#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_Confidence	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_NVarRat	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_TVarRat	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_dbSNP_PopFreq	i_dbSNP_Strength	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
TRIM63	84676	hgsc.bcm.edu	37	1	26386776	26386776	+	Missense_Mutation	SNP	T	T	A			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr1:26386776T>A	ENST00000374272.3	-	4	716	c.578A>T	c.(577-579)gAt>gTt	p.D193V	TRIM63_ENST00000483052.1_5'Flank	NM_032588.3	NP_115977.2	Q969Q1	TRI63_HUMAN	tripartite motif containing 63, E3 ubiquitin protein ligase	193	Interaction with TTN.				cellular response to dexamethasone stimulus (GO:0071549)|muscle contraction (GO:0006936)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of gene expression (GO:0010468)|response to electrical stimulus involved in regulation of muscle adaptation (GO:0014878)|response to interleukin-1 (GO:0070555)|signal transduction (GO:0007165)|skeletal muscle atrophy (GO:0014732)	contractile fiber (GO:0043292)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|titin binding (GO:0031432)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(1)|ovary(1)|skin(1)|stomach(1)	5		Colorectal(325;3.46e-05)|Lung NSC(340;0.000154)|all_lung(284;0.00021)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0133)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;9.15e-26)|Colorectal(126;3.16e-08)|COAD - Colon adenocarcinoma(152;1.72e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000767)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)		TCGACGGGAATCCTCCAGCTG	0.572																																					p.D193V		Atlas-SNP	.											.	TRIM63	33	.	0			c.A578T						PASS	.						122.0	113.0	116.0					1																	26386776		2203	4300	6503	SO:0001583	missense	84676	exon4			CGGGAATCCTCCA	AF353673	CCDS273.1	1p34-p33	2014-09-17	2012-02-23	2004-11-17	ENSG00000158022	ENSG00000158022		"""RING-type (C3HC4) zinc fingers"", ""Tripartite motif containing / Tripartite motif containing"""	16007	protein-coding gene	gene with protein product	"""muscle-specific RING finger protein 1"", ""iris ring finger protein"", ""striated muscle RING zinc finger protein"""	606131	"""ring finger protein 28"", ""tripartite motif-containing 63"", ""tripartite motif containing 63"""	RNF28		11243782, 11283016	Standard	NM_032588		Approved	MURF-1, IRF, SMRZ	uc001bli.2	Q969Q1	OTTHUMG00000007510	ENST00000374272.3:c.578A>T	chr1.hg19:g.26386776T>A	ENSP00000363390:p.Asp193Val	156.0	0.0	.		125.0	25.0	.	NM_032588	B4DN95|Q5T2I1|Q96BD3|Q96KD9|Q9BYV4	Missense_Mutation	SNP	ENST00000374272.3	hg19	CCDS273.1	.	.	.	.	.	.	.	.	.	.	T	18.01	3.528379	0.64860	.	.	ENSG00000158022	ENST00000374272	T	0.39787	1.06	5.21	5.21	0.72293	.	0.086183	0.85682	D	0.000000	T	0.50222	0.1603	M	0.68593	2.085	0.80722	D	1	B	0.32893	0.389	B	0.40741	0.339	T	0.55792	-0.8085	10	0.87932	D	0	.	15.0417	0.71796	0.0:0.0:0.0:1.0	.	193	Q969Q1	TRI63_HUMAN	V	193	ENSP00000363390:D193V	ENSP00000363390:D193V	D	-	2	0	TRIM63	26259363	1.000000	0.71417	1.000000	0.80357	0.774000	0.43823	5.828000	0.69307	2.081000	0.62600	0.379000	0.24179	GAT	.	.	.	none		0.572	TRIM63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019750.1	NM_032588	
