#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_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	i_BAM_File	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_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	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_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	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_NTotCov	i_NVarCov	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	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_dbSNPPopFreq	i_dbSNP_AF	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
MACF1	23499	hgsc.bcm.edu	37	1	39907974	39907974	+	Missense_Mutation	SNP	G	G	T			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr1:39907974G>T	ENST00000372915.3	+	75	18714	c.18627G>T	c.(18625-18627)gaG>gaT	p.E6209D	MACF1_ENST00000567887.1_Missense_Mutation_p.E6347D|MACF1_ENST00000539005.1_Missense_Mutation_p.E4121D|MACF1_ENST00000564288.1_Missense_Mutation_p.E6310D|MACF1_ENST00000289893.4_Missense_Mutation_p.E4753D|MACF1_ENST00000545844.1_Missense_Mutation_p.E4251D|MACF1_ENST00000317713.7_Missense_Mutation_p.E4251D|MACF1_ENST00000361689.2_Missense_Mutation_p.E4251D			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	6209					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			ACCTGGGTGAGAAAATTGCCC	0.438																																					p.E4251D		Atlas-SNP	.											.	MACF1	909	.	0			c.G12753T						.						46.0	48.0	47.0					1																	39907974		2203	4300	6503	SO:0001583	missense	23499	exon73			GGGTGAGAAAATT	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"""EF-hand domain containing"""	13664	protein-coding gene	gene with protein product	"""actin cross-linking factor"", ""620 kDa actin binding protein"", ""macrophin 1"", ""trabeculin-alpha"", ""actin cross-linking family protein 7"""	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.18627G>T	chr1.hg19:g.39907974G>T	ENSP00000362006:p.Glu6209Asp	128.0	0.0		123.0	39.0	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.61|12.61	1.989737|1.989737	0.35131|0.35131	.|.	.|.	ENSG00000127603|ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893|ENST00000372925	T;T;T;T;T;T|.	0.53640|.	0.61;0.61;0.61;0.61;0.61;0.61|.	6.03|6.03	0.646|0.646	0.17789|0.17789	.|.	0.090504|0.090504	0.47852|0.47852	D|D	0.000217|0.000217	T|.	0.26448|.	0.0646|.	N|N	0.11927|0.11927	0.2|0.2	0.80722|0.80722	D|D	1|1	B;B|.	0.32800|.	0.27;0.385|.	B;B|.	0.38842|.	0.241;0.283|.	T|.	0.09335|.	-1.0679|.	10|.	0.34782|0.07175	T|T	0.22|0.84	.|.	6.3831|6.3831	0.21546|0.21546	0.4178:0.1188:0.4634:0.0|0.4178:0.1188:0.4634:0.0	.|.	6209;4251|.	Q9UPN3;F8W8Q1|.	MACF1_HUMAN;.|.	D|X	4251;6209;4251;4251;4121;4753|3255	ENSP00000439537:E4251D;ENSP00000362006:E6209D;ENSP00000354573:E4251D;ENSP00000313438:E4251D;ENSP00000444364:E4121D;ENSP00000289893:E4753D|.	ENSP00000289893:E4753D|ENSP00000362016:E3255X	E|E	+|+	3|1	2|0	MACF1|MACF1	39680561|39680561	0.969000|0.969000	0.33509|0.33509	0.995000|0.995000	0.50966|0.50966	0.993000|0.993000	0.82548|0.82548	0.116000|0.116000	0.15561|0.15561	-0.132000|-0.132000	0.11557|0.11557	0.655000|0.655000	0.94253|0.94253	GAG|GAA	.	.		0.438	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044	
STXBP3	6814	hgsc.bcm.edu	37	1	109339272	109339272	+	Missense_Mutation	SNP	T	T	A			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr1:109339272T>A	ENST00000370008.3	+	15	1330	c.1280T>A	c.(1279-1281)aTc>aAc	p.I427N		NM_007269.2	NP_009200.2	O00186	STXB3_HUMAN	syntaxin binding protein 3	427					blood coagulation (GO:0007596)|membrane organization (GO:0061024)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|neutrophil degranulation (GO:0043312)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein heterooligomerization (GO:0051291)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|specific granule (GO:0042581)|tertiary granule (GO:0070820)	syntaxin binding (GO:0019905)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(3)|urinary_tract(1)	13		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0386)|Lung(183;0.104)|COAD - Colon adenocarcinoma(174;0.137)|Epithelial(280;0.231)		GACAGGTTGATCCAGAATGTA	0.358																																					p.I427N		Atlas-SNP	.											.	STXBP3	44	.	0			c.T1280A						.						137.0	134.0	135.0					1																	109339272		2203	4300	6503	SO:0001583	missense	6814	exon15			GGTTGATCCAGAA	D63506	CCDS790.1	1p13.3	2008-02-05			ENSG00000116266	ENSG00000116266			11446	protein-coding gene	gene with protein product		608339				10194441	Standard	NM_007269		Approved	UNC-18C	uc001dvy.3	O00186	OTTHUMG00000011122	ENST00000370008.3:c.1280T>A	chr1.hg19:g.109339272T>A	ENSP00000359025:p.Ile427Asn	230.0	0.0		208.0	62.0	NM_007269	A8K269|A8K5K7|Q53FW1|Q86YJ3|Q9UPD7	Missense_Mutation	SNP	ENST00000370008.3	hg19	CCDS790.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.422713	0.83559	.	.	ENSG00000116266	ENST00000370008	T	0.79141	-1.24	5.44	5.44	0.79542	.	0.149746	0.64402	D	0.000017	T	0.77758	0.4178	M	0.78049	2.395	0.58432	D	0.999996	B	0.27765	0.188	B	0.40101	0.319	T	0.80462	-0.1372	10	0.72032	D	0.01	-1.0014	15.4851	0.75560	0.0:0.0:0.0:1.0	.	427	O00186	STXB3_HUMAN	N	427	ENSP00000359025:I427N	ENSP00000359025:I427N	I	+	2	0	STXBP3	109140795	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.999000	0.76283	2.060000	0.61445	0.383000	0.25322	ATC	.	.		0.358	STXBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030591.1	NM_007269	
KPRP	448834	hgsc.bcm.edu	37	1	152732812	152732812	+	Missense_Mutation	SNP	C	C	T			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr1:152732812C>T	ENST00000606109.1	+	1	776	c.748C>T	c.(748-750)Cgg>Tgg	p.R250W	KPRP_ENST00000368773.1_Missense_Mutation_p.R250W			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	250						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				NS(1)|breast(1)|endometrium(9)|kidney(1)|large_intestine(10)|lung(21)|ovary(6)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCACCGCTCTCGGAGCACCAG	0.607																																					p.R250W		Atlas-SNP	.											.	KPRP	152	.	0			c.C748T						.						52.0	58.0	56.0					1																	152732812		2203	4300	6503	SO:0001583	missense	448834	exon2			CGCTCTCGGAGCA	AY960854	CCDS30862.1	1q21.3	2008-02-05	2007-02-02	2006-12-07	ENSG00000203786	ENSG00000203786			31823	protein-coding gene	gene with protein product		613260	"""chromosome 1 open reading frame 45"""	C1orf45		16297201	Standard	NM_001025231		Approved		uc001fal.1	Q5T749	OTTHUMG00000012402	ENST00000606109.1:c.748C>T	chr1.hg19:g.152732812C>T	ENSP00000475216:p.Arg250Trp	58.0	0.0		82.0	26.0	NM_001025231		Missense_Mutation	SNP	ENST00000606109.1	hg19	CCDS30862.1	.	.	.	.	.	.	.	.	.	.	C	11.34	1.609401	0.28623	.	.	ENSG00000203786	ENST00000368773	T	0.13657	2.57	5.56	2.67	0.31697	.	0.921332	0.08935	N	0.872419	T	0.02848	0.0085	N	0.19112	0.55	0.09310	N	1	B	0.23650	0.089	B	0.21546	0.035	T	0.46048	-0.9219	10	0.87932	D	0	-0.0836	5.188	0.15195	0.1647:0.6645:0.0:0.1708	.	250	Q5T749	KPRP_HUMAN	W	250	ENSP00000357762:R250W	ENSP00000357762:R250W	R	+	1	2	KPRP	150999436	0.106000	0.21978	0.010000	0.14722	0.008000	0.06430	1.379000	0.34340	0.390000	0.25115	-0.140000	0.14226	CGG	.	.		0.607	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	NM_001025231	
CD1E	913	hgsc.bcm.edu	37	1	158325699	158325699	+	Silent	SNP	C	C	T			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr1:158325699C>T	ENST00000368167.3	+	4	947	c.708C>T	c.(706-708)taC>taT	p.Y236Y	CD1E_ENST00000368163.3_Silent_p.Y236Y|CD1E_ENST00000444681.2_Silent_p.Y137Y|CD1E_ENST00000368161.3_Silent_p.Y236Y|CD1E_ENST00000368155.3_Silent_p.Y146Y|CD1E_ENST00000368166.3_Silent_p.Y47Y|CD1E_ENST00000368165.3_Silent_p.Y146Y|CD1E_ENST00000368160.3_Silent_p.Y236Y|CD1E_ENST00000434258.1_Silent_p.Y234Y|CD1E_ENST00000368164.3_Silent_p.Y47Y|CD1E_ENST00000368156.1_Silent_p.Y146Y|CD1E_ENST00000368157.1_Silent_p.Y47Y|CD1E_ENST00000368154.1_Silent_p.Y47Y|CD1E_ENST00000452291.2_Silent_p.Y47Y	NM_030893.3	NP_112155.2	P15812	CD1E_HUMAN	CD1e molecule	236	Ig-like.				antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(27)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|urinary_tract(1)	49	all_hematologic(112;0.0378)					CAGGATTCTACCCAAAGCCCG	0.607																																					p.Y236Y		Atlas-SNP	.											.	CD1E	129	.	0			c.C708T						.						74.0	73.0	74.0					1																	158325699		2203	4298	6501	SO:0001819	synonymous_variant	913	exon4			ATTCTACCCAAAG	AJ289111	CCDS41417.1, CCDS41418.1, CCDS41419.1, CCDS41420.1, CCDS41421.1, CCDS41422.1, CCDS53387.1, CCDS53388.1, CCDS53389.1, CCDS53390.1, CCDS53384.1, CCDS53385.1, CCDS53386.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158488	ENSG00000158488		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	1638	protein-coding gene	gene with protein product		188411	"""CD1E antigen, e polypeptide"", ""CD1e antigen"""			10948205	Standard	NM_001042585		Approved		uc001fse.3	P15812	OTTHUMG00000017515	ENST00000368167.3:c.708C>T	chr1.hg19:g.158325699C>T		273.0	0.0		320.0	14.0	NM_001042584	B4DZV3|E7EP01|Q5TDJ9|Q5TDK3|Q5TDK4|Q5TDK5|Q5TDK6|Q5TDK8|Q5TDL1|Q712E4|Q712E5|Q712E6|Q712E7|Q712E8|Q712E9|Q712F0|Q712F1|Q712F2|Q712F3|Q712F4|Q712F5|Q96TD0|Q96TD1|Q9UMM1|Q9Y5M3	Silent	SNP	ENST00000368167.3	hg19	CCDS41417.1	.	.	.	.	.	.	.	.	.	.	C	9.848	1.193006	0.21954	.	.	ENSG00000158488	ENST00000368162	.	.	.	4.83	0.315	0.15852	.	.	.	.	.	T	0.38081	0.1027	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.25222	-1.0138	4	.	.	.	-10.221	6.8541	0.24030	0.0:0.5054:0.0:0.4946	.	.	.	.	S	6	.	.	P	+	1	0	CD1E	156592323	0.070000	0.21116	0.886000	0.34754	0.996000	0.88848	-0.738000	0.04871	-0.099000	0.12263	0.563000	0.77884	CCC	.	.		0.607	CD1E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046353.3	NM_030893	
ABCG5	64240	hgsc.bcm.edu	37	2	44053584	44053584	+	Missense_Mutation	SNP	T	T	G			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr2:44053584T>G	ENST00000260645.1	-	6	850	c.711A>C	c.(709-711)gaA>gaC	p.E237D	ABCG5_ENST00000543989.1_Intron|ABCG5_ENST00000405322.1_Intron	NM_022436.2	NP_071881.1	Q9H222	ABCG5_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 5	237	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|excretion (GO:0007588)|intestinal cholesterol absorption (GO:0030299)|negative regulation of intestinal cholesterol absorption (GO:0045796)|negative regulation of intestinal phytosterol absorption (GO:0010949)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cholesterol transporter activity (GO:0017127)|protein heterodimerization activity (GO:0046982)			breast(1)|kidney(2)|large_intestine(4)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	33		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)			Ezetimibe(DB00973)	TGCGAGCCAGTTCCACCAGGA	0.532																																					p.E237D		Atlas-SNP	.											.	ABCG5	72	.	0			c.A711C						.						146.0	126.0	133.0					2																	44053584		2203	4300	6503	SO:0001583	missense	64240	exon6			AGCCAGTTCCACC	T93792	CCDS1814.1	2p21	2012-03-14	2008-07-31		ENSG00000138075	ENSG00000138075		"""ATP binding cassette transporters / subfamily G"""	13886	protein-coding gene	gene with protein product	"""sterolin 1"""	605459				11099417, 11452359	Standard	NM_022436		Approved	STSL	uc002rtn.3	Q9H222	OTTHUMG00000128758	ENST00000260645.1:c.711A>C	chr2.hg19:g.44053584T>G	ENSP00000260645:p.Glu237Asp	150.0	0.0		184.0	61.0	NM_022436	Q2T9G2|Q96QZ2|Q96QZ3	Missense_Mutation	SNP	ENST00000260645.1	hg19	CCDS1814.1	.	.	.	.	.	.	.	.	.	.	T	11.50	1.657373	0.29425	.	.	ENSG00000138075	ENST00000260645	T	0.42131	0.98	5.56	2.31	0.28768	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.300661	0.40222	N	0.001146	T	0.25344	0.0616	N	0.20845	0.615	0.80722	D	1	P	0.46395	0.877	B	0.43194	0.411	T	0.02560	-1.1141	10	0.13853	T	0.58	.	9.2504	0.37551	0.0:0.6013:0.0:0.3987	.	237	Q9H222	ABCG5_HUMAN	D	237	ENSP00000260645:E237D	ENSP00000260645:E237D	E	-	3	2	ABCG5	43907088	1.000000	0.71417	0.985000	0.45067	0.195000	0.23768	1.080000	0.30779	0.689000	0.31550	-0.242000	0.12053	GAA	.	.		0.532	ABCG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250675.1	NM_022436	
CHRNA1	1134	hgsc.bcm.edu	37	2	175624066	175624066	+	Missense_Mutation	SNP	A	A	T			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr2:175624066A>T	ENST00000261007.5	-	3	293	c.227T>A	c.(226-228)cTg>cAg	p.L76Q	CHRNA1_ENST00000409542.1_Missense_Mutation_p.L76Q|CHRNA1_ENST00000409323.1_Missense_Mutation_p.L76Q|CHRNA1_ENST00000409219.1_Missense_Mutation_p.L76Q|CHRNA1_ENST00000348749.5_Missense_Mutation_p.L76Q|AC018890.6_ENST00000442996.1_RNA	NM_001039523.2	NP_001034612.1	P02708	ACHA_HUMAN	cholinergic receptor, nicotinic, alpha 1 (muscle)	76					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|muscle cell cellular homeostasis (GO:0046716)|musculoskeletal movement (GO:0050881)|neuromuscular junction development (GO:0007528)|neuromuscular process (GO:0050905)|neuromuscular synaptic transmission (GO:0007274)|neuron cellular homeostasis (GO:0070050)|neuronal action potential (GO:0019228)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue growth (GO:0048630)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cell surface (GO:0009986)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ion channel activity (GO:0005216)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(3)|prostate(3)|skin(4)	37					Galantamine(DB00674)	TACCTGTTTCAGACGCACATT	0.428																																					p.L76Q		Atlas-SNP	.											.	CHRNA1	92	.	0			c.T227A						.						106.0	101.0	102.0					2																	175624066		2203	4300	6503	SO:0001583	missense	1134	exon3			TGTTTCAGACGCA	Y00762	CCDS2261.1, CCDS33331.1	2q31.1	2012-02-11	2006-02-01		ENSG00000138435	ENSG00000138435		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1955	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 1 (muscle)"""	100690	"""cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle)"""	CHRNA			Standard	NM_001039523		Approved		uc002uje.2	P02708	OTTHUMG00000132357	ENST00000261007.5:c.227T>A	chr2.hg19:g.175624066A>T	ENSP00000261007:p.Leu76Gln	216.0	0.0		247.0	78.0	NM_001039523	B4DRV6|D3DPE8	Missense_Mutation	SNP	ENST00000261007.5	hg19	CCDS33331.1	.	.	.	.	.	.	.	.	.	.	A	28.0	4.883238	0.91740	.	.	ENSG00000138435	ENST00000348749;ENST00000261007;ENST00000409542;ENST00000409219;ENST00000409323	D;D;D;D;D	0.82167	-1.58;-1.58;-1.58;-1.58;-1.58	5.95	5.95	0.96441	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	D	0.93245	0.7848	M	0.92738	3.34	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;0.997;1.0	D	0.94649	0.7837	10	0.87932	D	0	.	16.4101	0.83708	1.0:0.0:0.0:0.0	.	76;76;76	G5E9G9;Q53SH4;P02708	.;.;ACHA_HUMAN	Q	76	ENSP00000261008:L76Q;ENSP00000261007:L76Q;ENSP00000387026:L76Q;ENSP00000386611:L76Q;ENSP00000386684:L76Q	ENSP00000261007:L76Q	L	-	2	0	CHRNA1	175332312	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	9.277000	0.95755	2.280000	0.76307	0.460000	0.39030	CTG	.	.		0.428	CHRNA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000334116.1		
