPG*		NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	415					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						TGAATGTGGCAAAGCATTTAGA	0.411																																						ENST00000422689.2		NA																	0				breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						c.(1243-1245)aaa>aTGAGGTCAGGAGATCGAGACCATCCTGGCTaa		zinc finger protein 880																																				SO:0001652	inframe_insertion	400713				regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding	g.chr19:52888076_52888077insTGAGGTCAGGAGATCGAGACCATCCTGGCT	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"""Zinc fingers, C2H2-type"", ""-"""	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	Exception_encountered	19.37:g.52888076_52888077insTGAGGTCAGGAGATCGAGACCATCCTGGCT	ENSP00000406318:p.Lys415delinsMetArgSerGlyAspArgAspHisProGly*	True	False		Somatic	0					p.415_415K>MRSGDRDHPG*	NM_001145434.1	NP_001138906.1	WXS	Illumina HiSeq	Phase_I	Q6PDB4	ZN880_HUMAN			4	1258_1259	+			415					B4DNA6	In_Frame_Ins	INS	ENST00000422689.2	37	c.1243_1244insTGAGGTCAGGAGATCGAGACCATCCTGGCT	CCDS46164.1																																																																																				0.411	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	0	NM_001145434		19:52888076
SHROOM4	57477	broad.mit.edu	37	X	50350672	50350674	+	In_Frame_Del	DEL	TCT	TCT	-	rs3747282	byFrequency	TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	TCT	TCT	-	-	TCT	TCT	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chrX:50350672_50350674delTCT	ENST00000289292.7	-	6	3751_3753	c.3468_3470delAGA	c.(3466-3471)gaagag>gag	p.1156_1157EE>E	SHROOM4_ENST00000376020.2_In_Frame_Del_p.1156_1157EE>E|SHROOM4_ENST00000460112.3_In_Frame_Del_p.1040_1041EE>E			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1156	Glu-rich.				actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)	p.E1156E(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					TGGCAGctcctcttcctcctcct	0.557																																						ENST00000460112.3		NA																	1	Substitution - coding silent(1)	p.E1156E(1)	skin(1)	breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52						c.(3118-3123)gaagag>gag		shroom family member 4																																				SO:0001651	inframe_deletion	57477				actin filament organization|brain development|cell morphogenesis|cognition	apical plasma membrane|basal plasma membrane|internal side of plasma membrane|nucleus	actin filament binding	g.chrX:50350672_50350674delTCT	AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.3468_3470delAGA	X.37:g.50350672_50350674delTCT	ENSP00000289292:p.Glu1158del	False	False		Somatic	1				SHROOM4_ENST00000376020.2_In_Frame_Del_p.1156_1157EE>E|SHROOM4_ENST00000289292.7_In_Frame_Del_p.1156_1157EE>E	p.1040_1041EE>E			WXS	Illumina HiSeq	Phase_I	Q9ULL8	SHRM4_HUMAN			5	3574_3576	-	Ovarian(276;0.236)		1156					A7E2X9|D6RFW0|Q96LA0	In_Frame_Del	DEL	ENST00000289292.7	37	c.3120_3122delAGA	CCDS35277.1																																																																																				0.557	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	0	NM_020717		X:50350672
HUWE1	10075	broad.mit.edu	37	X	53634624	53634625	+	Frame_Shift_Ins	INS	-	-	ATATA			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chrX:53634624_53634625insATATA	ENST00000342160.3	-	24	2812_2813	c.2355_2356insTATAT	c.(2353-2358)acaacafs	p.T786fs	HUWE1_ENST00000218328.8_Frame_Shift_Ins_p.T786fs|HUWE1_ENST00000262854.6_Frame_Shift_Ins_p.T786fs			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	786					base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						TGGTCATCTGTTGTATTGTTGC	0.411																																						ENST00000342160.3		NA																	0				NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						c.(2353-2358)acaacafs		HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase																																				SO:0001589	frameshift_variant	10075				base-excision repair|cell differentiation|histone ubiquitination|protein monoubiquitination|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	DNA binding|protein binding|ubiquitin-protein ligase activity	g.chrX:53634624_53634625insATATA	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"""HECT, UBA and WWE domain containing 1"""			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.2355_2356insTATAT	X.37:g.53634624_53634625insATATA	ENSP00000340648:p.Thr786fs	False	False		Somatic	0				HUWE1_ENST00000218328.8_Frame_Shift_Ins_p.T786fs|HUWE1_ENST00000262854.6_Frame_Shift_Ins_p.T786fs	p.T786fs			WXS	Illumina HiSeq	Phase_I	Q7Z6Z7	HUWE1_HUMAN			24	2812_2813	-			786					O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Frame_Shift_Ins	INS	ENST00000342160.3	37	c.2355_2356insTATAT	CCDS35301.1																																																																																				0.411	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	0	XM_497119		X:53634624
HUWE1	10075	broad.mit.edu	37	X	53634626	53634627	+	Frame_Shift_Ins	INS	-	-	TTTT			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chrX:53634626_53634627insTTTT	ENST00000342160.3	-	24	2810_2811	c.2353_2354insAAAA	c.(2353-2355)acafs	p.T785fs	HUWE1_ENST00000218328.8_Frame_Shift_Ins_p.T785fs|HUWE1_ENST00000262854.6_Frame_Shift_Ins_p.T785fs			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	785					base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						GTCATCTGTTGTATTGTTGCTC	0.401																																						ENST00000342160.3		NA																	0				NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						c.(2353-2355)acafs		HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase																																				SO:0001589	frameshift_variant	10075				base-excision repair|cell differentiation|histone ubiquitination|protein monoubiquitination|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	DNA binding|protein binding|ubiquitin-protein ligase activity	g.chrX:53634626_53634627insTTTT	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"""HECT, UBA and WWE domain containing 1"""			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.2353_2354insAAAA	X.37:g.53634626_53634627insTTTT	ENSP00000340648:p.Thr785fs	False	False		Somatic	1				HUWE1_ENST00000218328.8_Frame_Shift_Ins_p.T785fs|HUWE1_ENST00000262854.6_Frame_Shift_Ins_p.T785fs	p.T785fs			WXS	Illumina HiSeq	Phase_I	Q7Z6Z7	HUWE1_HUMAN			24	2810_2811	-			785					O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Frame_Shift_Ins	INS	ENST00000342160.3	37	c.2353_2354insAAAA	CCDS35301.1																																																																																				0.401	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	0	XM_497119		X:53634626
OR2T2	401992	broad.mit.edu	37	1	248616705	248616711	+	Frame_Shift_Del	DEL	TGCTGCG	TGCTGCG	-	rs199823862|rs372931983		TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	TGCTGCG	TGCTGCG	-	-	TGCTGCG	TGCTGCG	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr1:248616705_248616711delTGCTGCG	ENST00000342927.3	+	1	629_635	c.607_613delTGCTGCG	c.(607-615)tgctgcgtgfs	p.CCV203fs		NM_001004136.1	NP_001004136.1	Q6IF00	OR2T2_HUMAN	olfactory receptor, family 2, subfamily T, member 2	203						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(21)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	37	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GATGTATGCCTGCTGCGTGCTGATGCT	0.527																																						ENST00000342927.3		NA																	0				cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(21)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	37						c.(607-615)tgctgcgtgfs		olfactory receptor, family 2, subfamily T, member 2				51,3755		2,47,1854						-2.5	0.6			76	261,7371		12,237,3567	no	frameshift	OR2T2	NM_001004136.1		14,284,5421	A1A1,A1R,RR		3.4198,1.34,2.7277				312,11126				SO:0001589	frameshift_variant	401992				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr1:248616705_248616711delTGCTGCG	BK004462	CCDS31116.1	1q44	2012-08-09	2002-11-13	2002-11-15	ENSG00000196240	ENSG00000196240		"""GPCR / Class A : Olfactory receptors"""	14725	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily T, member 2 pseudogene"""	OR2T2P		14983052	Standard	NM_001004136		Approved		uc001iek.1	Q6IF00	OTTHUMG00000040480	ENST00000342927.3:c.607_613delTGCTGCG	1.37:g.248616705_248616711delTGCTGCG	ENSP00000343062:p.Cys203fs	False	False		Somatic	1					p.CCV203fs	NM_001004136.1	NP_001004136.1	WXS	Illumina HiSeq	Phase_I	Q6IF00	OR2T2_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.0265)		1	629_635	+	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		203					B2RNM1|B9EH01	Frame_Shift_Del	DEL	ENST00000342927.3	37	c.607_613delTGCTGCG	CCDS31116.1																																																																																				0.527	OR2T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097421.1	0	NM_001004136		1:248616705
AAK1	22848	broad.mit.edu	37	2	69741760	69741765	+	In_Frame_Del	DEL	TGTTGC	TGTTGC	-	rs77547121		TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	TGTTGC	TGTTGC	-	-	TGTTGC	TGTTGC	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr2:69741760_69741765delTGTTGC	ENST00000409085.4	-	13	1990_1995	c.1614_1619delGCAACA	c.(1612-1620)cagcaacaa>caa	p.538_540QQQ>Q	AAK1_ENST00000409068.1_In_Frame_Del_p.538_540QQQ>Q|RN7SL604P_ENST00000492589.2_RNA|AAK1_ENST00000406297.3_In_Frame_Del_p.538_540QQQ>Q	NM_014911.3	NP_055726	Q2M2I8	AAK1_HUMAN	AP2 associated kinase 1	538	Gln-rich.				endocytosis (GO:0006897)|positive regulation of Notch signaling pathway (GO:0045747)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of clathrin-mediated endocytosis (GO:2000369)|regulation of protein localization (GO:0032880)	cell leading edge (GO:0031252)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extrinsic component of plasma membrane (GO:0019897)|terminal bouton (GO:0043195)	AP-2 adaptor complex binding (GO:0035612)|ATP binding (GO:0005524)|Notch binding (GO:0005112)|protein serine/threonine kinase activity (GO:0004674)	p.Q538Q(2)		NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)	17						ttgctgttgttgttgctgctgctgct	0.544																																						ENST00000409085.4		NA																	2	Substitution - coding silent(2)	p.Q538Q(2)	kidney(2)	NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)	17						c.(1612-1620)cagcaacaa>caa		AP2 associated kinase 1																																				SO:0001651	inframe_deletion	22848					coated pit|mitochondrion|plasma membrane	ATP binding|protein serine/threonine kinase activity	g.chr2:69741760_69741765delTGTTGC	AB028971	CCDS1893.2	2p13.3	2012-07-10			ENSG00000115977	ENSG00000115977			19679	protein-coding gene	gene with protein product						11877461, 12471243	Standard	NM_014911		Approved	KIAA1048, DKFZp686K16132	uc002sfp.2	Q2M2I8	OTTHUMG00000129648	ENST00000409085.4:c.1614_1619delGCAACA	2.37:g.69741760_69741765delTGTTGC	ENSP00000386456:p.Gln544_Gln545del	True	False		Somatic	1				AAK1_ENST00000409068.1_In_Frame_Del_p.538_540QQQ>Q|AAK1_ENST00000406297.3_In_Frame_Del_p.538_540QQQ>Q	p.538_540QQQ>Q	NM_014911.3	NP_055726.3	WXS	Illumina HiSeq	Phase_I	Q2M2I8	AAK1_HUMAN			13	1990_1995	-			538			Gln-rich.		Q4ZFZ3|Q53RX6|Q9UPV4	In_Frame_Del	DEL	ENST00000409085.4	37	c.1614_1619delGCAACA	CCDS1893.2																																																																																				0.544	AAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251847.4	0	NM_014911		2:69741760
WDR33	55339	broad.mit.edu	37	2	128477233	128477234	+	Frame_Shift_Ins	INS	-	-	AGAT			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr2:128477233_128477234insAGAT	ENST00000322313.4	-	16	2523_2524	c.2365_2366insATCT	c.(2365-2367)ggcfs	p.G789fs		NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33	789					mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		CTCCCGGGGGCCTGGAGGCCCC	0.604																																						ENST00000322313.4		NA																	0				NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39						c.(2365-2367)ggcfs		WD repeat domain 33																																				SO:0001589	frameshift_variant	55339				postreplication repair|spermatogenesis	collagen|nucleus	protein binding	g.chr2:128477233_128477234insAGAT		CCDS2150.1, CCDS42746.1, CCDS46407.1	2q21.1	2013-01-09			ENSG00000136709	ENSG00000136709		"""WD repeat domain containing"""	25651	protein-coding gene	gene with protein product						11162572	Standard	NM_001006622		Approved	FLJ11294, WDC146, NET14	uc002tpg.2	Q9C0J8	OTTHUMG00000131534	ENST00000322313.4:c.2365_2366insATCT	2.37:g.128477233_128477234insAGAT	ENSP00000325377:p.Gly789fs	False	False		Somatic	0					p.G789fs	NM_018383.4	NP_060853.3	WXS	Illumina HiSeq	Phase_I	Q9C0J8	WDR33_HUMAN		BRCA - Breast invasive adenocarcinoma(221;0.0695)	16	2523_2524	-	Colorectal(110;0.1)		789					Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Frame_Shift_Ins	INS	ENST00000322313.4	37	c.2365_2366insATCT	CCDS2150.1																																																																																				0.604	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	0	NM_018383		2:128477233
PPIG	9360	broad.mit.edu	37	2	170493042	170493043	+	Frame_Shift_Ins	INS	-	-	TTGGGGAAATGTT			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr2:170493042_170493043insTTGGGGAAATGTT	ENST00000260970.3	+	14	1494_1495	c.1274_1275insTTGGGGAAATGTT	c.(1273-1278)aaagttfs	p.KV425fs	PPIG_ENST00000448752.2_Frame_Shift_Ins_p.KV425fs|PPIG_ENST00000409714.3_Frame_Shift_Ins_p.KV410fs|PPIG_ENST00000482772.1_3'UTR	NM_004792.2	NP_004783.2	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G (cyclophilin G)	425					protein folding (GO:0006457)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(17)|ovary(2)|stomach(1)|urinary_tract(1)	43					L-Proline(DB00172)	AAGGAGAAGAAAGTTAAAGACC	0.322																																						ENST00000260970.3		NA																	0				NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(17)|ovary(2)|stomach(1)|urinary_tract(1)	43						c.(1273-1278)aaagttfs		peptidylprolyl isomerase G (cyclophilin G)	L-Proline(DB00172)																																			SO:0001589	frameshift_variant	9360				protein folding|RNA splicing	nuclear matrix|nuclear speck	cyclosporin A binding|peptidyl-prolyl cis-trans isomerase activity	g.chr2:170493042_170493043insTTGGGGAAATGTT	X99717	CCDS2235.1	2q31.1	2010-07-23	2006-01-12		ENSG00000138398	ENSG00000138398	6.1.1.16		14650	protein-coding gene	gene with protein product	"""SR-related CTD-associated factor 10"""	606093	"""peptidyl-prolyl isomerase G (cyclophilin G)"""			8973360, 9153302	Standard	NM_004792		Approved	CARS-Cyp, SRCyp, SCAF10	uc002uez.3	Q13427	OTTHUMG00000132206	Exception_encountered	2.37:g.170493042_170493043insTTGGGGAAATGTT	ENSP00000260970:p.Lys425fs	True	False		Somatic	0				PPIG_ENST00000409714.3_Frame_Shift_Ins_p.KV410fs|PPIG_ENST00000482772.1_3'UTR|PPIG_ENST00000448752.2_Frame_Shift_Ins_p.KV425fs	p.KV425fs	NM_004792.2	NP_004783.2	WXS	Illumina HiSeq	Phase_I	Q13427	PPIG_HUMAN			14	1494_1495	+			425					D3DPC5|D3DPC6|O00706|Q53R40|Q53SN4|Q96DG9	Frame_Shift_Ins	INS	ENST00000260970.3	37	c.1274_1275insTTGGGGAAATGTT	CCDS2235.1																																																																																				0.322	PPIG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255264.2	0			2:170493042
GIGYF2	26058	broad.mit.edu	37	2	233708804	233708806	+	In_Frame_Del	DEL	CAA	CAA	-	rs3816334	byFrequency	TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	CAA	CAA	-	-	CAA	CAA	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr2:233708804_233708806delCAA	ENST00000409547.1	+	26	3249_3251	c.2938_2940delCAA	c.(2938-2940)caadel	p.Q984del	GIGYF2_ENST00000409480.1_In_Frame_Del_p.Q1006del|GIGYF2_ENST00000409451.3_In_Frame_Del_p.Q1005del|GIGYF2_ENST00000409196.3_In_Frame_Del_p.Q978del|GIGYF2_ENST00000452341.2_In_Frame_Del_p.T823del|GIGYF2_ENST00000373566.3_In_Frame_Del_p.Q1006del|GIGYF2_ENST00000373563.4_In_Frame_Del_p.Q984del	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	984	Gln-rich.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		gcagcagcagcaacagcaacagc	0.483																																						ENST00000409547.1		NA																	0				NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63						c.(2938-2940)caadel		GRB10 interacting GYF protein 2																																				SO:0001651	inframe_deletion	26058				cell death		protein binding	g.chr2:233708804_233708806delCAA	U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"""Trinucleotide (CAG) repeat containing"""	11960	protein-coding gene	gene with protein product	"""GYF domain containing 2"""	612003	"""PERQ amino acid rich, with GYF domain 2"", ""PERQ amino acid rich, with GYF domain 3"", ""trinucleotide repeat containing 15"", ""Parkinson disease (autosomal recessive, early onset) 11"""	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.2938_2940delCAA	2.37:g.233708804_233708806delCAA	ENSP00000386537:p.Gln984del	True	False		Somatic	1				GIGYF2_ENST00000409196.3_In_Frame_Del_p.Q978del|GIGYF2_ENST00000452341.2_In_Frame_Del_p.T823del|GIGYF2_ENST00000373563.4_In_Frame_Del_p.Q984del|GIGYF2_ENST00000409451.3_In_Frame_Del_p.Q1005del|GIGYF2_ENST00000373566.3_In_Frame_Del_p.Q1006del|GIGYF2_ENST00000409480.1_In_Frame_Del_p.Q1006del	p.Q984del	NM_015575.3	NP_056390.2	WXS	Illumina HiSeq	Phase_I	Q6Y7W6	PERQ2_HUMAN		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)	26	3249_3251	+		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)	984			Gln-rich.		A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	In_Frame_Del	DEL	ENST00000409547.1	37	c.2938_2940delCAA	CCDS33401.1																																																																																				0.483	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	0	NM_001103146		2:233708804
FOXL2	668	broad.mit.edu	37	3	138665464	138665540	+	Frame_Shift_Del	DEL	GGGCTCGGCGGCGGCCCTTCTGGCTCCTTGACTGTGCGACCGGTCTCTGGGGCCAGCAGGGCCCCCGCCGCGTCCTC	GGGCTCGGCGGCGGCCCTTCTGGCTCCTTGACTGTGCGACCGGTCTCTGGGGCCAGCAGGGCCCCCGCCGCGTCCTC	-	rs111967494|rs569790915|rs551580060		TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	GGGCTCGGCGGCGGCCCTTCTGGCTCCTTGACTGTGCGACCGGTCTCTGGGGCCAGCAGGGCCCCCGCCGCGTCCTC	GGGCTCGGCGGCGGCCCTTCTGGCTCCTTGACTGTGCGACCGGTCTCTGGGGCCAGCAGGGCCCCCGCCGCGTCCTC	-	-	GGGCTCGGCGGCGGCCCTTCTGGCTCCTTGACTGTGCGACCGGTCTCTGGGGCCAGCAGGGCCCCCGCCGCGTCCTC	GGGCTCGGCGGCGGCCCTTCTGGCTCCTTGACTGTGCGACCGGTCTCTGGGGCCAGCAGGGCCCCCGCCGCGTCCTC	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr3:138665464_138665540delGGGCTCGGCGGCGGCCCTTCTGGCTCCTTGACTGTGCGACCGGTCTCTGGGGCCAGCAGGGCCCCCGCCGCGTCCTC	ENST00000330315.3	-	1	442_518	c.25_101delGAGGACGCGGCGGGGGCCCTGCTGGCCCCAGAGACCGGTCGCACAGTCAAGGAGCCAGAAGGGCCGCCGCCGAGCCC	c.(25-102)gaggacgcggcgggggccctgctggccccagagaccggtcgcacagtcaaggagccagaagggccgccgccgagcccafs	p.EDAAGALLAPETGRTVKEPEGPPPSP9fs	RP11-548O1.3_ENST00000495287.1_lincRNA|C3orf72_ENST00000383165.3_5'Flank	NM_023067.3	NP_075555.1	P58012	FOXL2_HUMAN	forkhead box L2	9					apoptotic DNA fragmentation (GO:0006309)|cell differentiation (GO:0030154)|embryonic eye morphogenesis (GO:0048048)|extraocular skeletal muscle development (GO:0002074)|female somatic sex determination (GO:0019101)|granulosa cell differentiation (GO:0060014)|menstruation (GO:0042703)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|ovarian follicle development (GO:0001541)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	cysteine-type endopeptidase regulator activity involved in apoptotic process (GO:0043028)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin conjugating enzyme binding (GO:0031624)			large_intestine(1)|lung(1)|ovary(333)|skin(1)	336						GCCCTTGCCTGGGCTCGGCGGCGGCCCTTCTGGCTCCTTGACTGTGCGACCGGTCTCTGGGGCCAGCAGGGCCCCCGCCGCGTCCTCGGGCTCGGGG	0.747			Mis		granulosa-cell tumour of the ovary		"""Blepharophimosis, ptosis and epicanthus inversus Types I, II; Premature ovarian failure type III"""																															ENST00000330315.3		NA		Dom	yes		3	3q23	668	Mis	forkhead box L2	yes	"""Blepharophimosis, ptosis and epicanthus inversus Types I, II; Premature ovarian failure type III"""	O			granulosa-cell tumour of the ovary		0				large_intestine(1)|lung(1)|ovary(333)|skin(1)	336	GRCh37	CD012523|CD025238|CD032465|CD084129	FOXL2	D		c.(25-102)gaggacgcggcgggggccctgctggccccagagaccggtcgcacagtcaaggagccagaagggccgccgccgagcccafs		forkhead box L2																																				SO:0001589	frameshift_variant	668				convergent extension|DNA fragmentation involved in apoptotic nuclear change|embryonic eye morphogenesis|extraocular skeletal muscle development|female somatic sex determination|induction of apoptosis|menstruation|negative regulation of transcription, DNA-dependent|ovarian follicle development|pattern specification process|positive regulation of caspase activity|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity	transcription factor complex	caspase regulator activity|DNA bending activity|double-stranded DNA binding|estrogen receptor binding|promoter binding|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|ubiquitin conjugating enzyme binding	g.chr3:138665464_138665540delGGGCTCGGCGGCGGCCCTTCTGGCTCCTTGACTGTGCGACCGGTCTCTGGGGCCAGCAGGGCCCCCGCCGCGTCCTC	AF301906	CCDS3105.1	3q23	2008-04-10			ENSG00000183770	ENSG00000183770		"""Forkhead boxes"""	1092	protein-coding gene	gene with protein product		605597		BPES		1941972	Standard	NM_023067		Approved	BPES1	uc003esw.3	P58012	OTTHUMG00000159889	ENST00000330315.3:c.25_101delGAGGACGCGGCGGGGGCCCTGCTGGCCCCAGAGACCGGTCGCACAGTCAAGGAGCCAGAAGGGCCGCCGCCGAGCCC	3.37:g.138665464_138665540delGGGCTCGGCGGCGGCCCTTCTGGCTCCTTGACTGTGCGACCGGTCTCTGGGGCCAGCAGGGCCCCCGCCGCGTCCTC	ENSP00000333188:p.Glu9fs	False	False		Somatic	1					p.EDAAGALLAPETGRTVKEPEGPPPSP9fs	NM_023067.3	NP_075555.1	WXS	Illumina HiSeq	Phase_I	P58012	FOXL2_HUMAN			1	442_518	-			9					Q4ZGJ3	Frame_Shift_Del	DEL	ENST00000330315.3	37	c.25_101delGAGGACGCGGCGGGGGCCCTGCTGGCCCCAGAGACCGGTCGCACAGTCAAGGAGCCAGAAGGGCCGCCGCCGAGCCC	CCDS3105.1																																																																																				0.747	FOXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357999.1	0			3:138665464