KIF2C	11004	hgsc.bcm.edu	37	1	45206651	45206651	+	Missense_Mutation	SNP	C	C	A			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr1:45206651C>A	ENST00000372224.4	+	2	250	c.137C>A	c.(136-138)gCa>gAa	p.A46E	KIF2C_ENST00000372218.4_Missense_Mutation_p.A46E|KIF2C_ENST00000493027.1_3'UTR	NM_006845.3	NP_006836.2	Q99661	KIF2C_HUMAN	kinesin family member 2C	46	Globular. {ECO:0000255}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of chromosome segregation (GO:0051983)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|microtubule motor activity (GO:0003777)|microtubule plus-end binding (GO:0051010)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(16)|ovary(1)|skin(1)|urinary_tract(1)	34	Acute lymphoblastic leukemia(166;0.155)					GTGGAATGGGCAGAAGGAGGT	0.413																																					p.A46E		Atlas-SNP	.											.	KIF2C	68	.	0			c.C137A						PASS	.						106.0	102.0	103.0					1																	45206651		2203	4300	6503	SO:0001583	missense	11004	exon2			AATGGGCAGAAGG	U63743	CCDS512.1, CCDS72774.1	1p34.1	2014-01-21	2003-01-13	2003-01-17	ENSG00000142945	ENSG00000142945		"""Kinesins"""	6393	protein-coding gene	gene with protein product		604538	"""kinesin-like 6 (mitotic centromere-associated kinesin)"""	KNSL6		9434124	Standard	NM_006845		Approved	MCAK, CT139	uc001cmg.4	Q99661	OTTHUMG00000008416	ENST00000372224.4:c.137C>A	chr1.hg19:g.45206651C>A	ENSP00000361298:p.Ala46Glu	69.0	0.0	.		75.0	8.0	.	NM_006845	B3ITR9|Q5JR88|Q6ICU1|Q96C18|Q96HB8|Q9BWV8	Missense_Mutation	SNP	ENST00000372224.4	hg19	CCDS512.1	.	.	.	.	.	.	.	.	.	.	c	15.02	2.708022	0.48412	.	.	ENSG00000142945	ENST00000452259;ENST00000372224;ENST00000372218;ENST00000455186	T;T;T;T	0.74947	1.14;-0.89;-0.72;0.9	5.95	0.825	0.18824	.	1.230180	0.05208	N	0.506277	T	0.64864	0.2637	L	0.43152	1.355	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.17098	0.017;0.017	T	0.55554	-0.8123	10	0.52906	T	0.07	.	2.3087	0.04181	0.1215:0.4871:0.1181:0.2733	.	46;46	B7Z6Q6;Q99661	.;KIF2C_HUMAN	E	46;46;46;37	ENSP00000410346:A46E;ENSP00000361298:A46E;ENSP00000361292:A46E;ENSP00000395050:A37E	ENSP00000361292:A46E	A	+	2	0	KIF2C	44979238	0.981000	0.34729	0.990000	0.47175	0.995000	0.86356	-0.030000	0.12308	-0.083000	0.12618	0.655000	0.94253	GCA	.	.	.	none		0.413	KIF2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023180.1	NM_006845	
TXNDC12	51060	hgsc.bcm.edu	37	1	52494277	52494277	+	Missense_Mutation	SNP	G	G	T			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr1:52494277G>T	ENST00000371626.4	-	3	1258	c.184C>A	c.(184-186)Cat>Aat	p.H62N		NM_015913.3	NP_056997.1	O95881	TXD12_HUMAN	thioredoxin domain containing 12 (endoplasmic reticulum)	62					cell redox homeostasis (GO:0045454)	endoplasmic reticulum (GO:0005783)	protein-disulfide reductase (glutathione) activity (GO:0019153)			endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	7					Glutathione(DB00143)	CAGGATTTATGAATAATCACC	0.299																																					p.H62N		Atlas-SNP	.											.	TXNDC12	18	.	0			c.C184A						PASS	.						86.0	85.0	85.0					1																	52494277		2203	4300	6503	SO:0001583	missense	51060	exon3			ATTTATGAATAAT	AF131758	CCDS561.1	1p32.3	2011-10-19			ENSG00000117862	ENSG00000117862		"""Protein disulfide isomerases"""	24626	protein-coding gene	gene with protein product	"""endoplasmic reticulum thioredoxin superfamily member, 18 kDa"", ""anterior gradient homolog 1 (Xenopus laevis)"", ""protein disulfide isomerase family A, member 16"""	609448				8619474, 9110174	Standard	NM_015913		Approved	TLP19, ERP18, ERP19, hAG-1, AGR1, PDIA16	uc001cti.4	O95881	OTTHUMG00000008629	ENST00000371626.4:c.184C>A	chr1.hg19:g.52494277G>T	ENSP00000360688:p.His62Asn	103.0	0.0	.		69.0	9.0	.	NM_015913	B3KQS0|Q5T1T4|Q96H50	Missense_Mutation	SNP	ENST00000371626.4	hg19	CCDS561.