IDH1	3417	hgsc.bcm.edu	37	2	209113113	209113113	+	Missense_Mutation	SNP	G	G	A	rs121913499		TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr2:209113113G>A	ENST00000415913.1	-	4	775	c.394C>T	c.(394-396)Cgt>Tgt	p.R132C	IDH1_ENST00000446179.1_Missense_Mutation_p.R132C|IDH1_ENST00000345146.2_Missense_Mutation_p.R132C	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132C(446)|p.R132G(125)|p.R132S(106)|p.G131_R132>VL(1)|p.R132V(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		TAAGCATGACGACCTATGATG	0.398			Mis		gliobastoma																																p.R132C	Pancreas(158;264 1958 3300 35450 36047)	Atlas-SNP	.		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	IDH1,NS,haematopoietic_neoplasm,0,788	IDH1	6310	.	679	Substitution - Missense(678)|Complex - compound substitution(1)	haematopoietic_and_lymphoid_tissue(280)|central_nervous_system(181)|bone(177)|biliary_tract(21)|soft_tissue(12)|large_intestine(2)|skin(2)|autonomic_ganglia(1)|endometrium(1)|NS(1)|prostate(1)	c.C394T						.						81.0	74.0	76.0					2																	209113113		2203	4300	6503	SO:0001583	missense	3417	exon4			CATGACGACCTAT		CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.394C>T	chr2.hg19:g.209113113G>A	ENSP00000390265:p.Arg132Cys	267.0	0.0		294.0	87.0	NM_005896	Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	hg19	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.550898	0.86127	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.87029	-2.2;-2.2;-2.2;-2.2	5.57	5.57	0.84162	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.94049	0.8093	H	0.99379	4.54	0.80722	D	1	B	0.29862	0.259	B	0.31245	0.126	D	0.94048	0.7315	10	0.87932	D	0	-20.0399	19.5341	0.95242	0.0:0.0:1.0:0.0	.	132	O75874	IDHC_HUMAN	C	132	ENSP00000260985:R132C;ENSP00000410513:R132C;ENSP00000390265:R132C;ENSP00000391075:R132C	ENSP00000260985:R132C	R	-	1	0	IDH1	208821358	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	7.074000	0.76791	2.616000	0.88540	0.555000	0.69702	CGT	.	.		0.398	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1		
TMPRSS7	344805	hgsc.bcm.edu	37	3	111797619	111797619	+	Missense_Mutation	SNP	C	C	T			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr3:111797619C>T	ENST00000452346.2	+	17	2258	c.2255C>T	c.(2254-2256)gCg>gTg	p.A752V	TMPRSS7_ENST00000419127.1_Missense_Mutation_p.A626V			Q7RTY8	TMPS7_HUMAN	transmembrane protease, serine 7	752	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(2)|endometrium(6)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						CTGCAGCAAGCGGAGGTAGAG	0.463																																					p.A626V		Atlas-SNP	.											.	TMPRSS7	126	.	0			c.C1877T						.						112.0	111.0	112.0					3																	111797619		1942	4131	6073	SO:0001583	missense	344805	exon15			AGCAAGCGGAGGT	BN000125	CCDS43129.2	3q13.2	2010-04-13	2004-03-16		ENSG00000176040	ENSG00000176040		"""Serine peptidases / Transmembrane"""	30846	protein-coding gene	gene with protein product			"""type II transmembrane serine protease 7"""			12838346	Standard	NM_001042575		Approved		uc010hqb.2	Q7RTY8	OTTHUMG00000157148	ENST00000452346.2:c.2255C>T	chr3.hg19:g.111797619C>T	ENSP00000398236:p.Ala752Val	218.0	0.0		231.0	64.0	NM_001042575	C9J8P7|E9PAS3|Q17RH4	Missense_Mutation	SNP	ENST00000452346.2	hg19		.	.	.	.	.	.	.	.	.	.	C	35	5.518493	0.96416	.	.	ENSG00000176040	ENST00000452346;ENST00000443106;ENST00000437906;ENST00000419127	T;T	0.58940	0.3;0.3	5.79	5.79	0.91817	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.85682	D	0.000000	T	0.54647	0.1871	N	0.02765	-0.5	0.58432	D	0.999997	D;D	0.89917	1.0;0.996	D;P	0.80764	0.994;0.794	T	0.64968	-0.6282	10	0.39692	T	0.17	.	16.9482	0.86236	0.0:1.0:0.0:0.0	.	752;626	Q7RTY8;Q7RTY8-2	TMPS7_HUMAN;.	V	752;740;726;626	ENSP00000398236:A752V;ENSP00000411645:A626V	ENSP00000411645:A626V	A	+	2	0	TMPRSS7	113280309	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.884000	0.75600	2.716000	0.92895	0.655000	0.94253	GCG	.	.		0.463	TMPRSS7-003	NOVEL	NAGNAG_splice_site|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000347592.2	XM_293599	
SEMA5B	54437	hgsc.bcm.edu	37	3	122629075	122629075	+	Missense_Mutation	SNP	G	G	A	rs369693926		TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr3:122629075G>A	ENST00000357599.3	-	23	3757	c.3371C>T	c.(3370-3372)aCg>aTg	p.T1124M	SEMA5B_ENST00000195173.4_3'UTR|SEMA5B_ENST00000451055.2_Missense_Mutation_p.T1178M	NM_001031702.3|NM_001256348.1	NP_001026872.2|NP_001243277.1	Q9P283	SEM5B_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	1124					cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		GTAAGTAGTCGTGTACACATT	0.542																																					p.T1178M		Atlas-SNP	.											.	SEMA5B	303	.	0			c.C3533T						.	G	MET/THR	1,4405	2.1+/-5.4	0,1,2202	206.0	173.0	184.0		3371	5.1	1.0	3		184	0,8600		0,0,4300	no	missense	SEMA5B	NM_001031702.2	81	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	1124/1152	122629075	1,13005	2203	4300	6503	SO:0001583	missense	54437	exon23			GTAGTCGTGTACA	AB040878	CCDS35491.1, CCDS58848.1, CCDS74995.1	3q21.1	2008-07-18			ENSG00000082684	ENSG00000082684		"""Semaphorins"""	10737	protein-coding gene	gene with protein product		609298		SEMAG		8817451	Standard	NM_001256346		Approved	SemG, KIAA1445, FLJ10372	uc031sbm.1	Q9P283	OTTHUMG00000140392	ENST00000357599.3:c.3371C>T	chr3.hg19:g.122629075G>A	ENSP00000350215:p.Thr1124Met	620.0	0.0		705.0	231.0	NM_001256347	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Missense_Mutation	SNP	ENST00000357599.3	hg19	CCDS35491.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.7|22.7	4.323460|4.323460	0.81580|0.81580	2.27E-4|2.27E-4	0.0|0.0	ENSG00000082684|ENSG00000082684	ENST00000451541|ENST00000357599;ENST00000418793;ENST00000451055	.|T;T	.|0.37584	.|1.19;1.23	5.06|5.06	5.06|5.06	0.68205|0.68205	.|.	.|0.052354	.|0.85682	.|D	.|0.000000	.|T	.|0.48786	.|0.1519	L|L	0.29908|0.29908	0.895|0.895	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.72338	.|0.977;0.95	.|T	.|0.46693	.|-0.9173	.|10	.|0.52906	.|T	.|0.07	.|.	17.1675|17.1675	0.86820|0.86820	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1030;1124	.|D3YTI7;Q9P283	.|.;SEM5B_HUMAN	X|M	170|1124;1030;1178	.|ENSP00000350215:T1124M;ENSP00000389588:T1178M	.|ENSP00000350215:T1124M	R|T	-|-	1|2	2|0	SEMA5B|SEMA5B	124111765|124111765	1.000000|1.000000	0.71417|0.71417	0.991000|0.991000	0.47740|0.47740	0.981000|0.981000	0.71138|0.71138	9.263000|9.263000	0.95617|0.95617	2.643000|2.643000	0.89663|0.89663	0.650000|0.650000	0.86243|0.86243	CGA|ACG	.	.		0.542	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702	
ZNF518B	85460	hgsc.bcm.edu	37	4	10446101	10446101	+	Missense_Mutation	SNP	A	A	T			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr4:10446101A>T	ENST00000326756.3	-	3	2290	c.1852T>A	c.(1852-1854)Tta>Ata	p.L618I		NM_053042.2	NP_444270.2	Q9C0D4	Z518B_HUMAN	zinc finger protein 518B	618					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)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	42						GAATTCTTTAATTCCAAAGGC	0.398																																					p.L618I		Atlas-SNP	.											.	ZNF518B	116	.	0			c.T1852A						.						144.0	144.0	144.0					4																	10446101		2203	4300	6503	SO:0001583	missense	85460	exon3			TCTTTAATTCCAA	AB051516	CCDS33960.1	4p16.1	2007-12-07				ENSG00000178163		"""Zinc fingers, C2H2-type"""	29365	protein-coding gene	gene with protein product						11214970	Standard	XM_005248193		Approved	KIAA1729	uc003gmn.3	Q9C0D4		ENST00000326756.3:c.1852T>A	chr4.hg19:g.10446101A>T	ENSP00000317614:p.Leu618Ile	403.0	1.0		293.0	77.0	NM_053042	Q96LN8	Missense_Mutation	SNP	ENST00000326756.3	hg19	CCDS33960.1	.	.	.	.	.	.	.	.	.	.	A	17.67	3.446832	0.63178	.	.	ENSG00000178163	ENST00000326756	T	0.01902	4.57	6.06	-10.4	0.00318	.	0.495160	0.13666	N	0.371205	T	0.02267	0.0070	L	0.42245	1.32	0.09310	N	1	P	0.42456	0.78	B	0.36666	0.23	T	0.09552	-1.0669	10	0.51188	T	0.08	-0.1159	20.4514	0.99126	0.1311:0.0867:0.7822:0.0	.	618	Q9C0D4	Z518B_HUMAN	I	618	ENSP00000317614:L618I	ENSP00000317614:L618I	L	-	1	2	ZNF518B	10055199	0.000000	0.05858	0.000000	0.03702	0.599000	0.36880	-0.202000	0.09451	-1.789000	0.01264	-0.250000	0.11733	TTA	.	.		0.398	ZNF518B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359040.1	NM_053042	
GYPB	2994	hgsc.bcm.edu	37	4	145039884	145039884	+	Intron	SNP	T	T	A			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr4:145039884T>A	ENST00000283126.7	-	1	93				GYPA_ENST00000360771.4_Missense_Mutation_p.H85L|RP11-673E1.4_ENST00000506982.1_RNA|GYPA_ENST00000324022.10_Missense_Mutation_p.H52L|GYPA_ENST00000512789.1_Missense_Mutation_p.H20L|GYPA_ENST00000503627.1_Intron|GYPA_ENST00000535709.1_Missense_Mutation_p.H59L|GYPA_ENST00000512064.1_Intron|GYPA_ENST00000504786.1_Missense_Mutation_p.H53L			P06028	GLPB_HUMAN	glycophorin B (MNS blood group)							integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|large_intestine(2)|skin(1)	4	all_hematologic(180;0.158)					AGAGAAATGATGGGCAAGTTG	0.313																																					p.H85L		Atlas-SNP	.											GYPA,right_upper_lobe,carcinoma,0,1	GYPA	27	.	0			c.A254T						.						109.0	109.0	109.0					4																	145039884		2203	4300	6503	SO:0001627	intron_variant	2993	exon4			AAATGATGGGCAA		CCDS54809.1	4q31.21	2014-09-17	2006-02-23			ENSG00000250361		"""CD molecules"", ""Blood group antigens"""	4703	protein-coding gene	gene with protein product		111740	"""glycophorin B (includes Ss blood group)"", ""glycophorin B (Ss blood group)"""	MNS			Standard	NM_002100		Approved	GPB, SS, CD235b		P06028		ENST00000283126.7:c.37+21867A>T	chr4.hg19:g.145039884T>A		722.0	0.0		370.0	87.0	NM_002099	B8Q174|E2QBW7|Q0VAF4|Q58HE9|Q58HF0|Q58HF1|Q9UCH7	Missense_Mutation	SNP	ENST00000283126.7	hg19		.	.	.	.	.	.	.	.	.	.	T	9.261	1.043323	0.19748	.	.	ENSG00000170180	ENST00000360771;ENST00000324022;ENST00000535709;ENST00000512789;ENST00000504786;ENST00000394119	T;T;T;T;T	0.19250	2.16;2.16;2.16;2.16;2.16	3.94	1.33	0.21861	.	0.000000	0.42682	D	0.000668	T	0.35711	0.0941	M	0.68952	2.095	0.09310	N	1	D;D;D;B;D	0.89917	0.996;0.992;0.999;0.007;1.0	D;D;D;B;D	0.72338	0.934;0.912;0.955;0.022;0.977	T	0.08743	-1.0707	10	0.87932	D	0	-13.6461	4.5091	0.11903	0.1971:0.0:0.2052:0.5976	.	52;20;53;85;85	B8Q185;Q13030;E7EQF3;P02724;Q16336	.;.;.;GLPA_HUMAN;.	L	85;52;59;20;53;53	ENSP00000354003:H85L;ENSP00000324483:H52L;ENSP00000445398:H59L;ENSP00000425193:H20L;ENSP00000425549:H53L	ENSP00000324483:H52L	H	-	2	0	GYPA	145259334	0.029000	0.19370	0.000000	0.03702	0.001000	0.01503	1.046000	0.30354	0.288000	0.22398	0.482000	0.46254	CAT	.	.		0.313	GYPB-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_002100	
FAM53C	51307	hgsc.bcm.edu	37	5	137681062	137681062	+	Missense_Mutation	SNP	C	C	T			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr5:137681062C>T	ENST00000239906.5	+	4	1113	c.685C>T	c.(685-687)Cgc>Tgc	p.R229C	FAM53C_ENST00000507506.1_3'UTR|FAM53C_ENST00000513056.1_Intron|RP11-256P1.1_ENST00000504539.1_RNA|FAM53C_ENST00000434981.2_Missense_Mutation_p.R229C	NM_016605.2	NP_057689.1	Q9NYF3	FA53C_HUMAN	family with sequence similarity 53, member C	229										breast(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			CCCACCTCAGCGCCGCTTCTC	0.677																																					p.R229C		Atlas-SNP	.											.	FAM53C	35	.	0			c.C685T						.						85.0	97.0	93.0					5																	137681062		2203	4300	6503	SO:0001583	missense	51307	exon4			CCTCAGCGCCGCT	AF251040	CCDS4204.1	5q31	2008-02-05	2004-11-24	2004-11-26	ENSG00000120709	ENSG00000120709			1336	protein-coding gene	gene with protein product		609372	"""chromosome 5 open reading frame 6"""	C5orf6		11087669, 11161817	Standard	NM_001135647		Approved		uc003lcv.3	Q9NYF3	OTTHUMG00000129201	ENST00000239906.5:c.685C>T	chr5.hg19:g.137681062C>T	ENSP00000239906:p.Arg229Cys	29.0	0.0		49.0	14.0	NM_001135647	B2RDJ5|D3DQB9	Missense_Mutation	SNP	ENST00000239906.5	hg19	CCDS4204.1	.	.	.	.	.	.	.	.	.	.	C	19.99	3.929458	0.73327	.	.	ENSG00000120709	ENST00000434981;ENST00000239906	T;T	0.57907	0.37;0.37	5.55	5.55	0.83447	.	0.252298	0.39834	N	0.001253	T	0.70937	0.3281	M	0.75615	2.305	0.80722	D	1	D	0.89917	1.0	P	0.62298	0.9	T	0.70156	-0.4949	9	.	.	.	-9.4919	18.4386	0.90656	0.0:1.0:0.0:0.0	.	229	Q9NYF3	FA53C_HUMAN	C	229	ENSP00000403705:R229C;ENSP00000239906:R229C	.	R	+	1	0	FAM53C	137708961	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.135000	0.50546	2.894000	0.99253	0.655000	0.94253	CGC	.	.		0.677	FAM53C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251278.2	NM_016605	
TYW1	55253	hgsc.bcm.edu	37	7	66582482	66582482	+	Silent	SNP	G	G	A	rs13221716		TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr7:66582482G>A	ENST00000359626.5	+	13	1739	c.1575G>A	c.(1573-1575)ccG>ccA	p.P525P		NM_018264.2	NP_060734.2	Q9NV66	TYW1_HUMAN	tRNA-yW synthesizing protein 1 homolog (S. cerevisiae)	525					tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|lyase activity (GO:0016829)|oxidoreductase activity (GO:0016491)			breast(1)|endometrium(8)|kidney(10)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(3)|stomach(2)|urinary_tract(2)	46		Lung NSC(55;0.0846)|all_lung(88;0.183)				ACCTCGAGCCGGTTACTCAGC	0.398																																					p.P525P		Atlas-SNP	.											.	TYW1	71	.	0			c.G1575A						.						73.0	72.0	72.0					7																	66582482		2203	4300	6503	SO:0001819	synonymous_variant	55253	exon13			CGAGCCGGTTACT	AK001762	CCDS5538.1	7q11.21	2007-11-29	2007-11-29	2007-11-29	ENSG00000198874	ENSG00000198874			25598	protein-coding gene	gene with protein product	"""tRNA-yW synthesizing protein 1 homolog A (S. cerevisiae)"""	611243	"""radical S-adenosyl methionine and flavodoxin domains 1"""	RSAFD1		16162496, 17150819	Standard	NM_018264		Approved	FLJ10900, MGC23001, MGC60291, YPL207W, TYW1A	uc003tvn.4	Q9NV66	OTTHUMG00000129723	ENST00000359626.5:c.1575G>A	chr7.hg19:g.66582482G>A		186.0	0.0		198.0	8.0	NM_018264	Q6PJG8|Q75MG8|Q75MN3|Q86V12|Q8IVS7|Q9H9C4	Silent	SNP	ENST00000359626.5	hg19	CCDS5538.1																																																																																			.	.		0.398	TYW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251932.2	NM_018264	