AP3S1	1176	broad.mit.edu	37	5	115202418	115202421	+	Frame_Shift_Del	DEL	AAGA	AAGA	-	rs80118146		TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	AAGA	AAGA	-	-	AAGA	AAGA	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr5:115202418_115202421delAAGA	ENST00000316788.7	+	2	678_681	c.121_124delAAGA	c.(121-126)aagagafs	p.KR41fs		NM_001284.2	NP_001275.1	Q92572	AP3S1_HUMAN	adaptor-related protein complex 3, sigma 1 subunit	41					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|insulin receptor signaling pathway (GO:0008286)|intracellular protein transport (GO:0006886)	AP-3 adaptor complex (GO:0030123)|AP-type membrane coat adaptor complex (GO:0030119)|Golgi apparatus (GO:0005794)|transport vesicle (GO:0030133)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|pancreas(1)|prostate(1)	12		all_cancers(142;0.00377)|all_epithelial(76;0.000129)|Prostate(80;0.0132)|Ovarian(225;0.0776)|Lung NSC(810;0.245)		OV - Ovarian serous cystadenocarcinoma(64;1.08e-07)|Epithelial(69;1.11e-06)|all cancers(49;5.2e-05)		TTTGGTATCTAAGAGAGATGAAAA	0.304																																						ENST00000316788.7		NA																	0				cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|pancreas(1)|prostate(1)	12						c.(121-126)aagagafs		adaptor-related protein complex 3, sigma 1 subunit																																				SO:0001589	frameshift_variant	1176				insulin receptor signaling pathway|intracellular protein transport|vesicle-mediated transport	AP-type membrane coat adaptor complex|cytoplasmic vesicle membrane|Golgi apparatus|transport vesicle	protein binding|protein transporter activity	g.chr5:115202418_115202421delAAGA	D63643	CCDS4123.1	5q22	2010-06-29			ENSG00000177879	ENSG00000177879			2013	protein-coding gene	gene with protein product		601507		CLAPS3		8697810, 9118953	Standard	NM_001284		Approved		uc003krl.3	Q92572	OTTHUMG00000128887	ENST00000316788.7:c.121_124delAAGA	5.37:g.115202418_115202421delAAGA	ENSP00000325369:p.Lys41fs	True	False		Somatic	1					p.KR41fs	NM_001284.2	NP_001275.1	WXS	Illumina HiSeq	Phase_I	Q92572	AP3S1_HUMAN		OV - Ovarian serous cystadenocarcinoma(64;1.08e-07)|Epithelial(69;1.11e-06)|all cancers(49;5.2e-05)	2	678_681	+		all_cancers(142;0.00377)|all_epithelial(76;0.000129)|Prostate(80;0.0132)|Ovarian(225;0.0776)|Lung NSC(810;0.245)	41					O00647|O00676|O00721|O00727|Q53XL4|Q6ICQ2	Frame_Shift_Del	DEL	ENST00000316788.7	37	c.121_124delAAGA	CCDS4123.1																																																																																				0.304	AP3S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250847.2	0			5:115202418
FNDC1	84624	broad.mit.edu	37	6	159655079	159655081	+	In_Frame_Del	DEL	GAC	GAC	-	rs547492676	byFrequency	TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	GAC	GAC	-	-	GAC	GAC	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr6:159655079_159655081delGAC	ENST00000297267.9	+	11	3735_3737	c.3535_3537delGAC	c.(3535-3537)gacdel	p.D1180del	FNDC1_ENST00000340366.6_In_Frame_Del_p.D1117del	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	1180			D -> E (in dbSNP:rs420054). {ECO:0000269|PubMed:11347906, ECO:0000269|PubMed:15489334}.		cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		CTCAGCCGAGGACGACGAGGAGG	0.65																																						ENST00000297267.9		NA																	0				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93						c.(3535-3537)gacdel		fibronectin type III domain containing 1																																				SO:0001651	inframe_deletion	84624					extracellular region		g.chr6:159655079_159655081delGAC	AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"""Fibronectin type III domain containing"""	21184	protein-coding gene	gene with protein product		609991	"""fibronectin type III domain containing 2"""	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.3535_3537delGAC	6.37:g.159655082_159655084delGAC	ENSP00000297267:p.Asp1180del	False	False		Somatic	2				FNDC1_ENST00000340366.6_In_Frame_Del_p.D1117del	p.D1180del	NM_032532.2	NP_115921.2	WXS	Illumina HiSeq	Phase_I	Q4ZHG4	FNDC1_HUMAN		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)	11	3735_3737	+		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)	1180		D -> E (in dbSNP:rs420054).			A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	In_Frame_Del	DEL	ENST00000297267.9	37	c.3535_3537delGAC	CCDS47512.1																																																																																				0.650	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	0	NM_032532		6:159655079
DTX2P1-UPK3BP1-PMS2P11	441263	broad.mit.edu	37	7	76652971	76652972	+	RNA	INS	-	-	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr7:76652971_76652972insA	ENST00000584900.1	+	0	1529_1530					NR_023383.1				DTX2P1-UPK3BP1-PMS2P11 readthrough transcribed pseudogene																		TCACTGTATTCAGCTCCATCAA	0.48																																						ENST00000584900.1		NA																	0					NA																																														0							g.chr7:76652971_76652972insA	U38980		7q11.23	2014-09-10	2012-12-07		ENSG00000265479	ENSG00000265479			42360	other	readthrough			"""DTX2P1-UPK3BP1-PMS2P11 readthrough (non-protein coding)"""				Standard	NR_023383		Approved		uc003ufw.4		OTTHUMG00000179528		7.37:g.76652972_76652972dupA		False	False		Somatic	1						NR_023383.1		WXS	Illumina HiSeq	Phase_I					0	1529_1530	+			NA						RNA	INS	ENST00000584900.1	37																																																																																						0.480	DTX2P1-UPK3BP1-PMS2P11-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000446923.2	0	NR_023383		7:76652971
MYOM2	9172	broad.mit.edu	37	8	2000419	2000433	+	Splice_Site	DEL	AGAACAGAAGCAGGT	AGAACAGAAGCAGGT	-	rs35022521|rs374547578	byFrequency	TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	AGAACAGAAGCAGGT	AGAACAGAAGCAGGT	-	-	AGAACAGAAGCAGGT	AGAACAGAAGCAGGT	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr8:2000419_2000433delAGAACAGAAGCAGGT	ENST00000262113.4	+	3	392_404	c.251_263delAGAACAGAAGCAGGT	c.(250-264)gagaacagaagcagg>gg	p.ENRSR84del	MYOM2_ENST00000523438.1_Intron	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	84					muscle contraction (GO:0006936)	M band (GO:0031430)|mitochondrion (GO:0005739)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3)	104		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		GAGGAGCAGGAGAACAGAAGCAGGTGAGCACATGG	0.605																																						ENST00000262113.4		NA																	0				autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3)	104						c.(250-264)gagaacagaagcagg>gg		myomesin 2																																				SO:0001630	splice_region_variant	9172				muscle contraction	myosin filament	structural constituent of muscle	g.chr8:2000419_2000433delAGAACAGAAGCAGGT		CCDS5957.1	8p23.3	2014-06-06	2012-10-17		ENSG00000036448	ENSG00000036448		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7614	protein-coding gene	gene with protein product		603509	"""myomesin (M-protein) 2 (165kD)"", ""myomesin (M-protein) 2, 165kDa"""				Standard	XM_006716237		Approved		uc003wpx.4	P54296	OTTHUMG00000129175	ENST00000262113.4:c.263+1AGAACAGAAGCAGGT>-	8.37:g.2000419_2000433delAGAACAGAAGCAGGT		False	False		Somatic	1				MYOM2_ENST00000523438.1_Intron	p.ENRSR84del	NM_003970.2	NP_003961.2	WXS	Illumina HiSeq	Phase_I	P54296	MYOM2_HUMAN		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)	3	392_404	+		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)	84					Q7Z3Y2	Splice_Site	DEL	ENST00000262113.4	37	c.251_263delAGAACAGAAGCAGGT	CCDS5957.1																																																																																				0.605	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	0	NM_003970	In_Frame_Del	8:2000419
LZTS1	11178	broad.mit.edu	37	8	20107683	20107730	+	In_Frame_Del	DEL	CAGCTCCAGGCCCTTGGTGCGCAGGGCGCCCTCCAGGTCCTGGGTCCT	CAGCTCCAGGCCCTTGGTGCGCAGGGCGCCCTCCAGGTCCTGGGTCCT	-	rs372940217|rs141716809|rs373668156|rs148039718	byFrequency	TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	CAGCTCCAGGCCCTTGGTGCGCAGGGCGCCCTCCAGGTCCTGGGTCCT	CAGCTCCAGGCCCTTGGTGCGCAGGGCGCCCTCCAGGTCCTGGGTCCT	-	-	CAGCTCCAGGCCCTTGGTGCGCAGGGCGCCCTCCAGGTCCTGGGTCCT	CAGCTCCAGGCCCTTGGTGCGCAGGGCGCCCTCCAGGTCCTGGGTCCT	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr8:20107683_20107730delCAGCTCCAGGCCCTTGGTGCGCAGGGCGCCCTCCAGGTCCTGGGTCCT	ENST00000381569.1	-	4	1651_1698	c.1294_1341delAGGACCCAGGACCTGGAGGGCGCCCTGCGCACCAAGGGCCTGGAGCTG	c.(1294-1341)aggacccaggacctggagggcgccctgcgcaccaagggcctggagctgdel	p.RTQDLEGALRTKGLEL432del	LZTS1_ENST00000265801.6_In_Frame_Del_p.RTQDLEGALRTKGLEL432del|LZTS1_ENST00000522290.1_In_Frame_Del_p.RTQDLEGALRTKGLEL432del			Q9Y250	LZTS1_HUMAN	leucine zipper, putative tumor suppressor 1	432					cell cycle (GO:0007049)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of macroautophagy (GO:0016242)|positive regulation of type I interferon production (GO:0032481)|regulation of dendrite morphogenesis (GO:0048814)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|nucleoplasm (GO:0005654)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(16)|ovary(2)|skin(1)|urinary_tract(1)	29				Colorectal(74;0.0511)|COAD - Colon adenocarcinoma(73;0.207)		CACAGACCTCCAGCTCCAGGCCCTTGGTGCGCAGGGCGCCCTCCAGGTCCTGGGTCCTCAGCTCCAGG	0.657																																						ENST00000381569.1		NA																	0				breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(16)|ovary(2)|skin(1)|urinary_tract(1)	29						c.(1294-1341)aggacccaggacctggagggcgccctgcgcaccaagggcctggagctgdel		leucine zipper, putative tumor suppressor 1																																				SO:0001651	inframe_deletion	11178				cell cycle|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	cell junction|dendritic spine|Golgi apparatus|nucleolus|nucleoplasm|postsynaptic density|postsynaptic membrane	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity	g.chr8:20107683_20107730delCAGCTCCAGGCCCTTGGTGCGCAGGGCGCCCTCCAGGTCCTGGGTCCT	AF123659	CCDS6015.1	8p22	2012-10-05			ENSG00000061337	ENSG00000061337			13861	protein-coding gene	gene with protein product		606551	"""F37/Esophageal cancer-related gene-coding leucine-zipper motif"""			10097140, 17349584	Standard	NM_021020		Approved	FEZ1	uc003wzr.3	Q9Y250	OTTHUMG00000097027	ENST00000381569.1:c.1294_1341delAGGACCCAGGACCTGGAGGGCGCCCTGCGCACCAAGGGCCTGGAGCTG	8.37:g.20107683_20107730delCAGCTCCAGGCCCTTGGTGCGCAGGGCGCCCTCCAGGTCCTGGGTCCT	ENSP00000370981:p.Arg432_Leu447del	True	False		Somatic	1				LZTS1_ENST00000522290.1_In_Frame_Del_p.RTQDLEGALRTKGLEL432del|LZTS1_ENST00000265801.6_In_Frame_Del_p.RTQDLEGALRTKGLEL432del	p.RTQDLEGALRTKGLEL432del			WXS	Illumina HiSeq	Phase_I	Q9Y250	LZTS1_HUMAN		Colorectal(74;0.0511)|COAD - Colon adenocarcinoma(73;0.207)	4	1651_1698	-			432					D3DSQ6|Q9Y5V7|Q9Y5V8|Q9Y5V9|Q9Y5W0|Q9Y5W1|Q9Y5W2	In_Frame_Del	DEL	ENST00000381569.1	37	c.1294_1341delAGGACCCAGGACCTGGAGGGCGCCCTGCGCACCAAGGGCCTGGAGCTG	CCDS6015.1																																																																																				0.657	LZTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214122.1	0	NM_021020		8:20107683
PHPT1	29085	broad.mit.edu	37	9	139748277	139748296	+	IGR	DEL	CCCTGTGGCAGAGCACAGGG	CCCTGTGGCAGAGCACAGGG	-	rs547669049|rs143877651|rs533545675	byFrequency	TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	CCCTGTGGCAGAGCACAGGG	CCCTGTGGCAGAGCACAGGG	-	-	CCCTGTGGCAGAGCACAGGG	CCCTGTGGCAGAGCACAGGG	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr9:139748277_139748296delCCCTGTGGCAGAGCACAGGG	ENST00000247665.10	+	0	890				MAMDC4_ENST00000317446.2_Frame_Shift_Del_p.TLWQSTG168fs|MAMDC4_ENST00000485732.1_3'UTR|MAMDC4_ENST00000445819.1_Frame_Shift_Del_p.TLWQSTG168fs	NM_014172.4	NP_054891.2	Q9NRX4	PHP14_HUMAN	phosphohistidine phosphatase 1						negative regulation of ATP citrate synthase activity (GO:2000984)|negative regulation of lyase activity (GO:0051350)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-histidine dephosphorylation (GO:0035971)|positive regulation of cell motility (GO:2000147)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|protein dephosphorylation (GO:0006470)|regulation of actin cytoskeleton reorganization (GO:2000249)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	calcium channel inhibitor activity (GO:0019855)|ion channel binding (GO:0044325)|phosphohistidine phosphatase activity (GO:0008969)|phosphoprotein phosphatase activity (GO:0004721)			NS(1)|large_intestine(1)|lung(1)	3	all_cancers(76;0.0763)|all_epithelial(76;0.198)	Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171)		GAGACCCTGACCCTGTGGCAGAGCACAGGGCCCTGGGGCC	0.677														24	0.00479233	0.0	0.0014	5008	,	,		13843	0.0		0.0229	False		,,,				2504	0.0					ENST00000317446.2		NA																	0				breast(4)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	19						c.(502-522)accctgtggcagagcacagggfs		MAM domain containing 4				6,4248		0,6,2121						0.9	0.1			25	146,8098		3,140,3979	no	frameshift	MAMDC4	NM_206920.2		3,146,6100	A1A1,A1R,RR		1.771,0.141,1.2162				152,12346				SO:0001628	intergenic_variant	158056				protein transport	integral to membrane		g.chr9:139748277_139748296delCCCTGTGGCAGAGCACAGGG	AF131857	CCDS7009.1, CCDS48060.1	9q34.3	2008-02-05			ENSG00000054148	ENSG00000054148	3.1.3.-		30033	protein-coding gene	gene with protein product	"""phosphohistidine phosphatase 14kDa"", "" sex-regulated protein janus-a"""	610167				11042152, 8619474	Standard	NM_014172		Approved	PHP14, HSPC141, CGI-202, DKFZp564M173, bA216L13.10	uc004cjq.4	Q9NRX4	OTTHUMG00000020950		9.37:g.139748277_139748296delCCCTGTGGCAGAGCACAGGG		False	False		Somatic	1				MAMDC4_ENST00000445819.1_Frame_Shift_Del_p.TLWQSTG168fs|MAMDC4_ENST00000485732.1_3'UTR	p.TLWQSTG168fs	NM_206920.2	NP_996803.2	WXS	Illumina HiSeq	Phase_I	Q6UXC1	AEGP_HUMAN		OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171)	5	553_572	+	all_cancers(76;0.0763)|all_epithelial(76;0.198)	Myeloproliferative disorder(178;0.0511)	168			MAM 1.		B1AMX0|B1AMX1|Q9H0Y3	Frame_Shift_Del	DEL	ENST00000247665.10	37	c.503_522delCCCTGTGGCAGAGCACAGGG	CCDS7009.1																																																																																				0.677	PHPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055150.1	0	NM_014172		9:139748277
TMPRSS3	64699	broad.mit.edu	37	21	43796648	43796648	+	Splice_Site	SNP	A	A	T			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	A	A	-	-	A	A	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr21:43796648A>T	ENST00000291532.3	-	11	2150		c.e11+1		TMPRSS3_ENST00000398405.1_Splice_Site|TMPRSS3_ENST00000380399.1_Splice_Site|TMPRSS3_ENST00000433957.2_Splice_Site|TMPRSS3_ENST00000474596.1_Splice_Site	NM_032404.2	NP_115780.1	P57727	TMPS3_HUMAN	transmembrane protease, serine 3						cellular sodium ion homeostasis (GO:0006883)|proteolysis (GO:0006508)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(4)|skin(1)	13						GCGGCCCCGTACCTGGCAGCT	0.622											OREG0031642	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																										ENST00000291532.3		NA																	0				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(4)|skin(1)	13						c.e11+1		transmembrane protease, serine 3							68.0	59.0	62.0					21																	43796648		2203	4300	6503	SO:0001630	splice_region_variant	64699				cellular sodium ion homeostasis|proteolysis	endoplasmic reticulum membrane|integral to membrane	scavenger receptor activity|serine-type endopeptidase activity|sodium channel regulator activity	g.chr21:43796648A>T	AF201380	CCDS13686.1, CCDS42939.1, CCDS58790.1	21q22.3	2010-04-13			ENSG00000160183	ENSG00000160183		"""Serine peptidases / Transmembrane"""	11877	protein-coding gene	gene with protein product		605511		DFNB10, DFNB8		11462234, 11907649	Standard	NM_032405		Approved		uc002zbc.3	P57727	OTTHUMG00000086796	ENST00000291532.3:c.1194+1T>A	21.37:g.43796648A>T		False	False		Somatic	0	OREG0031642	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	919	TMPRSS3_ENST00000398405.1_Splice_Site|TMPRSS3_ENST00000474596.1_Splice_Site|TMPRSS3_ENST00000380399.1_Splice_Site|TMPRSS3_ENST00000433957.2_Splice_Site		NM_032404.2	NP_115780.1	WXS	Illumina HiSeq	Phase_I	P57727	TMPS3_HUMAN			11	2150	-			NA					D3DSJ6|Q5USC7|Q6ZMC3	Splice_Site	SNP	ENST00000291532.3	37		CCDS13686.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.329752	0.81690	.	.	ENSG00000160183	ENST00000291532;ENST00000433957;ENST00000398405;ENST00000380399	.	.	.	4.94	4.94	0.65067	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5997	0.68432	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TMPRSS3	42669717	1.000000	0.71417	0.945000	0.38365	0.866000	0.49608	8.554000	0.90689	1.840000	0.53500	0.482000	0.46254	.		0.622	TMPRSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195347.1	0		Intron	21:43796648
TUB	7275	broad.mit.edu	37	11	8123100	8123100	+	Silent	SNP	G	G	A	rs147880022	byFrequency	TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr11:8123100G>A	ENST00000299506.2	+	12	1604	c.1455G>A	c.(1453-1455)ccG>ccA	p.P485P	TUB_ENST00000305253.4_Silent_p.P540P|TUB_ENST00000534099.1_Silent_p.P491P	NM_177972.2	NP_813977.1	P50607	TUB_HUMAN	tubby bipartite transcription factor	485					multicellular organismal macromolecule metabolic process (GO:0044259)|phagocytosis (GO:0006909)|phototransduction (GO:0007602)|positive regulation of phagocytosis (GO:0050766)|response to hormone (GO:0009725)|retina development in camera-type eye (GO:0060041)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled photoreceptor activity (GO:0008020)|protein complex binding (GO:0032403)			breast(1)|cervix(1)|endometrium(9)|large_intestine(7)|lung(5)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	26		all_lung(207;6.91e-20)|Lung NSC(207;3.36e-17)		Epithelial(150;1.69e-62)|BRCA - Breast invasive adenocarcinoma(625;8.54e-06)|LUSC - Lung squamous cell carcinoma(625;0.000184)		ACAACTACCCGCTGTGTGCAC	0.582													G|||	4	0.000798722	0.0	0.0	5008	,	,		20364	0.0		0.0	False		,,,				2504	0.0041					ENST00000305253.4		NA																	0				breast(1)|cervix(1)|endometrium(9)|large_intestine(7)|lung(5)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	26						c.(1618-1620)ccG>ccA		tubby bipartite transcription factor		G	,	4,4398	8.1+/-20.4	0,4,2197	170.0	125.0	141.0		1620,1455	-3.8	1.0	11	dbSNP_134	141	2,8590	2.2+/-6.3	0,2,4294	no	coding-synonymous,coding-synonymous	TUB	NM_003320.4,NM_177972.2	,	0,6,6491	AA,AG,GG		0.0233,0.0909,0.0462	,	540/562,485/507	8123100	6,12988	2201	4296	6497	SO:0001819	synonymous_variant	7275				phagocytosis|positive regulation of phagocytosis|response to stimulus	cytoplasm|extracellular region|nucleus|plasma membrane		g.chr11:8123100G>A	U54644	CCDS7786.1, CCDS7787.1	11p15.5	2013-08-06	2013-08-06		ENSG00000166402	ENSG00000166402			12406	protein-coding gene	gene with protein product		601197	"""tubby (mouse) homolog"", ""tubby homolog (mouse)"""			8612280	Standard	NM_003320		Approved	rd5	uc001mfy.3	P50607	OTTHUMG00000165690	ENST00000299506.2:c.1455G>A	11.37:g.8123100G>A		True	False		Somatic	0				TUB_ENST00000534099.1_Silent_p.P491P|TUB_ENST00000299506.2_Silent_p.P485P	p.P540P	NM_003320.4	NP_003311.2	WXS	Illumina HiSeq	Phase_I	P50607	TUB_HUMAN		Epithelial(150;1.69e-62)|BRCA - Breast invasive adenocarcinoma(625;8.54e-06)|LUSC - Lung squamous cell carcinoma(625;0.000184)	13	1861	+		all_lung(207;6.91e-20)|Lung NSC(207;3.36e-17)	485					D3DQU4|O00293|Q6B007	Silent	SNP	ENST00000299506.2	37	c.1620G>A	CCDS7787.1																																																																																				0.582	TUB-003	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385823.1	0	NM_003320		11:8123100