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.570676	0.86542	.	.	ENSG00000117862	ENST00000371626	T	0.52754	0.65	5.6	5.6	0.85130	Thioredoxin domain (1);Thioredoxin, conserved site (1);Thioredoxin-like fold (3);	0.000000	0.85682	D	0.000000	T	0.73682	0.3618	M	0.87269	2.87	0.58432	D	0.999996	D	0.89917	1.0	D	0.97110	1.0	T	0.76705	-0.2861	10	0.52906	T	0.07	.	17.7823	0.88527	0.0:0.0:1.0:0.0	.	62	O95881	TXD12_HUMAN	N	62	ENSP00000360688:H62N	ENSP00000360688:H62N	H	-	1	0	TXNDC12	52266865	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	8.150000	0.89634	2.622000	0.88805	0.655000	0.94253	CAT	.	.	.	none		0.299	TXNDC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023818.1	NM_015913	
ANKRD35	148741	hgsc.bcm.edu	37	1	145561665	145561665	+	Silent	SNP	C	C	T			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr1:145561665C>T	ENST00000355594.4	+	10	1440	c.1353C>T	c.(1351-1353)acC>acT	p.T451T		NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	451										NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(16)|ovary(4)|prostate(3)|skin(2)|urinary_tract(1)	47	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GGGCACAGACCTTTGGCCCTG	0.587																																					p.T451T	Melanoma(9;127 754 22988 51047)	Atlas-SNP	.											.	ANKRD35	96	.	0			c.C1353T						PASS	.						59.0	67.0	64.0					1																	145561665		2203	4300	6503	SO:0001819	synonymous_variant	148741	exon10			ACAGACCTTTGGC	AK091120	CCDS72867.1, CCDS72868.1	1q21.1	2013-01-10			ENSG00000198483	ENSG00000198483		"""Ankyrin repeat domain containing"""	26323	protein-coding gene	gene with protein product							Standard	NM_144698		Approved	FLJ25124	uc001eob.1	Q8N283	OTTHUMG00000013743	ENST00000355594.4:c.1353C>T	chr1.hg19:g.145561665C>T		113.0	0.0	.		97.0	22.0	.	NM_144698	A6NEU0|B4DL62|Q3MJ10|Q96LS3	Silent	SNP	ENST00000355594.4	hg19	CCDS919.1																																																																																			.	.	.	none		0.587	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038515.1	NM_144698	
FLAD1	80308	hgsc.bcm.edu	37	1	154961016	154961016	+	Missense_Mutation	SNP	G	G	A			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr1:154961016G>A	ENST00000292180.3	+	2	1130	c.808G>A	c.(808-810)Gga>Aga	p.G270R	FLAD1_ENST00000368432.1_Missense_Mutation_p.G173R|FLAD1_ENST00000368433.1_Missense_Mutation_p.G270R|FLAD1_ENST00000368428.1_5'Flank|FLAD1_ENST00000295530.2_Missense_Mutation_p.G3R|FLAD1_ENST00000405236.2_Missense_Mutation_p.G171R|FLAD1_ENST00000368431.3_Missense_Mutation_p.G171R|FLAD1_ENST00000315144.10_Missense_Mutation_p.G173R	NM_025207.4	NP_079483.3	Q8NFF5	FAD1_HUMAN	flavin adenine dinucleotide synthetase 1	270					FAD biosynthetic process (GO:0006747)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|riboflavin metabolic process (GO:0006771)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|FMN adenylyltransferase activity (GO:0003919)			endometrium(3)|kidney(4)|large_intestine(2)|lung(7)|ovary(3)|skin(3)	22	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			GGGGATGAAGGGACTATTCCA	0.572																																					p.G270R		Atlas-SNP	.											.	FLAD1	52	.	0			c.G808A						PASS	.						43.0	41.0	42.0					1																	154961016		2203	4300	6503	SO:0001583	missense	80308	exon2			ATGAAGGGACTAT		CCDS1078.1, CCDS1079.1, CCDS53371.1, CCDS53372.1	1q22	2013-03-05	2013-03-05		ENSG00000160688	ENSG00000160688	2.7.7.2		24671	protein-coding gene	gene with protein product		610595	"""Fad1, flavin adenine dinucleotide synthetase, homolog (yeast)"", ""FAD1 flavin adenine dinucleotide synthetase homolog (S. cerevisiae)"", ""flavin adenine dinucleotide synthetase"""				Standard	NM_001184891		Approved	PP591, FAD1	uc001fgf.2	Q8NFF5	OTTHUMG00000037416	ENST00000292180.3:c.808G>A	chr1.hg19:g.154961016G>A	ENSP00000292180:p.Gly270Arg	69.0	0.0	.		