CHPF2	54480	hgsc.bcm.edu	37	7	150934562	150934562	+	Missense_Mutation	SNP	G	G	A	rs139379425	byFrequency	TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr7:150934562G>A	ENST00000035307.2	+	4	2627	c.1114G>A	c.(1114-1116)Gtg>Atg	p.V372M	MIR671_ENST00000390183.1_RNA|RP4-548D19.3_ENST00000607902.1_RNA|CHPF2_ENST00000495645.1_Missense_Mutation_p.V364M	NM_019015.1	NP_061888.1	Q9P2E5	CHPF2_HUMAN	chondroitin polymerizing factor 2	372					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			breast(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(4)|prostate(1)|skin(3)	17						TCGCTTTGAGGTGCTGGGCTG	0.637																																					p.V372M		Atlas-SNP	.											.	CHPF2	52	.	0			c.G1114A						.						81.0	81.0	81.0					7																	150934562		2203	4300	6503	SO:0001583	missense	54480	exon4			TTTGAGGTGCTGG	AB037823	CCDS34779.1, CCDS64803.1	7q36.1	2013-02-19			ENSG00000033100	ENSG00000033100	2.4.1.226	"""Beta 3-glycosyltransferases"", ""Beta 4-glycosyltransferases"""	29270	protein-coding gene	gene with protein product		608037				10718198, 12145278, 18316376	Standard	NM_019015		Approved	KIAA1402, ChSy-3, CSGlcA-T	uc003wjr.1	Q9P2E5	OTTHUMG00000157380	ENST00000035307.2:c.1114G>A	chr7.hg19:g.150934562G>A	ENSP00000035307:p.Val372Met	97.0	0.0		236.0	62.0	NM_019015	B2DBD8|Q6P2I4|Q6UXD2	Missense_Mutation	SNP	ENST00000035307.2	hg19	CCDS34779.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.025532	0.75390	.	.	ENSG00000033100	ENST00000495645;ENST00000035307;ENST00000377851	T;T	0.25579	1.79;1.79	5.63	5.63	0.86233	.	0.058009	0.64402	D	0.000002	T	0.49047	0.1534	M	0.67953	2.075	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.81914	0.995;0.925	T	0.45381	-0.9265	10	0.62326	D	0.03	-22.7659	14.3202	0.66482	0.0:0.1479:0.8521:0.0	.	372;364	Q9P2E5;G5E9W2	CHPF2_HUMAN;.	M	364;372;372	ENSP00000418914:V364M;ENSP00000035307:V372M	ENSP00000035307:V372M	V	+	1	0	CHPF2	150565495	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.884000	0.87274	2.652000	0.90054	0.655000	0.94253	GTG	.	G|1.000;T|0.000		0.637	CHPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348648.2	NM_019015	
TNKS	8658	hgsc.bcm.edu	37	8	9627614	9627614	+	Splice_Site	SNP	A	A	T			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr8:9627614A>T	ENST00000310430.6	+	26	3766		c.e26-1		TNKS_ENST00000518281.1_Splice_Site	NM_003747.2	NP_003738.2	O95271	TNKS1_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase						mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|mRNA transport (GO:0051028)|negative regulation of DNA binding (GO:0043392)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein poly-ADP-ribosylation (GO:0070212)|protein polyubiquitination (GO:0000209)|protein transport (GO:0015031)|regulation of telomere maintenance via telomerase (GO:0032210)|spindle assembly (GO:0051225)|Wnt signaling pathway (GO:0016055)	chromosome, centromeric region (GO:0000775)|chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nuclear chromosome, telomeric region (GO:0000784)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	NAD+ ADP-ribosyltransferase activity (GO:0003950)|zinc ion binding (GO:0008270)			NS(1)|endometrium(10)|kidney(6)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	49				COAD - Colon adenocarcinoma(149;0.0467)		CTTTTTCCTTAGACAAATGCT	0.373																																					.		Atlas-SNP	.											.	TNKS	198	.	0			c.3741-2A>T						.						45.0	48.0	47.0					8																	9627614		2202	4300	6502	SO:0001630	splice_region_variant	8658	exon26			TTCCTTAGACAAA	AF082556	CCDS5974.1	8p23.1	2013-01-10			ENSG00000173273	ENSG00000173273		"""Poly (ADP-ribose) polymerases"", ""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	11941	protein-coding gene	gene with protein product		603303				9822378, 10198177	Standard	XM_006716263		Approved	TIN1, TINF1, TNKS1, PARP-5a, PARP5A, pART5	uc003wss.3	O95271	OTTHUMG00000090481	ENST00000310430.6:c.3741-1A>T	chr8.hg19:g.9627614A>T		28.0	0.0		38.0	21.0	NM_003747	O95272|Q4G0F2	Splice_Site	SNP	ENST00000310430.6	hg19	CCDS5974.1	.	.	.	.	.	.	.	.	.	.	A	19.91	3.914815	0.72983	.	.	ENSG00000173273	ENST00000310430;ENST00000518281	.	.	.	5.42	5.42	0.78866	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7698	0.78157	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TNKS	9665024	1.000000	0.71417	0.990000	0.47175	0.930000	0.56654	9.287000	0.95975	2.189000	0.69895	0.533000	0.62120	.	.	.		0.373	TNKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206935.1	NM_003747	Intron
RAB11FIP1	80223	hgsc.bcm.edu	37	8	37756823	37756823	+	Missense_Mutation	SNP	T	T	A			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr8:37756823T>A	ENST00000330843.4	-	1	149	c.137A>T	c.(136-138)cAg>cTg	p.Q46L	RAB11FIP1_ENST00000522727.1_5'UTR|RAB11FIP1_ENST00000287263.4_Missense_Mutation_p.Q46L	NM_001002814.2	NP_001002814.2	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 (class I)	46	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(4)|endometrium(3)|large_intestine(6)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	49		Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;3.62e-11)			CTTGCCCACCTGGATCACCGC	0.731																																					p.Q46L		Atlas-SNP	.											.	RAB11FIP1	105	.	0			c.A137T						.						14.0	17.0	16.0					8																	37756823		2192	4286	6478	SO:0001583	missense	80223	exon1			CCCACCTGGATCA	AK092296	CCDS34881.1, CCDS34882.1	8p11.22	2005-10-04			ENSG00000156675	ENSG00000156675			30265	protein-coding gene	gene with protein product		608737				11786538, 11495908	Standard	NM_001002814		Approved	RCP, FLJ22622, FLJ22524, Rab11-FIP1	uc003xkm.2	Q6WKZ4	OTTHUMG00000164026	ENST00000330843.4:c.137A>T	chr8.hg19:g.37756823T>A	ENSP00000331342:p.Gln46Leu	24.0	0.0		79.0	26.0	NM_025151	J3KNP0|Q307T1|Q6AZK4|Q6WKZ2|Q6WKZ6|Q86YV4|Q8TDL1|Q9H642	Missense_Mutation	SNP	ENST00000330843.4	hg19	CCDS34882.1	.	.	.	.	.	.	.	.	.	.	t	31	5.069606	0.93950	.	.	ENSG00000156675	ENST00000287263;ENST00000330843;ENST00000343853	T;T	0.69806	-0.43;-0.43	5.05	5.05	0.67936	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.335659	0.25948	N	0.027275	T	0.75398	0.3844	M	0.71581	2.175	0.80722	D	1	P;D	0.54772	0.763;0.968	B;P	0.56960	0.3;0.81	T	0.77555	-0.2544	10	0.56958	D	0.05	-11.3897	11.0281	0.47757	0.0:0.0:0.2031:0.7969	.	46;46	Q6WKZ4-3;Q6WKZ4	.;RFIP1_HUMAN	L	46	ENSP00000287263:Q46L;ENSP00000331342:Q46L	ENSP00000287263:Q46L	Q	-	2	0	RAB11FIP1	37875981	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.035000	0.57297	1.902000	0.55061	0.524000	0.50904	CAG	.	.		0.731	RAB11FIP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376816.1	NM_025151	
MMP16	4325	hgsc.bcm.edu	37	8	89180036	89180036	+	Missense_Mutation	SNP	C	C	T			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr8:89180036C>T	ENST00000286614.6	-	4	852	c.571G>A	c.(571-573)Ggt>Agt	p.G191S	MMP16_ENST00000544227.1_5'UTR	NM_005941.4	NP_005932.2	P51512	MMP16_HUMAN	matrix metallopeptidase 16 (membrane-inserted)	191					chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of catalytic activity (GO:0043085)	Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(1)|lung(51)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	81					Marimastat(DB00786)	CCATGGAAACCAGATGCAAAA	0.443																																					p.G191S		Atlas-SNP	.											.	MMP16	176	.	0			c.G571A						.						89.0	80.0	83.0					8																	89180036		2203	4300	6503	SO:0001583	missense	4325	exon4			GGAAACCAGATGC	D85511	CCDS6246.1	8q21	2009-01-09	2005-08-08		ENSG00000156103	ENSG00000156103			7162	protein-coding gene	gene with protein product		602262	"""matrix metalloproteinase 16 (membrane-inserted)"", ""chromosome 8 open reading frame 57"""	C8orf57		7559440	Standard	NM_005941		Approved	MT3-MMP, DKFZp761D112	uc003yeb.4	P51512	OTTHUMG00000163769	ENST00000286614.6:c.571G>A	chr8.hg19:g.89180036C>T	ENSP00000286614:p.Gly191Ser	188.0	0.0		135.0	33.0	NM_005941	B2RAN7|Q14824|Q52H48	Missense_Mutation	SNP	ENST00000286614.6	hg19	CCDS6246.1	.	.	.	.	.	.	.	.	.	.	C	36	5.750365	0.96890	.	.	ENSG00000156103	ENST00000286614	T	0.21543	2.0	5.91	5.91	0.95273	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.085161	0.85682	D	0.000000	T	0.49541	0.1563	M	0.73217	2.22	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.35500	-0.9786	10	0.52906	T	0.07	.	20.3829	0.98937	0.0:1.0:0.0:0.0	.	191;191	P51512-2;P51512	.;MMP16_HUMAN	S	191	ENSP00000286614:G191S	ENSP00000286614:G191S	G	-	1	0	MMP16	89249152	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.751000	0.85126	2.823000	0.97156	0.644000	0.83932	GGT	.	.		0.443	MMP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375304.2	NM_005941	
TMC1	117531	hgsc.bcm.edu	37	9	75355074	75355074	+	Silent	SNP	T	T	A			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr9:75355074T>A	ENST00000297784.5	+	9	942	c.402T>A	c.(400-402)ctT>ctA	p.L134L	TMC1_ENST00000340019.3_Silent_p.L134L|TMC1_ENST00000396237.3_Silent_p.L134L	NM_138691.2	NP_619636.2	Q8TDI8	TMC1_HUMAN	transmembrane channel-like 1	134	Arg/Asp/Glu/Lys-rich (highly charged).				auditory receptor cell development (GO:0060117)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(21)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	36						AAGGGGCTCTTGGGAAAGGAA	0.373																																					p.L134L	Pancreas(75;173 1345 14232 34245 43413)	Atlas-SNP	.											.	TMC1	87	.	0			c.T402A						.						103.0	106.0	105.0					9																	75355074		2203	4300	6503	SO:0001819	synonymous_variant	117531	exon9			GGCTCTTGGGAAA	AF417578	CCDS6643.1	9q21	2014-01-28			ENSG00000165091	ENSG00000165091			16513	protein-coding gene	gene with protein product		606706	"""transmembrane, cochlear expressed, 1"""	DFNA36, DFNB7, DFNB11		11850618, 11850623	Standard	NM_138691		Approved		uc004aiz.1	Q8TDI8	OTTHUMG00000020014	ENST00000297784.5:c.402T>A	chr9.hg19:g.75355074T>A		271.0	0.0		275.0	67.0	NM_138691	A8MVZ2|B1AM91	Silent	SNP	ENST00000297784.5	hg19	CCDS6643.1																																																																																			.	.		0.373	TMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052655.1		
HEMGN	55363	hgsc.bcm.edu	37	9	100693389	100693389	+	Missense_Mutation	SNP	T	T	C	rs201990544	byFrequency	TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr9:100693389T>C	ENST00000259456.3	-	4	431	c.288A>G	c.(286-288)atA>atG	p.I96M		NM_018437.3|NM_197978.2	NP_060907.2|NP_932095.1	Q9BXL5	HEMGN_HUMAN	hemogen	96				IV -> M (in Ref. 6; AAH48324). {ECO:0000305}.	cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)	nucleus (GO:0005634)				NS(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|skin(2)|urinary_tract(1)	27		Acute lymphoblastic leukemia(62;0.0559)				CTTTCTCCACTATTTCCTTTT	0.458																																					p.I96M		Atlas-SNP	.											.	HEMGN	55	.	0			c.A288G						.						154.0	145.0	148.0					9																	100693389		2203	4300	6503	SO:0001583	missense	55363	exon3			CTCCACTATTTCC	AF228713	CCDS6731.1	9q22.33	2014-01-21			ENSG00000136929	ENSG00000136929			17509	protein-coding gene	gene with protein product		610715					Standard	NM_018437		Approved	EDAG, CT155, NDR	uc004axy.4	Q9BXL5	OTTHUMG00000020336	ENST00000259456.3:c.288A>G	chr9.hg19:g.100693389T>C	ENSP00000259456:p.Ile96Met	197.0	0.0		166.0	21.0	NM_197978	Q6XAR3|Q86XY5|Q9NPC0	Missense_Mutation	SNP	ENST00000259456.3	hg19	CCDS6731.1	.	.	.	.	.	.	.	.	.	.	T	9.069	0.996436	0.19043	.	.	ENSG00000136929	ENST00000375112;ENST00000259456	.	.	.	4.84	-0.593	0.11667	.	1.389330	0.04154	N	0.321907	T	0.16685	0.0401	N	0.05124	-0.11	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.14643	-1.0465	9	0.29301	T	0.29	5.0598	2.682	0.05096	0.3468:0.3265:0.0:0.3267	.	96	Q9BXL5	HEMGN_HUMAN	M	96	.	ENSP00000259456:I96M	I	-	3	3	HEMGN	99733210	0.000000	0.05858	0.000000	0.03702	0.176000	0.22953	-0.528000	0.06193	0.015000	0.14971	-1.251000	0.01509	ATA	.	.		0.458	HEMGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053344.2	NM_197978	
CDK5RAP2	55755	hgsc.bcm.edu	37	9	123177407	123177407	+	Missense_Mutation	SNP	C	C	T			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr9:123177407C>T	ENST00000349780.4	-	28	4387	c.4208G>A	c.(4207-4209)cGa>cAa	p.R1403Q	CDK5RAP2_ENST00000359309.3_Missense_Mutation_p.R1362Q|CDK5RAP2_ENST00000360822.3_Missense_Mutation_p.R1371Q|CDK5RAP2_ENST00000360190.4_Missense_Mutation_p.R1403Q	NM_018249.4	NP_060719.4	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	1403					brain development (GO:0007420)|centrosome organization (GO:0051297)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of centriole replication (GO:0046600)|negative regulation of neuron differentiation (GO:0045665)|neurogenesis (GO:0022008)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of spindle checkpoint (GO:0090231)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)	p.R1403Q(1)		breast(6)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	58						TCTCAAAGTTCGAATTTCCTG	0.348																																					p.R1403Q		Atlas-SNP	.											CDK5RAP2,NS,carcinoma,0,2	CDK5RAP2	157	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4208A						.						130.0	120.0	123.0					9																	123177407		2203	4300	6503	SO:0001583	missense	55755	exon28			AAAGTTCGAATTT	BK005504	CCDS6823.1, CCDS43871.1, CCDS75888.1	9q33.3	2014-02-21			ENSG00000136861	ENSG00000136861			18672	protein-coding gene	gene with protein product	"""centrosomin"""	608201	"""microcephaly, primary autosomal recessive 3"""	MCPH3		10721722, 17764569, 24466316	Standard	NM_018249		Approved	C48, FLJ10867, CEP215	uc004bkf.4	Q96SN8	OTTHUMG00000021043	ENST00000349780.4:c.4208G>A	chr9.hg19:g.123177407C>T	ENSP00000343818:p.Arg1403Gln	209.0	0.0		280.0	32.0	NM_018249	Q5JV18|Q7Z3L4|Q7Z3U1|Q7Z7I6|Q9BSW0|Q9H6J6|Q9HCD9|Q9NV90|Q9UIW9	Missense_Mutation	SNP	ENST00000349780.4	hg19	CCDS6823.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.045848	0.93685	.	.	ENSG00000136861	ENST00000360822;ENST00000359309;ENST00000349780;ENST00000360190;ENST00000416449;ENST00000425647;ENST00000345313	T;T;T;T;T;T	0.35605	1.3;1.3;1.3;1.3;1.3;1.3	5.97	5.97	0.96955	.	0.000000	0.43747	D	0.000528	T	0.60287	0.2257	M	0.64997	1.995	0.42278	D	0.99208	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.91635	0.997;0.999;0.999;0.998;0.998;0.997	T	0.60326	-0.7285	10	0.87932	D	0	.	18.6193	0.91316	0.0:1.0:0.0:0.0	.	413;1172;1371;1403;1403;797	Q5JTU8;Q6MZT4;Q96SN8-2;Q96SN8-4;Q96SN8;B1AMJ5	.;.;.;.;CK5P2_HUMAN;.	Q	1371;1362;1403;1403;797;413;1175	ENSP00000354065:R1371Q;ENSP00000352258:R1362Q;ENSP00000343818:R1403Q;ENSP00000353317:R1403Q;ENSP00000400395:R797Q;ENSP00000409941:R413Q	ENSP00000341695:R1175Q	R	-	2	0	CDK5RAP2	122217228	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.941000	0.70195	2.836000	0.97738	0.655000	0.94253	CGA	.	.		0.348	CDK5RAP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055535.1	NM_018249	