HLA-DMA	3108	broad.mit.edu	37	6	32917503	32917503	+	Silent	SNP	G	G	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr6:32917503G>A	ENST00000374843.4	-	3	622	c.537C>T	c.(535-537)gtC>gtT	p.V179V	HLA-DMA_ENST00000395305.3_Silent_p.V84V|XXbac-BPG181M17.5_ENST00000429234.1_Intron|HLA-DMA_ENST00000464392.1_5'UTR|HLA-DMA_ENST00000395303.3_Silent_p.V145V	NM_006120.3	NP_006111.2	P28067	DMA_HUMAN	major histocompatibility complex, class II, DM alpha	179	Alpha-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|chaperone mediated protein folding requiring cofactor (GO:0051085)|immunoglobulin mediated immune response (GO:0016064)|inner ear development (GO:0048839)|peptide antigen assembly with MHC class II protein complex (GO:0002503)|positive regulation of immune response (GO:0050778)|positive regulation of T cell differentiation (GO:0045582)|positive thymic T cell selection (GO:0045059)|protein transport (GO:0015031)	cell surface (GO:0009986)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|multivesicular body (GO:0005771)	MHC class II protein complex binding (GO:0023026)			kidney(1)|large_intestine(2)|lung(8)	11						TGAGTCCATCGACAGCTGAGA	0.473																																						ENST00000374843.4		NA																	0				kidney(1)|large_intestine(2)|lung(8)	11						c.(535-537)gtC>gtT		major histocompatibility complex, class II, DM alpha							75.0	68.0	71.0					6																	32917503		1509	2709	4218	SO:0001819	synonymous_variant	3108					integral to membrane|MHC class II protein complex		g.chr6:32917503G>A		CCDS4761.1	6p21.3	2013-01-11			ENSG00000204257	ENSG00000204257		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4934	protein-coding gene	gene with protein product		142855				1922385	Standard	NM_006120		Approved	D6S222E, RING6	uc003ocm.2	P28067	OTTHUMG00000031173	ENST00000374843.4:c.537C>T	6.37:g.32917503G>A		False	False		Somatic	0				XXbac-BPG181M17.5_ENST00000429234.1_Intron|HLA-DMA_ENST00000395305.3_Silent_p.V84V|HLA-DMA_ENST00000395303.3_Silent_p.V145V|HLA-DMA_ENST00000464392.1_5'UTR	p.V179V	NM_006120.3	NP_006111.2	WXS	Illumina HiSeq	Phase_I	Q31604	Q31604_HUMAN			3	622	-			179					Q29639|Q29640	Silent	SNP	ENST00000374843.4	37	c.537C>T	CCDS4761.1																																																																																				0.473	HLA-DMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076325.2	0	NM_006120		6:32917503
NALCN	259232	broad.mit.edu	37	13	101755619	101755619	+	Silent	SNP	G	G	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr13:101755619G>A	ENST00000251127.6	-	26	3042	c.2961C>T	c.(2959-2961)gtC>gtT	p.V987V		NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	987					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					GGCACCGAAGGACCATTAGAA	0.443																																						ENST00000251127.6		NA																	0				NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177						c.(2959-2961)gtC>gtT		sodium leak channel, non-selective							91.0	89.0	90.0					13																	101755619		2203	4300	6503	SO:0001819	synonymous_variant	259232					integral to membrane	sodium channel activity|voltage-gated ion channel activity	g.chr13:101755619G>A	AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"""Ion channels / Sodium leak channels, non-selective"""	19082	protein-coding gene	gene with protein product		611549	"""voltage gated channel like 1"""	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.2961C>T	13.37:g.101755619G>A		False	False		Somatic	0					p.V987V	NM_052867.2	NP_443099.1	WXS	Illumina HiSeq	Phase_I	Q8IZF0	NALCN_HUMAN			26	3042	-	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		987					Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Silent	SNP	ENST00000251127.6	37	c.2961C>T	CCDS9498.1																																																																																				0.443	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	0	NM_052867		13:101755619
DYX1C1	161582	broad.mit.edu	37	15	55731755	55731755	+	Nonsense_Mutation	SNP	G	G	A	rs397515621		TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr15:55731755G>A	ENST00000321149.3	-	7	1175	c.808C>T	c.(808-810)Cga>Tga	p.R270*	DYX1C1-CCPG1_ENST00000565113.1_RNA|DYX1C1_ENST00000448430.2_Nonsense_Mutation_p.R270*|DYX1C1_ENST00000348518.3_Nonsense_Mutation_p.R270*|DYX1C1_ENST00000380679.1_Nonsense_Mutation_p.R270*|DYX1C1_ENST00000457155.2_Nonsense_Mutation_p.R270*	NM_130810.3	NP_570722.2	Q8WXU2	DYXC1_HUMAN	dyslexia susceptibility 1 candidate 1	270					cilium movement (GO:0003341)|determination of left/right symmetry (GO:0007368)|inner dynein arm assembly (GO:0036159)|neuron migration (GO:0001764)|outer dynein arm assembly (GO:0036158)|regulation of intracellular estrogen receptor signaling pathway (GO:0033146)|regulation of proteasomal protein catabolic process (GO:0061136)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	estrogen receptor binding (GO:0030331)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18				all cancers(107;0.0118)|GBM - Glioblastoma multiforme(80;0.171)		ATTGCTCTTCGTGCCTCAGCT	0.333																																						ENST00000321149.3		NA																	0				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18						c.(808-810)Cga>Tga		dyslexia susceptibility 1 candidate 1							78.0	78.0	78.0					15																	55731755		2193	4291	6484	SO:0001587	stop_gained	161582				neuron migration|regulation of estrogen receptor signaling pathway|regulation of proteasomal protein catabolic process	cytoplasm|nucleus	estrogen receptor binding	g.chr15:55731755G>A		CCDS10154.1, CCDS32243.1, CCDS32244.1	15q21.3	2014-09-11			ENSG00000256061	ENSG00000256061		"""Tetratricopeptide (TTC) repeat domain containing"""	21493	protein-coding gene	gene with protein product		608706				12954984	Standard	NM_130810		Approved	EKN1, FLJ37882, CILD25	uc002adc.3	Q8WXU2	OTTHUMG00000132008	ENST00000321149.3:c.808C>T	15.37:g.55731755G>A	ENSP00000323275:p.Arg270*	False	False		Somatic	0				DYX1C1_ENST00000380679.1_Nonsense_Mutation_p.R270*|DYX1C1_ENST00000448430.2_Nonsense_Mutation_p.R270*|DYX1C1_ENST00000348518.3_Nonsense_Mutation_p.R270*|DYX1C1-CCPG1_ENST00000565113.1_RNA|DYX1C1_ENST00000457155.2_Nonsense_Mutation_p.R270*	p.R270*	NM_130810.3	NP_570722.2	WXS	Illumina HiSeq	Phase_I	Q8WXU2	DYXC1_HUMAN		all cancers(107;0.0118)|GBM - Glioblastoma multiforme(80;0.171)	7	1175	-			270					Q6P5Y9|Q8N1S6	Nonsense_Mutation	SNP	ENST00000321149.3	37	c.808C>T	CCDS10154.1	.	.	.	.	.	.	.	.	.	.	G	39	7.385981	0.98252	.	.	ENSG00000256061	ENST00000420792;ENST00000448430;ENST00000380679;ENST00000457155;ENST00000321149;ENST00000348518	.	.	.	5.09	1.99	0.26369	.	0.000000	0.64402	U	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.1133	0.30928	0.0749:0.0:0.6445:0.2806	.	.	.	.	X	270	.	ENSP00000323275:R270X	R	-	1	2	DYX1C1	53519047	0.943000	0.32029	0.693000	0.30195	0.986000	0.74619	1.674000	0.37544	0.196000	0.20367	0.563000	0.77884	CGA		0.333	DYX1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254976.1	0	NM_130810		15:55731755
FGB	2244	broad.mit.edu	37	4	155487741	155487741	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr4:155487741C>A	ENST00000302068.4	+	3	470	c.407C>A	c.(406-408)gCt>gAt	p.A136D	FGB_ENST00000502545.1_3'UTR|FGB_ENST00000509493.1_Intron	NM_005141.4	NP_005132.2	P02675	FIBB_HUMAN	fibrinogen beta chain	136					blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|cellular response to interleukin-1 (GO:0071347)|cellular response to leptin stimulus (GO:0044320)|extracellular matrix organization (GO:0030198)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	chaperone binding (GO:0051087)|structural molecule activity (GO:0005198)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(2)|lung(22)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34	all_hematologic(180;0.215)	Renal(120;0.0458)			Sucralfate(DB00364)	AATGTGGAAGCTGTTTCCCAG	0.433																																					NSCLC(106;1133 1613 21870 46110 52656)	ENST00000302068.4		NA																	0				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(2)|lung(22)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						c.(406-408)gCt>gAt		fibrinogen beta chain	Sucralfate(DB00364)						170.0	159.0	163.0					4																	155487741		2203	4300	6503	SO:0001583	missense	2244				platelet activation|platelet degranulation|protein polymerization|response to calcium ion|signal transduction	external side of plasma membrane|fibrinogen complex|platelet alpha granule lumen|soluble fraction	chaperone binding|eukaryotic cell surface binding|protein binding, bridging|receptor binding	g.chr4:155487741C>A		CCDS3786.1	4q28	2014-09-17			ENSG00000171564	ENSG00000171564		"""Fibrinogen C domain containing"", ""Endogenous ligands"""	3662	protein-coding gene	gene with protein product		134830	"""fibrinogen, B beta polypeptide"""				Standard	NM_005141		Approved		uc003ioa.4	P02675	OTTHUMG00000150331	ENST00000302068.4:c.407C>A	4.37:g.155487741C>A	ENSP00000306099:p.Ala136Asp	False	False		Somatic	0				FGB_ENST00000509493.1_Intron|FGB_ENST00000502545.1_3'UTR	p.A136D	NM_005141.4	NP_005132.2	WXS	Illumina HiSeq	Phase_I	P02675	FIBB_HUMAN			3	470	+	all_hematologic(180;0.215)	Renal(120;0.0458)	136					A0JLR9|B2R7G3|Q32Q65|Q3KPF2	Missense_Mutation	SNP	ENST00000302068.4	37	c.407C>A	CCDS3786.1	.	.	.	.	.	.	.	.	.	.	C	0.023	-1.403604	0.01165	.	.	ENSG00000171564	ENST00000302068;ENST00000537843	T	0.80738	-1.41	5.14	0.887	0.19200	Fibrinogen, alpha/beta/gamma chain, coiled coil domain (2);	1.797860	0.02358	N	0.076577	T	0.57799	0.2078	N	0.02539	-0.55	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.53739	-0.8396	10	0.07325	T	0.83	.	9.2198	0.37370	0.4197:0.5032:0.0:0.0771	.	119;136	B4E1D3;P02675	.;FIBB_HUMAN	D	136;119	ENSP00000306099:A136D	ENSP00000306099:A136D	A	+	2	0	FGB	155707191	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.058000	0.11750	-0.020000	0.14032	-1.151000	0.01829	GCT		0.433	FGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317595.1	0	NM_005141		4:155487741
ZNF749	388567	broad.mit.edu	37	19	57955950	57955950	+	Silent	SNP	T	T	C			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	T	T	-	-	T	T	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr19:57955950T>C	ENST00000334181.4	+	3	1684	c.1434T>C	c.(1432-1434)atT>atC	p.I478I	AC004076.9_ENST00000596831.1_Intron	NM_001023561.2	NP_001018855.2	O43361	ZN749_HUMAN	zinc finger protein 749	478					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|kidney(2)|lung(3)|prostate(1)	13		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0264)|Lung(386;0.177)		GGATTGACATTAGGCCAAGGC	0.458																																						ENST00000334181.4		NA																	0				breast(1)|endometrium(6)|kidney(2)|lung(3)|prostate(1)	13						c.(1432-1434)atT>atC		zinc finger protein 749							84.0	78.0	80.0					19																	57955950		2203	4300	6503	SO:0001819	synonymous_variant	388567				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:57955950T>C	AK122740	CCDS33132.2	19q13.43	2013-01-08			ENSG00000186230	ENSG00000186230		"""Zinc fingers, C2H2-type"", ""-"""	32783	protein-coding gene	gene with protein product							Standard	NM_001023561		Approved	FLJ16360	uc002qoq.2	O43361	OTTHUMG00000150372	ENST00000334181.4:c.1434T>C	19.37:g.57955950T>C		False	False		Somatic	0				AC004076.9_ENST00000596831.1_Intron	p.I478I	NM_001023561.2	NP_001018855.2	WXS	Illumina HiSeq	Phase_I	O43361	ZN749_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0264)|Lung(386;0.177)	3	1684	+		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)	478						Silent	SNP	ENST00000334181.4	37	c.1434T>C	CCDS33132.2																																																																																				0.458	ZNF749-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317879.1	0	NM_001023561		19:57955950
HERC6	55008	broad.mit.edu	37	4	89349856	89349856	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr4:89349856G>A	ENST00000264346.7	+	16	2119	c.2060G>A	c.(2059-2061)cGt>cAt	p.R687H	HERC6_ENST00000380265.5_Missense_Mutation_p.R651H	NM_017912.3	NP_060382.3	Q8IVU3	HERC6_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 6	687					hematopoietic progenitor cell differentiation (GO:0002244)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)	11		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000222)		GATGCTCTGCGTCAATTAAGT	0.388																																						ENST00000380265.5		NA																	0				endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)	11						c.(1951-1953)cGt>cAt		HECT and RLD domain containing E3 ubiquitin protein ligase family member 6							30.0	28.0	29.0					4																	89349856		1855	4099	5954	SO:0001583	missense	55008				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytosol	ubiquitin-protein ligase activity	g.chr4:89349856G>A	AF336798	CCDS47098.1, CCDS54777.1	4q22	2012-02-23	2012-02-23		ENSG00000138642	ENSG00000138642			26072	protein-coding gene	gene with protein product		609249	"""hect domain and RLD 6"""				Standard	NM_001165136		Approved	FLJ20637	uc011cdi.2	Q8IVU3	OTTHUMG00000160983	ENST00000264346.7:c.2060G>A	4.37:g.89349856G>A	ENSP00000264346:p.Arg687His	False	False		Somatic	0				HERC6_ENST00000264346.7_Missense_Mutation_p.R687H	p.R651H	NM_001165136.1	NP_001158608.1	WXS	Illumina HiSeq	Phase_I	Q8IVU3	HERC6_HUMAN		OV - Ovarian serous cystadenocarcinoma(123;0.000222)	15	2135	+		Hepatocellular(203;0.114)	687					B4DIY5|Q5GC90|Q5GRH3|Q5HYM6|Q5JPB6|Q6PIF4|Q8NAN3|Q9NWS4	Missense_Mutation	SNP	ENST00000264346.7	37	c.1952G>A	CCDS47098.1	.	.	.	.	.	.	.	.	.	.	G	10.40	1.340412	0.24339	.	.	ENSG00000138642	ENST00000380265;ENST00000264346	T;T	0.77877	0.88;-1.13	4.25	4.25	0.50352	HECT (1);	0.116551	0.34002	N	0.004344	T	0.63129	0.2485	L	0.41710	1.295	0.80722	D	1	B;B	0.31817	0.341;0.231	B;B	0.19148	0.024;0.01	T	0.60078	-0.7333	10	0.10902	T	0.67	.	12.3559	0.55176	0.0:0.0:1.0:0.0	.	651;687	Q8IVU3-2;Q8IVU3	.;HERC6_HUMAN	H	651;687	ENSP00000369617:R651H;ENSP00000264346:R687H	ENSP00000264346:R687H	R	+	2	0	HERC6	89568879	0.046000	0.20272	0.997000	0.53966	0.863000	0.49368	0.184000	0.16939	2.356000	0.79943	0.467000	0.42956	CGT		0.388	HERC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363259.2	0			4:89349856
FEM1A	55527	broad.mit.edu	37	19	4793864	4793864	+	Silent	SNP	C	C	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr19:4793864C>A	ENST00000269856.3	+	1	2137	c.1998C>A	c.(1996-1998)atC>atA	p.I666I	AC005523.3_ENST00000598782.1_lincRNA|AC005523.2_ENST00000596170.1_RNA|AC005523.2_ENST00000601192.1_RNA	NM_018708.2	NP_061178.1	Q9BSK4	FEM1A_HUMAN	fem-1 homolog a (C. elegans)	666					negative regulation of inflammatory response (GO:0050728)|regulation of ubiquitin-protein transferase activity (GO:0051438)	cytoplasm (GO:0005737)	EP4 subtype prostaglandin E2 receptor binding (GO:0031867)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	17		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0139)		AGGCGTTCATCGAACTGCACT	0.592																																						ENST00000269856.3		NA																	0				breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	17						c.(1996-1998)atC>atA		fem-1 homolog a (C. elegans)							16.0	15.0	15.0					19																	4793864		2202	4297	6499	SO:0001819	synonymous_variant	55527				regulation of ubiquitin-protein ligase activity	cytoplasm	binding|ubiquitin-protein ligase activity	g.chr19:4793864C>A	BC004988	CCDS12135.1	19p13.3	2013-01-10	2006-11-08		ENSG00000141965	ENSG00000141965		"""Ankyrin repeat domain containing"""	16934	protein-coding gene	gene with protein product		613538				11441184	Standard	NM_018708		Approved		uc002mbf.3	Q9BSK4		ENST00000269856.3:c.1998C>A	19.37:g.4793864C>A		False	False		Somatic	0				AC005523.2_ENST00000601192.1_RNA	p.I666I	NM_018708.2	NP_061178.1	WXS	Illumina HiSeq	Phase_I	Q9BSK4	FEM1A_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0139)	1	2137	+		Hepatocellular(1079;0.137)	666					B2RDI3|Q711P8|Q9NPN7|Q9NPW8	Silent	SNP	ENST00000269856.3	37	c.1998C>A	CCDS12135.1																																																																																				0.592	FEM1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459000.1	0			19:4793864
AKAP3	10566	broad.mit.edu	37	12	4737445	4737445	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr12:4737445C>A	ENST00000545990.2	-	5	1147	c.623G>T	c.(622-624)aGt>aTt	p.S208I	RP11-500M8.7_ENST00000536588.1_Intron|AKAP3_ENST00000228850.1_Missense_Mutation_p.S208I	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	208					acrosome reaction (GO:0007340)|cellular component movement (GO:0006928)|protein localization (GO:0008104)|single fertilization (GO:0007338)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	acrosomal vesicle (GO:0001669)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	protein kinase A binding (GO:0051018)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|liver(1)|lung(17)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	51						ATTTGGGGGACTTTGTGATGA	0.488																																						ENST00000545990.2		NA																	0				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|liver(1)|lung(17)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	51						c.(622-624)aGt>aTt		A kinase (PRKA) anchor protein 3							94.0	94.0	94.0					12																	4737445		2203	4300	6503	SO:0001583	missense	10566				acrosome reaction|cellular component movement	acrosomal vesicle	protein kinase A binding	g.chr12:4737445C>A	U85715	CCDS8531.1	12p13.3	2009-03-12				ENSG00000111254		"""A-kinase anchor proteins"""	373	protein-coding gene	gene with protein product	"""Fibrous Sheath Protein of 95 kDa"", ""cancer/testis antigen 82"""	604689				10334916, 10319321	Standard	NM_001278309		Approved	FSP95, SOB1, AKAP110, CT82	uc001qnb.4	O75969		ENST00000545990.2:c.623G>T	12.37:g.4737445C>A	ENSP00000440994:p.Ser208Ile	True	False		Somatic	0				AKAP3_ENST00000228850.1_Missense_Mutation_p.S208I|RP11-500M8.7_ENST00000536588.1_Intron	p.S208I	NM_001278309.1	NP_001265238.1	WXS	Illumina HiSeq	Phase_I	O75969	AKAP3_HUMAN			5	1147	-			208					O75945|Q86X01|Q9UM61	Missense_Mutation	SNP	ENST00000545990.2	37	c.623G>T	CCDS8531.1	.	.	.	.	.	.	.	.	.	.	C	4.255	0.046299	0.08243	.	.	ENSG00000111254	ENST00000228850;ENST00000545990	T;T	0.10668	2.85;2.85	4.61	-1.24	0.09435	A-kinase anchor 110kDa, C-terminal (1);	0.765712	0.12130	N	0.496807	T	0.09335	0.0230	L	0.57536	1.79	0.09310	N	1	B	0.12630	0.006	B	0.12837	0.008	T	0.37663	-0.9696	10	0.87932	D	0	.	1.3901	0.02249	0.303:0.3889:0.1314:0.1767	.	208	O75969	AKAP3_HUMAN	I	208	ENSP00000228850:S208I;ENSP00000440994:S208I	ENSP00000228850:S208I	S	-	2	0	AKAP3	4607706	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-0.674000	0.05233	-0.341000	0.08376	-0.459000	0.05422	AGT		0.488	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2	0	NM_006422		12:4737445
PTGS1	5742	broad.mit.edu	37	9	125148756	125148756	+	Silent	SNP	C	C	T	rs201795484		TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr9:125148756C>T	ENST00000362012.2	+	9	1046	c.1041C>T	c.(1039-1041)taC>taT	p.Y347Y	AL162424.1_ENST00000600713.1_Intron|PTGS1_ENST00000223423.4_Silent_p.Y347Y|PTGS1_ENST00000540753.1_Silent_p.Y322Y|PTGS1_ENST00000373698.5_Silent_p.Y238Y	NM_000962.3|NM_001271164.1|NM_001271367.1|NM_080591.2	NP_000953.2|NP_001258093.1|NP_001258296.1|NP_542158.1	P23219	PGH1_HUMAN	prostaglandin-endoperoxide synthase 1 (prostaglandin G/H synthase and cyclooxygenase)	347					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|prostaglandin biosynthetic process (GO:0001516)|regulation of blood pressure (GO:0008217)|regulation of cell proliferation (GO:0042127)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|photoreceptor outer segment (GO:0001750)	dioxygenase activity (GO:0051213)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)|prostaglandin-endoperoxide synthase activity (GO:0004666)			large_intestine(3)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	8					Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Antipyrine(DB01435)|Antrafenine(DB01419)|Balsalazide(DB01014)|Bortezomib(DB00188)|Bromfenac(DB00963)|Candesartan(DB00796)|Carprofen(DB00821)|Carvedilol(DB01136)|Chlorpropamide(DB00672)|Dapsone(DB00250)|Desmopressin(DB00035)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylcarbamazine(DB00711)|Diflunisal(DB00861)|Dihomo-gamma-linolenic acid(DB00154)|Diphenhydramine(DB01075)|Dronabinol(DB00470)|Eletriptan(DB00216)|Eszopiclone(DB00402)|Etodolac(DB00749)|Etoposide(DB00773)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|Hexobarbital(DB01355)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Icosapent(DB00159)|Ifosfamide(DB01181)|Imatinib(DB00619)|Indomethacin(DB00328)|Irbesartan(DB01029)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lornoxicam(DB06725)|Lumiracoxib(DB01283)|Magnesium salicylate(DB01397)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mesalazine(DB00244)|Minoxidil(DB00350)|Montelukast(DB00471)|Nabumetone(DB00461)|Naproxen(DB00788)|Nateglinide(DB00731)|Nepafenac(DB06802)|Niflumic Acid(DB04552)|Nortriptyline(DB00540)|Oxaprozin(DB00991)|Phenylbutazone(DB00812)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Rosiglitazone(DB00412)|Salicylate-sodium(DB01398)|Salicylic acid(DB00936)|Salsalate(DB01399)|Sulfamethoxazole(DB01015)|Sulfasalazine(DB00795)|Sulindac(DB00605)|Suprofen(DB00870)|Tenoxicam(DB00469)|Terbinafine(DB00857)|Thalidomide(DB01041)|Tiaprofenic acid(DB01600)|Tolmetin(DB00500)|Torasemide(DB00214)|Trabectedin(DB05109)|Triflusal(DB08814)|Trisalicylate-choline(DB01401)|Valproic Acid(DB00313)|Voriconazole(DB00582)|Zafirlukast(DB00549)|Zileuton(DB00744)|Zolpidem(DB00425)|Zopiclone(DB01198)	TCGAGGAGTACGTGCAGCAGC	0.527																																						ENST00000362012.2		NA																	0				large_intestine(3)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	8						c.(1039-1041)taC>taT		prostaglandin-endoperoxide synthase 1 (prostaglandin G/H synthase and cyclooxygenase)	Acetaminophen(DB00316)|Aspirin(DB00945)|Balsalazide(DB01014)|Bromfenac(DB00963)|Ciclopirox(DB01188)|Diclofenac(DB00586)|Diflunisal(DB00861)|Dipyrone(DB04817)|Etodolac(DB00749)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|gamma-Homolinolenic acid(DB00154)|Ibuprofen(DB01050)|Icosapent(DB00159)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lumiracoxib(DB01283)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Mesalazine(DB00244)|Minoxidil(DB00350)|Nabumetone(DB00461)|Naproxen(DB00788)|Phenacetin(DB03783)|Piroxicam(DB00554)|Rofecoxib(DB00533)|Salicyclic acid(DB00936)|Salsalate(DB01399)|Sulindac(DB00605)|Suprofen(DB00870)|Tenoxicam(DB00469)|Tolmetin(DB00500)						147.0	149.0	148.0					9																	125148756		2203	4300	6503	SO:0001819	synonymous_variant	5742				cyclooxygenase pathway|hormone biosynthetic process|regulation of blood pressure|response to oxidative stress|xenobiotic metabolic process	endoplasmic reticulum membrane|Golgi apparatus|microsome|plasma membrane	heme binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peroxidase activity|prostaglandin-endoperoxide synthase activity	g.chr9:125148756C>T	M59979	CCDS6842.1, CCDS6843.1, CCDS59520.1, CCDS59521.1, CCDS75895.1	9q32-q33.3	2008-02-05			ENSG00000095303	ENSG00000095303	1.14.99.1		9604	protein-coding gene	gene with protein product		176805				2512924, 1907252	Standard	NM_000962		Approved	COX1, PGHS-1, PTGHS	uc004bmg.2	P23219	OTTHUMG00000020605	ENST00000362012.2:c.1041C>T	9.37:g.125148756C>T		False	False		Somatic	0				AL162424.1_ENST00000600713.1_Intron|PTGS1_ENST00000373698.5_Silent_p.Y238Y|PTGS1_ENST00000540753.1_Silent_p.Y322Y|PTGS1_ENST00000223423.4_Silent_p.Y347Y	p.Y347Y	NM_000962.3|NM_001271164.1|NM_001271367.1|NM_080591.2	NP_000953.2|NP_001258093.1|NP_001258296.1|NP_542158.1	WXS	Illumina HiSeq	Phase_I	P23219	PGH1_HUMAN			9	1046	+			347					A8K1V7|B4DHQ2|B4E2S5|Q15122|Q3HY28|Q3HY29|Q5T7T6|Q5T7T7|Q5T7T8	Silent	SNP	ENST00000362012.2	37	c.1041C>T	CCDS6842.1																																																																																				0.527	PTGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053933.1	0			9:125148756