69.0	9.0	.	NM_025207	Q8N5J1|Q8N686|Q8WU93|Q8WUJ4|Q96CR8|Q99764|Q9HBN6	Missense_Mutation	SNP	ENST00000292180.3	hg19	CCDS1078.1	.	.	.	.	.	.	.	.	.	.	G	10.59	1.391696	0.25118	.	.	ENSG00000160688	ENST00000368433;ENST00000315144;ENST00000368432;ENST00000368431;ENST00000292180;ENST00000405236;ENST00000295530	.	.	.	5.51	1.43	0.22495	Molybdopterin binding (2);	0.470755	0.24384	N	0.038987	T	0.05777	0.0151	N	0.25890	0.77	0.09310	N	1	P;B;P	0.45474	0.859;0.05;0.491	B;B;B	0.37304	0.246;0.124;0.076	T	0.32188	-0.9916	9	0.21014	T	0.42	-1.0E-4	6.7182	0.23314	0.2278:0.3684:0.4038:0.0	.	3;270;171	Q5T191;Q8NFF5;Q8NFF5-4	.;FAD1_HUMAN;.	R	270;173;173;171;270;171;3	.	ENSP00000292180:G270R	G	+	1	0	FLAD1	153227640	0.089000	0.21612	0.069000	0.20011	0.879000	0.50718	1.889000	0.39718	0.419000	0.25927	0.561000	0.74099	GGA	.	.	.	none		0.572	FLAD1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000091089.1	NM_025207	
LOXL3	84695	hgsc.bcm.edu	37	2	74761483	74761483	+	Silent	SNP	G	G	A			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr2:74761483G>A	ENST00000264094.3	-	11	1970	c.1899C>T	c.(1897-1899)caC>caT	p.H633H	LOXL3_ENST00000393937.2_Silent_p.H488H|LOXL3_ENST00000409986.1_Silent_p.H488H|LOXL3_ENST00000409549.1_Silent_p.H577H|LOXL3_ENST00000409249.1_Intron	NM_032603.2	NP_115992.1	P58215	LOXL3_HUMAN	lysyl oxidase-like 3	633	Lysyl-oxidase like.				epithelial to mesenchymal transition (GO:0001837)|negative regulation of transcription, DNA-templated (GO:0045892)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|nucleus (GO:0005634)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)			endometrium(7)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30						AACTAGCTTTGTGGCCCTCAG	0.502																																					p.H633H		Atlas-SNP	.											.	LOXL3	73	.	0			c.C1899T						PASS	.						190.0	183.0	185.0					2																	74761483		2203	4300	6503	SO:0001819	synonymous_variant	84695	exon11			AGCTTTGTGGCCC	AF282619	CCDS1953.1, CCDS74527.1	2p13	2008-05-23			ENSG00000115318	ENSG00000115318			13869	protein-coding gene	gene with protein product		607163				11386757	Standard	NM_032603		Approved		uc002smp.1	P58215	OTTHUMG00000129953	ENST00000264094.3:c.1899C>T	chr2.hg19:g.74761483G>A		117.0	0.0	.		121.0	20.0	.	NM_032603	D6W5J1|Q2EHP2|Q6IPL7|Q96RS1	Silent	SNP	ENST00000264094.3	hg19	CCDS1953.1																																																																																			.	.	.	none		0.502	LOXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252215.1	NM_032603	
TUBA3D	113457	hgsc.bcm.edu	37	2	132236969	132236969	+	Silent	SNP	G	G	A			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr2:132236969G>A	ENST00000321253.6	+	3	422	c.315G>A	c.(313-315)agG>agA	p.R105R	TUBA3D_ENST00000409047.2_3'UTR	NM_080386.3	NP_525125.2	Q13748	TBA3C_HUMAN	tubulin, alpha 3d	105					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	32				BRCA - Breast invasive adenocarcinoma(221;0.13)		ATTACGCCAGGGGCCATTACA	0.527																																					p.R105R	Ovarian(137;2059 2432 35543 39401)	Atlas-SNP	.											.	TUBA3D	60	.	0			c.G315A						PASS	.						