MAPKAP1	79109	hgsc.bcm.edu	37	9	128230302	128230302	+	Missense_Mutation	SNP	T	T	C			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr9:128230302T>C	ENST00000373498.1	-	9	1362	c.1294A>G	c.(1294-1296)Atc>Gtc	p.I432V	MAPKAP1_ENST00000373511.2_Missense_Mutation_p.I385V|MAPKAP1_ENST00000394063.1_Missense_Mutation_p.I240V|MAPKAP1_ENST00000350766.3_Missense_Mutation_p.I396V|MAPKAP1_ENST00000373503.3_Missense_Mutation_p.I240V|MAPKAP1_ENST00000373497.5_Missense_Mutation_p.I145V|MAPKAP1_ENST00000483937.1_5'UTR|MAPKAP1_ENST00000265960.3_Missense_Mutation_p.I432V			Q9BPZ7	SIN1_HUMAN	mitogen-activated protein kinase associated protein 1	432					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|negative regulation of Ras protein signal transduction (GO:0046580)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|substantia nigra development (GO:0021762)|T cell costimulation (GO:0031295)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein kinase binding (GO:0019901)|Ras GTPase binding (GO:0017016)			endometrium(2)|kidney(1)|large_intestine(2)|lung(15)|ovary(3)	23						TCGGAATCGATTGAGATGGGT	0.453																																					p.I432V		Atlas-SNP	.											.	MAPKAP1	68	.	0			c.A1294G						.						205.0	196.0	199.0					9																	128230302		2203	4300	6503	SO:0001583	missense	79109	exon10			AATCGATTGAGAT	M37191	CCDS6864.1, CCDS35139.1, CCDS35140.1, CCDS35141.1, CCDS48020.1	9q34.11	2008-02-05			ENSG00000119487	ENSG00000119487			18752	protein-coding gene	gene with protein product	"""stress-activated protein kinase-interacting 1"""	610558				15363842	Standard	NM_001006620		Approved	MGC2745, SIN1, MIP1	uc004bpv.3	Q9BPZ7	OTTHUMG00000020683	ENST00000373498.1:c.1294A>G	chr9.hg19:g.128230302T>C	ENSP00000362597:p.Ile432Val	384.0	0.0		394.0	30.0	NM_001006617	A8K1Z5|B1AMA4|B7Z309|Q00426|Q5JSV5|Q5JSV6|Q5JSV9|Q658R0|Q699U1|Q699U2|Q699U3|Q699U4|Q6GVJ0|Q6GVJ1|Q6GVJ2	Missense_Mutation	SNP	ENST00000373498.1	hg19	CCDS35140.1	.	.	.	.	.	.	.	.	.	.	T	16.35	3.097275	0.56075	.	.	ENSG00000119487	ENST00000373511;ENST00000350766;ENST00000373503;ENST00000373498;ENST00000265960;ENST00000394063;ENST00000373497;ENST00000420643	.	.	.	6.07	3.72	0.42706	.	0.000000	0.85682	D	0.000000	T	0.64735	0.2625	M	0.65975	2.015	0.52099	D	0.999941	D;D;P;D	0.58268	0.971;0.971;0.936;0.982	P;P;P;P	0.57283	0.795;0.816;0.698;0.817	T	0.60454	-0.7260	9	0.15952	T	0.53	-3.9461	10.8112	0.46549	0.0:0.1281:0.0:0.8719	.	145;385;396;432	B7Z5E5;Q9BPZ7-3;Q9BPZ7-2;Q9BPZ7	.;.;.;SIN1_HUMAN	V	385;396;240;432;432;240;145;204	.	ENSP00000265960:I432V	I	-	1	0	MAPKAP1	127270123	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.298000	0.72763	0.523000	0.28482	0.533000	0.62120	ATC	.	.		0.453	MAPKAP1-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054092.1		
PCDH15	65217	hgsc.bcm.edu	37	10	55839135	55839135	+	Missense_Mutation	SNP	G	G	A	rs573043647		TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr10:55839135G>A	ENST00000320301.6	-	17	2441	c.2047C>T	c.(2047-2049)Cgc>Tgc	p.R683C	PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000395430.1_Missense_Mutation_p.R683C|PCDH15_ENST00000373957.3_Missense_Mutation_p.R661C|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000409834.1_Missense_Mutation_p.R294C|PCDH15_ENST00000395446.1_Missense_Mutation_p.R683C|PCDH15_ENST00000395445.1_Missense_Mutation_p.R690C|PCDH15_ENST00000414778.1_Missense_Mutation_p.R688C|PCDH15_ENST00000395432.2_Missense_Mutation_p.R646C|PCDH15_ENST00000373955.1_Missense_Mutation_p.R683C|PCDH15_ENST00000395438.1_Missense_Mutation_p.R683C|PCDH15_ENST00000437009.1_Missense_Mutation_p.R612C|PCDH15_ENST00000373965.2_Missense_Mutation_p.R690C|PCDH15_ENST00000395433.1_Missense_Mutation_p.R661C|PCDH15_ENST00000361849.3_Missense_Mutation_p.R683C	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	683	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				AGAATGTAGCGATCAGTGCTT	0.428										HNSCC(58;0.16)			G|||	1	0.000199681	0.0	0.0	5008	,	,		18679	0.0		0.001	False		,,,				2504	0.0				p.R688C		Atlas-SNP	.											PCDH15_ENST00000417177,caecum,carcinoma,+1,3	PCDH15	1715	.	0			c.C2062T						.						259.0	232.0	241.0					10																	55839135		2203	4300	6503	SO:0001583	missense	65217	exon18			TGTAGCGATCAGT	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"""Cadherins / Cadherin-related"""	14674	protein-coding gene	gene with protein product	"""cadherin-related family member 15"""	605514	"""deafness, autosomal recessive 23"", ""protocadherin 15"""	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.2047C>T	chr10.hg19:g.55839135G>A	ENSP00000322604:p.Arg683Cys	264.0	1.0		151.0	61.0	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	hg19	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.763231	0.89932	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000409834;ENST00000395445;ENST00000395446;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000373957;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009;ENST00000373955	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.58940	0.63;0.63;0.63;0.63;0.63;0.63;0.63;0.63;0.63;0.63;0.63;0.63;0.3;0.63	5.9	5.9	0.94986	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.72779	0.3503	L	0.45744	1.44	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;1.0;1.0;1.0;1.0;1.0;0.999;0.998;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.91635	0.999;0.978;0.978;0.964;0.973;0.978;0.999;0.935;0.964;0.964;0.935;0.935;0.931;0.959;0.964	T	0.73225	-0.4050	9	0.87932	D	0	.	19.8634	0.96793	0.0:0.0:1.0:0.0	.	661;683;683;688;612;646;683;683;690;690;683;688;683;661;683	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1-3;A2A3D8;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	C	690;688;683;683;294;690;683;646;683;661;661;683;683;688;612;683	ENSP00000363076:R690C;ENSP00000410304:R688C;ENSP00000378826:R683C;ENSP00000386693:R294C;ENSP00000378832:R690C;ENSP00000378833:R683C;ENSP00000378820:R646C;ENSP00000354950:R683C;ENSP00000378821:R661C;ENSP00000363068:R661C;ENSP00000322604:R683C;ENSP00000378818:R683C;ENSP00000412628:R612C;ENSP00000363066:R683C	ENSP00000322604:R683C	R	-	1	0	PCDH15	55509141	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	4.963000	0.63694	2.800000	0.96347	0.591000	0.81541	CGC	.	.		0.428	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056	
MKI67	4288	hgsc.bcm.edu	37	10	129901092	129901092	+	Silent	SNP	T	T	A			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr10:129901092T>A	ENST00000368654.3	-	13	9387	c.9012A>T	c.(9010-9012)ggA>ggT	p.G3004G	MKI67_ENST00000368653.3_Silent_p.G2644G	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	3004					cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				CCGTGACGCTTCCATCTTTGC	0.572																																					p.G3004G		Atlas-SNP	.											.	MKI67	363	.	0			c.A9012T						.						88.0	80.0	83.0					10																	129901092		2203	4300	6503	SO:0001819	synonymous_variant	4288	exon13			GACGCTTCCATCT	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.9012A>T	chr10.hg19:g.129901092T>A		107.0	0.0		73.0	32.0	NM_002417	Q5VWH2	Silent	SNP	ENST00000368654.3	hg19	CCDS7659.1																																																																																			.	.		0.572	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
OR8H2	390151	hgsc.bcm.edu	37	11	55872687	55872687	+	Missense_Mutation	SNP	C	C	T			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr11:55872687C>T	ENST00000313503.1	+	1	169	c.169C>T	c.(169-171)Cac>Tac	p.H57Y		NM_001005200.1	NP_001005200.1	Q8N162	OR8H2_HUMAN	olfactory receptor, family 8, subfamily H, member 2	57						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.H57Y(1)		breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(38)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	61	Esophageal squamous(21;0.00693)					CCTCCAGCTTCACACTCCCAT	0.423										HNSCC(53;0.14)																											p.H57Y		Atlas-SNP	.											OR8H2,NS,carcinoma,0,1	OR8H2	117	.	1	Substitution - Missense(1)	lung(1)	c.C169T						.						264.0	239.0	248.0					11																	55872687		2201	4293	6494	SO:0001583	missense	390151	exon1			CAGCTTCACACTC	AB065657	CCDS31518.1	11q11	2012-08-09			ENSG00000181767	ENSG00000181767		"""GPCR / Class A : Olfactory receptors"""	15308	protein-coding gene	gene with protein product							Standard	NM_001005200		Approved		uc010riy.2	Q8N162	OTTHUMG00000166832	ENST00000313503.1:c.169C>T	chr11.hg19:g.55872687C>T	ENSP00000323982:p.His57Tyr	301.0	1.0		302.0	33.0	NM_001005200	Q6IFC1	Missense_Mutation	SNP	ENST00000313503.1	hg19	CCDS31518.1	.	.	.	.	.	.	.	.	.	.	c	13.22	2.172220	0.38315	.	.	ENSG00000181767	ENST00000313503	T	0.15952	2.38	3.58	3.58	0.41010	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000030	T	0.42517	0.1206	M	0.90542	3.125	0.30664	N	0.754128	D	0.76494	0.999	D	0.70487	0.969	T	0.51108	-0.8747	10	0.87932	D	0	.	6.5232	0.22287	0.1797:0.7187:0.0:0.1016	.	57	Q8N162	OR8H2_HUMAN	Y	57	ENSP00000323982:H57Y	ENSP00000323982:H57Y	H	+	1	0	OR8H2	55629263	0.976000	0.34144	0.954000	0.39281	0.234000	0.25298	2.543000	0.45752	1.952000	0.56665	0.440000	0.28878	CAC	.	.		0.423	OR8H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391540.1	NM_001005200	
SUV420H1	51111	hgsc.bcm.edu	37	11	67957441	67957441	+	Missense_Mutation	SNP	T	T	A			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr11:67957441T>A	ENST00000304363.4	-	2	456	c.103A>T	c.(103-105)Acg>Tcg	p.T35S	SUV420H1_ENST00000402789.1_Missense_Mutation_p.T35S|SUV420H1_ENST00000401547.2_Missense_Mutation_p.T35S|SUV420H1_ENST00000402185.2_Missense_Mutation_p.T35S|SUV420H1_ENST00000405515.1_Missense_Mutation_p.T35S	NM_017635.3	NP_060105	Q4FZB7	SV421_HUMAN	suppressor of variegation 4-20 homolog 1 (Drosophila)	35					histone H4-K20 trimethylation (GO:0034773)|muscle organ development (GO:0007517)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome, centromeric region (GO:0000780)	histone methyltransferase activity (H4-K20 specific) (GO:0042799)|histone-lysine N-methyltransferase activity (GO:0018024)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(15)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46						TCCTTCCCCGTGTGCTGTAAT	0.453																																					p.T35S		Atlas-SNP	.											.	SUV420H1	125	.	0			c.A103T						.						370.0	320.0	337.0					11																	67957441		2200	4294	6494	SO:0001583	missense	51111	exon2			TCCCCGTGTGCTG	AL512763	CCDS31623.1, CCDS44660.1	11q13.2	2011-07-01			ENSG00000110066	ENSG00000110066		"""Chromatin-modifying enzymes / K-methyltransferases"""	24283	protein-coding gene	gene with protein product		610881				10810093, 11401438	Standard	NM_016028		Approved	CGI-85, KMT5B	uc001onm.1	Q4FZB7	OTTHUMG00000150484	ENST00000304363.4:c.103A>T	chr11.hg19:g.67957441T>A	ENSP00000305899:p.Thr35Ser	538.0	0.0		462.0	122.0	NM_017635	B7WNX7|Q3SX56|Q4V775|Q6P150|Q96E44|Q9BUL0|Q9H022|Q9H2K3|Q9NXV3|Q9Y393	Missense_Mutation	SNP	ENST00000304363.4	hg19	CCDS31623.1	.	.	.	.	.	.	.	.	.	.	T	5.134	0.210418	0.09757	.	.	ENSG00000110066	ENST00000304363;ENST00000401547;ENST00000405515;ENST00000402789;ENST00000402185;ENST00000434573	T;T;T;T;T;T	0.40476	1.04;1.04;1.04;1.04;1.03;1.04	5.77	-11.5	0.00074	.	1.182760	0.05656	N	0.586013	T	0.19967	0.0480	L	0.29908	0.895	0.18873	N	0.999987	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.08055	0.001;0.003;0.002;0.001	T	0.06463	-1.0825	10	0.08179	T	0.78	0.5301	5.4972	0.16809	0.3645:0.3961:0.1218:0.1176	.	35;35;35;35	B7WNX0;B5MCB3;Q4FZB7-2;Q4FZB7	.;.;.;SV421_HUMAN	S	35	ENSP00000305899:T35S;ENSP00000385965:T35S;ENSP00000385640:T35S;ENSP00000385005:T35S;ENSP00000384724:T35S;ENSP00000402921:T35S	ENSP00000305899:T35S	T	-	1	0	SUV420H1	67714017	0.000000	0.05858	0.002000	0.10522	0.950000	0.60333	-3.146000	0.00584	-4.185000	0.00066	-0.386000	0.06593	ACG	.	.		0.453	SUV420H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318319.1	NM_017635	
ANAPC15	25906	hgsc.bcm.edu	37	11	71819726	71819726	+	IGR	SNP	C	C	A			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr11:71819726C>A	ENST00000227618.4	-	0	886				LRTOMT_ENST00000439209.1_3'UTR|LRTOMT_ENST00000419228.1_Missense_Mutation_p.L171M|LRTOMT_ENST00000307198.7_Missense_Mutation_p.L211M|ANAPC15_ENST00000543015.1_5'Flank|ANAPC15_ENST00000543050.1_Intron|ANAPC15_ENST00000502597.2_Intron|LRTOMT_ENST00000435085.1_Missense_Mutation_p.L211M	NM_001278487.1|NM_001278491.1|NM_014042.2	NP_001265416.1|NP_001265420.1|NP_054761.1	P60006	APC15_HUMAN	anaphase promoting complex subunit 15						mitotic nuclear division (GO:0007067)|regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090266)	anaphase-promoting complex (GO:0005680)|intracellular (GO:0005622)											TCGGGCAGACCTGGTGCTCCT	0.652																																					p.L211M		Atlas-SNP	.											.	LRTOMT	20	.	0			c.C631A						.						54.0	51.0	52.0					11																	71819726		692	1591	2283	SO:0001628	intergenic_variant	220074	exon9			GCAGACCTGGTGC	AL080071	CCDS8210.1, CCDS60880.1	11q13.4	2012-10-17	2012-05-31	2012-05-31	ENSG00000110200	ENSG00000110200		"""Anaphase promoting complex subunits"""	24531	protein-coding gene	gene with protein product		614717	"""chromosome 11 open reading frame 51"""	C11orf51		21926987	Standard	NM_014042		Approved	HSPC020, DKFZP564M082, APC15	uc001orw.3	P60006	OTTHUMG00000167865		chr11.hg19:g.71819726C>A		28.0	0.0		36.0	9.0	NM_001145309	G3V1Q3|Q9CXK2|Q9Y269	Missense_Mutation	SNP	ENST00000227618.4	hg19	CCDS8210.1	.	.	.	.	.	.	.	.	.	.	C	11.60	1.687934	0.29962	.	.	ENSG00000184154	ENST00000419228;ENST00000435085;ENST00000307198	T;T;T	0.29142	1.58;1.58;1.58	5.17	3.21	0.36854	.	.	.	.	.	T	0.39384	0.1076	L	0.44542	1.39	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.75020	0.985;0.974	T	0.14090	-1.0485	9	0.18710	T	0.47	-3.6591	7.6386	0.28280	0.0:0.6301:0.0:0.3699	.	211;171	Q8WZ04;Q8WZ04-2	TOMT_HUMAN;.	M	171;211;211	ENSP00000392233:L171M;ENSP00000409789:L211M;ENSP00000305742:L211M	ENSP00000305742:L171M	L	+	1	2	LRTOMT	71497374	0.483000	0.25956	0.988000	0.46212	0.915000	0.54546	0.730000	0.26043	0.647000	0.30713	-0.144000	0.13903	CTG	.	.		0.652	ANAPC15-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396695.1	NM_014042	