CYB5RL	606495	broad.mit.edu	37	1	54640404	54640404	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr1:54640404C>T	ENST00000534324.1	-	6	835	c.836G>A	c.(835-837)tGc>tAc	p.C279Y	RP11-446E24.4_ENST00000525949.1_5'Flank|CYB5RL_ENST00000401046.3_Missense_Mutation_p.C131Y|AL357673.1_ENST00000536061.1_5'Flank|CYB5RL_ENST00000542737.1_Missense_Mutation_p.C279Y|CYB5RL_ENST00000287899.8_Missense_Mutation_p.C211Y|CYB5RL_ENST00000419823.2_Missense_Mutation_p.C279Y|RP11-446E24.4_ENST00000311841.7_Intron|CYB5RL_ENST00000537208.1_Missense_Mutation_p.C211Y			Q6IPT4	NB5R5_HUMAN	cytochrome b5 reductase-like	279							cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)			endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|urinary_tract(1)	8						TCTCCGACAGCAGCTGACCAG	0.552																																						ENST00000419823.2		NA																	0				endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|urinary_tract(1)	8						c.(835-837)tGc>tAc		cytochrome b5 reductase-like							43.0	45.0	44.0					1																	54640404		1937	4156	6093	SO:0001583	missense	606495						cytochrome-b5 reductase activity	g.chr1:54640404C>T		CCDS44151.1	1p32.3	2011-04-08			ENSG00000215883	ENSG00000215883			32220	protein-coding gene	gene with protein product						12477932	Standard	NM_001031672		Approved	LOC606495	uc009vzo.3	Q6IPT4	OTTHUMG00000008082	ENST00000534324.1:c.836G>A	1.37:g.54640404C>T	ENSP00000434343:p.Cys279Tyr	False	False		Somatic	0				CYB5RL_ENST00000534324.1_Missense_Mutation_p.C279Y|RP11-446E24.4_ENST00000311841.7_Intron|CYB5RL_ENST00000287899.8_Missense_Mutation_p.C211Y|CYB5RL_ENST00000401046.3_Missense_Mutation_p.C131Y|CYB5RL_ENST00000537208.1_Missense_Mutation_p.C211Y|CYB5RL_ENST00000542737.1_Missense_Mutation_p.C279Y	p.C279Y	NM_001031672.2	NP_001026842.2	WXS	Illumina HiSeq	Phase_I	Q6IPT4	NB5R5_HUMAN			7	1060	-			279					B7ZBS4|Q8NF25	Missense_Mutation	SNP	ENST00000534324.1	37	c.836G>A	CCDS44151.1	.	.	.	.	.	.	.	.	.	.	C	7.486	0.649652	0.14516	.	.	ENSG00000215883	ENST00000419823;ENST00000401046;ENST00000534324;ENST00000287899;ENST00000542737;ENST00000537208	D;D;D;D;D;D	0.85861	-2.04;-2.04;-2.04;-1.9;-2.04;-1.9	5.14	3.21	0.36854	Oxidoreductase FAD/NAD(P)-binding (1);	0.413252	0.17337	U	0.177898	T	0.77356	0.4118	L	0.36672	1.1	0.24354	N	0.994901	B;B	0.22414	0.069;0.001	B;B	0.28553	0.091;0.001	T	0.64219	-0.6459	10	0.32370	T	0.25	-19.4038	7.8496	0.29446	0.0:0.2439:0.6084:0.1477	.	279;131	Q6IPT4;Q6IPT4-3	NB5R5_HUMAN;.	Y	279;131;279;211;279;211	ENSP00000409075:C279Y;ENSP00000383825:C131Y;ENSP00000434343:C279Y;ENSP00000287899:C211Y;ENSP00000438151:C279Y;ENSP00000443797:C211Y	ENSP00000287899:C211Y	C	-	2	0	CYB5RL	54412992	0.984000	0.35163	0.465000	0.27155	0.376000	0.30014	2.109000	0.41863	0.696000	0.31696	0.555000	0.69702	TGC		0.552	CYB5RL-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388318.1	0	NM_001031672		1:54640404
SPATA31D5P	347127	broad.mit.edu	37	9	84533928	84533928	+	RNA	SNP	G	G	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr9:84533928G>A	ENST00000527857.1	+	0	3950					NR_026851.1				SPATA31 subfamily D, member 5, pseudogene																		TTCACCAGCTGCAAAGAGAGT	0.532																																						ENST00000527857.1		NA																	0					NA																																														0							g.chr9:84533928G>A			9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000240632	ENSG00000240632			38602	pseudogene	pseudogene			"""family with sequence similarity 75, member D5"", ""family with sequence similarity 75, member D5, pseudogene"""	FAM75D5			Standard	NR_026851		Approved	FLJ43950, FAM75D5P	uc011lst.2		OTTHUMG00000020087		9.37:g.84533928G>A		False	False		Somatic	0						NR_026851.1		WXS	Illumina HiSeq	Phase_I					0	3950	+			NA						RNA	SNP	ENST00000527857.1	37																																																																																						0.532	SPATA31D5P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000052810.2	0	NR_026851		9:84533928
RPTOR	57521	broad.mit.edu	37	17	78914377	78914377	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr17:78914377C>A	ENST00000306801.3	+	25	3363	c.3001C>A	c.(3001-3003)Cag>Aag	p.Q1001K	CTD-2561B21.4_ENST00000576032.1_RNA|RPTOR_ENST00000575542.1_3'UTR|RPTOR_ENST00000544334.2_Missense_Mutation_p.Q843K	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	1001					cell cycle arrest (GO:0007050)|cell growth (GO:0016049)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nutrient levels (GO:0031669)|insulin receptor signaling pathway (GO:0008286)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of TOR signaling (GO:0032008)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|regulation of cell size (GO:0008361)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|TORC1 complex (GO:0031931)	14-3-3 protein binding (GO:0071889)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	44						TGTCAGGAGGCAGGCCCAGCA	0.632																																						ENST00000306801.3		NA																	0				breast(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	44						c.(3001-3003)Cag>Aag		regulatory associated protein of MTOR, complex 1							45.0	39.0	41.0					17																	78914377		2200	4299	6499	SO:0001583	missense	57521				cell cycle arrest|cell growth|cellular response to amino acid stimulus|cellular response to nutrient levels|insulin receptor signaling pathway|positive regulation of protein serine/threonine kinase activity|positive regulation of TOR signaling cascade|TOR signaling cascade	cytosol|lysosome|TORC1 complex	protein complex binding	g.chr17:78914377C>A		CCDS11773.1, CCDS54175.1	17q25.3	2013-01-10				ENSG00000141564		"""WD repeat domain containing"""	30287	protein-coding gene	gene with protein product	"""regulatory associated protein of mTOR"""	607130				10718198, 12150926	Standard	NM_001163034		Approved	KOG1, Mip1, KIAA1303, raptor	uc002jyt.1	Q8N122		ENST00000306801.3:c.3001C>A	17.37:g.78914377C>A	ENSP00000307272:p.Gln1001Lys	True	False		Somatic	0				CTD-2561B21.4_ENST00000576032.1_RNA|RPTOR_ENST00000575542.1_3'UTR|RPTOR_ENST00000544334.2_Missense_Mutation_p.Q843K	p.Q1001K	NM_020761.2	NP_065812.1	WXS	Illumina HiSeq	Phase_I	Q8N122	RPTOR_HUMAN			25	3363	+			1001					B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Missense_Mutation	SNP	ENST00000306801.3	37	c.3001C>A	CCDS11773.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.165535	0.78339	.	.	ENSG00000141564	ENST00000306801;ENST00000544334	T;T	0.41758	1.01;0.99	4.8	4.8	0.61643	.	0.070570	0.64402	D	0.000019	T	0.56804	0.2010	L	0.50333	1.59	0.80722	D	1	P;B	0.43578	0.811;0.111	P;B	0.57846	0.828;0.026	T	0.55173	-0.8182	10	0.42905	T	0.14	.	17.8504	0.88746	0.0:1.0:0.0:0.0	.	843;1001	F5H7J5;Q8N122	.;RPTOR_HUMAN	K	1001;843	ENSP00000307272:Q1001K;ENSP00000442479:Q843K	ENSP00000307272:Q1001K	Q	+	1	0	RPTOR	76528972	1.000000	0.71417	0.962000	0.40283	0.334000	0.28698	6.977000	0.76141	2.209000	0.71365	0.561000	0.74099	CAG		0.632	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	0	NM_020761		17:78914377
ROR2	4920	broad.mit.edu	37	9	94486741	94486741	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr9:94486741C>T	ENST00000375708.3	-	9	2233	c.2035G>A	c.(2035-2037)Ggt>Agt	p.G679S	ROR2_ENST00000375715.1_Missense_Mutation_p.G539S|ROR2_ENST00000550066.1_5'UTR	NM_004560.3	NP_004551.2	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	679	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|embryonic genitalia morphogenesis (GO:0030538)|inner ear morphogenesis (GO:0042472)|JNK cascade (GO:0007254)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	clathrin-coated endocytic vesicle membrane (GO:0030669)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						AGGACCACACCGTAGGACCAG	0.607																																						ENST00000375708.3		NA																	0				autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						c.(2035-2037)Ggt>Agt		receptor tyrosine kinase-like orphan receptor 2							75.0	61.0	65.0					9																	94486741		2203	4300	6503	SO:0001583	missense	4920				negative regulation of cell proliferation|positive regulation of cell migration|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding	g.chr9:94486741C>T	M97639	CCDS6691.1	9q22	2013-01-11			ENSG00000169071	ENSG00000169071		"""Immunoglobulin superfamily / I-set domain containing"""	10257	protein-coding gene	gene with protein product		602337		NTRKR2, BDB, BDB1		1334494, 10700182	Standard	NM_004560		Approved		uc004arj.2	Q01974	OTTHUMG00000020211	ENST00000375708.3:c.2035G>A	9.37:g.94486741C>T	ENSP00000364860:p.Gly679Ser	False	False		Somatic	0				ROR2_ENST00000550066.1_5'UTR|ROR2_ENST00000375715.1_Missense_Mutation_p.G539S	p.G679S	NM_004560.3	NP_004551.2	WXS	Illumina HiSeq	Phase_I	Q01974	ROR2_HUMAN			9	2233	-			679			Protein kinase.		Q59GF5|Q5SPI5|Q9HAY7|Q9HB61	Missense_Mutation	SNP	ENST00000375708.3	37	c.2035G>A	CCDS6691.1	.	.	.	.	.	.	.	.	.	.	C	17.59	3.427881	0.62733	.	.	ENSG00000169071	ENST00000375715;ENST00000375708	D;D	0.99150	-5.49;-5.49	4.86	4.86	0.63082	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.42420	D	0.000712	D	0.99471	0.9812	M	0.93638	3.44	0.80722	D	1	D;D	0.76494	0.995;0.999	P;D	0.75020	0.797;0.985	D	0.98372	1.0554	10	0.87932	D	0	.	18.2087	0.89863	0.0:1.0:0.0:0.0	.	679;539	Q01974;B1APY4	ROR2_HUMAN;.	S	539;679	ENSP00000364867:G539S;ENSP00000364860:G679S	ENSP00000364860:G679S	G	-	1	0	ROR2	93526562	1.000000	0.71417	1.000000	0.80357	0.446000	0.32137	5.842000	0.69417	2.526000	0.85167	0.561000	0.74099	GGT		0.607	ROR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053040.1	0			9:94486741
CCDC180	100499483	broad.mit.edu	37	9	100053719	100053719	+	Silent	SNP	C	C	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr9:100053719C>A	ENST00000357054.1	+	12	971	c.36C>A	c.(34-36)acC>acA	p.T12T	CCDC180_ENST00000395220.1_Silent_p.T12T|CCDC180_ENST00000375205.2_Silent_p.T12T|RP11-23J9.5_ENST00000375204.2_RNA|CCDC180_ENST00000375202.2_5'UTR|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000411667.2_5'UTR			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	12						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											CTGGTGCTACCCATCGTCCAA	0.537																																						ENST00000357054.1		NA																	0					NA						c.(34-36)acC>acA		coiled-coil domain containing 180							228.0	197.0	207.0					9																	100053719		2203	4300	6503	SO:0001819	synonymous_variant	100499483							g.chr9:100053719C>A	AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"""Behcet's Disease Associated Gene 1"""		"""KIAA1529"", ""chromosome 9 open reading frame 174"""	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	ENST00000357054.1:c.36C>A	9.37:g.100053719C>A		True	False		Somatic	0				RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000375205.2_Silent_p.T12T|CCDC180_ENST00000411667.2_5'UTR|CCDC180_ENST00000375202.2_5'UTR|RP11-23J9.5_ENST00000375204.2_RNA|CCDC180_ENST00000395220.1_Silent_p.T12T	p.T12T			WXS	Illumina HiSeq	Phase_I					12	971	+			NA					Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Silent	SNP	ENST00000357054.1	37	c.36C>A																																																																																					0.537	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		0	NM_020893		9:100053719
PINK1	65018	broad.mit.edu	37	1	20975596	20975596	+	Missense_Mutation	SNP	T	T	G			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	T	T	-	-	T	T	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr1:20975596T>G	ENST00000321556.4	+	7	1454	c.1360T>G	c.(1360-1362)Tac>Gac	p.Y454D	PINK1-AS_ENST00000451424.1_RNA|PINK1_ENST00000492302.1_3'UTR	NM_032409.2	NP_115785.1	Q9BXM7	PINK1_HUMAN	PTEN induced putative kinase 1	454	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159, ECO:0000305}.				activation of protein kinase B activity (GO:0032148)|cell death (GO:0008219)|cellular response to hypoxia (GO:0071456)|cellular response to toxic substance (GO:0097237)|intracellular signal transduction (GO:0035556)|mitochondrion degradation (GO:0000422)|mitochondrion organization (GO:0007005)|negative regulation of gene expression (GO:0010629)|negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway (GO:1903384)|negative regulation of JNK cascade (GO:0046329)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of oxidative stress-induced cell death (GO:1903202)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of oxidative stress-induced neuron death (GO:1903204)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|peptidyl-serine autophosphorylation (GO:0036289)|peptidyl-serine phosphorylation (GO:0018105)|phosphorylation (GO:0016310)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of mitochondrial electron transport, NADH to ubiquinone (GO:1902958)|positive regulation of peptidase activity (GO:0010952)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of synaptic transmission, dopaminergic (GO:0032226)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of mitochondrion degradation (GO:1903146)|regulation of protein complex assembly (GO:0043254)|regulation of protein ubiquitination (GO:0031396)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|TORC2 signaling (GO:0038203)|ubiquitin-dependent protein catabolic process (GO:0006511)	astrocyte projection (GO:0097449)|axon (GO:0030424)|cell body (GO:0044297)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of mitochondrial outer membrane (GO:0031307)|Lewy body (GO:0097413)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|C3HC4-type RING finger domain binding (GO:0055131)|calcium-dependent protein kinase activity (GO:0010857)|kinase activity (GO:0016301)|magnesium ion binding (GO:0000287)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)|protein kinase B binding (GO:0043422)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)	14		all_lung(284;2.72e-05)|Lung NSC(340;2.94e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.21e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000146)|Kidney(64;0.000182)|GBM - Glioblastoma multiforme(114;0.000497)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		CAATCCCTTCTACGGCCAGGG	0.607																																					Esophageal Squamous(145;853 1803 8146 34412 35011)	ENST00000321556.4		NA																	0				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)	14						c.(1360-1362)Tac>Gac		PTEN induced putative kinase 1							69.0	61.0	64.0					1																	20975596		2203	4300	6503	SO:0001583	missense	65018				cell death|intracellular protein kinase cascade|mitochondrion degradation|peptidyl-serine phosphorylation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of release of cytochrome c from mitochondria|regulation of protein complex assembly|regulation of protein ubiquitination|response to stress	cytosol|integral to membrane|mitochondrial outer membrane	ATP binding|C3HC4-type RING finger domain binding|calcium-dependent protein kinase activity|magnesium ion binding|protein serine/threonine kinase activity|ubiquitin protein ligase binding	g.chr1:20975596T>G	AB053323	CCDS211.1	1p36.12	2011-07-21			ENSG00000158828	ENSG00000158828		"""Parkinson disease"""	14581	protein-coding gene	gene with protein product		608309	"""Parkinson disease (autosomal recessive) 6"""	PARK6		11494141, 15349860	Standard	NM_032409		Approved		uc001bdm.3	Q9BXM7	OTTHUMG00000002841	ENST00000321556.4:c.1360T>G	1.37:g.20975596T>G	ENSP00000364204:p.Tyr454Asp	False	False		Somatic	0				PINK1_ENST00000492302.1_3'UTR|PINK1-AS_ENST00000451424.1_RNA	p.Y454D	NM_032409.2	NP_115785.1	WXS	Illumina HiSeq	Phase_I	Q9BXM7	PINK1_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.21e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000146)|Kidney(64;0.000182)|GBM - Glioblastoma multiforme(114;0.000497)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)	7	1454	+		all_lung(284;2.72e-05)|Lung NSC(340;2.94e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)	454			Protein kinase.		Q8N6T9|Q8NBU3|Q96DE4	Missense_Mutation	SNP	ENST00000321556.4	37	c.1360T>G	CCDS211.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.986271	0.74589	.	.	ENSG00000158828	ENST00000321556	T	0.64260	-0.09	6.05	6.05	0.98169	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.057544	0.64402	D	0.000001	T	0.72922	0.3521	L	0.45470	1.425	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.993;0.998	T	0.74225	-0.3734	10	0.56958	D	0.05	-10.0039	12.9918	0.58622	0.0:0.0:0.0:1.0	.	147;454	Q9BXM7-2;Q9BXM7	.;PINK1_HUMAN	D	454	ENSP00000364204:Y454D	ENSP00000364204:Y454D	Y	+	1	0	PINK1	20848183	1.000000	0.71417	0.970000	0.41538	0.633000	0.38033	7.179000	0.77665	2.323000	0.78572	0.533000	0.62120	TAC		0.607	PINK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007954.1	0	NM_032409		1:20975596
IGHV2-26	28455	broad.mit.edu	37	14	106757880	106757880	+	RNA	SNP	C	C	T	rs146488407	byFrequency	TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr14:106757880C>T	ENST00000390611.2	-	0	150									immunoglobulin heavy variable 2-26																		AACCCAGAGACGGTGCAGGTC	0.552													c|||	10	0.00199681	0.0068	0.0	5008	,	,		14914	0.0		0.001	False		,,,				2504	0.0					ENST00000390611.2		NA																	0					NA										T		27,3959		0,27,1966	48.0	46.0	47.0			-5.4	0.0	14	dbSNP_134	47	3,8325		1,1,4162	no	intergenic				1,28,6128	TT,TC,CC		0.036,0.6774,0.2436			106757880	30,12284	1993	4164	6157			0							g.chr14:106757880C>T	M99648		14q32.33	2012-02-08			ENSG00000211951	ENSG00000211951		"""Immunoglobulins / IGH locus"""	5575	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000152100		14.37:g.106757880C>T		False	False		Somatic	0								WXS	Illumina HiSeq	Phase_I					0	150	-			NA						RNA	SNP	ENST00000390611.2	37																																																																																						0.552	IGHV2-26-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene	OTTHUMT00000325197.1	0	NG_001019		14:106757880