209.0	172.0	184.0					2																	132236969		2203	4300	6503	SO:0001819	synonymous_variant	113457	exon3			CGCCAGGGGCCAT	K03460	CCDS33290.1	2q21.1	2007-03-16			ENSG00000075886	ENSG00000075886		"""Tubulins"""	24071	protein-coding gene	gene with protein product	"""alpha-tubulin isotype H2-alpha"""					3785200	Standard	NM_080386		Approved	H2-ALPHA	uc002tsu.4	Q13748	OTTHUMG00000153600	ENST00000321253.6:c.315G>A	chr2.hg19:g.132236969G>A		273.0	0.0	.		256.0	40.0	.	NM_080386	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Silent	SNP	ENST00000321253.6	hg19	CCDS33290.1																																																																																			.	.	.	none		0.527	TUBA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331800.2	NM_080386	
FIGN	55137	hgsc.bcm.edu	37	2	164466515	164466515	+	Missense_Mutation	SNP	A	A	T			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr2:164466515A>T	ENST00000333129.3	-	3	2141	c.1827T>A	c.(1825-1827)ttT>ttA	p.F609L	FIGN_ENST00000482917.1_5'Flank|FIGN_ENST00000409634.1_Intron	NM_018086.2	NP_060556.2	Q5HY92	FIGN_HUMAN	fidgetin	609					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)			breast(2)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(1)|prostate(2)|skin(1)	47						GTTGCATCAGAAATTCGGTTC	0.458																																					p.F609L		Atlas-SNP	.											.	FIGN	106	.	0			c.T1827A						PASS	.						105.0	99.0	101.0					2																	164466515		1948	4151	6099	SO:0001583	missense	55137	exon3			CATCAGAAATTCG	AK001267	CCDS2221.2	2q24	2010-04-21			ENSG00000182263	ENSG00000182263		"""ATPases / AAA-type"""	13285	protein-coding gene	gene with protein product		605295				11017077	Standard	XM_005246661		Approved		uc002uck.1	Q5HY92	OTTHUMG00000074059	ENST00000333129.3:c.1827T>A	chr2.hg19:g.164466515A>T	ENSP00000333836:p.Phe609Leu	153.0	0.0	.		105.0	23.0	.	NM_018086	B3KWM0|Q9H6M5|Q9NVZ9	Missense_Mutation	SNP	ENST00000333129.3	hg19	CCDS2221.2	.	.	.	.	.	.	.	.	.	.	A	12.72	2.023844	0.35701	.	.	ENSG00000182263	ENST00000333129	D	0.86865	-2.18	5.47	2.81	0.32909	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.055714	0.64402	D	0.000001	T	0.74504	0.3725	N	0.00771	-1.2	0.58432	D	0.999996	B	0.32324	0.364	P	0.51999	0.687	T	0.66767	-0.5840	10	0.21014	T	0.42	-19.2916	5.9791	0.19397	0.6913:0.0:0.3087:0.0	.	609	Q5HY92	FIGN_HUMAN	L	609	ENSP00000333836:F609L	ENSP00000333836:F609L	F	-	3	2	FIGN	164174761	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	1.691000	0.37721	1.009000	0.39289	0.383000	0.25322	TTT	.	.	.	none		0.458	FIGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157220.2	NM_018086	
TTN	7273	hgsc.bcm.edu	37	2	179650403	179650403	+	Missense_Mutation	SNP	T	T	A			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr2:179650403T>A	ENST00000591111.1	-	15	2661	c.2437A>T	c.(2437-2439)Agc>Tgc	p.S813C	TTN_ENST00000359218.5_Missense_Mutation_p.S767C|TTN_ENST00000360870.5_Missense_Mutation_p.S813C|TTN_ENST00000460472.2_Missense_Mutation_p.S767C|TTN_ENST00000589042.1_Missense_Mutation_p.S813C|TTN_ENST00000342175.6_Missense_Mutation_p.S767C|TTN_ENST00000342992.6_Missense_Mutation_p.S813C			Q8WZ42	TITIN_HUMAN	titin	33644					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AAGTGAGGGCTAGCTGTGCGG	0.373																																					p.S813C		Atlas-SNP	.											.	TTN	18412	.	0			c.A2437T						PASS	.						172.0	167.0	169.0					2																	179650403		2203	4300	6503	SO:0001583	missense	7273	exon15			GAGGGCTAGCTGT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.2437A>T	chr2.hg19:g.179650403T>A	ENSP00000465570:p.Ser813Cys	94.0	0.0	.		88.0	16.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	T	12.88	2.071468	0.36566	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.67523	-0.27;-0.03;-0.03;-0.04;0.15	5.51	5.51	0.81932	Ribonuclease H-like (1);	.	