PICALM	8301	hgsc.bcm.edu	37	11	85712084	85712084	+	Silent	SNP	A	A	G			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr11:85712084A>G	ENST00000393346.3	-	10	1159	c.1011T>C	c.(1009-1011)gcT>gcC	p.A337A	PICALM_ENST00000356360.5_Silent_p.A337A|PICALM_ENST00000532317.1_Silent_p.A337A|PICALM_ENST00000526033.1_Silent_p.A337A|PICALM_ENST00000528398.1_Silent_p.A286A			Q13492	PICAL_HUMAN	phosphatidylinositol binding clathrin assembly protein	337					axonogenesis (GO:0007409)|cargo loading into vesicle (GO:0035459)|cell proliferation (GO:0008283)|clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|hemopoiesis (GO:0030097)|iron ion homeostasis (GO:0055072)|iron ion import into cell (GO:0097459)|negative regulation of gene expression (GO:0010629)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of receptor-mediated endocytosis (GO:0048261)|positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902961)|positive regulation of beta-amyloid formation (GO:1902004)|positive regulation of neuron death (GO:1901216)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902959)|regulation of endocytosis (GO:0030100)|regulation of protein localization (GO:0032880)|synaptic vesicle maturation (GO:0016188)|vesicle-mediated transport (GO:0016192)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neurofibrillary tangle (GO:0097418)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|vesicle (GO:0031982)	1-phosphatidylinositol binding (GO:0005545)|clathrin adaptor activity (GO:0035615)|clathrin binding (GO:0030276)|clathrin heavy chain binding (GO:0032050)			endometrium(1)|kidney(2)|large_intestine(2)|liver(1)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	19		Acute lymphoblastic leukemia(157;7.42e-07)|all_hematologic(158;0.00092)				TTACCTTTAAAGCTTTCAAAC	0.423			T	"""MLLT10, MLL"""	"""TALL, AML, """																																p.A337A		Atlas-SNP	.		Dom	yes		11	11q14	8301	phosphatidylinositol binding clathrin assembly protein (CALM)		L	.	PICALM	82	.	0			c.T1011C						.						269.0	245.0	253.0					11																	85712084		2203	4299	6502	SO:0001819	synonymous_variant	8301	exon10			CTTTAAAGCTTTC	BC048259	CCDS8272.1, CCDS31653.1, CCDS55783.1, CCDS55784.1	11q14	2008-02-01			ENSG00000073921	ENSG00000073921			15514	protein-coding gene	gene with protein product		603025				8643484	Standard	NM_001206947		Approved	CALM, CLTH	uc001pbm.3	Q13492	OTTHUMG00000166981	ENST00000393346.3:c.1011T>C	chr11.hg19:g.85712084A>G		520.0	0.0		584.0	158.0	NM_007166	B4DTM3|E9PN05|F8VPG7|O60700|Q4LE54|Q6GMQ6|Q86XZ9	Silent	SNP	ENST00000393346.3	hg19	CCDS8272.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.46|11.46	1.645177|1.645177	0.29246|0.29246	.|.	.|.	ENSG00000073921|ENSG00000073921	ENST00000529760;ENST00000530542|ENST00000529016	.|.	.|.	.|.	5.83|5.83	4.68|4.68	0.58851|0.58851	.|.	.|.	.|.	.|.	.|.	T|T	0.63546|0.63546	0.2520|0.2520	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.60606|0.60606	-0.7230|-0.7230	4|4	.|.	.|.	.|.	-10.6027|-10.6027	11.9757|11.9757	0.53089|0.53089	0.8663:0.0:0.0:0.1337|0.8663:0.0:0.0:0.1337	.|.	.|.	.|.	.|.	L|P	40|34	.|.	.|.	F|L	-|-	1|2	0|0	PICALM|PICALM	85389732|85389732	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	2.021000|2.021000	0.41020|0.41020	0.992000|0.992000	0.38840|0.38840	0.533000|0.533000	0.62120|0.62120	TTT|CTT	.	.		0.423	PICALM-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392224.1	NM_007166	
PRMT8	56341	hgsc.bcm.edu	37	12	3702274	3702274	+	Missense_Mutation	SNP	G	G	A			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr12:3702274G>A	ENST00000382622.3	+	10	1501	c.1111G>A	c.(1111-1113)Gat>Aat	p.D371N	PRMT8_ENST00000261252.4_3'UTR|PRMT8_ENST00000452611.2_Missense_Mutation_p.D362N	NM_019854.4	NP_062828.3	Q9NR22	ANM8_HUMAN	protein arginine methyltransferase 8	371	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				histone arginine methylation (GO:0034969)|histone H4-R3 methylation (GO:0043985)|histone methylation (GO:0016571)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|regulation of protein binding (GO:0043393)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	histone methyltransferase activity (H4-R3 specific) (GO:0044020)|histone-arginine N-methyltransferase activity (GO:0008469)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(9)|lung(14)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)	37			OV - Ovarian serous cystadenocarcinoma(31;0.0109)|COAD - Colon adenocarcinoma(12;0.0264)			GCGAGACCTCGATTTCACAGT	0.532																																					p.D371N		Atlas-SNP	.											.	PRMT8	97	.	0			c.G1111A						.						99.0	82.0	87.0					12																	3702274		2203	4300	6503	SO:0001583	missense	56341	exon10			GACCTCGATTTCA	AF263539	CCDS8521.2, CCDS58200.1	12p13.3	2006-03-03	2006-02-16	2006-02-16	ENSG00000111218	ENSG00000111218		"""Protein arginine methyltransferases"""	5188	protein-coding gene	gene with protein product		610086	"""HMT1 hnRNP methyltransferase-like 3 (S. cerevisiae)"", ""HMT1 hnRNP methyltransferase-like 4 (S. cerevisiae)"""	HRMT1L3, HRMT1L4		16051612	Standard	NM_019854		Approved		uc001qmf.4	Q9NR22	OTTHUMG00000128493	ENST00000382622.3:c.1111G>A	chr12.hg19:g.3702274G>A	ENSP00000372067:p.Asp371Asn	108.0	0.0		126.0	15.0	NM_019854	B2RDP0|Q8TBJ8	Missense_Mutation	SNP	ENST00000382622.3	hg19	CCDS8521.2	.	.	.	.	.	.	.	.	.	.	G	21.8	4.199887	0.79015	.	.	ENSG00000111218	ENST00000452611;ENST00000382622	D;D	0.86627	-2.15;-2.15	5.22	5.22	0.72569	.	0.044150	0.85682	D	0.000000	D	0.86389	0.5921	L	0.54965	1.715	0.80722	D	1	P;B	0.47841	0.901;0.41	B;B	0.44044	0.439;0.133	D	0.87923	0.2705	10	0.59425	D	0.04	.	16.2763	0.82644	0.0:0.0:1.0:0.0	.	362;371	Q9NR22-2;Q9NR22	.;ANM8_HUMAN	N	362;371	ENSP00000414507:D362N;ENSP00000372067:D371N	ENSP00000372067:D371N	D	+	1	0	PRMT8	3572535	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	9.732000	0.98816	2.445000	0.82738	0.313000	0.20887	GAT	.	.		0.532	PRMT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250297.2	NM_019854	
PCDH20	64881	hgsc.bcm.edu	37	13	61987587	61987587	+	Silent	SNP	C	C	T	rs201107730		TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr13:61987587C>T	ENST00000409186.1	-	5	2750	c.645G>A	c.(643-645)tcG>tcA	p.S215S	PCDH20_ENST00000409204.4_Silent_p.S215S			Q8N6Y1	PCD20_HUMAN	protocadherin 20	215	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)	p.S188S(1)|p.S215S(1)		breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(14)|liver(1)|lung(23)|ovary(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	58		Breast(118;0.195)|Prostate(109;0.229)		GBM - Glioblastoma multiforme(99;0.000118)		GGACCCACACCGAGATCTGGG	0.527																																					p.S215S		Atlas-SNP	.											PCDH20_ENST00000409186,caecum,carcinoma,0,2	PCDH20	265	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G645A						.						110.0	99.0	102.0					13																	61987587		2203	4300	6503	SO:0001819	synonymous_variant	64881	exon2			CCACACCGAGATC	AF169693	CCDS9442.2	13q21	2010-01-26			ENSG00000197991	ENSG00000197991		"""Cadherins / Protocadherins : Non-clustered"""	14257	protein-coding gene	gene with protein product		614449					Standard	NM_022843		Approved	PCDH13, FLJ22218	uc001vid.4	Q8N6Y1	OTTHUMG00000017012	ENST00000409186.1:c.645G>A	chr13.hg19:g.61987587C>T		107.0	1.0		92.0	20.0	NM_022843	A8K1K9|B1AQU2|Q8NDN4|Q9NRT9	Silent	SNP	ENST00000409186.1	hg19	CCDS9442.2																																																																																			.	C|1.000;A|0.000		0.527	PCDH20-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333054.2	NM_022843	
TMEM260	54916	hgsc.bcm.edu	37	14	57075883	57075883	+	Silent	SNP	C	C	G			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr14:57075883C>G	ENST00000261556.6	+	6	818	c.696C>G	c.(694-696)ccC>ccG	p.P232P	TMEM260_ENST00000538838.1_Silent_p.P232P|TMEM260_ENST00000536419.1_5'UTR	NM_017799.3	NP_060269.3	Q9NX78	TM260_HUMAN	transmembrane protein 260	232						integral component of membrane (GO:0016021)											GTTTGCTGCCCTATGTCCACC	0.478																																					p.P232P		Atlas-SNP	.											.	.	.	.	0			c.C696G						.						309.0	295.0	300.0					14																	57075883		2203	4300	6503	SO:0001819	synonymous_variant	0	exon6			GCTGCCCTATGTC	AK000399	CCDS9727.2	14q22.2	2013-03-08	2013-03-08	2013-03-08	ENSG00000070269	ENSG00000070269			20185	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 101"""	C14orf101			Standard	XR_245695		Approved	FLJ20392	uc001xcm.3	Q9NX78	OTTHUMG00000152337	ENST00000261556.6:c.696C>G	chr14.hg19:g.57075883C>G		582.0	0.0		610.0	133.0	NM_017799	A8KAN4|B3KPF5|Q86XE1	Silent	SNP	ENST00000261556.6	hg19	CCDS9727.2																																																																																			.	.		0.478	TMEM260-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276924.1	NM_017799	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79063584	79063584	+	Missense_Mutation	SNP	C	C	T			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr15:79063584C>T	ENST00000388820.4	-	16	2648	c.2438G>A	c.(2437-2439)gGt>gAt	p.G813D	ADAMTS7_ENST00000566303.1_Intron	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	813					cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						GTCGTGGCCACCTGCCTCCCT	0.652																																					p.G813D		Atlas-SNP	.											.	ADAMTS7	142	.	0			c.G2438A						.						44.0	33.0	37.0					15																	79063584		2196	4291	6487	SO:0001583	missense	11173	exon16			TGGCCACCTGCCT	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	223	protein-coding gene	gene with protein product	"""COMPase"", ""a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"""	605009	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"""			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.2438G>A	chr15.hg19:g.79063584C>T	ENSP00000373472:p.Gly813Asp	142.0	0.0		208.0	39.0	NM_014272	Q14F51|Q6P7J9	Missense_Mutation	SNP	ENST00000388820.4	hg19	CCDS32303.1	.	.	.	.	.	.	.	.	.	.	C	0.003	-2.568149	0.00133	.	.	ENSG00000136378	ENST00000388820	T	0.58506	0.33	3.28	-1.88	0.07713	.	0.734180	0.12442	N	0.468536	T	0.14356	0.0347	N	0.00496	-1.435	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.29549	-1.0008	10	0.02654	T	1	.	1.6689	0.02808	0.1567:0.1053:0.189:0.549	.	813	Q9UKP4	ATS7_HUMAN	D	813	ENSP00000373472:G813D	ENSP00000373472:G813D	G	-	2	0	ADAMTS7	76850639	0.004000	0.15560	0.000000	0.03702	0.019000	0.09904	1.364000	0.34171	-0.341000	0.08376	-0.768000	0.03414	GGT	.	.		0.652	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
CDH1	999	hgsc.bcm.edu	37	16	68856129	68856129	+	Splice_Site	SNP	G	G	A			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr16:68856129G>A	ENST00000261769.5	+	12	2127		c.e12+1		CDH1_ENST00000422392.2_Splice_Site|RP11-354M1.2_ENST00000563916.1_RNA|CDH1_ENST00000562836.1_Splice_Site	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)						adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)			NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		AACGACCCAAGTGGGTACCTG	0.488			"""Mis, N, F, S"""		"""lobular breast, gastric"""	gastric			Hereditary Diffuse Gastric Cancer																												.		Atlas-SNP	.	yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"""cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"""		E	CDH1,NS,carcinoma,0,2	CDH1	535	.	0			c.1936+1G>A						.						72.0	60.0	64.0					16																	68856129		2198	4300	6498	SO:0001630	splice_region_variant	999	exon12	Familial Cancer Database	HDGC	ACCCAAGTGGGTA	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"""CD molecules"", ""Cadherins / Major cadherins"""	1748	protein-coding gene	gene with protein product	"""E-Cadherin"""	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.1936+1G>A	chr16.hg19:g.68856129G>A		82.0	0.0		89.0	17.0	NM_004360	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Splice_Site	SNP	ENST00000261769.5	hg19	CCDS10869.1	.	.	.	.	.	.	.	.	.	.	G	12.73	2.025419	0.35701	.	.	ENSG00000039068	ENST00000261769;ENST00000379120;ENST00000422392	.	.	.	5.68	5.68	0.88126	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.4194	0.90584	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CDH1	67413630	1.000000	0.71417	0.540000	0.28089	0.048000	0.14542	7.958000	0.87877	2.697000	0.92050	0.632000	0.83419	.	.	.		0.488	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360	Intron
SGCA	6442	hgsc.bcm.edu	37	17	48244792	48244792	+	Missense_Mutation	SNP	G	G	T	rs371675217		TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr17:48244792G>T	ENST00000262018.3	+	2	137	c.101G>T	c.(100-102)cGt>cTt	p.R34L	SGCA_ENST00000543315.1_Missense_Mutation_p.R34L|SGCA_ENST00000513942.1_Intron|SGCA_ENST00000451235.2_5'UTR|SGCA_ENST00000344627.6_Missense_Mutation_p.R34L|RP11-893F2.14_ENST00000572855.1_RNA	NM_000023.2	NP_000014.1	Q16586	SGCA_HUMAN	sarcoglycan, alpha (50kDa dystrophin-associated glycoprotein)	34			R -> C (in LGMD2D). {ECO:0000269|PubMed:9192266}.|R -> H (in LGMD2D). {ECO:0000269|PubMed:7663524}.		muscle contraction (GO:0006936)|muscle organ development (GO:0007517)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(7)|ovary(2)|skin(1)	14						CTTGTGGGCCGTGTCTTTGTG	0.642																																					p.R34L		Atlas-SNP	.											SGCA,colon,carcinoma,0,1	SGCA	35	.	0			c.G101T	GRCh37	CM951149	SGCA	M		.						104.0	87.0	92.0					17																	48244792		2203	4300	6503	SO:0001583	missense	6442	exon2			TGGGCCGTGTCTT	L34355	CCDS32679.1, CCDS45729.1	17q21	2014-09-17	2002-08-29		ENSG00000108823	ENSG00000108823			10805	protein-coding gene	gene with protein product	"""50kD DAG"", ""Sarcoglycan, alpha (50kD dystrophin-associated glycoprotein; adhalin)"", ""adhalin (limb girdle muscular dystrophy 2D)"""	600119	"""sarcoglycan, alpha (50kD dystrophin-associated glycoprotein)"""	ADL		7937874	Standard	NM_000023		Approved	SCARMD1, LGMD2D, adhalin, DMDA2, A2	uc002iqi.3	Q16586	OTTHUMG00000162024	ENST00000262018.3:c.101G>T	chr17.hg19:g.48244792G>T	ENSP00000262018:p.Arg34Leu	130.0	0.0		219.0	51.0	NM_001135697	A6NEB8|A8K3K7|Q13710|Q13712	Missense_Mutation	SNP	ENST00000262018.3	hg19	CCDS32679.1	.	.	.	.	.	.	.	.	.	.	G	15.52	2.857415	0.51376	.	.	ENSG00000108823	ENST00000344627;ENST00000262018;ENST00000543315	D;D;D	0.98531	-4.98;-4.98;-4.98	4.47	4.47	0.54385	Dystroglycan-type cadherin-like (1);Cadherin-like (1);	0.144240	0.43579	D	0.000544	D	0.95990	0.8694	L	0.46157	1.445	0.80722	D	1	B;B	0.28636	0.218;0.004	B;B	0.26864	0.074;0.007	D	0.95008	0.8149	10	0.42905	T	0.14	-15.278	12.9801	0.58559	0.0:0.0:1.0:0.0	.	34;34	Q16586-2;Q16586	.;SGCA_HUMAN	L	34	ENSP00000345522:R34L;ENSP00000262018:R34L;ENSP00000444539:R34L	ENSP00000262018:R34L	R	+	2	0	SGCA	45599791	0.584000	0.26766	0.960000	0.40013	0.753000	0.42808	2.894000	0.48640	2.184000	0.69523	0.407000	0.27541	CGT	.	.		0.642	SGCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366841.1	NM_000023	