SLC35F3	148641	broad.mit.edu	37	1	234454518	234454518	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr1:234454518G>A	ENST00000366617.3	+	5	997	c.769G>A	c.(769-771)Ggc>Agc	p.G257S	SLC35F3_ENST00000366618.3_Missense_Mutation_p.G326S			Q8IY50	S35F3_HUMAN	solute carrier family 35, member F3	257					thiamine transport (GO:0015888)	integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|urinary_tract(1)	32	Ovarian(103;0.0454)	all_cancers(173;0.145)|Prostate(94;0.0885)	OV - Ovarian serous cystadenocarcinoma(106;0.00531)			GCTCCTCCTGGGCAGTGCTAA	0.468																																						ENST00000366618.3		NA																	0				breast(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|urinary_tract(1)	32						c.(976-978)Ggc>Agc		solute carrier family 35, member F3							174.0	168.0	170.0					1																	234454518		2203	4300	6503	SO:0001583	missense	148641				transport	integral to membrane		g.chr1:234454518G>A		CCDS1600.1, CCDS73050.1	1q42.3	2013-05-22			ENSG00000183780	ENSG00000183780		"""Solute carriers"""	23616	protein-coding gene	gene with protein product							Standard	XM_005273070		Approved	FLJ37712	uc001hvy.1	Q8IY50	OTTHUMG00000037929	ENST00000366617.3:c.769G>A	1.37:g.234454518G>A	ENSP00000355576:p.Gly257Ser	True	False		Somatic	0				SLC35F3_ENST00000366617.3_Missense_Mutation_p.G257S	p.G326S	NM_173508.2	NP_775779.1	WXS	Illumina HiSeq	Phase_I	Q8IY50	S35F3_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.00531)		6	1121	+	Ovarian(103;0.0454)	all_cancers(173;0.145)|Prostate(94;0.0885)	257					Q5TDD6|Q8N9C9	Missense_Mutation	SNP	ENST00000366617.3	37	c.976G>A		.	.	.	.	.	.	.	.	.	.	G	36	5.759291	0.96898	.	.	ENSG00000183780	ENST00000366618;ENST00000366617	T;T	0.73469	-0.75;-0.75	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	D	0.87736	0.6252	M	0.83483	2.645	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.86546	0.1831	10	0.40728	T	0.16	-24.7144	19.8559	0.96758	0.0:0.0:1.0:0.0	.	257;326	Q8IY50;Q8IY50-2	S35F3_HUMAN;.	S	326;257	ENSP00000355577:G326S;ENSP00000355576:G257S	ENSP00000355576:G257S	G	+	1	0	SLC35F3	232521141	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.693000	0.91896	0.655000	0.94253	GGC		0.468	SLC35F3-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000128322.1	0	NM_173508		1:234454518
C2orf71	388939	broad.mit.edu	37	2	29295748	29295748	+	Silent	SNP	C	C	T			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr2:29295748C>T	ENST00000331664.5	-	1	1379	c.1380G>A	c.(1378-1380)ggG>ggA	p.G460G		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	460					response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						AGACCCCAATCCCAAAGGAAT	0.557																																						ENST00000331664.5		NA																	0				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						c.(1378-1380)ggG>ggA		chromosome 2 open reading frame 71							83.0	87.0	85.0					2																	29295748		1992	4172	6164	SO:0001819	synonymous_variant	388939				response to stimulus|visual perception	photoreceptor outer segment		g.chr2:29295748C>T		CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.1380G>A	2.37:g.29295748C>T		True	False		Somatic	0					p.G460G	NM_001029883.2	NP_001025054.1	WXS	Illumina HiSeq	Phase_I	A6NGG8	CB071_HUMAN			1	1379	-			460						Silent	SNP	ENST00000331664.5	37	c.1380G>A	CCDS42669.1																																																																																				0.557	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	0	NM_001029883		2:29295748
FOXP2	93986	broad.mit.edu	37	7	114298280	114298280	+	Nonsense_Mutation	SNP	C	C	T			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr7:114298280C>T	ENST00000393494.2	+	11	1705	c.1426C>T	c.(1426-1428)Cga>Tga	p.R476*	FOXP2_ENST00000393489.3_Nonsense_Mutation_p.R384*|FOXP2_ENST00000393500.3_3'UTR|FOXP2_ENST00000408937.3_Nonsense_Mutation_p.R501*|FOXP2_ENST00000393498.2_Nonsense_Mutation_p.R455*|FOXP2_ENST00000403559.4_Nonsense_Mutation_p.R493*|FOXP2_ENST00000393491.3_Intron|FOXP2_ENST00000350908.4_Nonsense_Mutation_p.R476*			O15409	FOXP2_HUMAN	forkhead box P2	476					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)			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						GGGAGCCATACGAAGGCGACA	0.507																																						ENST00000408937.3		NA																	0				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.(1501-1503)Cga>Tga		forkhead box P2							116.0	99.0	105.0					7																	114298280		2203	4300	6503	SO:0001587	stop_gained	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.chr7:114298280C>T	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.1426C>T	7.37:g.114298280C>T	ENSP00000377132:p.Arg476*	False	False		Somatic	0				FOXP2_ENST00000403559.4_Nonsense_Mutation_p.R493*|FOXP2_ENST00000393498.2_Nonsense_Mutation_p.R455*|FOXP2_ENST00000393491.3_Intron|FOXP2_ENST00000393489.3_Nonsense_Mutation_p.R384*|FOXP2_ENST00000393494.2_Nonsense_Mutation_p.R476*|FOXP2_ENST00000393500.3_3'UTR|FOXP2_ENST00000350908.4_Nonsense_Mutation_p.R476*	p.R501*	NM_001172766.2|NM_014491.3|NM_148898.3	NP_001166237.1|NP_055306.1|NP_683696.2	WXS	Illumina HiSeq	Phase_I	O15409	FOXP2_HUMAN			12	1875	+			476					A0AUV6|A4D0U8|A6NNW4|B4DLD9|Q6ZND1|Q75MJ3|Q8IZE0|Q8N0W2|Q8N6B7|Q8N6B8|Q8NFQ1|Q8NFQ2|Q8NFQ3|Q8NFQ4|Q8TD74	Nonsense_Mutation	SNP	ENST00000393494.2	37	c.1501C>T	CCDS5760.1	.	.	.	.	.	.	.	.	.	.	C	39	7.583133	0.98371	.	.	ENSG00000128573	ENST00000393494;ENST00000408937;ENST00000403559;ENST00000350908;ENST00000393498;ENST00000393489	.	.	.	5.71	5.71	0.89125	.	0.113270	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.2245	0.98337	0.0:1.0:0.0:0.0	.	.	.	.	X	476;501;493;476;453;384	.	ENSP00000265436:R476X	R	+	1	2	FOXP2	114085516	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.664000	0.54525	2.861000	0.98227	0.650000	0.86243	CGA		0.507	FOXP2-014	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317366.1	0	NM_014491		7:114298280
LRRC3	81543	broad.mit.edu	37	21	45877295	45877295	+	Silent	SNP	G	G	T			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr21:45877295G>T	ENST00000291592.4	+	2	1085	c.768G>T	c.(766-768)ggG>ggT	p.G256G	LRRC3-AS1_ENST00000426578.1_RNA|LRRC3DN_ENST00000596691.1_5'Flank	NM_030891.3	NP_112153.1	Q9BY71	LRRC3_HUMAN	leucine rich repeat containing 3	256						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|lung(1)|urinary_tract(1)	5		Breast(209;0.00908)		COAD - Colon adenocarcinoma(84;0.148)|Lung(125;0.195)		TCGGCCCGGGGCCCTAGCGCC	0.637																																						ENST00000291592.4		NA																	0				endometrium(2)|kidney(1)|lung(1)|urinary_tract(1)	5						c.(766-768)ggG>ggT		leucine rich repeat containing 3							17.0	22.0	20.0					21																	45877295		2134	4179	6313	SO:0001819	synonymous_variant	81543					integral to membrane	protein binding	g.chr21:45877295G>T	AB058646	CCDS13711.1	21q22.3	2011-12-07	2002-06-20		ENSG00000160233	ENSG00000160233			14965	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 102"""	C21orf102		12036297	Standard	NM_030891		Approved		uc002zfa.3	Q9BY71	OTTHUMG00000040847	ENST00000291592.4:c.768G>T	21.37:g.45877295G>T		True	False		Somatic	0					p.G256G	NM_030891.3	NP_112153.1	WXS	Illumina HiSeq	Phase_I	Q9BY71	LRRC3_HUMAN		COAD - Colon adenocarcinoma(84;0.148)|Lung(125;0.195)	2	1085	+		Breast(209;0.00908)	256					Q0VDJ2	Silent	SNP	ENST00000291592.4	37	c.768G>T	CCDS13711.1																																																																																				0.637	LRRC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098095.3	0			21:45877295
NIPBL	25836	broad.mit.edu	37	5	37044451	37044451	+	Silent	SNP	G	G	T			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr5:37044451G>T	ENST00000282516.8	+	35	6610	c.6111G>T	c.(6109-6111)acG>acT	p.T2037T	NIPBL_ENST00000448238.2_Silent_p.T2037T	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	2037					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			TCTTATAGACGCAAAATGATT	0.358																																						ENST00000282516.8		NA																	0				autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128						c.(6109-6111)acG>acT		Nipped-B homolog (Drosophila)							49.0	49.0	49.0					5																	37044451		2203	4299	6502	SO:0001819	synonymous_variant	25836				brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis	SMC loading complex	chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding	g.chr5:37044451G>T	AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"""sister chromatid cohesion 2 homolog (yeast)"""	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.6111G>T	5.37:g.37044451G>T		False	False		Somatic	0				NIPBL_ENST00000448238.2_Silent_p.T2037T	p.T2037T	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	WXS	Illumina HiSeq	Phase_I	Q6KC79	NIPBL_HUMAN	Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)		35	6610	+	all_lung(31;0.000447)|Hepatocellular(1;0.108)		2037					Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Silent	SNP	ENST00000282516.8	37	c.6111G>T	CCDS3920.1																																																																																				0.358	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	0	NM_015384		5:37044451
PNMAL2	57469	broad.mit.edu	37	19	46998201	46998201	+	Silent	SNP	G	G	C			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr19:46998201G>C	ENST00000377655.2	-	1	521	c.522C>G	c.(520-522)acC>acG	p.T174T	AC011484.1_ENST00000377652.3_Missense_Mutation_p.W104C|PNMAL2_ENST00000594749.1_Intron|PNMAL2_ENST00000599531.1_Silent_p.T174T			Q9ULN7	PNML2_HUMAN	paraneoplastic Ma antigen family-like 2	174	Arg-rich.									central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(4)	8		Ovarian(192;0.00965)|all_neural(266;0.0459)		OV - Ovarian serous cystadenocarcinoma(262;0.000322)|all cancers(93;0.00233)|GBM - Glioblastoma multiforme(486;0.0421)|Epithelial(262;0.0427)		TGCCCTTCTGGGTCAACCTGT	0.647																																						ENST00000377652.3		NA																	0					NA						c.(310-312)tgG>tgC									69.0	68.0	69.0					19																	46998201		2203	4300	6503	SO:0001819	synonymous_variant	0							g.chr19:46998201G>C	AB033009	CCDS59400.1	19q13.32	2014-02-12	2012-02-09		ENSG00000204851	ENSG00000204851		"""Paraneoplastic Ma antigens"""	29206	protein-coding gene	gene with protein product			"""PNMA-like 2"""			10574461	Standard	NM_020709		Approved	KIAA1183	uc002pes.2	Q9ULN7		ENST00000377655.2:c.522C>G	19.37:g.46998201G>C		True	False		Somatic	0				PNMAL2_ENST00000377655.2_Silent_p.T174T|PNMAL2_ENST00000599531.1_Silent_p.T174T|PNMAL2_ENST00000594749.1_Intron	p.W104C			WXS	Illumina HiSeq	Phase_I					1	437	+			NA					C9JGD5|M0R374|Q08E79|Q0D2F9|Q6ZVD1	Missense_Mutation	SNP	ENST00000377655.2	37	c.312G>C		.	.	.	.	.	.	.	.	.	.	G	13.41	2.229867	0.39399	.	.	ENSG00000204850	ENST00000377652	.	.	.	2.83	-0.738	0.11125	.	.	.	.	.	T	0.34658	0.0905	.	.	.	0.52501	D	0.999953	D	0.56968	0.978	B	0.42030	0.373	T	0.29701	-1.0003	7	0.87932	D	0	-1.6491	3.1252	0.06405	0.2934:0.2286:0.478:0.0	.	104	Q6ZVU4	.	C	104	.	ENSP00000366880:W104C	W	+	3	0	AC011484.1	51690041	0.576000	0.26700	0.626000	0.29213	0.859000	0.49053	-0.415000	0.07106	-0.071000	0.12886	-0.424000	0.05967	TGG		0.647	PNMAL2-201	KNOWN	basic	protein_coding	protein_coding		0	NM_020709		19:46998201
SCN5A	6331	broad.mit.edu	37	3	38591931	38591931	+	Missense_Mutation	SNP	C	C	G			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr3:38591931C>G	ENST00000333535.4	-	28	6081	c.5932G>C	c.(5932-5934)Gac>Cac	p.D1978H	SCN5A_ENST00000455624.2_Missense_Mutation_p.D1945H|SCN5A_ENST00000449557.2_Missense_Mutation_p.D1924H|SCN5A_ENST00000414099.2_Missense_Mutation_p.D1960H|SCN5A_ENST00000423572.2_Missense_Mutation_p.D1977H|SCN5A_ENST00000450102.2_Missense_Mutation_p.D1924H|SCN5A_ENST00000451551.2_Missense_Mutation_p.D1924H|SCN5A_ENST00000464652.1_5'Flank|SCN5A_ENST00000413689.1_Missense_Mutation_p.D1978H|SCN5A_ENST00000443581.1_Missense_Mutation_p.D1977H|SCN5A_ENST00000425664.1_Missense_Mutation_p.D1960H			Q14524	SCN5A_HUMAN	sodium channel, voltage-gated, type V, alpha subunit	1978					AV node cell to bundle of His cell communication (GO:0086067)|brainstem development (GO:0003360)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|cardiac ventricle development (GO:0003231)|cellular response to calcium ion (GO:0071277)|cerebellum development (GO:0021549)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane depolarization during SA node cell action potential (GO:0086046)|neuronal action potential (GO:0019228)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of action potential (GO:0045760)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of sodium ion transport (GO:0010765)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|telencephalon development (GO:0021537)|ventricular cardiac muscle cell action potential (GO:0086005)	caveola (GO:0005901)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	ankyrin binding (GO:0030506)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|fibroblast growth factor binding (GO:0017134)|ion channel binding (GO:0044325)|nitric-oxide synthase binding (GO:0050998)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)			NS(3)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|lung(27)|ovary(6)|pancreas(3)|prostate(10)|skin(9)|upper_aerodigestive_tract(4)	107	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Ajmaline(DB01426)|Aprindine(DB01429)|Benzonatate(DB00868)|Carbamazepine(DB00564)|Cinchocaine(DB00527)|Cocaine(DB00907)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lidocaine(DB00281)|Mexiletine(DB00379)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine barbiturate(DB01346)|Quinidine(DB00908)|Ranolazine(DB00243)|Riluzole(DB00740)|Tocainide(DB01056)|Valproic Acid(DB00313)|Verapamil(DB00661)|Zonisamide(DB00909)	GTGACACTGTCATAGGAGGGT	0.602																																						ENST00000413689.1		NA																	0				NS(3)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|lung(27)|ovary(6)|pancreas(3)|prostate(10)|skin(9)|upper_aerodigestive_tract(4)	107						c.(5932-5934)Gac>Cac		sodium channel, voltage-gated, type V, alpha subunit	Benzonatate(DB00868)|Bepridil(DB01244)|Carbamazepine(DB00564)|Cocaine(DB00907)|Dibucaine(DB00527)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lamotrigine(DB00555)|Lidocaine(DB00281)|Mephenytoin(DB00532)|Mexiletine(DB00379)|Mibefradil(DB01388)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine(DB00908)|Riluzole(DB00740)|Tocainide(DB01056)|Verapamil(DB00661)						42.0	47.0	45.0					3																	38591931		2022	4172	6194	SO:0001583	missense	6331				blood circulation|cellular response to calcium ion|muscle contraction|regulation of heart contraction	sarcolemma|voltage-gated sodium channel complex	protein binding|voltage-gated sodium channel activity	g.chr3:38591931C>G	AJ310893	CCDS46796.1, CCDS46797.1, CCDS46798.1, CCDS46799.1, CCDS54569.1, CCDS54570.1	3p21	2014-09-17	2007-01-23		ENSG00000183873	ENSG00000183873		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10593	protein-coding gene	gene with protein product	"""long QT syndrome 3"""	600163	"""sodium channel, voltage-gated, type V, alpha (long QT syndrome 3)"""	CMD1E		7842012, 15466643, 16382098	Standard	NM_198056		Approved	Nav1.5, LQT3, HB1, HBBD, PFHB1, IVF, HB2, HH1, SSS1, CDCD2, CMPD2, ICCD	uc021wvl.1	Q14524	OTTHUMG00000156166	ENST00000333535.4:c.5932G>C	3.37:g.38591931C>G	ENSP00000328968:p.Asp1978His	False	False		Somatic	0				SCN5A_ENST00000443581.1_Missense_Mutation_p.D1977H|SCN5A_ENST00000425664.1_Missense_Mutation_p.D1960H|SCN5A_ENST00000450102.2_Missense_Mutation_p.D1924H|SCN5A_ENST00000449557.2_Missense_Mutation_p.D1924H|SCN5A_ENST00000333535.4_Missense_Mutation_p.D1978H|SCN5A_ENST00000451551.2_Missense_Mutation_p.D1924H|SCN5A_ENST00000414099.2_Missense_Mutation_p.D1960H|SCN5A_ENST00000423572.2_Missense_Mutation_p.D1977H|SCN5A_ENST00000455624.2_Missense_Mutation_p.D1945H	p.D1978H	NM_001099404.1|NM_001160160.1	NP_001092874.1|NP_001153632.1	WXS	Illumina HiSeq	Phase_I	Q14524	SCN5A_HUMAN		KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	28	6125	-	Medulloblastoma(35;0.163)		1978					A5H1P8|A6N922|A6N923|B2RTU0|E7ET19|E9PEF3|E9PEK2|E9PFW7|Q59H93|Q75RX9|Q75RY0|Q86UR3|Q8IZC9|Q96J69	Missense_Mutation	SNP	ENST00000333535.4	37	c.5932G>C	CCDS46796.1	.	.	.	.	.	.	.	.	.	.	C	18.18	3.565807	0.65651	.	.	ENSG00000183873	ENST00000414099;ENST00000423572;ENST00000413689;ENST00000451551;ENST00000443581;ENST00000425664;ENST00000333535;ENST00000455624;ENST00000450102;ENST00000449557	D;D;D;D;D;D;D;D;D;D	0.96856	-4.02;-4.03;-4.03;-4.08;-4.03;-4.02;-4.03;-4.15;-4.08;-4.08	4.95	4.95	0.65309	.	0.058474	0.64402	D	0.000003	D	0.95529	0.8547	N	0.08118	0	0.54753	D	0.999986	D;D;P;D;D;D	0.89917	0.959;1.0;0.64;0.999;0.958;1.0	P;D;B;D;P;D	0.85130	0.496;0.997;0.387;0.973;0.693;0.996	D	0.97067	0.9775	10	0.62326	D	0.03	.	18.3714	0.90408	0.0:1.0:0.0:0.0	.	1924;1945;1960;1978;1977;1978	E9PEF3;E9PHB6;E9PG18;Q14524;Q14524-2;E9PEK2	.;.;.;SCN5A_HUMAN;.;.	H	1960;1977;1978;1924;1977;1960;1978;1945;1924;1924	ENSP00000398962:D1960H;ENSP00000398266:D1977H;ENSP00000410257:D1978H;ENSP00000388797:D1924H;ENSP00000397915:D1977H;ENSP00000416634:D1960H;ENSP00000328968:D1978H;ENSP00000399524:D1945H;ENSP00000403355:D1924H;ENSP00000413996:D1924H	ENSP00000328968:D1978H	D	-	1	0	SCN5A	38566935	1.000000	0.71417	0.993000	0.49108	0.998000	0.95712	4.781000	0.62389	2.573000	0.86826	0.655000	0.94253	GAC		0.602	SCN5A-014	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377958.1	0	NM_198056		3:38591931
CLEC4A	50856	broad.mit.edu	37	12	8276535	8276535	+	Missense_Mutation	SNP	A	A	G			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	A	A	-	-	A	A	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr12:8276535A>G	ENST00000229332.5	+	1	308	c.61A>G	c.(61-63)Atc>Gtc	p.I21V	CLEC4A_ENST00000345999.3_Missense_Mutation_p.I21V|CLEC4A_ENST00000360500.3_Missense_Mutation_p.I21V|CLEC4A_ENST00000352620.3_Missense_Mutation_p.I21V	NM_016184.3|NM_194447.2|NM_194450.2	NP_057268.1|NP_919429.2|NP_919432.1	Q9UMR7	CLC4A_HUMAN	C-type lectin domain family 4, member A	21					cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(3)|large_intestine(2)|lung(4)|prostate(1)	11				Kidney(36;0.0915)		GTCCTCAGGCATCAACACAGC	0.418																																						ENST00000229332.5		NA																	0				cervix(1)|endometrium(3)|large_intestine(2)|lung(4)|prostate(1)	11						c.(61-63)Atc>Gtc		C-type lectin domain family 4, member A							92.0	80.0	84.0					12																	8276535		2203	4300	6503	SO:0001583	missense	50856				cell adhesion|cell surface receptor linked signaling pathway|innate immune response	integral to plasma membrane	sugar binding|transmembrane receptor activity	g.chr12:8276535A>G	AJ133532	CCDS8590.1, CCDS8591.1, CCDS8592.1, CCDS41745.1	12p13	2005-02-09	2005-02-09	2005-02-09	ENSG00000111729	ENSG00000111729		"""C-type lectin domain containing"""	13257	protein-coding gene	gene with protein product		605306	"""C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 6"""	CLECSF6		10438934	Standard	NM_016184		Approved	DCIR, DDB27	uc001qtz.1	Q9UMR7	OTTHUMG00000168571	ENST00000229332.5:c.61A>G	12.37:g.8276535A>G	ENSP00000229332:p.Ile21Val	False	False		Somatic	0				CLEC4A_ENST00000360500.3_Missense_Mutation_p.I21V|CLEC4A_ENST00000345999.3_Missense_Mutation_p.I21V|CLEC4A_ENST00000352620.3_Missense_Mutation_p.I21V	p.I21V	NM_016184.3|NM_194447.2|NM_194450.2	NP_057268.1|NP_919429.2|NP_919432.1	WXS	Illumina HiSeq	Phase_I	Q9UMR7	CLC4A_HUMAN		Kidney(36;0.0915)	1	308	+			21					Q17R69|Q8WXW9|Q9H2Z9|Q9NS33|Q9UI34	Missense_Mutation	SNP	ENST00000229332.5	37	c.61A>G	CCDS8590.1	.	.	.	.	.	.	.	.	.	.	A	5.547	0.285885	0.10513	.	.	ENSG00000111729	ENST00000229332;ENST00000345999;ENST00000352620;ENST00000360500;ENST00000546339	T;T;T;T;T	0.44083	5.49;5.5;5.33;5.33;0.93	4.07	-0.299	0.12808	.	.	.	.	.	T	0.26882	0.0658	L	0.43152	1.355	0.09310	N	1	B;B;B;P	0.36990	0.32;0.048;0.32;0.577	B;B;B;B	0.31442	0.058;0.024;0.129;0.13	T	0.11842	-1.0571	9	0.27785	T	0.31	.	5.5206	0.16931	0.5456:0.3515:0.1029:0.0	.	21;21;21;21	Q9UMR7-3;Q9UMR7-4;Q9UMR7-2;Q9UMR7	.;.;.;CLC4A_HUMAN	V	21;21;21;21;10	ENSP00000229332:I21V;ENSP00000344646:I21V;ENSP00000247243:I21V;ENSP00000353690:I21V;ENSP00000443082:I10V	ENSP00000229332:I21V	I	+	1	0	CLEC4A	8167802	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.061000	0.11693	-0.051000	0.13334	0.528000	0.53228	ATC		0.418	CLEC4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400257.1	0	NM_194450		12:8276535
SLC16A9	220963	broad.mit.edu	37	10	61424005	61424005	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr10:61424005G>A	ENST00000395348.3	-	4	1052	c.416C>T	c.(415-417)gCg>gTg	p.A139V	SLC16A9_ENST00000395347.1_Missense_Mutation_p.A139V	NM_194298.2	NP_919274.1	Q7RTY1	MOT9_HUMAN	solute carrier family 16, member 9	139					urate metabolic process (GO:0046415)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			kidney(3)|large_intestine(5)|lung(5)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	23						CAGGCCAAGCGCTAGGCCTCG	0.398																																						ENST00000395348.3		NA																	0				kidney(3)|large_intestine(5)|lung(5)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	23						c.(415-417)gCg>gTg		solute carrier family 16, member 9							118.0	112.0	114.0					10																	61424005		2203	4300	6503	SO:0001583	missense	220963				urate metabolic process	integral to membrane|plasma membrane	symporter activity	g.chr10:61424005G>A	AK125791	CCDS7256.1	10q21.3	2013-07-18	2013-07-18	2004-01-21	ENSG00000165449	ENSG00000165449		"""Solute carriers"""	23520	protein-coding gene	gene with protein product	"""monocarboxylic acid transporter 9"""	614242	"""chromosome 10 open reading frame 36"", ""solute carrier family 16 (monocarboxylic acid transporters), member 9"", ""solute carrier family 16, member 9 (monocarboxylic acid transporter 9)"""	C10orf36			Standard	NM_194298		Approved	FLJ43803, MCT9	uc010qig.1	Q7RTY1	OTTHUMG00000018283	ENST00000395348.3:c.416C>T	10.37:g.61424005G>A	ENSP00000378757:p.Ala139Val	False	False		Somatic	0				SLC16A9_ENST00000395347.1_Missense_Mutation_p.A139V	p.A139V	NM_194298.2	NP_919274.1	WXS	Illumina HiSeq	Phase_I	Q7RTY1	MOT9_HUMAN			4	1052	-			139					Q6ZMI2|Q9UFH8	Missense_Mutation	SNP	ENST00000395348.3	37	c.416C>T	CCDS7256.1	.	.	.	.	.	.	.	.	.	.	G	35	5.415996	0.96092	.	.	ENSG00000165449	ENST00000395348;ENST00000395347	T;T	0.50813	0.73;0.73	5.34	5.34	0.76211	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.050554	0.85682	D	0.000000	T	0.65291	0.2677	L	0.54323	1.7	0.80722	D	1	D	0.89917	1.0	D	0.71414	0.973	T	0.64824	-0.6316	10	0.49607	T	0.09	.	19.0182	0.92902	0.0:0.0:1.0:0.0	.	139	Q7RTY1	MOT9_HUMAN	V	139	ENSP00000378757:A139V;ENSP00000378756:A139V	ENSP00000378756:A139V	A	-	2	0	SLC16A9	61094011	1.000000	0.71417	0.997000	0.53966	0.967000	0.64934	9.428000	0.97476	2.487000	0.83934	0.655000	0.94253	GCG		0.398	SLC16A9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048174.2	0	NM_194298		10:61424005