.	.	.	T	0.70159	0.3192	L	0.27053	0.805	0.24564	N	0.993953	D;D;D;D;D	0.89917	0.993;0.993;0.993;0.993;1.0	P;P;P;P;D	0.69479	0.628;0.628;0.628;0.628;0.964	T	0.62699	-0.6799	9	0.87932	D	0	.	10.3027	0.43661	0.0:0.0737:0.0:0.9263	.	767;767;767;813;813	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	C	813;767;767;767;767;813	ENSP00000343764:S813C;ENSP00000434586:S767C;ENSP00000340554:S767C;ENSP00000352154:S767C;ENSP00000354117:S813C	ENSP00000340554:S767C	S	-	1	0	TTN	179358648	1.000000	0.71417	0.998000	0.56505	0.978000	0.69477	2.566000	0.45948	2.210000	0.71456	0.533000	0.62120	AGC	.	.	.	none		0.373	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
COL6A3	1293	hgsc.bcm.edu	37	2	238303376	238303376	+	Missense_Mutation	SNP	A	A	G			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr2:238303376A>G	ENST00000295550.4	-	3	1015	c.563T>C	c.(562-564)aTa>aCa	p.I188T	COL6A3_ENST00000472056.1_Intron|COL6A3_ENST00000347401.3_Missense_Mutation_p.I188T|COL6A3_ENST00000346358.4_Missense_Mutation_p.I188T|COL6A3_ENST00000409809.1_Intron|COL6A3_ENST00000353578.4_Intron|COL6A3_ENST00000392003.2_Intron|COL6A3_ENST00000392004.3_Intron	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	188	Nonhelical region.|VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		TTCACTTGCTATTTCTTTTAA	0.433																																					p.I188T		Atlas-SNP	.											.	COL6A3	608	.	0			c.T563C						PASS	.						127.0	124.0	125.0					2																	238303376		2203	4300	6503	SO:0001583	missense	1293	exon3			CTTGCTATTTCTT	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"""Collagens"""	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.563T>C	chr2.hg19:g.238303376A>G	ENSP00000295550:p.Ile188Thr	122.0	0.0	.		85.0	13.0	.	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	hg19	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	A	6.536	0.467096	0.12402	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000346358;ENST00000433762	D;D;D;D	0.84146	-1.81;-1.81;-1.81;-1.81	4.9	3.72	0.42706	von Willebrand factor, type A (3);	0.267710	0.25584	U	0.029678	D	0.88437	0.6436	H	0.94886	3.595	0.47778	D	0.999513	B;B	0.19445	0.009;0.036	B;B	0.20767	0.021;0.031	D	0.85506	0.1194	10	0.62326	D	0.03	.	10.6923	0.45877	0.9233:0.0:0.0766:0.0	.	188;188	E9PCV6;P12111	.;CO6A3_HUMAN	T	188	ENSP00000295550:I188T;ENSP00000315609:I188T;ENSP00000295546:I188T;ENSP00000389539:I188T	ENSP00000295550:I188T	I	-	2	0	COL6A3	237968115	1.000000	0.71417	0.997000	0.53966	0.219000	0.24729	6.121000	0.71602	0.699000	0.31761	0.374000	0.22700	ATA	.	.	.	none		0.433	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
RNPEPL1	57140	hgsc.bcm.edu	37	2	241516157	241516157	+	Silent	SNP	C	C	T			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr2:241516157C>T	ENST00000270357.4	+	9	1616	c.1023C>T	c.(1021-1023)ctC>ctT	p.L341L	RNPEPL1_ENST00000464550.1_3'UTR	NM_018226.4	NP_060696.4	Q9HAU8	RNPL1_HUMAN	arginyl aminopeptidase (aminopeptidase B)-like 1	341					leukotriene biosynthetic process (GO:0019370)		aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(1)|lung(3)|prostate(1)|skin(1)	13		all_epithelial(40;1.13e-11)|Breast(86;0.000169)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.204)|Melanoma(123;0.238)		Epithelial(32;3.05e-31)|all cancers(36;8.2e-29)|OV - Ovarian serous cystadenocarcinoma(60;8.55e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;5.12e-06)|Lung(119;0.00168)|Colorectal(34;0.005)|LUSC - Lung squamous cell carcinoma(224;0.00813)|COAD - Colon adenocarcinoma(134;0.0322)		TGGACCGGCTCCTGGATGGGT	0.687																																					p.L572L		Atlas-SNP	.											