SIPA1L3	23094	hgsc.bcm.edu	37	19	38610466	38610466	+	Silent	SNP	C	C	T			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr19:38610466C>T	ENST00000222345.6	+	9	3321	c.2812C>T	c.(2812-2814)Cta>Tta	p.L938L		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	938					hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			CCACATCTTCCTACAGGCGAC	0.532																																					p.L938L		Atlas-SNP	.											.	SIPA1L3	150	.	0			c.C2812T						.						44.0	47.0	46.0					19																	38610466		2203	4300	6503	SO:0001819	synonymous_variant	23094	exon9			ATCTTCCTACAGG	AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738			23801	protein-coding gene	gene with protein product							Standard	XM_005258671		Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.2812C>T	chr19.hg19:g.38610466C>T		47.0	0.0		76.0	31.0	NM_015073	Q2TV87	Silent	SNP	ENST00000222345.6	hg19	CCDS33007.1																																																																																			.	.		0.532	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278	
KRTAP10-11	386678	hgsc.bcm.edu	37	21	46066650	46066650	+	Missense_Mutation	SNP	C	C	G			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr21:46066650C>G	ENST00000334670.8	+	1	320	c.275C>G	c.(274-276)tCc>tGc	p.S92C	TSPEAR_ENST00000323084.4_Intron	NM_198692.2	NP_941965.2	P60412	KR10B_HUMAN	keratin associated protein 10-11	92	25 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)	12						TGCTGCACCTCCTCCCcctgc	0.657																																					p.S92C		Atlas-SNP	.											.	KRTAP10-11	36	.	0			c.C275G						.						85.0	87.0	86.0					21																	46066650		2203	4298	6501	SO:0001583	missense	386678	exon1			GCACCTCCTCCCC	AB076359	CCDS42962.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000243489	ENSG00000243489		"""Keratin associated proteins"""	20528	protein-coding gene	gene with protein product			"""keratin associated protein 10-11"""	KRTAP18-11			Standard	NM_198692		Approved	KRTAP18.11, KAP18.11, KAP10.11	uc002zfr.4	P60412	OTTHUMG00000057626	ENST00000334670.8:c.275C>G	chr21.hg19:g.46066650C>G	ENSP00000334197:p.Ser92Cys	191.0	0.0		247.0	23.0	NM_198692	A2RRF9	Missense_Mutation	SNP	ENST00000334670.8	hg19	CCDS42962.1	.	.	.	.	.	.	.	.	.	.	c	9.733	1.162758	0.21538	.	.	ENSG00000243489	ENST00000334670	T	0.00695	5.83	3.57	0.12	0.14691	.	.	.	.	.	T	0.01627	0.0052	M	0.80422	2.495	0.09310	N	1	B	0.12013	0.005	B	0.12837	0.008	T	0.28713	-1.0035	9	0.49607	T	0.09	.	12.8421	0.57809	0.0:0.4303:0.5697:0.0	.	92	P60412	KR10B_HUMAN	C	92	ENSP00000334197:S92C	ENSP00000334197:S92C	S	+	2	0	KRTAP10-11	44891078	0.000000	0.05858	0.018000	0.16275	0.822000	0.46500	0.194000	0.17135	0.008000	0.14787	0.456000	0.33151	TCC	.	.		0.657	KRTAP10-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128029.1	NM_198692	
GPR82	27197	hgsc.bcm.edu	37	X	41586732	41586732	+	Missense_Mutation	SNP	T	T	A			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chrX:41586732T>A	ENST00000302548.4	+	3	693	c.453T>A	c.(451-453)ttT>ttA	p.F151L	CASK_ENST00000361962.4_Intron|CASK_ENST00000442742.2_Intron|CASK_ENST00000378166.4_Intron|CASK_ENST00000378158.1_Intron|CASK_ENST00000318588.9_Intron|CASK_ENST00000421587.2_Intron|CASK_ENST00000378154.1_Intron|CASK_ENST00000378163.1_Intron	NM_080817.4	NP_543007.1	Q96P67	GPR82_HUMAN	G protein-coupled receptor 82	151						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	10						AGCCCAACTTTGCTAGAAAAC	0.388																																					p.F151L		Atlas-SNP	.											.	GPR82	52	.	0			c.T453A						.						49.0	50.0	50.0					X																	41586732		2202	4299	6501	SO:0001583	missense	27197	exon3			CAACTTTGCTAGA	AF411111	CCDS14259.1	Xp11.4	2012-08-21			ENSG00000171657	ENSG00000171657		"""GPCR / Class A : Orphans"""	4533	protein-coding gene	gene with protein product		300748				11574155	Standard	NM_080817		Approved		uc004dft.3	Q96P67	OTTHUMG00000021373	ENST00000302548.4:c.453T>A	chrX.hg19:g.41586732T>A	ENSP00000303549:p.Phe151Leu	182.0	0.0		100.0	13.0	NM_080817	Q5VT13	Missense_Mutation	SNP	ENST00000302548.4	hg19	CCDS14259.1	.	.	.	.	.	.	.	.	.	.	T	17.23	3.336319	0.60963	.	.	ENSG00000171657	ENST00000302548	T	0.35236	1.32	5.73	2.07	0.26955	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000005	T	0.46014	0.1371	L	0.54323	1.7	0.31162	N	0.704282	D	0.69078	0.997	D	0.80764	0.994	T	0.48091	-0.9065	10	0.12430	T	0.62	-14.8389	8.3659	0.32387	0.0:0.3226:0.0:0.6774	.	151	Q96P67	GPR82_HUMAN	L	151	ENSP00000303549:F151L	ENSP00000303549:F151L	F	+	3	2	GPR82	41471676	1.000000	0.71417	0.949000	0.38748	0.948000	0.59901	1.063000	0.30567	0.015000	0.14971	-0.323000	0.08544	TTT	.	.		0.388	GPR82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056261.1	NM_080817	
SMC1A	8243	hgsc.bcm.edu	37	X	53409455	53409455	+	Missense_Mutation	SNP	T	T	A			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chrX:53409455T>A	ENST00000322213.4	-	21	3384	c.3257A>T	c.(3256-3258)aAg>aTg	p.K1086M	SMC1A_ENST00000469129.1_5'UTR	NM_006306.2	NP_006297.2	Q14683	SMC1A_HUMAN	structural maintenance of chromosomes 1A	1086					DNA repair (GO:0006281)|gene expression (GO:0010467)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic sister chromatid cohesion (GO:0007064)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of DNA endoreduplication (GO:0032876)|response to radiation (GO:0009314)|RNA splicing (GO:0008380)|signal transduction in response to DNA damage (GO:0042770)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin core heterodimer (GO:0008280)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|meiotic cohesin complex (GO:0030893)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(8)|ovary(5)|upper_aerodigestive_tract(2)	49						GGACAGGGCCTTATAGATCTC	0.522																																					p.K1086M		Atlas-SNP	.											.	SMC1A	112	.	0			c.A3257T						.						76.0	61.0	66.0					X																	53409455		2203	4300	6503	SO:0001583	missense	8243	exon21			AGGGCCTTATAGA	S78271	CCDS14352.1, CCDS75985.1	Xp11.22-p11.21	2014-09-17	2006-07-06	2006-07-06	ENSG00000072501	ENSG00000072501		"""Structural maintenance of chromosomes proteins"""	11111	protein-coding gene	gene with protein product		300040	"""SMC1 (structural maintenance of chromosomes 1, yeast)-like 1"", ""SMC1 structural maintenance of chromosomes 1-like 1 (yeast)"""	SMC1L1		7757074	Standard	NM_006306		Approved	DXS423E, KIAA0178, SB1.8, Smcb	uc004dsg.3	Q14683	OTTHUMG00000021614	ENST00000322213.4:c.3257A>T	chrX.hg19:g.53409455T>A	ENSP00000323421:p.Lys1086Met	137.0	0.0		139.0	38.0	NM_006306	O14995|Q16351|Q2M228	Missense_Mutation	SNP	ENST00000322213.4	hg19	CCDS14352.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.226692	0.79576	.	.	ENSG00000072501	ENST00000322213	T	0.79845	-1.31	5.45	5.45	0.79879	RecF/RecN/SMC (1);	0.000000	0.85682	D	0.000000	D	0.91905	0.7437	M	0.93939	3.475	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93744	0.7053	10	0.87932	D	0	.	13.6717	0.62430	0.0:0.0:0.0:1.0	.	1086	Q14683	SMC1A_HUMAN	M	1086	ENSP00000323421:K1086M	ENSP00000323421:K1086M	K	-	2	0	SMC1A	53426180	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	6.162000	0.71874	1.940000	0.56252	0.486000	0.48141	AAG	.	.		0.522	SMC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056756.2	NM_006306	
TCEANC2	127428	hgsc.bcm.edu	37	1	54520147	54520148	+	Frame_Shift_Ins	INS	-	-	T			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr1:54520147_54520148insT	ENST00000234827.1	+	2	252_253	c.52_53insT	c.(52-54)aaafs	p.K18fs	TCEANC2_ENST00000371331.1_Frame_Shift_Ins_p.K48fs|TMEM59_ENST00000234831.5_5'Flank|TCEANC2_ENST00000498272.1_3'UTR|TMEM59_ENST00000371337.3_5'Flank|TMEM59_ENST00000371341.1_5'Flank|MIR4781_ENST00000585250.1_RNA	NM_153035.1	NP_694580.1	Q96MN5	TEAN2_HUMAN	transcription elongation factor A (SII) N-terminal and central domain containing 2	18					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			kidney(1)|lung(3)|pancreas(1)	5						CCCTCAGAAGAAAGATTCTGGA	0.485																																					p.K18fs		Atlas-Indel,Pindel	.											.	TCEANC2	17	.	0			c.52_53insT						.																																			SO:0001589	frameshift_variant	127428	exon2			.	AK056674	CCDS587.1	1p32.3	2011-01-25	2011-01-25	2011-01-25	ENSG00000116205	ENSG00000116205			26494	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 83"""	C1orf83		12477932	Standard	NM_153035		Approved	FLJ32112	uc001cwt.1	Q96MN5	OTTHUMG00000008434	Exception_encountered	chr1.hg19:g.54520147_54520148insT	ENSP00000234827:p.Lys18fs	110.0	0.0		151.0	43.0	NM_153035	Q5T702|Q8N8N2	Frame_Shift_Ins	INS	ENST00000234827.1	hg19	CCDS587.1																																																																																			.	.		0.485	TCEANC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023245.1	NM_153035	
C18orf8	29919	hgsc.bcm.edu	37	18	21104108	21104109	+	Frame_Shift_Ins	INS	-	-	C			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr18:21104108_21104109insC	ENST00000269221.3	+	11	1086_1087	c.976_977insC	c.(976-978)accfs	p.T326fs	C18orf8_ENST00000590868.1_Frame_Shift_Ins_p.T278fs	NM_013326.3	NP_037458.3	Q96DM3	MIC1_HUMAN	chromosome 18 open reading frame 8	326						lysosomal membrane (GO:0005765)				endometrium(9)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	21	all_cancers(21;0.000122)|all_epithelial(16;8.08e-07)|Lung NSC(20;0.00206)|all_lung(20;0.00659)|Colorectal(14;0.0202)|Ovarian(20;0.127)					TGCTGCCGTGACCAGCCAGTCT	0.46																																					p.T326fs		Atlas-INDEL	.											.	C18orf8	58	.	0			c.976_977insC						.																																			SO:0001589	frameshift_variant	29919	exon11			.	AK057192	CCDS32803.1, CCDS74199.1	18q11.2	2013-12-13			ENSG00000141452	ENSG00000141452			24326	protein-coding gene	gene with protein product	"""colon cancer associated protein Mic1"", ""macrophage inhibitory cytokine 1"""					12477932	Standard	NM_013326		Approved	MIC1, MIC-1, HsT2591	uc021uie.2	Q96DM3		ENST00000269221.3:c.978dupC	chr18.hg19:g.21104110_21104110dupC	ENSP00000269221:p.Thr326fs	155.0	0.0		170.0	10.0	NM_013326	Q9BU17|Q9Y5M0	Frame_Shift_Ins	INS	ENST00000269221.3	hg19	CCDS32803.1																																																																																			.	.		0.460	C18orf8-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445386.1	NM_013326	
ANKRD17	26057	hgsc.bcm.edu	37	4	74043114	74043115	+	Frame_Shift_Ins	INS	-	-	C			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr4:74043114_74043115insC	ENST00000358602.4	-	2	645_646	c.529_530insG	c.(529-531)gctfs	p.A177fs	ANKRD17_ENST00000330838.6_Frame_Shift_Ins_p.A177fs|ANKRD17_ENST00000509867.2_Frame_Shift_Ins_p.A64fs	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	177					blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TTCTAGTAAAGCTTCCAGTCTA	0.391																																					p.A177fs		Atlas-INDEL	.											.	ANKRD17	214	.	0			c.530_531insG						.																																			SO:0001589	frameshift_variant	26057	exon2			.	AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"""Ankyrin repeat domain containing"""	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.530dupG	chr4.hg19:g.74043115_74043115dupC	ENSP00000351416:p.Ala177fs	158.0	0.0		129.0	10.0	NM_198889	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Frame_Shift_Ins	INS	ENST00000358602.4	hg19	CCDS34004.1																																																																																			.	.		0.391	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217	
KAT2A	2648	hgsc.bcm.edu	37	17	40272817	40272818	+	Frame_Shift_Ins	INS	-	-	C	rs200262131		TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr17:40272817_40272818insC	ENST00000225916.5	-	2	422_423	c.369_370insG	c.(367-372)tggaaafs	p.K124fs	CTD-2132N18.3_ENST00000592574.1_Frame_Shift_Ins_p.K158fs|HSPB9_ENST00000355067.3_5'Flank	NM_021078.2	NP_066564.2	Q92830	KAT2A_HUMAN	K(lysine) acetyltransferase 2A	124					cell proliferation (GO:0008283)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|histone deubiquitination (GO:0016578)|histone H3 acetylation (GO:0043966)|histone H3-K14 acetylation (GO:0044154)|in utero embryonic development (GO:0001701)|metencephalon development (GO:0022037)|midbrain development (GO:0030901)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|positive regulation of gluconeogenesis (GO:0045722)|regulation of protein stability (GO:0031647)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|somitogenesis (GO:0001756)|telencephalon development (GO:0021537)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|extracellular space (GO:0005615)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|STAGA complex (GO:0030914)|transcription factor TFTC complex (GO:0033276)	chromatin binding (GO:0003682)|H3 histone acetyltransferase activity (GO:0010484)|histone acetyltransferase activity (GO:0004402)|histone acetyltransferase activity (H4-K12 specific) (GO:0043997)|histone deacetylase binding (GO:0042826)|transcription coactivator activity (GO:0003713)	p.K124E(1)		central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						TTGGGGTTTTTCCAGCCATTAC	0.584																																					p.K124fs		Atlas-INDEL	.											KAT2A,NS,carcinoma,0,2	KAT2A	54	.	1	Substitution - Missense(1)	prostate(1)	c.370_371insG						.																																			SO:0001589	frameshift_variant	2648	exon2			.	AF029777	CCDS11417.1	17q12-q21	2011-07-01	2008-07-04	2008-07-04	ENSG00000108773	ENSG00000108773		"""Chromatin-modifying enzymes / K-acetyltransferases"""	4201	protein-coding gene	gene with protein product		602301	"""GCN5 general control of amino-acid synthesis 5-like 2 (yeast)"""	GCN5L2		8552087	Standard	NM_021078		Approved	GCN5, PCAF-b	uc002hyx.2	Q92830	OTTHUMG00000133504	ENST00000225916.5:c.370dupG	chr17.hg19:g.40272819_40272819dupC	ENSP00000225916:p.Lys124fs	106.0	0.0		166.0	34.0	NM_021078	Q8N1A2|Q9UCW1	Frame_Shift_Ins	INS	ENST00000225916.5	hg19	CCDS11417.1																																																																																			.	.		0.584	KAT2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257458.1	NM_021078	