UQCR11	10975	broad.mit.edu	37	19	1605381	1605381	+	Missense_Mutation	SNP	A	A	G			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	A	A	-	-	A	A	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr19:1605381A>G	ENST00000591899.3	-	1	99	c.28T>C	c.(28-30)Tac>Cac	p.Y10H	UQCR11_ENST00000593029.1_5'UTR|UQCR11_ENST00000589880.1_Missense_Mutation_p.Y10H|UQCR11_ENST00000585671.1_Missense_Mutation_p.Y10H|UQCR11_ENST00000585937.1_Missense_Mutation_p.Y10H	NM_006830.3	NP_006821.1	O14957	QCR10_HUMAN	ubiquinol-cytochrome c reductase, complex III subunit XI	10					cellular metabolic process (GO:0044237)|generation of precursor metabolites and energy (GO:0006091)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|respiratory chain (GO:0070469)	electron carrier activity (GO:0009055)|ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(1)|lung(2)|ovary(1)|prostate(1)	5						AGCTCCCGGTAGCGTGGGCCC	0.731																																						ENST00000591899.3		NA																	0				breast(1)|lung(2)|ovary(1)|prostate(1)	5						c.(28-30)Tac>Cac		ubiquinol-cytochrome c reductase, complex III subunit XI							20.0	20.0	20.0					19																	1605381		2192	4287	6479	SO:0001583	missense	10975				respiratory electron transport chain	integral to membrane|mitochondrial inner membrane|respiratory chain	electron carrier activity	g.chr19:1605381A>G	D55636	CCDS12073.1	19p13.3	2011-07-04	2010-01-26	2010-01-26	ENSG00000127540	ENSG00000127540		"""Mitochondrial respiratory chain complex / Complex III"""	30862	protein-coding gene	gene with protein product	"""complex III subunit 10"""	609711	"""ubiquinol-cytochrome c reductase, 6.4kDa subunit"""	UQCR		9161705	Standard	NM_006830		Approved	QCR10	uc002ltm.3	O14957		ENST00000591899.3:c.28T>C	19.37:g.1605381A>G	ENSP00000467262:p.Tyr10His	False	False		Somatic	0				UQCR11_ENST00000585937.1_Missense_Mutation_p.Y10H|UQCR11_ENST00000589880.1_Missense_Mutation_p.Y10H|UQCR11_ENST00000585671.1_Missense_Mutation_p.Y10H|UQCR11_ENST00000593029.1_5'UTR	p.Y10H	NM_006830.3	NP_006821.1	WXS	Illumina HiSeq	Phase_I	O14957	QCR10_HUMAN			1	99	-			10					B2R542|D6W5Z4|Q9UEA3|Q9UPK4	Missense_Mutation	SNP	ENST00000591899.3	37	c.28T>C	CCDS12073.1	.	.	.	.	.	.	.	.	.	.	A	16.30	3.083359	0.55861	.	.	ENSG00000127540	ENST00000262946	.	.	.	4.76	4.76	0.60689	.	0.169791	0.39083	N	0.001465	T	0.62539	0.2436	.	.	.	0.32763	N	0.504898	D	0.59767	0.986	P	0.60541	0.876	T	0.68903	-0.5286	8	0.28530	T	0.3	-13.3155	12.1352	0.53966	1.0:0.0:0.0:0.0	.	10	O14957	QCR10_HUMAN	H	10	.	ENSP00000262946:Y10H	Y	-	1	0	UQCR11	1556381	0.990000	0.36364	0.970000	0.41538	0.042000	0.13812	4.876000	0.63079	2.002000	0.58637	0.533000	0.62120	TAC		0.731	UQCR11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449668.3	0	NM_006830		19:1605381
PLEC	5339	broad.mit.edu	37	8	145006714	145006714	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr8:145006714G>A	ENST00000322810.4	-	16	2411	c.2242C>T	c.(2242-2244)Cgc>Tgc	p.R748C	PLEC_ENST00000354958.2_Missense_Mutation_p.R589C|PLEC_ENST00000354589.3_Missense_Mutation_p.R611C|PLEC_ENST00000436759.2_Missense_Mutation_p.R638C|PLEC_ENST00000356346.3_Missense_Mutation_p.R597C|PLEC_ENST00000527096.1_Missense_Mutation_p.R634C|PLEC_ENST00000345136.3_Missense_Mutation_p.R611C|PLEC_ENST00000357649.2_Missense_Mutation_p.R615C|PLEC_ENST00000398774.2_Missense_Mutation_p.R579C	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	748	Globular 1.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)	p.R611C(1)|p.R748C(1)|p.R638C(1)		NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						GACCTGAGGCGGGCCTTGGAG	0.657																																						ENST00000322810.4		NA																	3	Substitution - Missense(3)	p.R611C(1)|p.R748C(1)|p.R638C(1)	lung(3)	NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						c.(2242-2244)Cgc>Tgc		plectin							45.0	52.0	50.0					8																	145006714		1981	4143	6124	SO:0001583	missense	5339				cellular component disassembly involved in apoptosis|hemidesmosome assembly	cytosol|focal adhesion|hemidesmosome|intermediate filament cytoskeleton|sarcolemma	actin binding|structural constituent of muscle	g.chr8:145006714G>A	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.2242C>T	8.37:g.145006714G>A	ENSP00000323856:p.Arg748Cys	True	False		Somatic	0				PLEC_ENST00000345136.3_Missense_Mutation_p.R611C|PLEC_ENST00000357649.2_Missense_Mutation_p.R615C|PLEC_ENST00000354589.3_Missense_Mutation_p.R611C|PLEC_ENST00000398774.2_Missense_Mutation_p.R579C|PLEC_ENST00000527096.1_Missense_Mutation_p.R634C|PLEC_ENST00000356346.3_Missense_Mutation_p.R597C|PLEC_ENST00000436759.2_Missense_Mutation_p.R638C|PLEC_ENST00000354958.2_Missense_Mutation_p.R589C	p.R748C	NM_201380.2	NP_958782.1	WXS	Illumina HiSeq	Phase_I	Q15149	PLEC_HUMAN			16	2411	-			748			Globular 1.		Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	37	c.2242C>T	CCDS43772.1	.	.	.	.	.	.	.	.	.	.	G	12.41	1.930956	0.34096	.	.	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096;ENST00000528025	T;T;T;T;T;T;T;T;T;D	0.96334	-0.02;-0.02;-0.02;-0.02;-0.02;-0.02;-0.02;-0.02;-0.02;-3.98	4.6	3.71	0.42584	.	0.000000	0.64402	U	0.000005	D	0.97838	0.9290	M	0.84773	2.715	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.85130	0.997;0.997;0.997;0.994;0.997;0.997;0.997;0.997	D	0.97902	1.0303	10	0.87932	D	0	.	11.3503	0.49583	0.0925:0.0:0.9075:0.0	.	638;597;589;748;579;611;615;611	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	C	611;615;611;579;748;589;597;638;634;655	ENSP00000344848:R611C;ENSP00000350277:R615C;ENSP00000346602:R611C;ENSP00000381756:R579C;ENSP00000323856:R748C;ENSP00000347044:R589C;ENSP00000348702:R597C;ENSP00000388180:R638C;ENSP00000434583:R634C;ENSP00000437303:R655C	ENSP00000323856:R748C	R	-	1	0	PLEC	145078702	1.000000	0.71417	1.000000	0.80357	0.558000	0.35554	6.203000	0.72137	2.271000	0.75665	0.453000	0.30009	CGC		0.657	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	0	NM_000445		8:145006714
FCGBP	8857	broad.mit.edu	37	19	40398010	40398010	+	Silent	SNP	G	G	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr19:40398010G>A	ENST00000221347.6	-	14	6964	c.6957C>T	c.(6955-6957)gcC>gcT	p.A2319A		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2319						extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GGGCCCCAGCGGCCTGACAGG	0.652																																						ENST00000221347.6		NA																	0				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165						c.(6955-6957)gcC>gcT		Fc fragment of IgG binding protein							37.0	38.0	38.0					19																	40398010		2102	3822	5924	SO:0001819	synonymous_variant	8857					extracellular region	protein binding	g.chr19:40398010G>A	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.6957C>T	19.37:g.40398010G>A		False	False		Somatic	0					p.A2319A	NM_003890.2	NP_003881.2	WXS	Illumina HiSeq	Phase_I	Q9Y6R7	FCGBP_HUMAN	Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)		14	6964	-	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		2319					O95784	Silent	SNP	ENST00000221347.6	37	c.6957C>T	CCDS12546.1																																																																																				0.652	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	0	NM_003890		19:40398010
RBM6	10180	broad.mit.edu	37	3	50005374	50005374	+	Silent	SNP	A	A	T			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	A	A	-	-	A	A	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr3:50005374A>T	ENST00000266022.4	+	3	775	c.516A>T	c.(514-516)ccA>ccT	p.P172P	RBM6_ENST00000441115.1_Intron|RBM6_ENST00000539992.1_Intron|RBM6_ENST00000442092.1_Intron|RBM6_ENST00000422955.1_Intron|RBM6_ENST00000443081.1_Silent_p.P40P	NM_005777.2	NP_005768.1	P78332	RBM6_HUMAN	RNA binding motif protein 6	172					RNA processing (GO:0006396)	nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(3)|prostate(1)|skin(4)|urinary_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)		ATGCTCCTCCATCTGACTTCA	0.468																																						ENST00000443081.1		NA																	0				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(3)|prostate(1)|skin(4)|urinary_tract(1)	33						c.(118-120)ccA>ccT		RNA binding motif protein 6							59.0	62.0	61.0					3																	50005374		2203	4300	6503	SO:0001819	synonymous_variant	10180				RNA processing	nucleus	DNA binding|nucleotide binding|RNA binding|zinc ion binding	g.chr3:50005374A>T	AF069517	CCDS2809.1, CCDS54586.1	3p21.3	2013-01-28			ENSG00000004534	ENSG00000004534		"""RNA binding motif (RRM) containing"", ""G patch domain containing"""	9903	protein-coding gene	gene with protein product		606886				10352938	Standard	NM_001167582		Approved	DEF-3, 3G2, NY-LU-12, g16, DEF3	uc003cyc.3	P78332	OTTHUMG00000156736	ENST00000266022.4:c.516A>T	3.37:g.50005374A>T		False	False		Somatic	0				RBM6_ENST00000539992.1_Intron|RBM6_ENST00000266022.4_Silent_p.P172P|RBM6_ENST00000442092.1_Intron|RBM6_ENST00000422955.1_Intron|RBM6_ENST00000441115.1_Intron	p.P40P			WXS	Illumina HiSeq	Phase_I	P78332	RBM6_HUMAN		BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)	3	1039	+			172					O60549|O75524|Q86SS3	Silent	SNP	ENST00000266022.4	37	c.120A>T	CCDS2809.1																																																																																				0.468	RBM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345528.4	0	NM_005777		3:50005374
MAGEA3	4102	broad.mit.edu	37	X	151935609	151935609	+	Silent	SNP	G	G	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chrX:151935609G>A	ENST00000393902.3	-	3	1125	c.558C>T	c.(556-558)taC>taT	p.Y186Y	MAGEA3_ENST00000370278.3_Silent_p.Y186Y			P43357	MAGA3_HUMAN	melanoma antigen family A, 3	186	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.									endometrium(4)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)	15	Acute lymphoblastic leukemia(192;6.56e-05)					GCAGGCCATCGTAGGAGAGGC	0.572																																						ENST00000393902.3		NA																	0				endometrium(4)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)	15						c.(556-558)taC>taT		melanoma antigen family A, 3							103.0	102.0	102.0					X																	151935609		2202	4294	6496	SO:0001819	synonymous_variant	4102							g.chrX:151935609G>A		CCDS76045.1	Xq28	2009-03-13			ENSG00000221867	ENSG00000221867			6801	protein-coding gene	gene with protein product	"""melanoma-associated antigen 3"", ""antigen MZ2-D"", ""MAGE-3 antigen"", ""cancer/testis antigen family 1, member 3"""	300174		MAGE3		1840703, 8575766	Standard	NM_005362		Approved	HYPD, HIP8, MGC14613, CT1.3	uc004fgp.3	P43357	OTTHUMG00000022640	ENST00000393902.3:c.558C>T	X.37:g.151935609G>A		False	False		Somatic	0				MAGEA3_ENST00000370278.3_Silent_p.Y186Y	p.Y186Y			WXS	Illumina HiSeq	Phase_I	P43357	MAGA3_HUMAN			3	1125	-	Acute lymphoblastic leukemia(192;6.56e-05)		186			MAGE.		Q6FHI6	Silent	SNP	ENST00000393902.3	37	c.558C>T	CCDS14715.1																																																																																				0.572	MAGEA3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058744.1	0	NM_005362		X:151935609
LRP12	29967	broad.mit.edu	37	8	105502937	105502937	+	Silent	SNP	G	G	A	rs532435409		TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr8:105502937G>A	ENST00000276654.5	-	7	2652	c.2544C>T	c.(2542-2544)aaC>aaT	p.N848N	LRP12_ENST00000518375.1_5'UTR|LRP12_ENST00000424843.2_Silent_p.N829N	NM_013437.4	NP_038465.1	Q9Y561	LRP12_HUMAN	low density lipoprotein receptor-related protein 12	848					endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48			OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)			CACTCGTTTCGTTTTTCAGTG	0.418																																						ENST00000276654.5		NA																	0				NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48						c.(2542-2544)aaC>aaT		low density lipoprotein receptor-related protein 12							143.0	130.0	134.0					8																	105502937		2203	4300	6503	SO:0001819	synonymous_variant	29967				endocytosis|regulation of growth	coated pit|integral to plasma membrane	low-density lipoprotein receptor activity|protein binding	g.chr8:105502937G>A	AF166350	CCDS6303.1, CCDS47907.1	8q22.2	2013-02-27	2010-01-26		ENSG00000147650	ENSG00000147650		"""Low density lipoprotein receptors"""	31708	protein-coding gene	gene with protein product						12809483, 14676824	Standard	NM_013437		Approved	ST7, FLJ12929	uc003yma.3	Q9Y561	OTTHUMG00000164892	ENST00000276654.5:c.2544C>T	8.37:g.105502937G>A		True	False		Somatic	0				LRP12_ENST00000424843.2_Silent_p.N829N|LRP12_ENST00000518375.1_5'UTR	p.N848N	NM_013437.4	NP_038465.1	WXS	Illumina HiSeq	Phase_I	Q9Y561	LRP12_HUMAN	OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)		7	2652	-			848					A8K137|B4DRQ2	Silent	SNP	ENST00000276654.5	37	c.2544C>T	CCDS6303.1																																																																																				0.418	LRP12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380821.1	0	NM_013437		8:105502937
LTBR	4055	broad.mit.edu	37	12	6494502	6494502	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr12:6494502G>T	ENST00000228918.4	+	4	755	c.429G>T	c.(427-429)gaG>gaT	p.E143D	LTBR_ENST00000541102.1_Missense_Mutation_p.E36D|LTBR_ENST00000543190.1_Missense_Mutation_p.E36D|LTBR_ENST00000539925.1_Missense_Mutation_p.E124D	NM_002342.2	NP_002333.1	P36941	TNR3_HUMAN	lymphotoxin beta receptor (TNFR superfamily, member 3)	143					apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of JNK cascade (GO:0046330)|signal transduction (GO:0007165)|viral process (GO:0016032)	integral component of membrane (GO:0016021)	identical protein binding (GO:0042802)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|cervix(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)	15						CACACTGCGAGCTACTTTCTG	0.607																																						ENST00000228918.4		NA																	0				breast(1)|cervix(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)	15						c.(427-429)gaG>gaT		lymphotoxin beta receptor (TNFR superfamily, member 3)							48.0	49.0	49.0					12																	6494502		2203	4300	6503	SO:0001583	missense	4055				apoptosis|cellular response to mechanical stimulus|interspecies interaction between organisms|positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to membrane	protein binding|receptor activity	g.chr12:6494502G>T	L04270	CCDS8544.1, CCDS59233.1	12p13	2013-05-22				ENSG00000111321		"""Tumor necrosis factor receptor superfamily"""	6718	protein-coding gene	gene with protein product		600979		D12S370		8171323, 8486360	Standard	NM_002342		Approved	TNFCR, TNFR-RP, TNFR2-RP, TNF-R-III, TNFRSF3	uc001qny.2	P36941		ENST00000228918.4:c.429G>T	12.37:g.6494502G>T	ENSP00000228918:p.Glu143Asp	False	False		Somatic	0				LTBR_ENST00000539925.1_Missense_Mutation_p.E124D|LTBR_ENST00000543190.1_Missense_Mutation_p.E36D|LTBR_ENST00000541102.1_Missense_Mutation_p.E36D	p.E143D	NM_002342.2	NP_002333.1	WXS	Illumina HiSeq	Phase_I	P36941	TNR3_HUMAN			4	755	+			143					B7Z1D2|D3DUR2|F5GXE7	Missense_Mutation	SNP	ENST00000228918.4	37	c.429G>T	CCDS8544.1	.	.	.	.	.	.	.	.	.	.	G	13.66	2.303124	0.40795	.	.	ENSG00000111321	ENST00000539925;ENST00000228918;ENST00000540343;ENST00000536876;ENST00000543190;ENST00000541102	T;T;T;T;T	0.73047	0.12;0.12;0.12;-0.71;0.12	4.79	1.89	0.25635	TNFR/CD27/30/40/95 cysteine-rich region (1);	0.432883	0.23340	N	0.049255	T	0.78227	0.4250	M	0.69358	2.11	0.09310	N	0.999996	D;D;D	0.76494	0.996;0.993;0.999	D;D;D	0.76071	0.986;0.967;0.987	T	0.66913	-0.5803	9	.	.	.	-1.2798	6.5625	0.22493	0.1755:0.0:0.6788:0.1457	.	124;124;143	F5GXE7;B7Z1D2;P36941	.;.;TNR3_HUMAN	D	124;143;36;138;36;36	ENSP00000440875:E124D;ENSP00000228918:E143D;ENSP00000437647:E138D;ENSP00000438955:E36D;ENSP00000438605:E36D	.	E	+	3	2	LTBR	6364763	0.749000	0.28305	0.076000	0.20297	0.307000	0.27823	0.698000	0.25571	-0.127000	0.11661	-1.134000	0.01955	GAG		0.607	LTBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399422.1	0			12:6494502
KLHDC4	54758	broad.mit.edu	37	16	87790046	87790046	+	Nonsense_Mutation	SNP	C	C	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr16:87790046C>A	ENST00000270583.5	-	3	287	c.229G>T	c.(229-231)Gag>Tag	p.E77*	KLHDC4_ENST00000347925.5_Nonsense_Mutation_p.E77*|KLHDC4_ENST00000353170.5_Intron	NM_017566.3	NP_060036.2	Q8TBB5	KLDC4_HUMAN	kelch domain containing 4	77										breast(2)|endometrium(3)|lung(10)|pancreas(2)|prostate(1)|skin(1)|urinary_tract(2)	21				BRCA - Breast invasive adenocarcinoma(80;0.0283)		AGGATTAACTCATCTTTCTCA	0.438																																						ENST00000270583.5		NA																	0				breast(2)|endometrium(3)|lung(10)|pancreas(2)|prostate(1)|skin(1)|urinary_tract(2)	21						c.(229-231)Gag>Tag		kelch domain containing 4							68.0	66.0	66.0					16																	87790046		2198	4300	6498	SO:0001587	stop_gained	54758							g.chr16:87790046C>A	AK001742	CCDS10963.1, CCDS54050.1, CCDS54051.1	16q24	2008-02-05			ENSG00000104731	ENSG00000104731			25272	protein-coding gene	gene with protein product							Standard	NM_001184854		Approved	DKFZp434G0522	uc002fki.3	Q8TBB5	OTTHUMG00000137657	ENST00000270583.5:c.229G>T	16.37:g.87790046C>A	ENSP00000270583:p.Glu77*	False	False		Somatic	0				KLHDC4_ENST00000347925.5_Nonsense_Mutation_p.E77*|KLHDC4_ENST00000353170.5_Intron	p.E77*	NM_017566.3	NP_060036.2	WXS	Illumina HiSeq	Phase_I	Q8TBB5	KLDC4_HUMAN		BRCA - Breast invasive adenocarcinoma(80;0.0283)	3	287	-			77					D3DUN3|D3DUN4|D3DUN5|Q96F29|Q9BVN3	Nonsense_Mutation	SNP	ENST00000270583.5	37	c.229G>T	CCDS10963.1	.	.	.	.	.	.	.	.	.	.	C	36	5.966446	0.97156	.	.	ENSG00000104731	ENST00000270583;ENST00000347925	.	.	.	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30078	T	0.28	-15.5645	15.8539	0.78960	0.0:1.0:0.0:0.0	.	.	.	.	X	77	.	ENSP00000270583:E77X	E	-	1	0	KLHDC4	86347547	1.000000	0.71417	0.998000	0.56505	0.925000	0.55904	7.019000	0.76412	2.417000	0.82017	0.655000	0.94253	GAG		0.438	KLHDC4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269109.2	0	NM_017566		16:87790046
PHACTR4	65979	broad.mit.edu	37	1	28807088	28807088	+	Silent	SNP	C	C	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr1:28807088C>A	ENST00000373839.3	+	9	1993	c.1732C>A	c.(1732-1734)Cgg>Agg	p.R578R	RNU6ATAC27P_ENST00000408289.1_RNA|PHACTR4_ENST00000493669.1_3'UTR|PHACTR4_ENST00000373836.3_Silent_p.R588R	NM_001048183.1	NP_001041648.1	Q8IZ21	PHAR4_HUMAN	phosphatase and actin regulator 4	578					actin cytoskeleton organization (GO:0030036)|closure of optic fissure (GO:0061386)|enteric nervous system development (GO:0048484)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of catalytic activity (GO:0043085)|regulation of cell cycle (GO:0051726)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)	actin binding (GO:0003779)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase type 1 activator activity (GO:0071862)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)		GAATGAAATACGGCACCAGAT	0.428																																						ENST00000373839.3		NA																	0				NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	32						c.(1732-1734)Cgg>Agg		phosphatase and actin regulator 4							225.0	207.0	213.0					1																	28807088		2001	4171	6172	SO:0001819	synonymous_variant	65979						actin binding|protein phosphatase inhibitor activity	g.chr1:28807088C>A	AF130081	CCDS41293.1, CCDS41294.1	1p35.2	2014-06-13			ENSG00000204138	ENSG00000204138		"""Phosphatase and actin regulators"""	25793	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 124"""	608726				11483580, 15107502	Standard	NM_023923		Approved	FLJ13171, PPP1R124	uc001bpy.3	Q8IZ21	OTTHUMG00000003541	ENST00000373839.3:c.1732C>A	1.37:g.28807088C>A		False	False		Somatic	0				PHACTR4_ENST00000373836.3_Silent_p.R588R|PHACTR4_ENST00000493669.1_3'UTR	p.R578R	NM_001048183.1	NP_001041648.1	WXS	Illumina HiSeq	Phase_I	Q8IZ21	PHAR4_HUMAN		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)	9	1993	+		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)	578					A2APK6|B9ZVW0|D3DPM3|Q68DD4|Q6NUN6|Q8N384|Q9H395|Q9H6X0|Q9H8W6	Silent	SNP	ENST00000373839.3	37	c.1732C>A	CCDS41293.1																																																																																				0.428	PHACTR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000009868.4	0	NM_023923		1:28807088