.	RNPEPL1	32	.	0			c.C1716T						PASS	.						29.0	33.0	32.0					2																	241516157		2196	4289	6485	SO:0001819	synonymous_variant	57140	exon9			CCGGCTCCTGGAT			2q37.3	2012-03-06			ENSG00000142327	ENSG00000142327			10079	protein-coding gene	gene with protein product		605287				19508204	Standard	NM_018226		Approved		uc002vzi.4	Q9HAU8	OTTHUMG00000133357	ENST00000270357.4:c.1023C>T	chr2.hg19:g.241516157C>T		99.0	0.0	.		83.0	11.0	.	NM_018226	Q5XKC3|Q6NX56|Q96AC9|Q9H033|Q9NVD0	Silent	SNP	ENST00000270357.4	hg19																																																																																				.	.	.	none		0.687	RNPEPL1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000257190.4	NM_018226	
SCAP	22937	hgsc.bcm.edu	37	3	47456625	47456625	+	Silent	SNP	C	C	T			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr3:47456625C>T	ENST00000265565.5	-	19	3514	c.3102G>A	c.(3100-3102)ttG>ttA	p.L1034L	SCAP_ENST00000441517.2_Silent_p.L778L|SCAP_ENST00000545718.1_Silent_p.L641L	NM_012235.2	NP_036367.2	Q12770	SCAP_HUMAN	SREBF chaperone	1034	Interaction with SREBF2. {ECO:0000250}.				aging (GO:0007568)|cholesterol metabolic process (GO:0008203)|negative regulation of cholesterol biosynthetic process (GO:0045541)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|regulation of fatty acid biosynthetic process (GO:0042304)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|SREBP signaling pathway (GO:0032933)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)	unfolded protein binding (GO:0051082)			endometrium(4)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	26				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.00592)|Kidney(197;0.00679)		TGTGGGTCTCCAAGGAGAAGA	0.632																																					p.L1034L	Pancreas(149;978 1908 29304 37806 46700)	Atlas-SNP	.											.	SCAP	88	.	0			c.G3102A						PASS	.						51.0	53.0	52.0					3																	47456625		2202	4299	6501	SO:0001819	synonymous_variant	22937	exon19			GGTCTCCAAGGAG	BC020987	CCDS2755.2	3p21.31	2013-01-10			ENSG00000114650	ENSG00000114650		"""WD repeat domain containing"""	30634	protein-coding gene	gene with protein product	"""SREBP cleavage activating protein"""	601510				8898195, 8724849, 10570913	Standard	XM_005264967		Approved	KIAA0199	uc003crh.1	Q12770	OTTHUMG00000125539	ENST00000265565.5:c.3102G>A	chr3.hg19:g.47456625C>T		65.0	0.0	.		69.0	17.0	.	NM_012235	Q8N2E0|Q8WUA1	Silent	SNP	ENST00000265565.5	hg19	CCDS2755.2																																																																																			.	.	.	none		0.632	SCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246872.2	NM_012235	
C3orf18	51161	hgsc.bcm.edu	37	3	50602964	50602964	+	Missense_Mutation	SNP	G	G	A	rs559763162		TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr3:50602964G>A	ENST00000357203.3	-	3	706	c.167C>T	c.(166-168)aCg>aTg	p.T56M	C3orf18_ENST00000441239.1_Missense_Mutation_p.T56M|C3orf18_ENST00000449241.1_Missense_Mutation_p.T56M|C3orf18_ENST00000486175.1_Intron|C3orf18_ENST00000426034.1_Missense_Mutation_p.T56M	NM_016210.4	NP_057294.2	Q9UK00	CC018_HUMAN	chromosome 3 open reading frame 18	56						integral component of membrane (GO:0016021)				lung(1)|pancreas(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.0175)|Kidney(197;0.0207)		CACGCCGGCCGTGCCACCAGC	0.607																																					p.T56M		Atlas-SNP	.											.	C3orf18	12	.	0			c.C167T						PASS	.						