VGF	7425	hgsc.bcm.edu	37	7	100807026	100807028	+	In_Frame_Del	DEL	CCT	CCT	-			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr7:100807026_100807028delCCT	ENST00000249330.2	-	2	1336_1338	c.1097_1099delAGG	c.(1096-1101)gaggcg>gcg	p.E366del	VGF_ENST00000445482.2_In_Frame_Del_p.E366del	NM_003378.3	NP_003369.2	O15240	VGF_HUMAN	VGF nerve growth factor inducible	366	Asp/Glu-rich (acidic).				defense response to bacterium (GO:0042742)|generation of precursor metabolites and energy (GO:0006091)|glucose homeostasis (GO:0042593)|insulin secretion (GO:0030073)|ovarian follicle development (GO:0001541)|response to cAMP (GO:0051591)|response to cold (GO:0009409)|response to dietary excess (GO:0002021)|response to insulin (GO:0032868)|sexual reproduction (GO:0019953)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)				cervix(1)|large_intestine(1)|lung(4)|prostate(2)|skin(1)	9	Lung NSC(181;0.168)|all_lung(186;0.215)					tcctgctccgcctcctcctcctc	0.744																																					p.366_367del		Atlas-INDEL	.											.	VGF	29	.	0			c.1098_1100del						.			10,3702		0,10,1846						0.9	1.0			9	28,7398		3,22,3688	no	coding	VGF	NM_003378.3		3,32,5534	A1A1,A1R,RR		0.3771,0.2694,0.3412				38,11100				SO:0001651	inframe_deletion	7425	exon2			.	Y12661	CCDS5712.1	7q22	2008-07-18			ENSG00000128564	ENSG00000128564			12684	protein-coding gene	gene with protein product	"""neuro-endocrine specific protein VGF"""	602186				9344675	Standard	NM_003378		Approved		uc003uxx.4	O15240	OTTHUMG00000157109	ENST00000249330.2:c.1097_1099delAGG	chr7.hg19:g.100807035_100807037delCCT	ENSP00000249330:p.Glu366del	46.0	0.0		126.0	11.0	NM_003378	Q9UDW8	In_Frame_Del	DEL	ENST00000249330.2	hg19	CCDS5712.1																																																																																			.	.		0.744	VGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347462.1	NM_003378	
USP37	57695	hgsc.bcm.edu	37	2	219423315	219423315	+	Frame_Shift_Del	DEL	T	T	-			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr2:219423315delT	ENST00000258399.3	-	4	474	c.62delA	c.(61-63)aagfs	p.K21fs	USP37_ENST00000454775.1_Frame_Shift_Del_p.K21fs|USP37_ENST00000418019.1_Frame_Shift_Del_p.K21fs|USP37_ENST00000338465.5_Frame_Shift_Del_p.K21fs|USP37_ENST00000415516.1_Intron	NM_020935.2	NP_065986	Q86T82	UBP37_HUMAN	ubiquitin specific peptidase 37	21					G1/S transition of mitotic cell cycle (GO:0000082)|mitotic nuclear division (GO:0007067)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)			NS(2)|breast(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|skin(5)|stomach(1)	35		Renal(207;0.0915)		Epithelial(149;1.08e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.00375)|Lung(261;0.00487)		TTCTTTCCACTTTGTAATCCC	0.343																																					p.K21fs		Atlas-Indel,Pindel	.											.	USP37	76	.	0			c.63delG						.						169.0	179.0	176.0					2																	219423315		2203	4300	6503	SO:0001589	frameshift_variant	57695	exon4			.	AB046814	CCDS2418.1	2q35	2008-02-05	2005-08-08		ENSG00000135913	ENSG00000135913		"""Ubiquitin-specific peptidases"""	20063	protein-coding gene	gene with protein product			"""ubiquitin specific protease 37"""			12838346	Standard	NM_020935		Approved	KIAA1594	uc010fvs.1	Q86T82	OTTHUMG00000133113	ENST00000258399.3:c.62delA	chr2.hg19:g.219423315delT	ENSP00000258399:p.Lys21fs	328.0	0.0		299.0	86.0	NM_020935	A2RUQ8|B7ZM38|B7ZM41|E9PHL3|Q2KHT2|Q53S10|Q7Z3A5|Q9HCH8	Frame_Shift_Del	DEL	ENST00000258399.3	hg19	CCDS2418.1																																																																																			.	.		0.343	USP37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256779.3	NM_020935	
HOXA10	3206	hgsc.bcm.edu	37	7	27213355	27213356	+	Frame_Shift_Ins	INS	-	-	G			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr7:27213355_27213356insG	ENST00000283921.4	-	1	569_570	c.570_571insC	c.(568-573)cccttcfs	p.F191fs	RP1-170O19.20_ENST00000465941.1_Intron|HOXA-AS4_ENST00000523790.1_RNA|HOXA-AS4_ENST00000519694.1_RNA|HOXA10_ENST00000521421.1_5'Flank|RP1-170O19.20_ENST00000470747.4_Intron|HOXA10_ENST00000396344.4_Intron|HOXA-AS4_ENST00000519935.1_RNA	NM_018951.3	NP_061824.3	P31260	HXA10_HUMAN	homeobox A10	191					anterior/posterior pattern specification (GO:0009952)|embryonic limb morphogenesis (GO:0030326)|male gonad development (GO:0008584)|multicellular organismal development (GO:0007275)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|single fertilization (GO:0007338)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|uterus development (GO:0060065)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase binding (GO:0042826)|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 positive regulation of transcription (GO:0001077)			breast(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	9						CCCCGCGGGAAGGGAGCCAGTT	0.673																																					p.F191fs		Atlas-INDEL	.											.	HOXA10	55	.	0			c.571_572insC						.																																			SO:0001589	frameshift_variant	3206	exon1			.		CCDS5410.2	7p15.2	2011-06-20	2005-12-22		ENSG00000253293	ENSG00000253293		"""Homeoboxes / ANTP class : HOXL subclass"""	5100	protein-coding gene	gene with protein product		142957	"""homeo box A10"""	HOX1H, HOX1		1973146, 1358459	Standard	NR_037939		Approved		uc011jzm.2	P31260	OTTHUMG00000023436	ENST00000283921.4:c.571dupC	chr7.hg19:g.27213358_27213358dupG	ENSP00000283921:p.Phe191fs	17.0	0.0		97.0	10.0	NM_018951	O43370|O43605|Q15949|Q504T1	Frame_Shift_Ins	INS	ENST00000283921.4	hg19	CCDS5410.2																																																																																			.	.		0.673	HOXA10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358724.2		
CDHR5	53841	hgsc.bcm.edu	37	11	618063	618064	+	Frame_Shift_Ins	INS	-	-	C			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr11:618063_618064insC	ENST00000358353.3	-	15	2330_2331	c.2008_2009insG	c.(2008-2010)gccfs	p.A670fs	IRF7_ENST00000397562.3_5'Flank|IRF7_ENST00000525445.1_5'Flank|CDHR5_ENST00000349570.7_Frame_Shift_Ins_p.A476fs|IRF7_ENST00000397570.1_5'Flank|IRF7_ENST00000397574.2_5'Flank|CDHR5_ENST00000397542.2_Frame_Shift_Ins_p.A670fs|IRF7_ENST00000397566.1_5'Flank|IRF7_ENST00000330243.5_5'Flank|IRF7_ENST00000348655.6_5'Flank			Q9HBB8	CDHR5_HUMAN	cadherin-related family member 5	670					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	23						CCCGCCCAGGGCCGCCATATCC	0.668																																					p.A670fs		Atlas-INDEL	.											.	CDHR5	77	.	0			c.2009_2010insG						.																																			SO:0001589	frameshift_variant	53841	exon14			.	AF258675	CCDS7707.1, CCDS7708.1	11p15.5	2011-07-01	2010-01-25	2010-01-25	ENSG00000099834	ENSG00000099834		"""Cadherins / Cadherin-related"""	7521	protein-coding gene	gene with protein product		606839	"""mucin and cadherin-like"", ""mucin-like protocadherin"""	MUCDHL, MUPCDH		11031102, 10801787	Standard	NM_021924		Approved	FLJ20219, MU-PCDH	uc001lqj.3	Q9HBB8	OTTHUMG00000132018	ENST00000358353.3:c.2009dupG	chr11.hg19:g.618065_618065dupC	ENSP00000351118:p.Ala670fs	68.0	0.0		95.0	17.0	NM_021924	C9J7X1|Q9H746|Q9HAU3|Q9HBB5|Q9HBB6|Q9HBB7|Q9NX86|Q9NXI9	Frame_Shift_Ins	INS	ENST00000358353.3	hg19	CCDS7707.1																																																																																			.	.		0.668	CDHR5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255023.2	NM_021924	
KRTAP5-11	440051	hgsc.bcm.edu	37	11	71293866	71293867	+	Frame_Shift_Ins	INS	-	-	C			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr11:71293866_71293867insC	ENST00000398530.1	-	1	54_55	c.17_18insG	c.(16-18)tgtfs	p.C6fs	KRTAP5-11_ENST00000526239.1_Intron|AP000867.1_ENST00000343767.3_Intron	NM_001005405.2	NP_001005405.1	Q6L8G4	KR511_HUMAN	keratin associated protein 5-11	6						keratin filament (GO:0045095)				endometrium(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						AGCCTCCAGAACAGCCACAGCA	0.644																																					p.C6fs		Atlas-INDEL	.											.	KRTAP5-11	36	.	0			c.18_19insG						.																																			SO:0001589	frameshift_variant	440051	exon1			.	AB126080	CCDS41685.1	11q13.4	2008-11-06			ENSG00000204571	ENSG00000204571		"""Keratin associated proteins"""	23606	protein-coding gene	gene with protein product						15144888	Standard	NM_001005405		Approved	KRTAP5.11, KRTAP5-6	uc001oqu.3	Q6L8G4	OTTHUMG00000057586	ENST00000398530.1:c.18dupG	chr11.hg19:g.71293867_71293867dupC	ENSP00000381541:p.Cys6fs	224.0	0.0		300.0	22.0	NM_001005405		Frame_Shift_Ins	INS	ENST00000398530.1	hg19	CCDS41685.1																																																																																			.	.		0.644	KRTAP5-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127969.1	NM_001005405	
SPTBN2	6712	hgsc.bcm.edu	37	11	66461311	66461312	+	Frame_Shift_Ins	INS	-	-	C			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr11:66461311_66461312insC	ENST00000533211.1	-	23	4855_4856	c.4524_4525insG	c.(4522-4527)ctgcccfs	p.P1509fs	SPTBN2_ENST00000529997.1_Frame_Shift_Ins_p.P1509fs|SPTBN2_ENST00000309996.2_Frame_Shift_Ins_p.P1509fs			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	1509					actin filament capping (GO:0051693)|adult behavior (GO:0030534)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|cell death (GO:0008219)|cerebellar Purkinje cell layer morphogenesis (GO:0021692)|multicellular organism growth (GO:0035264)|synapse assembly (GO:0007416)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|spectrin (GO:0008091)	actin binding (GO:0003779)|phospholipid binding (GO:0005543)|structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(15)|liver(1)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	74						CTGGCCATGGGCAGCCGCTCTG	0.589																																					p.P1509fs		Atlas-INDEL	.											.	SPTBN2	188	.	0			c.4525_4526insG						.																																			SO:0001589	frameshift_variant	6712	exon22			.	AB008567, AF026487, AF026488, AF079569	CCDS8150.1	11q13.2	2013-01-10			ENSG00000173898	ENSG00000173898		"""Pleckstrin homology (PH) domain containing"""	11276	protein-coding gene	gene with protein product		604985	"""spinocerebellar ataxia 5"""	SCA5		9826670, 16429157	Standard	NM_006946		Approved		uc001ojd.3	O15020	OTTHUMG00000167262	ENST00000533211.1:c.4525dupG	chr11.hg19:g.66461312_66461312dupC	ENSP00000432568:p.Pro1509fs	95.0	0.0		116.0	17.0	NM_006946	O14872|O14873	Frame_Shift_Ins	INS	ENST00000533211.1	hg19	CCDS8150.1																																																																																			.	.		0.589	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946	
BAP1	8314	hgsc.bcm.edu	37	3	52437456	52437456	+	Frame_Shift_Del	DEL	C	C	-			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr3:52437456delC	ENST00000460680.1	-	13	2176	c.1705delG	c.(1705-1707)gtgfs	p.V569fs	BAP1_ENST00000296288.5_Frame_Shift_Del_p.V551fs	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		GGACTCAGCACCCCATCCTCA	0.617			"""N, Mis, F, S, O"""		"""uveal melanoma, breast, NSCLC, RCC"""	"""mesothelioma, uveal melanoma"""																															p.V569fs	GBM(101;493 1458 7992 21037 25532)	Atlas-INDEL	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	.	BAP1	371	.	0			c.1706delT						.						60.0	56.0	58.0					3																	52437456		2203	4300	6503	SO:0001589	frameshift_variant	8314	exon13			.	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.1705delG	chr3.hg19:g.52437456delC	ENSP00000417132:p.Val569fs	47.0	0.0		53.0	19.0	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Frame_Shift_Del	DEL	ENST00000460680.1	hg19	CCDS2853.1																																																																																			.	.		0.617	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1		
CBS	875	hgsc.bcm.edu	37	21	44492127	44492128	+	Frame_Shift_Ins	INS	-	-	G			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr21:44492127_44492128insG	ENST00000398165.3	-	3	435_436	c.176_177insC	c.(175-177)cctfs	p.P59fs	CBS_ENST00000544202.1_5'Flank|CBS_ENST00000352178.5_Frame_Shift_Ins_p.P59fs|CBS_ENST00000398158.1_Frame_Shift_Ins_p.P59fs|CBS_ENST00000359624.3_Frame_Shift_Ins_p.P59fs|CBS_ENST00000398168.1_Frame_Shift_Ins_p.P59fs|CBS_ENST00000470912.1_5'UTR	NM_000071.2	NP_000062.1	P35520	CBS_HUMAN	cystathionine-beta-synthase	59					cellular nitrogen compound metabolic process (GO:0034641)|cysteine biosynthetic process from serine (GO:0006535)|cysteine biosynthetic process via cystathionine (GO:0019343)|homocysteine catabolic process (GO:0043418)|homocysteine metabolic process (GO:0050667)|hydrogen sulfide biosynthetic process (GO:0070814)|L-cysteine catabolic process (GO:0019448)|L-serine catabolic process (GO:0006565)|L-serine metabolic process (GO:0006563)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|transsulfuration (GO:0019346)	cytosol (GO:0005829)|nucleus (GO:0005634)	adenyl nucleotide binding (GO:0030554)|cystathionine beta-synthase activity (GO:0004122)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|modified amino acid binding (GO:0072341)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|ubiquitin protein ligase binding (GO:0031625)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(8)	17					L-Cysteine(DB00151)|L-Serine(DB00133)|S-Adenosylmethionine(DB00118)	ACTCGGAGGCAGGCCGGCCCAG	0.624																																					p.P59fs		Atlas-INDEL	.											.	CBS	85	.	0			c.177_178insC						.																																			SO:0001589	frameshift_variant	875	exon3			.	L14577	CCDS13693.1	21q22.3	2014-09-17			ENSG00000160200	ENSG00000160200	4.2.1.22		1550	protein-coding gene	gene with protein product		613381				9790750	Standard	NM_000071		Approved	HIP4	uc002zcv.2	P35520	OTTHUMG00000086834	ENST00000398165.3:c.177dupC	chr21.hg19:g.44492129_44492129dupG	ENSP00000381231:p.Pro59fs	123.0	0.0		191.0	13.0	NM_000071	B2R993|D3DSK4|Q99425|Q9BWC5	Frame_Shift_Ins	INS	ENST00000398165.3	hg19	CCDS13693.1																																																																																			.	.		0.624	CBS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195525.1	NM_000071	
MAPKBP1	23005	hgsc.bcm.edu	37	15	42110257	42110257	+	Frame_Shift_Del	DEL	A	A	-			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr15:42110257delA	ENST00000456763.2	+	18	2169	c.1973delA	c.(1972-1974)cagfs	p.Q658fs	MAPKBP1_ENST00000514566.1_Frame_Shift_Del_p.Q652fs|MAPKBP1_ENST00000221214.6_Frame_Shift_Del_p.Q535fs|MAPKBP1_ENST00000457542.2_Frame_Shift_Del_p.Q652fs|MAPKBP1_ENST00000260357.7_Frame_Shift_Del_p.Q491fs	NM_001128608.1	NP_001122080.1	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein 1	658										breast(6)|central_nervous_system(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)		AAAGGGTCACAGGGTGAGGAC	0.527																																					p.Q658fs		Atlas-Indel,Pindel	.											.	MAPKBP1	120	.	0			c.1972delC						.						116.0	119.0	118.0					15																	42110257		2203	4300	6503	SO:0001589	frameshift_variant	23005	exon18			.	AB011168	CCDS32201.1, CCDS45239.1, CCDS58359.1	15q15.1	2013-01-10	2008-01-30		ENSG00000137802	ENSG00000137802		"""WD repeat domain containing"""	29536	protein-coding gene	gene with protein product			"""mitogen activated protein kinase binding protein 1"""			9628581, 10471813	Standard	NM_014994		Approved	KIAA0596	uc001zok.4	O60336	OTTHUMG00000160227	ENST00000456763.2:c.1973delA	chr15.hg19:g.42110257delA	ENSP00000393099:p.Gln658fs	147.0	0.0		192.0	45.0	NM_001128608	A6NM93|A8K8P9|Q14CB5|Q14CD8|Q49AJ8|Q5W9G9	Frame_Shift_Del	DEL	ENST00000456763.2	hg19	CCDS45239.1																																																																																			.	.		0.527	MAPKBP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359745.1	NM_014994	