MKL1	57591	broad.mit.edu	37	22	40816901	40816901	+	Missense_Mutation	SNP	C	C	G			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr22:40816901C>G	ENST00000355630.3	-	10	1421	c.831G>C	c.(829-831)caG>caC	p.Q277H	MKL1_ENST00000402042.1_Missense_Mutation_p.Q227H|MKL1_ENST00000396617.3_Missense_Mutation_p.Q277H|MKL1_ENST00000407029.1_Missense_Mutation_p.Q277H	NM_020831.3	NP_065882.1	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia (translocation) 1	277	Gln-rich.				negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription via serum response element binding (GO:0010735)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	actin binding (GO:0003779)|actin monomer binding (GO:0003785)|leucine zipper domain binding (GO:0043522)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	30						GCTGCTGCTGCTGGTTGAGGA	0.657			T	RBM15	acute megakaryocytic leukemia																																	ENST00000396617.3		NA		Dom	yes		22	22q13	57591	T	megakaryoblastic leukemia (translocation) 1			L	RBM15		acute megakaryocytic leukemia		0				breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	30						c.(829-831)caG>caC		megakaryoblastic leukemia (translocation) 1							62.0	63.0	62.0					22																	40816901		2203	4300	6503	SO:0001583	missense	57591				positive regulation of transcription from RNA polymerase II promoter|smooth muscle cell differentiation|transcription, DNA-dependent	cytoplasm|nucleus	actin monomer binding|leucine zipper domain binding|nucleic acid binding|transcription coactivator activity	g.chr22:40816901C>G	AB037859	CCDS14003.1, CCDS74865.1, CCDS74866.1	22q13	2008-06-12			ENSG00000196588	ENSG00000196588			14334	protein-coding gene	gene with protein product	"""megakaryocytic acute leukemia"", ""myocardin-related transcription factor A"", ""basic, SAP and coiled-coil domain"""	606078				11431691, 12019265, 14970199	Standard	XM_005261692		Approved	KIAA1438, MAL, MRTF-A, BSAC	uc003ayw.1	Q969V6	OTTHUMG00000151146	ENST00000355630.3:c.831G>C	22.37:g.40816901C>G	ENSP00000347847:p.Gln277His	True	False		Somatic	0				MKL1_ENST00000402042.1_Missense_Mutation_p.Q227H|MKL1_ENST00000407029.1_Missense_Mutation_p.Q277H|MKL1_ENST00000355630.3_Missense_Mutation_p.Q277H	p.Q277H	NM_001282662.1	NP_001269591.1	WXS	Illumina HiSeq	Phase_I	Q969V6	MKL1_HUMAN			10	1421	-			277			Gln-rich.		Q8TCL1|Q96SC5|Q96SC6|Q9P2B0	Missense_Mutation	SNP	ENST00000355630.3	37	c.831G>C	CCDS14003.1	.	.	.	.	.	.	.	.	.	.	C	19.12	3.766193	0.69878	.	.	ENSG00000196588	ENST00000355630;ENST00000396617;ENST00000402042;ENST00000407029	T;T;T;T	0.61859	0.16;0.11;0.07;0.16	5.26	4.24	0.50183	.	0.000000	0.85682	D	0.000000	T	0.73353	0.3576	M	0.77616	2.38	0.48696	D	0.999692	P;D;P	0.67145	0.787;0.996;0.787	B;D;B	0.75484	0.294;0.986;0.294	T	0.75385	-0.3336	10	0.66056	D	0.02	-15.2355	9.9937	0.41887	0.0:0.8449:0.0:0.1551	.	227;277;277	B0QY83;E7ER32;Q969V6	.;.;MKL1_HUMAN	H	277;277;227;277	ENSP00000347847:Q277H;ENSP00000379861:Q277H;ENSP00000385584:Q227H;ENSP00000385835:Q277H	ENSP00000347847:Q277H	Q	-	3	2	MKL1	39146847	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.270000	0.51600	1.210000	0.43336	0.462000	0.41574	CAG		0.657	MKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321522.1	0	NM_020831		22:40816901
LRP1	4035	broad.mit.edu	37	12	57587450	57587450	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr12:57587450G>A	ENST00000243077.3	+	47	8252	c.7786G>A	c.(7786-7788)Gac>Aac	p.D2596N	MIR1228_ENST00000408438.1_RNA	NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	2596	LDL-receptor class A 12. {ECO:0000255|PROSITE-ProRule:PRU00124}.				aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	GGATGGCTCTGACGAGATCCC	0.622																																						ENST00000243077.3		NA																	0				NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184						c.(7786-7788)Gac>Aac		low density lipoprotein receptor-related protein 1	Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)						94.0	84.0	87.0					12																	57587450		2203	4300	6503	SO:0001583	missense	4035				aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity	coated pit|integral to plasma membrane|nucleus	apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity	g.chr12:57587450G>A	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.7786G>A	12.37:g.57587450G>A	ENSP00000243077:p.Asp2596Asn	False	False		Somatic	0					p.D2596N	NM_002332.2	NP_002323.2	WXS	Illumina HiSeq	Phase_I	Q07954	LRP1_HUMAN		BRCA - Breast invasive adenocarcinoma(357;0.0103)	47	8252	+			2596			LDL-receptor class A 12.		Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	37	c.7786G>A	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	G	14.42	2.529304	0.44969	.	.	ENSG00000123384	ENST00000243077	D	0.99214	-5.57	5.01	4.1	0.47936	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.64402	D	0.000001	D	0.99594	0.9853	H	0.97214	3.96	0.80722	D	1	D	0.69078	0.997	D	0.83275	0.996	D	0.97659	1.0159	10	0.59425	D	0.04	.	12.9517	0.58405	0.0821:0.0:0.9179:0.0	.	2596	Q07954	LRP1_HUMAN	N	2596	ENSP00000243077:D2596N	ENSP00000243077:D2596N	D	+	1	0	LRP1	55873717	1.000000	0.71417	0.100000	0.21137	0.069000	0.16628	7.767000	0.85331	2.606000	0.88127	0.655000	0.94253	GAC		0.622	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	0	NM_002332		12:57587450
MAP1S	55201	broad.mit.edu	37	19	17838243	17838243	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr19:17838243G>A	ENST00000324096.4	+	5	2201	c.2050G>A	c.(2050-2052)Gca>Aca	p.A684T	MAP1S_ENST00000597681.1_3'UTR|CTD-3149D2.4_ENST00000595363.1_RNA|MAP1S_ENST00000544059.2_Missense_Mutation_p.A658T	NM_018174.4	NP_060644.4	Q66K74	MAP1S_HUMAN	microtubule-associated protein 1S	684	Necessary for interaction with RASSF1 isoform A and isoform C.|Necessary for the microtubule-organizing center localization.|Pro-rich.				apoptotic DNA fragmentation (GO:0006309)|brain development (GO:0007420)|execution phase of apoptosis (GO:0097194)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|nervous system development (GO:0007399)|neuron projection morphogenesis (GO:0048812)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	actin filament binding (GO:0051015)|beta-tubulin binding (GO:0048487)|DNA binding (GO:0003677)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	25						CTCACTACCCGCAGAGGTGGG	0.711																																						ENST00000324096.4		NA																	0				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	25						c.(2050-2052)Gca>Aca		microtubule-associated protein 1S							15.0	13.0	14.0					19																	17838243		2179	4287	6466	SO:0001583	missense	55201				apoptosis|brain development|microtubule bundle formation|mitochondrion transport along microtubule|neuron projection morphogenesis	cytosol|dendrite|microtubule|neuronal cell body|nucleus|perinuclear region of cytoplasm|spindle|synapse	actin filament binding|beta-tubulin binding|DNA binding|microtubule binding	g.chr19:17838243G>A	BC067115	CCDS32954.1	19p13.12	2008-02-05	2006-07-04	2006-07-04		ENSG00000130479			15715	protein-coding gene	gene with protein product		607573	"""chromosome 19 open reading frame 5"", ""VCY2 interacting protein 1"", ""BPY2 interacting protein 1"""	C19orf5, VCY2IP1, BPY2IP1		11827465, 15528209, 16297881, 14627543	Standard	NM_018174		Approved	FLJ10669, MAP8	uc002nhe.1	Q66K74		ENST00000324096.4:c.2050G>A	19.37:g.17838243G>A	ENSP00000325313:p.Ala684Thr	True	False		Somatic	0				MAP1S_ENST00000544059.2_Missense_Mutation_p.A658T|MAP1S_ENST00000597681.1_3'UTR	p.A684T	NM_018174.4	NP_060644.4	WXS	Illumina HiSeq	Phase_I	Q66K74	MAP1S_HUMAN			5	2201	+			684			Necessary for interaction with RASSF1 isoform A and isoform C.|Necessary for the microtubule-organizing center localization.|Pro-rich.		B4DH53|Q27QB1|Q6NXF1|Q8N3L8|Q8N3W5|Q8NI88|Q96H94|Q96IT4|Q96SP8|Q9BRC6|Q9H928|Q9NVK7	Missense_Mutation	SNP	ENST00000324096.4	37	c.2050G>A	CCDS32954.1	.	.	.	.	.	.	.	.	.	.	G	16.43	3.120183	0.56613	.	.	ENSG00000130479	ENST00000324096;ENST00000544059	T;T	0.24350	1.86;1.87	4.16	3.11	0.35812	.	0.000000	0.49916	D	0.000137	T	0.43344	0.1243	L	0.61218	1.895	0.30145	N	0.80357	D;D	0.89917	1.0;1.0	D;D	0.72338	0.977;0.975	T	0.38779	-0.9645	10	0.46703	T	0.11	-18.582	10.0188	0.42031	0.1039:0.0:0.8961:0.0	.	658;684	B4DH53;Q66K74	.;MAP1S_HUMAN	T	684;658	ENSP00000325313:A684T;ENSP00000439243:A658T	ENSP00000325313:A684T	A	+	1	0	MAP1S	17699243	1.000000	0.71417	0.007000	0.13788	0.236000	0.25371	7.147000	0.77382	0.855000	0.35359	0.484000	0.47621	GCA		0.711	MAP1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466027.1	0	NM_018174		19:17838243
DAAM2	23500	broad.mit.edu	37	6	39847105	39847105	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr6:39847105C>T	ENST00000398904.2	+	14	1879	c.1697C>T	c.(1696-1698)cCg>cTg	p.P566L	RP11-61I13.3_ENST00000607675.1_RNA|DAAM2_ENST00000538976.1_Missense_Mutation_p.P566L|DAAM2_ENST00000274867.4_Missense_Mutation_p.P566L			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2	566	FH1.|Pro-rich.				actin cytoskeleton organization (GO:0030036)|determination of left/right symmetry (GO:0007368)					NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(18)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)	49	Ovarian(28;0.0355)|Colorectal(47;0.196)					GGGGGACCCCCGACTCCCCCA	0.672																																						ENST00000538976.1		NA																	0				NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(18)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)	49						c.(1696-1698)cCg>cTg		dishevelled associated activator of morphogenesis 2							22.0	23.0	23.0					6																	39847105		1832	4069	5901	SO:0001583	missense	23500				actin cytoskeleton organization		actin binding|Rho GTPase binding	g.chr6:39847105C>T	AB002379	CCDS54999.1, CCDS56426.1	6p21.1	2008-07-30			ENSG00000146122	ENSG00000146122			18143	protein-coding gene	gene with protein product		606627				11779461, 12632087	Standard	NM_015345		Approved	KIAA0381	uc003oow.3	Q86T65	OTTHUMG00000014653	ENST00000398904.2:c.1697C>T	6.37:g.39847105C>T	ENSP00000381876:p.Pro566Leu	True	False		Somatic	0				DAAM2_ENST00000274867.4_Missense_Mutation_p.P566L|DAAM2_ENST00000398904.2_Missense_Mutation_p.P566L	p.P566L	NM_015345.3	NP_056160.2	WXS	Illumina HiSeq	Phase_I	Q86T65	DAAM2_HUMAN			14	1879	+	Ovarian(28;0.0355)|Colorectal(47;0.196)		566			FH1.|Pro-rich.		G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	Missense_Mutation	SNP	ENST00000398904.2	37	c.1697C>T	CCDS56426.1	.	.	.	.	.	.	.	.	.	.	C	12.37	1.918426	0.33908	.	.	ENSG00000146122	ENST00000274867;ENST00000398904;ENST00000538976	D;D;D	0.92446	-3.04;-3.04;-3.04	4.63	4.63	0.57726	Actin-binding FH2 (1);	0.000000	0.85682	D	0.000000	D	0.90143	0.6920	L	0.47716	1.5	0.80722	D	1	D;D	0.61080	0.989;0.982	P;P	0.51170	0.661;0.459	D	0.89794	0.3970	10	0.42905	T	0.14	.	17.2629	0.87075	0.0:1.0:0.0:0.0	.	566;566	G5EA45;Q86T65	.;DAAM2_HUMAN	L	566	ENSP00000274867:P566L;ENSP00000381876:P566L;ENSP00000437808:P566L	ENSP00000274867:P566L	P	+	2	0	DAAM2	39955083	0.999000	0.42202	0.978000	0.43139	0.008000	0.06430	4.374000	0.59543	2.383000	0.81215	0.650000	0.86243	CCG		0.672	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1	0			6:39847105
VEZF1	7716	broad.mit.edu	37	17	56060697	56060697	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr17:56060697G>T	ENST00000581208.1	-	2	131	c.91C>A	c.(91-93)Ctg>Atg	p.L31M	VEZF1_ENST00000584396.1_Missense_Mutation_p.L22M	NM_007146.2	NP_009077.2	Q14119	VEZF1_HUMAN	vascular endothelial zinc finger 1	31					angiogenesis (GO:0001525)|cellular defense response (GO:0006968)|endothelial cell development (GO:0001885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(2)|lung(5)|ovary(1)	10						GCAGAGCTCAGGAGGGGCAGC	0.498																																						ENST00000584396.1		NA																	0				breast(1)|endometrium(1)|kidney(2)|lung(5)|ovary(1)	10						c.(64-66)Ctg>Atg		vascular endothelial zinc finger 1							84.0	92.0	90.0					17																	56060697		2203	4299	6502	SO:0001583	missense	7716				cellular defense response|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding	g.chr17:56060697G>T	D28118	CCDS32687.1	17q22	2012-10-05	2006-08-16	2006-08-16	ENSG00000136451	ENSG00000136451		"""Zinc fingers, C2H2-type"""	12949	protein-coding gene	gene with protein product		606747	"""zinc finger protein 161"""	ZNF161		8035792	Standard	XM_005257643		Approved	DB1	uc002ivf.1	Q14119	OTTHUMG00000178777	ENST00000581208.1:c.91C>A	17.37:g.56060697G>T	ENSP00000462337:p.Leu31Met	False	False		Somatic	0				VEZF1_ENST00000581208.1_Missense_Mutation_p.L31M	p.L22M			WXS	Illumina HiSeq	Phase_I	Q14119	VEZF1_HUMAN			2	152	-			31						Missense_Mutation	SNP	ENST00000581208.1	37	c.64C>A	CCDS32687.1	.	.	.	.	.	.	.	.	.	.	G	15.13	2.741196	0.49151	.	.	ENSG00000136451	ENST00000258963	.	.	.	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	T	0.61751	0.2372	L	0.27053	0.805	0.80722	D	1	D	0.65815	0.995	P	0.61874	0.895	T	0.63102	-0.6712	9	0.59425	D	0.04	-1.2014	13.5589	0.61777	0.0706:0.0:0.9294:0.0	.	31	Q14119	VEZF1_HUMAN	M	31	.	ENSP00000258963:L31M	L	-	1	2	VEZF1	53415696	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.455000	0.66658	2.823000	0.97156	0.643000	0.83706	CTG		0.498	VEZF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443321.1	0			17:56060697
LRRC71	149499	broad.mit.edu	37	1	156897772	156897772	+	Silent	SNP	A	A	G			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	A	A	-	-	A	A	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr1:156897772A>G	ENST00000337428.7	+	9	1126	c.972A>G	c.(970-972)aaA>aaG	p.K324K	LRRC71_ENST00000490146.1_3'UTR	NM_144702.2	NP_653303.2	Q8N4P6	LRC71_HUMAN	leucine rich repeat containing 71	324										endometrium(2)|large_intestine(3)|lung(5)|ovary(1)|stomach(1)	12						TGCTGGAAAAAGGGACACAGG	0.677											OREG0013892	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000337428.7		NA																	0				endometrium(2)|large_intestine(3)|lung(5)|ovary(1)|stomach(1)	12						c.(970-972)aaA>aaG		leucine rich repeat containing 71							25.0	37.0	33.0					1																	156897772		1978	4130	6108	SO:0001819	synonymous_variant	149499							g.chr1:156897772A>G	BC033790	CCDS44249.1	1q23.1	2011-02-14	2011-02-14	2011-02-14	ENSG00000160838	ENSG00000160838			26556	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 92"""	C1orf92		14702039	Standard	NM_144702		Approved	FLJ32884	uc001fqm.2	Q8N4P6	OTTHUMG00000041298	ENST00000337428.7:c.972A>G	1.37:g.156897772A>G		True	False		Somatic	0	OREG0013892	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1782	LRRC71_ENST00000490146.1_3'UTR	p.K324K	NM_144702.2	NP_653303.2	WXS	Illumina HiSeq	Phase_I	Q8N4P6	LRC71_HUMAN			9	1126	+			324					Q96M24	Silent	SNP	ENST00000337428.7	37	c.972A>G	CCDS44249.1																																																																																				0.677	LRRC71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098961.1	0	NM_144702		1:156897772
NRAP	4892	broad.mit.edu	37	10	115374049	115374049	+	Missense_Mutation	SNP	A	A	G			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	A	A	-	-	A	A	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr10:115374049A>G	ENST00000359988.3	-	29	3437	c.3193T>C	c.(3193-3195)Tac>Cac	p.Y1065H	NRAP_ENST00000369358.4_Missense_Mutation_p.Y1073H|NRAP_ENST00000369360.3_Missense_Mutation_p.Y1038H|NRAP_ENST00000360478.3_Missense_Mutation_p.Y1030H	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein											autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		GCCTCTTTGTATTTGTACTAA	0.453																																						ENST00000369358.4		NA																	0				autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95						c.(3217-3219)Tac>Cac		nebulin-related anchoring protein							150.0	134.0	140.0					10																	115374049		2203	4300	6503	SO:0001583	missense	4892					fascia adherens|muscle tendon junction	actin binding|muscle alpha-actinin binding|zinc ion binding	g.chr10:115374049A>G		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.3193T>C	10.37:g.115374049A>G	ENSP00000353078:p.Tyr1065His	True	False		Somatic	0				NRAP_ENST00000359988.3_Missense_Mutation_p.Y1065H|NRAP_ENST00000369360.3_Missense_Mutation_p.Y1038H|NRAP_ENST00000360478.3_Missense_Mutation_p.Y1030H	p.Y1073H			WXS	Illumina HiSeq	Phase_I	Q86VF7	NRAP_HUMAN		Epithelial(162;0.00392)|all cancers(201;0.00569)	29	3461	-		Colorectal(252;0.0233)|Breast(234;0.188)	1065						Missense_Mutation	SNP	ENST00000359988.3	37	c.3217T>C	CCDS7579.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.298801	0.81025	.	.	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478	D;D;D;D	0.99958	-9.03;-9.03;-9.03;-9.03	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	D	0.99955	0.9981	M	0.89601	3.045	0.48571	D	0.999672	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	D	0.95382	0.8474	10	0.87932	D	0	.	15.8761	0.79162	1.0:0.0:0.0:0.0	.	1065;1030;1065	A0AVL2;Q86VF7-4;Q86VF7	.;.;NRAP_HUMAN	H	1073;1038;1065;1030	ENSP00000358365:Y1073H;ENSP00000358367:Y1038H;ENSP00000353078:Y1065H;ENSP00000353666:Y1030H	ENSP00000353078:Y1065H	Y	-	1	0	NRAP	115364039	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.290000	0.89925	2.153000	0.67306	0.528000	0.53228	TAC		0.453	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	0	NM_006175		10:115374049
ACBD6	84320	broad.mit.edu	37	1	180461444	180461444	+	Missense_Mutation	SNP	A	A	G			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	A	A	-	-	A	A	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr1:180461444A>G	ENST00000367595.3	-	3	1031	c.344T>C	c.(343-345)aTc>aCc	p.I115T		NM_032360.3	NP_115736.1	Q9BR61	ACBD6_HUMAN	acyl-CoA binding domain containing 6	115	ACB. {ECO:0000255|PROSITE- ProRule:PRU00573}.					cytoplasm (GO:0005737)	fatty-acyl-CoA binding (GO:0000062)|lipid binding (GO:0008289)		ACBD6/RRP15(2)	haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|ovary(1)	7						AACTACTGCGATATATTCCTG	0.358																																						ENST00000367595.3		NA																ACBD6/RRP15(2)	0				haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|ovary(1)	7						c.(343-345)aTc>aCc		acyl-CoA binding domain containing 6							113.0	115.0	114.0					1																	180461444		2203	4300	6503	SO:0001583	missense	84320					cytoplasm|nucleus	fatty-acyl-CoA binding	g.chr1:180461444A>G	BC006505	CCDS1339.1	1q25.1	2013-10-11	2010-04-30		ENSG00000135847			"""Ankyrin repeat domain containing"""	23339	protein-coding gene	gene with protein product			"""acyl-Coenzyme A binding domain containing 6"""			18268358	Standard	NM_032360		Approved	MGC2404	uc001gog.3	Q9BR61	OTTHUMG00000035117	ENST00000367595.3:c.344T>C	1.37:g.180461444A>G	ENSP00000356567:p.Ile115Thr	True	False		Somatic	0					p.I115T	NM_032360.3	NP_115736.1	WXS	Illumina HiSeq	Phase_I	Q9BR61	ACBD6_HUMAN			3	1031	-			115			ACB.			Missense_Mutation	SNP	ENST00000367595.3	37	c.344T>C	CCDS1339.1	.	.	.	.	.	.	.	.	.	.	A	18.53	3.645038	0.67358	.	.	ENSG00000135847	ENST00000367595	T	0.33654	1.4	5.05	5.05	0.67936	FERM/acyl-CoA-binding protein, 3-helical bundle (1);Acyl-CoA-binding protein, ACBP (4);	0.228453	0.45126	D	0.000387	T	0.54159	0.1841	M	0.78223	2.4	0.49915	D	0.999832	B	0.28026	0.198	P	0.45712	0.491	T	0.57533	-0.7795	10	0.51188	T	0.08	-8.125	13.7956	0.63168	1.0:0.0:0.0:0.0	.	115	Q9BR61	ACBD6_HUMAN	T	115	ENSP00000356567:I115T	ENSP00000356567:I115T	I	-	2	0	ACBD6	178728067	1.000000	0.71417	0.961000	0.40146	0.726000	0.41606	6.617000	0.74210	1.903000	0.55091	0.528000	0.53228	ATC		0.358	ACBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084998.1	0	NM_032360		1:180461444
SNHG14	104472715	broad.mit.edu	37	15	25335130	25335130	+	RNA	SNP	T	T	C			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	T	T	-	-	T	T	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr15:25335130T>C	ENST00000546682.1	+	0	839				SNHG14_ENST00000549804.2_RNA|SNHG14_ENST00000384430.1_RNA|SNORD116-20_ENST00000384529.1_lincRNA|SNORD116-20_ENST00000384507.1_lincRNA|SNHG14_ENST00000553108.1_RNA|SNORD116-23_ENST00000384645.1_RNA	NR_003361.1				small nucleolar RNA host gene 14 (non-protein coding)																		GAGTGAAAACTCTATACCGTC	0.463																																						ENST00000546682.1		NA																	0					NA															305.0	261.0	275.0					15																	25335130		876	1991	2867			0							g.chr15:25335130T>C			15q11.2	2014-01-17	2011-08-22	2011-08-22	ENSG00000224078	ENSG00000224078		"""Long non-coding RNAs"""	37462	non-coding RNA	RNA, long non-coding	"""non-protein coding RNA 214"""		"""UBE3A antisense RNA 1 (non-protein coding)"""	UBE3A-AS1		23771028	Standard			Approved	NCRNA00214, UBE3A-AS			OTTHUMG00000056661		15.37:g.25335130T>C		False	False		Somatic	0				SNHG14_ENST00000553108.1_RNA|SNHG14_ENST00000549804.2_RNA|SNHG14_ENST00000384430.1_RNA		NR_003361.1		WXS	Illumina HiSeq	Phase_I					0	839	+			NA						RNA	SNP	ENST00000546682.1	37																																																																																						0.463	SNHG14-022	KNOWN	basic	antisense	processed_transcript	OTTHUMT00000408281.1	0			15:25335130
PUSL1	126789	broad.mit.edu	37	1	1244619	1244619	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr1:1244619G>A	ENST00000379031.5	+	3	366	c.289G>A	c.(289-291)Gcc>Acc	p.A97T	PUSL1_ENST00000470520.1_3'UTR|CPSF3L_ENST00000462432.1_5'Flank|ACAP3_ENST00000354700.5_5'Flank|ACAP3_ENST00000353662.3_5'Flank	NM_153339.1	NP_699170.1	Q8N0Z8	PUSL1_HUMAN	pseudouridylate synthase-like 1	97					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			lung(3)|skin(1)|urinary_tract(1)	5	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;4.95e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		CCTGGCCGAGGCCCTCAACAC	0.746																																						ENST00000379031.5		NA																	0				lung(3)|skin(1)|urinary_tract(1)	5						c.(289-291)Gcc>Acc		pseudouridylate synthase-like 1							5.0	6.0	6.0					1																	1244619		2017	4041	6058	SO:0001583	missense	126789				pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding	g.chr1:1244619G>A	AK027721	CCDS20.1	1p36.33	2008-02-05			ENSG00000169972	ENSG00000169972			26914	protein-coding gene	gene with protein product						12477932	Standard	NM_153339		Approved	FLJ90811	uc001aed.3	Q8N0Z8	OTTHUMG00000003361	ENST00000379031.5:c.289G>A	1.37:g.1244619G>A	ENSP00000368318:p.Ala97Thr	True	False		Somatic	0				PUSL1_ENST00000470520.1_3'UTR	p.A97T	NM_153339.1	NP_699170.1	WXS	Illumina HiSeq	Phase_I	Q8N0Z8	PUSL1_HUMAN		Epithelial(90;4.95e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)	3	366	+	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)	97					B4DP76|Q5TA41	Missense_Mutation	SNP	ENST00000379031.5	37	c.289G>A	CCDS20.1	.	.	.	.	.	.	.	.	.	.	g	16.09	3.025366	0.54683	.	.	ENSG00000169972	ENST00000379031	T	0.56275	0.47	4.63	2.5	0.30297	Pseudouridine synthase I, TruA, N-terminal (1);Pseudouridine synthase, catalytic domain (1);Pseudouridine synthase I, TruA, alpha/beta domain (1);	0.420768	0.18516	N	0.138901	T	0.73032	0.3535	M	0.90922	3.16	0.32924	D	0.516194	D	0.63880	0.993	P	0.61070	0.883	T	0.82554	-0.0399	10	0.87932	D	0	-24.0168	12.1582	0.54089	0.0:0.2825:0.7175:0.0	.	97	Q8N0Z8	PUSL1_HUMAN	T	97	ENSP00000368318:A97T	ENSP00000368318:A97T	A	+	1	0	PUSL1	1234482	0.975000	0.34042	0.971000	0.41717	0.211000	0.24417	2.775000	0.47702	2.141000	0.66446	0.450000	0.29827	GCC		0.746	PUSL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009438.1	0	NM_153339		1:1244619
GREM2	64388	broad.mit.edu	37	1	240656720	240656720	+	Missense_Mutation	SNP	G	G	A	rs200521974		TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr1:240656720G>A	ENST00000318160.4	-	2	322	c.56C>T	c.(55-57)gCg>gTg	p.A19V		NM_022469.3	NP_071914.3	Q9H772	GREM2_HUMAN	gremlin 2, DAN family BMP antagonist	19					BMP signaling pathway (GO:0030509)|cytokine-mediated signaling pathway (GO:0019221)|determination of dorsal identity (GO:0048263)|embryonic body morphogenesis (GO:0010172)|regulation of cytokine activity (GO:0060300)|sequestering of BMP from receptor via BMP binding (GO:0038098)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	heparin binding (GO:0008201)			endometrium(1)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	10		all_cancers(173;0.0196)	OV - Ovarian serous cystadenocarcinoma(106;0.0123)			CCGGGCTTCCGCCACCTTCAC	0.612																																						ENST00000318160.4		NA																	0				endometrium(1)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	10						c.(55-57)gCg>gTg		gremlin 2, DAN family BMP antagonist							10.0	12.0	12.0					1																	240656720		2175	4253	6428	SO:0001583	missense	64388				BMP signaling pathway	extracellular space	cytokine activity	g.chr1:240656720G>A	AK024848	CCDS31070.1	1q43	2013-02-26	2013-02-26		ENSG00000180875	ENSG00000180875			17655	protein-coding gene	gene with protein product	"""protein related to DAN and cerberus"""	608832	"""gremlin 2, cysteine knot superfamily, homolog (Xenopus laevis)"", ""gremlin 2"""			15039429	Standard	XM_005273226		Approved	Prdc, FLJ21195, CKTSF1B2, DAND3	uc001hys.3	Q9H772	OTTHUMG00000039909	ENST00000318160.4:c.56C>T	1.37:g.240656720G>A	ENSP00000318650:p.Ala19Val	False	False		Somatic	0					p.A19V	NM_022469.3	NP_071914.3	WXS	Illumina HiSeq	Phase_I	Q9H772	GREM2_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.0123)		2	322	-		all_cancers(173;0.0196)	19					Q86UD9	Missense_Mutation	SNP	ENST00000318160.4	37	c.56C>T	CCDS31070.1	.	.	.	.	.	.	.	.	.	.	G	17.33	3.361699	0.61403	.	.	ENSG00000180875	ENST00000318160	T	0.32753	1.44	5.15	3.22	0.36961	.	0.235752	0.35378	U	0.003251	T	0.22205	0.0535	L	0.38175	1.15	0.40552	D	0.981126	B	0.27971	0.196	B	0.16722	0.016	T	0.04708	-1.0932	10	0.48119	T	0.1	-3.9963	10.411	0.44294	0.0:0.1461:0.7017:0.1522	.	19	Q9H772	GREM2_HUMAN	V	19	ENSP00000318650:A19V	ENSP00000318650:A19V	A	-	2	0	GREM2	238723343	0.411000	0.25384	0.818000	0.32626	0.995000	0.86356	3.465000	0.53064	0.524000	0.28502	0.557000	0.71058	GCG		0.612	GREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096286.1	0	NM_022469		1:240656720
RPAP1	26015	broad.mit.edu	37	15	41815528	41815528	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr15:41815528G>T	ENST00000304330.4	-	18	2577	c.2461C>A	c.(2461-2463)Ctc>Atc	p.L821I	RPAP1_ENST00000561603.1_Missense_Mutation_p.L821I	NM_015540.2	NP_056355.2	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	821						nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)	p.L821I(1)		NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(16)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	45		all_cancers(109;6.59e-20)|all_epithelial(112;7.67e-17)|Lung NSC(122;5.34e-11)|all_lung(180;4.17e-10)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		OV - Ovarian serous cystadenocarcinoma(18;2.84e-17)|GBM - Glioblastoma multiforme(113;1.68e-06)|Colorectal(105;0.0163)|BRCA - Breast invasive adenocarcinoma(123;0.117)		ATGTCCTGGAGCCAATCCTCC	0.577																																						ENST00000304330.4		NA																	1	Substitution - Missense(1)	p.L821I(1)	kidney(1)	NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(16)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	45						c.(2461-2463)Ctc>Atc		RNA polymerase II associated protein 1							37.0	39.0	38.0					15																	41815528		2203	4300	6503	SO:0001583	missense	26015					nucleus	DNA binding|DNA-directed RNA polymerase activity	g.chr15:41815528G>T	BC000246	CCDS10079.1	15q14	2004-03-16			ENSG00000103932	ENSG00000103932			24567	protein-coding gene	gene with protein product		611475				10718198	Standard	XM_005254297		Approved	DKFZP727M111, KIAA1403, MGC858, FLJ12732	uc001zod.3	Q9BWH6	OTTHUMG00000130342	ENST00000304330.4:c.2461C>A	15.37:g.41815528G>T	ENSP00000306123:p.Leu821Ile	False	False		Somatic	0				RPAP1_ENST00000561603.1_Missense_Mutation_p.L821I	p.L821I	NM_015540.2	NP_056355.2	WXS	Illumina HiSeq	Phase_I	Q9BWH6	RPAP1_HUMAN		OV - Ovarian serous cystadenocarcinoma(18;2.84e-17)|GBM - Glioblastoma multiforme(113;1.68e-06)|Colorectal(105;0.0163)|BRCA - Breast invasive adenocarcinoma(123;0.117)	18	2577	-		all_cancers(109;6.59e-20)|all_epithelial(112;7.67e-17)|Lung NSC(122;5.34e-11)|all_lung(180;4.17e-10)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)	821					Q9H9I2|Q9NSQ5|Q9P2E4|Q9UFS7	Missense_Mutation	SNP	ENST00000304330.4	37	c.2461C>A	CCDS10079.1	.	.	.	.	.	.	.	.	.	.	G	18.00	3.525485	0.64860	.	.	ENSG00000103932	ENST00000304330	T	0.67345	-0.26	5.7	5.7	0.88788	.	0.218096	0.37577	N	0.002036	T	0.77805	0.4185	M	0.66939	2.045	0.36757	D	0.88309	D	0.89917	1.0	D	0.71184	0.972	T	0.82629	-0.0363	10	0.87932	D	0	-13.6196	10.1363	0.42708	0.0942:0.0:0.9058:0.0	.	821	Q9BWH6	RPAP1_HUMAN	I	821	ENSP00000306123:L821I	ENSP00000306123:L821I	L	-	1	0	RPAP1	39602820	1.000000	0.71417	1.000000	0.80357	0.450000	0.32258	4.664000	0.61540	2.679000	0.91253	0.655000	0.94253	CTC		0.577	RPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252694.2	0	NM_015540		15:41815528
CHD4	1108	broad.mit.edu	37	12	6686950	6686950	+	Splice_Site	SNP	C	C	T	rs529117126		TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr12:6686950C>T	ENST00000357008.2	-	37	5525		c.e37+1		CHD4_ENST00000544040.1_Splice_Site|CHD4_ENST00000309577.6_Splice_Site|RP5-940J5.6_ENST00000501075.2_RNA|CHD4_ENST00000544484.1_Splice_Site	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4						ATP-dependent chromatin remodeling (GO:0043044)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|RNA polymerase II repressing transcription factor binding (GO:0001103)|zinc ion binding (GO:0008270)	p.?(3)		central_nervous_system(2)	2						CAACCGCTCACCTTAAACCTT	0.463																																					Colon(32;586 792 4568 16848 45314)	ENST00000309577.6		NA																	3	Unknown(3)	p.?(3)	prostate(3)	central_nervous_system(2)	2						c.e36+1		chromodomain helicase DNA binding protein 4							103.0	102.0	102.0					12																	6686950		2203	4300	6503	SO:0001630	splice_region_variant	1108				chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	microtubule organizing center|NuRD complex	ATP binding|ATP-dependent DNA helicase activity|DNA binding|zinc ion binding	g.chr12:6686950C>T	X86691	CCDS8552.1	12p13	2013-01-28				ENSG00000111642		"""Zinc fingers, PHD-type"""	1919	protein-coding gene	gene with protein product		603277				7575689, 8843877	Standard	XM_006718958		Approved	Mi-2b, Mi2-BETA	uc001qpo.3	Q14839		ENST00000357008.2:c.5361+1G>A	12.37:g.6686950C>T		False	False		Somatic	0				CHD4_ENST00000544040.1_Splice_Site|CHD4_ENST00000544484.1_Splice_Site|CHD4_ENST00000357008.2_Splice_Site				WXS	Illumina HiSeq	Phase_I	Q14839	CHD4_HUMAN			36	5609	-			NA					Q8IXZ5	Splice_Site	SNP	ENST00000357008.2	37		CCDS8552.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.616076	0.87359	.	.	ENSG00000111642	ENST00000544484;ENST00000544040;ENST00000309577;ENST00000357008;ENST00000537464	.	.	.	5.51	5.51	0.81932	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.7859	0.96437	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CHD4	6557211	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	7.464000	0.80887	2.746000	0.94184	0.655000	0.94253	.		0.463	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		0	NM_001273	Intron	12:6686950
KNTC1	9735	broad.mit.edu	37	12	123019271	123019271	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr12:123019271G>T	ENST00000333479.7	+	3	367	c.190G>T	c.(190-192)Gac>Tac	p.D64Y	KNTC1_ENST00000450485.2_Missense_Mutation_p.D64Y	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	64					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|protein complex assembly (GO:0006461)|regulation of exit from mitosis (GO:0007096)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(1)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(8)|large_intestine(12)|lung(20)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	72	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)		TATTGTAGCCGACCAATCAGT	0.348																																						ENST00000333479.7		NA																	0				breast(1)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(8)|large_intestine(12)|lung(20)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	72						c.(190-192)Gac>Tac		kinetochore associated 1							162.0	145.0	150.0					12																	123019271		1876	4123	5999	SO:0001583	missense	9735				cell division|mitotic cell cycle checkpoint|mitotic prometaphase|protein complex assembly|regulation of exit from mitosis	condensed chromosome kinetochore|cytosol|kinetochore microtubule|nucleus|spindle pole	protein binding	g.chr12:123019271G>T		CCDS45002.1	12q24.31	2013-01-17			ENSG00000184445	ENSG00000184445			17255	protein-coding gene	gene with protein product	"""rough deal homolog (Drosophila)"""	607363				11146660, 11590237	Standard	NM_014708		Approved	KIAA0166, ROD	uc001ucv.3	P50748	OTTHUMG00000168861	ENST00000333479.7:c.190G>T	12.37:g.123019271G>T	ENSP00000328236:p.Asp64Tyr	False	False		Somatic	0				KNTC1_ENST00000450485.2_Missense_Mutation_p.D64Y	p.D64Y	NM_014708.4	NP_055523.1	WXS	Illumina HiSeq	Phase_I	P50748	KNTC1_HUMAN		OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)	3	367	+	all_neural(191;0.0837)|Medulloblastoma(191;0.163)		64					A7E2C4|B3KSG2	Missense_Mutation	SNP	ENST00000333479.7	37	c.190G>T	CCDS45002.1	.	.	.	.	.	.	.	.	.	.	G	18.11	3.551327	0.65311	.	.	ENSG00000184445	ENST00000450485;ENST00000333479	T;T	0.30448	1.53;1.53	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.48333	0.1494	L	0.34521	1.04	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.45862	-0.9232	10	0.87932	D	0	-20.8132	19.5419	0.95277	0.0:0.0:1.0:0.0	.	64;64	E7ES84;P50748	.;KNTC1_HUMAN	Y	64	ENSP00000397992:D64Y;ENSP00000328236:D64Y	ENSP00000328236:D64Y	D	+	1	0	KNTC1	121585224	1.000000	0.71417	0.861000	0.33841	0.985000	0.73830	6.059000	0.71133	2.714000	0.92807	0.650000	0.86243	GAC		0.348	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2	0			12:123019271
KRT26	353288	broad.mit.edu	37	17	38928255	38928255	+	Silent	SNP	C	C	T	rs376310686		TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr17:38928255C>T	ENST00000335552.4	-	1	159	c.111G>A	c.(109-111)tcG>tcA	p.S37S		NM_181539.4	NP_853517.2			keratin 26											central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(5)	16		Breast(137;0.00526)				TTCTTGCTCCCGATCCAACAC	0.557																																						ENST00000335552.4		NA																	0				central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(5)	16						c.(109-111)tcG>tcA		keratin 26		C		0,4406		0,0,2203	121.0	124.0	123.0		111	-11.3	0.0	17		123	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KRT26	NM_181539.4		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		37/469	38928255	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	353288					intermediate filament	structural molecule activity	g.chr17:38928255C>T	AJ564205	CCDS11374.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000186393	ENSG00000186393		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	30840	protein-coding gene	gene with protein product			"""keratin 25B"""	KRT25B		16831889	Standard	NM_181539		Approved		uc002hvf.3	Q7Z3Y9	OTTHUMG00000133370	ENST00000335552.4:c.111G>A	17.37:g.38928255C>T		True	False		Somatic	0					p.S37S	NM_181539.4	NP_853517.2	WXS	Illumina HiSeq	Phase_I	Q7Z3Y9	K1C26_HUMAN			1	159	-		Breast(137;0.00526)	37			Gly-rich.|Head.			Silent	SNP	ENST00000335552.4	37	c.111G>A	CCDS11374.1																																																																																				0.557	KRT26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257215.1	0	NM_181539		17:38928255
VARS2	57176	broad.mit.edu	37	6	30892256	30892256	+	Silent	SNP	C	C	G			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr6:30892256C>G	ENST00000321897.5	+	25	3224	c.2592C>G	c.(2590-2592)ctC>ctG	p.L864L	VARS2_ENST00000541562.1_Silent_p.L894L|VARS2_ENST00000416670.2_Silent_p.L864L|VARS2_ENST00000542001.1_Silent_p.L724L|VARS2_ENST00000476162.1_3'UTR			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	864					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(3)|prostate(3)|skin(4)|urinary_tract(1)	46						CTGAAGAGCTCTGGCAGAGGC	0.706																																						ENST00000321897.5		NA																	0				central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(3)|prostate(3)|skin(4)|urinary_tract(1)	46						c.(2590-2592)ctC>ctG		valyl-tRNA synthetase 2, mitochondrial							24.0	30.0	28.0					6																	30892256		1508	2708	4216	SO:0001819	synonymous_variant	57176				valyl-tRNA aminoacylation	mitochondrion	ATP binding|valine-tRNA ligase activity	g.chr6:30892256C>G	AB067472	CCDS34387.1, CCDS54980.1	6p21.33	2012-10-26	2012-10-26	2007-02-23	ENSG00000137411	ENSG00000137411	6.1.1.9	"""Aminoacyl tRNA synthetases / Class I"""	21642	protein-coding gene	gene with protein product	"""valine tRNA ligase 2, mitochondrial"""	612802	"""valyl-tRNA synthetase 2-like"", ""valyl-tRNA synthetase like"", ""valyl-tRNA synthetase 2, mitochondrial (putative)"""	VARS2L, VARSL		1898367, 11572484, 18400783	Standard	NM_001167734		Approved	DKFZP434L1435, KIAA1885, G7a	uc011dmz.2	Q5ST30	OTTHUMG00000031263	ENST00000321897.5:c.2592C>G	6.37:g.30892256C>G		False	False		Somatic	0				VARS2_ENST00000542001.1_Silent_p.L724L|VARS2_ENST00000416670.2_Silent_p.L864L|VARS2_ENST00000541562.1_Silent_p.L894L|VARS2_ENST00000476162.1_3'UTR	p.L864L			WXS	Illumina HiSeq	Phase_I	Q5ST30	SYVM_HUMAN			25	3224	+			864					A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Silent	SNP	ENST00000321897.5	37	c.2592C>G	CCDS34387.1																																																																																				0.706	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	0	NM_020442		6:30892256
GALNT16	57452	broad.mit.edu	37	14	69805396	69805396	+	Silent	SNP	T	T	C			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	T	T	-	-	T	T	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr14:69805396T>C	ENST00000337827.4	+	10	1323	c.996T>C	c.(994-996)ggT>ggC	p.G332G	GALNT16_ENST00000448469.3_Silent_p.G332G|GALNT16_ENST00000553669.1_Silent_p.G332G	NM_001168368.1|NM_020692.2	NP_001161840.1|NP_065743.2	Q8N428	GLT16_HUMAN	polypeptide N-acetylgalactosaminyltransferase 16	332	Catalytic subdomain B.				protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)										GGATGTGTGGTGGCAGTCTGG	0.592																																						ENST00000337827.4		NA																	0					NA						c.(994-996)ggT>ggC		UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 16							150.0	123.0	132.0					14																	69805396		2203	4300	6503	SO:0001819	synonymous_variant	57452							g.chr14:69805396T>C	AB032956	CCDS32107.1	14q24.1	2014-03-13	2014-03-13	2013-01-25	ENSG00000100626	ENSG00000100626	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	23233	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 16"""	615132	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 1"", ""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 16"""	GALNTL1		10574461, 22186971	Standard	NM_020692		Approved	KIAA1130, GalNAc-T16	uc010aqu.2	Q8N428	OTTHUMG00000171231	ENST00000337827.4:c.996T>C	14.37:g.69805396T>C		False	False		Somatic	0				GALNT16_ENST00000553669.1_Silent_p.G332G|GALNT16_ENST00000448469.3_Silent_p.G332G	p.G332G	NM_001168368.1|NM_020692.2	NP_001161840.1|NP_065743.2	WXS	Illumina HiSeq	Phase_I					10	1323	+			NA					Q4KMG3|Q58A55|Q9ULT9	Silent	SNP	ENST00000337827.4	37	c.996T>C	CCDS32107.1																																																																																				0.592	GALNT16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412434.1	0	NM_001168368		14:69805396
ASPSCR1	79058	broad.mit.edu	37	17	79973120	79973120	+	Intron	SNP	G	G	A			TCGA-IB-7897-01A-21D-2201-08	TCGA-IB-7897-10A-01D-2201-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Phase_I	WXS	none	NA	NA	Illumina GAIIx	1c284154-c3c3-4cd9-be15-7299b375fc83	e9687af7-9276-4f39-9f3d-5a96e305026f	g.chr17:79973120G>A	ENST00000306739.4	+	13	1450				ASPSCR1_ENST00000306729.7_Missense_Mutation_p.G508D|ASPSCR1_ENST00000580534.1_Intron|ASPSCR1_ENST00000582404.1_3'UTR	NM_024083.3	NP_076988.1	Q9BZE9	ASPC1_HUMAN	alveolar soft part sarcoma chromosome region, candidate 1						glucose homeostasis (GO:0042593)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|regulation of glucose import (GO:0046324)	cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)			ASPSCR1/TFE3(167)	breast(2)|large_intestine(2)	4	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191)			CCAAGCACTGGTCAGCCTCCA	0.627			T	TFE3	alveolar soft part sarcoma																																	ENST00000306729.7		NA		Dom	yes		17	17q25	79058	T	"""alveolar soft part sarcoma chromosome region, candidate 1"""			M	TFE3		alveolar soft part sarcoma	ASPSCR1/TFE3(167)	0				breast(2)|large_intestine(2)	4						c.(1522-1524)gGt>gAt		alveolar soft part sarcoma chromosome region, candidate 1							84.0	84.0	84.0					17																	79973120		876	1991	2867	SO:0001627	intron_variant	79058						protein binding	g.chr17:79973120G>A	AF324219	CCDS11796.1, CCDS58611.1	17q25	2011-06-28				ENSG00000169696		"""UBX domain containing"""	13825	protein-coding gene	gene with protein product	"""UBX domain protein 9"""	606236				11244503, 10506710	Standard	NM_024083		Approved	ASPS, ASPL, UBXD9, UBXN9	uc002kcy.3	Q9BZE9		ENST00000306739.4:c.1354-1232G>A	17.37:g.79973120G>A		False	False		Somatic	0				ASPSCR1_ENST00000580534.1_Intron|ASPSCR1_ENST00000582404.1_3'UTR|ASPSCR1_ENST00000306739.4_Intron	p.G508D	NM_001251888.1	NP_001238817.1	WXS	Illumina HiSeq	Phase_I	Q9BZE9	ASPC1_HUMAN	BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191)		13	1620	+	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.246)		505					A8K3K9|Q7Z6N7|Q8WV59|Q96LS5|Q96M40	Missense_Mutation	SNP	ENST00000306739.4	37	c.1523G>A	CCDS11796.1	.	.	.	.	.	.	.	.	.	.	G	6.957	0.546457	0.13312	.	.	ENSG00000169696	ENST00000306729	T	0.28069	1.63	0.53	-1.06	0.10002	.	.	.	.	.	T	0.17746	0.0426	.	.	.	0.09310	N	0.999999	P	0.49185	0.92	B	0.39805	0.31	T	0.12372	-1.0550	6	.	.	.	.	.	.	.	.	508	Q9BZE9-2	.	D	508	ENSP00000306625:G508D	.	G	+	2	0	ASPSCR1	77566409	0.000000	0.05858	0.001000	0.08648	0.027000	0.11550	-1.196000	0.03041	-0.573000	0.05998	0.205000	0.17691	GGT		0.627	ASPSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441972.1	0	NM_024083		17:79973120