GZMK	3003	hgsc.bcm.edu	37	5	54320547	54320548	+	Frame_Shift_Ins	INS	-	-	C			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr5:54320547_54320548insC	ENST00000231009.2	+	2	194_195	c.124_125insC	c.(124-126)gccfs	p.A42fs	CTD-2313F11.1_ENST00000608929.1_RNA|CTD-2313F11.1_ENST00000596137.1_RNA|CTD-2313F11.1_ENST00000607910.1_RNA|CTD-2313F11.1_ENST00000595218.1_RNA|CTD-2313F11.1_ENST00000609699.1_RNA|CTD-2313F11.1_ENST00000371487.3_RNA|CTD-2313F11.1_ENST00000608466.1_RNA|CTD-2313F11.1_ENST00000596909.2_RNA|ESM1_ENST00000598310.1_5'Flank	NM_002104.2	NP_002095.1	P49863	GRAK_HUMAN	granzyme K (granzyme 3; tryptase II)	42	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(4)	15		Lung NSC(810;4.08e-05)|Breast(144;0.0433)|Prostate(74;0.183)				GCCATTTATGGCCTCCATCCAG	0.46																																					p.A42fs		Atlas-INDEL	.											.	GZMK	39	.	0			c.124_125insC						.																																			SO:0001589	frameshift_variant	3003	exon2			.	BC035802	CCDS3964.1	5q11.2	2008-05-15	2005-08-17		ENSG00000113088	ENSG00000113088			4711	protein-coding gene	gene with protein product		600784	"""granzyme K (serine protease, granzyme 3; tryptase II)"""			7758581	Standard	NM_002104		Approved	TRYP2, PRSS	uc003jpl.1	P49863	OTTHUMG00000097009	ENST00000231009.2:c.126dupC	chr5.hg19:g.54320549_54320549dupC	ENSP00000231009:p.Ala42fs	159.0	0.0		174.0	11.0	NM_002104	B2R563	Frame_Shift_Ins	INS	ENST00000231009.2	hg19	CCDS3964.1																																																																																			.	.		0.460	GZMK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214098.1	NM_002104	
EFCC1	79825	hgsc.bcm.edu	37	3	128758638	128758639	+	Frame_Shift_Ins	INS	-	-	C			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr3:128758638_128758639insC	ENST00000480450.1	+	8	1744_1745	c.1744_1745insC	c.(1744-1746)gcafs	p.A582fs	EFCC1_ENST00000436022.2_Frame_Shift_Ins_p.A145fs			Q9HA90	EFCC1_HUMAN	EF-hand and coiled-coil domain containing 1	582	Poly-Ala.						calcium ion binding (GO:0005509)										ACAGCCCTCGGCACCAGCCTCT	0.658																																					p.A582fs		Atlas-INDEL	.											.	.	.	.	0			c.1744_1745insC						.																																			SO:0001589	frameshift_variant	79825	exon8			.	AK022119	CCDS3054.1, CCDS3054.2	3q21.3	2013-01-11	2013-01-11	2013-01-11	ENSG00000114654	ENSG00000114654		"""EF-hand domain containing"""	25692	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 73"", ""coiled-coil domain containing 48"""	C3orf73, CCDC48			Standard	NM_024768		Approved	FLJ12057	uc011bkt.2	Q9HA90	OTTHUMG00000158996	ENST00000480450.1:c.1745dupC	chr3.hg19:g.128758639_128758639dupC	ENSP00000420075:p.Ala582fs	151.0	0.0		172.0	14.0	NM_024768	A8MYE2	Frame_Shift_Ins	INS	ENST00000480450.1	hg19	CCDS3054.2																																																																																			.	.		0.658	EFCC1-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352832.1	NM_024768	
ZKSCAN8	7745	hgsc.bcm.edu	37	6	28121267	28121268	+	In_Frame_Ins	INS	-	-	AAA	rs200152195	byFrequency	TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr6:28121267_28121268insAAA	ENST00000330236.6	+	6	1393_1394	c.1209_1210insAAA	c.(1210-1212)aag>AAAaag	p.404_404K>KK	ZKSCAN8_ENST00000457389.2_In_Frame_Ins_p.404_404K>KK	NM_001278119.1|NM_001278121.1|NM_001278122.1|NM_006298.2	NP_001265048.1|NP_001265050.1|NP_001265051.1|NP_006289.2	Q15776	ZKSC8_HUMAN	zinc finger with KRAB and SCAN domains 8	404					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)										ACACTGGGGAGAAGCCATATCA	0.48																																					p.E403delinsEK		Atlas-INDEL	.											.	.	.	.	0			c.1209_1210insAAA						.																																			SO:0001652	inframe_insertion	7745	exon6			.		CCDS4645.1	6p21	2013-01-09	2013-01-09	2013-01-09	ENSG00000198315	ENSG00000198315		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	12983	protein-coding gene	gene with protein product		602240	"""zinc finger protein 192"""	ZNF192			Standard	NM_001278119		Approved	LD5-1, ZSCAN40	uc003nkn.2	Q15776	OTTHUMG00000014510	Exception_encountered	chr6.hg19:g.28121267_28121268insAAA	ENSP00000332750:p.Lys404dup	83.0	0.0		106.0	13.0	NM_006298	A1L3D4|B4DYF1|Q4VAR1|Q4VAR2|Q4VAR3|Q9H4T1	In_Frame_Ins	INS	ENST00000330236.6	hg19	CCDS4645.1																																																																																			.	.		0.480	ZKSCAN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040178.2		
COL12A1	1303	hgsc.bcm.edu	37	6	75806972	75806973	+	Frame_Shift_Ins	INS	-	-	G			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr6:75806972_75806973insG	ENST00000322507.8	-	59	8882_8883	c.8573_8574insC	c.(8572-8574)ccgfs	p.P2858fs	COL12A1_ENST00000511023.1_5'UTR|COL12A1_ENST00000345356.6_Frame_Shift_Ins_p.P1694fs|COL12A1_ENST00000416123.2_Frame_Shift_Ins_p.P2782fs|COL12A1_ENST00000483888.2_Intron	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	2858	Collagen-like 3.|Triple-helical region (COL2) with 1 imperfection.			P -> R (in Ref. 1; AAC51244). {ECO:0000305}.	cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						TTCTTACCGGCGGCCCTGGTGG	0.475																																					p.P2858fs		Atlas-INDEL	.											.	COL12A1	385	.	0			c.8574_8575insC						.																																			SO:0001589	frameshift_variant	1303	exon59			.	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"", ""Fibronectin type III domain containing"""	2188	protein-coding gene	gene with protein product	"""collagen type XII proteoglycan"""	120320	"""collagen, type XII, alpha 1-like"""	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.8574dupC	chr6.hg19:g.75806974_75806974dupG	ENSP00000325146:p.Pro2858fs	137.0	0.0		171.0	20.0	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Frame_Shift_Ins	INS	ENST00000322507.8	hg19	CCDS43482.1																																																																																			.	.		0.475	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370	
POU6F1	5463	hgsc.bcm.edu	37	12	51589910	51589911	+	Frame_Shift_Ins	INS	-	-	C			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr12:51589910_51589911insC	ENST00000389243.4	-	8	1030_1031	c.91_92insG	c.(91-93)gccfs	p.A31fs	POU6F1_ENST00000333640.10_Frame_Shift_Ins_p.A31fs|POU6F1_ENST00000550824.1_Frame_Shift_Ins_p.A31fs			Q14863	PO6F1_HUMAN	POU class 6 homeobox 1	31	Gln/Pro-rich.				brain development (GO:0007420)|heart development (GO:0007507)|muscle organ development (GO:0007517)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|cervix(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(1)	11						TGGTGCTGGGGCCGCCACACTA	0.629																																					p.A31fs		Atlas-INDEL	.											.	POU6F1	31	.	0			c.92_93insG						.																																			SO:0001589	frameshift_variant	5463	exon3			.	AL832881	CCDS31803.1	12q13.13	2011-06-20	2007-07-13			ENSG00000184271		"""Homeoboxes / POU class"""	9224	protein-coding gene	gene with protein product			"""POU domain, class 6, transcription factor 1"""			7908264	Standard	NM_002702		Approved	BRN5, MPOU, TCFB1	uc001rxz.3	Q14863		ENST00000389243.4:c.92dupG	chr12.hg19:g.51589912_51589912dupC	ENSP00000373895:p.Ala31fs	58.0	0.0		116.0	13.0	NM_002702	Q15944|Q6DK47|Q7Z7P6	Frame_Shift_Ins	INS	ENST00000389243.4	hg19	CCDS31803.1																																																																																			.	.		0.629	POU6F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405126.1	NM_002702	
CFAP36	112942	hgsc.bcm.edu	37	2	55772122	55772124	+	In_Frame_Del	DEL	AAG	AAG	-	rs528334905		TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr2:55772122_55772124delAAG	ENST00000349456.4	+	10	1155_1157	c.1007_1009delAAG	c.(1006-1011)aaagaa>aaa	p.E338del	CCDC104_ENST00000339012.3_In_Frame_Del_p.E363del|CCDC104_ENST00000407816.3_In_Frame_Del_p.E309del			Q96G28	CFA36_HUMAN		338										breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|liver(2)|lung(1)|ovary(2)	14			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			GAGAAACTCAAAGAAGAAGTTAT	0.286																																					p.336_336del		Atlas-Indel,Pindel	.											.	CCDC104	35	.	0			c.1006_1008del						.			3,4253		0,3,2125						5.7	1.0			35	0,8244		0,0,4122	no	coding	CCDC104	NM_080667.5		0,3,6247	A1A1,A1R,RR		0.0,0.0705,0.024				3,12497				SO:0001651	inframe_deletion	112942	exon10			.																												ENST00000349456.4:c.1007_1009delAAG	chr2.hg19:g.55772128_55772130delAAG	ENSP00000295117:p.Glu338del	439.0	0.0		259.0	59.0	NM_080667	Q53SF0|Q53ST9|Q6UY34	In_Frame_Del	DEL	ENST00000349456.4	hg19	CCDS1854.2																																																																																			.	.		0.286	CCDC104-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319610.2		
AMTN	401138	hgsc.bcm.edu	37	4	71396955	71396955	+	Frame_Shift_Del	DEL	C	C	-			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr4:71396955delC	ENST00000339336.4	+	8	687	c.557delC	c.(556-558)accfs	p.T186fs	AMTN_ENST00000504451.1_Frame_Shift_Del_p.T185fs	NM_212557.2	NP_997722.1	Q6UX39	AMTN_HUMAN	amelotin	186					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|odontogenesis of dentin-containing tooth (GO:0042475)	basal lamina (GO:0005605)|cell-cell junction (GO:0005911)|proteinaceous extracellular matrix (GO:0005578)				NS(3)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|prostate(3)|skin(1)	19			Lung(101;0.235)			GCAGTGACCACCCCTGCAGGC	0.552																																					p.T186fs		Atlas-INDEL	.											.	AMTN	28	.	0			c.556delA						.						69.0	56.0	61.0					4																	71396955		2203	4300	6503	SO:0001589	frameshift_variant	401138	exon8			.	AY358528	CCDS3542.1, CCDS68716.1	4q13.3	2006-12-12			ENSG00000187689	ENSG00000187689			33188	protein-coding gene	gene with protein product		610912				16304441	Standard	NM_001286731		Approved	UNQ689, RSTI689	uc003hfk.1	Q6UX39	OTTHUMG00000129906	ENST00000339336.4:c.557delC	chr4.hg19:g.71396955delC	ENSP00000341013:p.Thr186fs	184.0	0.0		202.0	14.0	NM_212557	Q0P503|Q0P506	Frame_Shift_Del	DEL	ENST00000339336.4	hg19	CCDS3542.1																																																																																			.	.		0.552	AMTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252157.1	NM_212557	
EPN1	29924	hgsc.bcm.edu	37	19	56206198	56206199	+	Frame_Shift_Del	DEL	TG	TG	-			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr19:56206198_56206199delTG	ENST00000270460.6	+	10	1682_1683	c.1371_1372delTG	c.(1369-1374)cctgcafs	p.A459fs	EPN1_ENST00000411543.2_Frame_Shift_Del_p.A545fs|AC010525.6_ENST00000587937.1_lincRNA|EPN1_ENST00000085079.7_Frame_Shift_Del_p.A433fs|AC010525.4_ENST00000585559.1_RNA|AC010525.7_ENST00000589698.1_lincRNA	NM_001130072.1	NP_001123544.1	Q9Y6I3	EPN1_HUMAN	epsin 1	459	Ala/Gly/Pro-rich.				embryonic organ development (GO:0048568)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|female pregnancy (GO:0007565)|in utero embryonic development (GO:0001701)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|Notch signaling pathway (GO:0007219)	coated pit (GO:0005905)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			endometrium(5)|kidney(1)|large_intestine(2)|lung(8)|skin(1)	17		Colorectal(82;0.00244)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.112)		GCCCCCCACCTGCAGCCACACC	0.693																																					p.543_543del		Atlas-INDEL	.											.	EPN1	98	.	0			c.1628_1629del						.																																			SO:0001589	frameshift_variant	29924	exon10			.	AF073727	CCDS46198.1, CCDS46199.1, CCDS46200.1	19q13.42	2014-08-12			ENSG00000063245	ENSG00000063245			21604	protein-coding gene	gene with protein product		607262				9723620, 10557078	Standard	NM_001130072		Approved		uc002qlx.3	Q9Y6I3	OTTHUMG00000180911	ENST00000270460.6:c.1371_1372delTG	chr19.hg19:g.56206198_56206199delTG	ENSP00000270460:p.Ala459fs	71.0	0.0		105.0	11.0	NM_001130071	Q86ST3|Q9HA18	Frame_Shift_Del	DEL	ENST00000270460.6	hg19	CCDS46199.1																																																																																			.	.		0.693	EPN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453610.1	NM_013333	
CHSY1	22856	hgsc.bcm.edu	37	15	101717654	101717655	+	Frame_Shift_Ins	INS	-	-	C			TCGA-CC-5260-01A-01D-A12Z-10	TCGA-CC-5260-10B-01D-A12Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3bacc189-01b8-46cc-a442-f393c0f428c6	bf471c04-91b1-4ccc-9cd2-101b7f008edc	g.chr15:101717654_101717655insC	ENST00000254190.3	-	3	2822_2823	c.2347_2348insG	c.(2347-2349)gaafs	p.E783fs	CHSY1_ENST00000543813.1_5'UTR	NM_014918.4	NP_055733.2	Q86X52	CHSS1_HUMAN	chondroitin sulfate synthase 1	783					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|negative regulation of ossification (GO:0030279)|response to nutrient levels (GO:0031667)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(5)|skin(1)	24	Lung NSC(78;0.00217)|all_lung(78;0.00271)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			ATCATTTTTTTCCAGCCACATC	0.436																																					p.E783fs		Atlas-INDEL	.											.	CHSY1	60	.	0			c.2348_2349insG						.																																			SO:0001589	frameshift_variant	22856	exon3			.	AB023207	CCDS10390.1	15q26.3	2013-02-19	2008-01-24	2008-01-24	ENSG00000131873	ENSG00000131873	2.4.1.175, 2.4.1.226	"""Beta 3-glycosyltransferases"", ""Beta 4-glycosyltransferases"""	17198	protein-coding gene	gene with protein product		608183	"""carbohydrate (chondroitin) synthase 1"""			11514575	Standard	NM_014918		Approved	KIAA0990, CSS1	uc021sxt.1	Q86X52	OTTHUMG00000149873	ENST00000254190.3:c.2348dupG	chr15.hg19:g.101717656_101717656dupC	ENSP00000254190:p.Glu783fs	240.0	0.0		302.0	28.0	NM_014918	Q6UX38|Q7LFU5|Q9Y2J5	Frame_Shift_Ins	INS	ENST00000254190.3	hg19	CCDS10390.1																																																																																			.	.		0.436	CHSY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313624.1	NM_014918	