88.0	76.0	80.0					3																	50602964		2202	4300	6502	SO:0001583	missense	51161	exon3			CCGGCCGTGCCAC	AF188706	CCDS2829.1, CCDS54589.1	3p21.3	2006-01-11			ENSG00000088543	ENSG00000088543			24837	protein-coding gene	gene with protein product						12477932	Standard	NM_016210		Approved	G20	uc010hlp.3	Q9UK00	OTTHUMG00000156854	ENST00000357203.3:c.167C>T	chr3.hg19:g.50602964G>A	ENSP00000349732:p.Thr56Met	67.0	0.0	.		65.0	13.0	.	NM_016210	C9JNP0	Missense_Mutation	SNP	ENST00000357203.3	hg19	CCDS2829.1	.	.	.	.	.	.	.	.	.	.	G	10.95	1.495028	0.26774	.	.	ENSG00000088543	ENST00000426034;ENST00000357203;ENST00000449241;ENST00000441239	T;T;T;T	0.42513	2.52;2.52;2.52;0.97	5.24	3.36	0.38483	.	0.821587	0.11279	N	0.580514	T	0.24851	0.0603	N	0.19112	0.55	0.21105	N	0.999781	P;P	0.52577	0.89;0.954	B;B	0.37780	0.258;0.251	T	0.05920	-1.0856	10	0.52906	T	0.07	-12.7022	7.5988	0.28065	0.0:0.3237:0.5385:0.1378	.	56;56	C9JNP0;Q9UK00	.;CC018_HUMAN	M	56	ENSP00000387606:T56M;ENSP00000349732:T56M;ENSP00000404913:T56M;ENSP00000414124:T56M	ENSP00000349732:T56M	T	-	2	0	C3orf18	50577968	0.019000	0.18553	0.001000	0.08648	0.388000	0.30384	2.265000	0.43311	1.193000	0.43086	0.462000	0.41574	ACG	.	.	.	none		0.607	C3orf18-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346260.2	NM_016210	
BBX	56987	hgsc.bcm.edu	37	3	107491690	107491690	+	Missense_Mutation	SNP	G	G	C			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr3:107491690G>C	ENST00000325805.8	+	11	1409	c.1122G>C	c.(1120-1122)gaG>gaC	p.E374D	BBX_ENST00000406780.1_Missense_Mutation_p.E374D|BBX_ENST00000416476.2_Intron|BBX_ENST00000402543.1_Missense_Mutation_p.E374D|BBX_ENST00000415149.2_Missense_Mutation_p.E374D			Q8WY36	BBX_HUMAN	bobby sox homolog (Drosophila)	374					bone development (GO:0060348)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(18)|ovary(4)|pancreas(1)|skin(2)	49			OV - Ovarian serous cystadenocarcinoma(3;0.112)			GAAATTTTGAGGCATTGCAAA	0.323																																					p.E374D		Atlas-SNP	.											.	BBX	156	.	0			c.G1122C						PASS	.						58.0	68.0	64.0					3																	107491690		2203	4298	6501	SO:0001583	missense	56987	exon11			TTTTGAGGCATTG	AF168718	CCDS2950.1, CCDS46881.1, CCDS63712.1	3q13.1	2008-07-18			ENSG00000114439	ENSG00000114439			14422	protein-coding gene	gene with protein product	"""x 001 protein"""					11680820	Standard	NM_001142568		Approved	MDS001, HSPC339, HBP2	uc010hpr.4	Q8WY36	OTTHUMG00000150360	ENST00000325805.8:c.1122G>C	chr3.hg19:g.107491690G>C	ENSP00000319974:p.Glu374Asp	99.0	0.0	.		109.0	48.0	.	NM_001142568	A2RRM7|Q2TAJ1|Q7L3J8|Q7LBY8|Q8NDB0|Q8WY35|Q9H0J6	Missense_Mutation	SNP	ENST00000325805.8	hg19	CCDS46881.1	.	.	.	.	.	.	.	.	.	.	G	4.952	0.176823	0.09443	.	.	ENSG00000114439	ENST00000415149;ENST00000325767;ENST00000402543;ENST00000325805;ENST00000402163;ENST00000406780	D;D;D;D;D	0.98747	-4.6;-4.6;-4.61;-5.11;-4.6	6.16	-0.709	0.11237	.	0.342008	0.33253	N	0.005119	D	0.94486	0.8225	N	0.24115	0.695	0.28521	N	0.91307	B;B;B	0.18461	0.012;0.028;0.009	B;B;B	0.14023	0.004;0.01;0.009	D	0.88666	0.3192	10	0.45353	T	0.12	-10.7263	7.4111	0.27017	0.5975:0.0:0.282:0.1205	.	374;374;374	C9JA69;Q8WY36;Q8WY36-2	.;BBX_HUMAN;.	D	374;225;374;374;374;374	ENSP00000408358:E374D;ENSP00000385317:E374D;ENSP00000319974:E374D;ENSP00000385518:E374D;ENSP00000385530:E374D	ENSP00000319742:E225D	E	+	3	2	BBX	108974380	0.991000	0.36638	0.873000	0.34254	0.130000	0.20726	0.223000	0.17719	-0.449000	0.07117	-1.871000	0.00553	GAG	.	.	.	none		0.323	BBX-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317820.1	NM_020235	
EHHADH	1962	hgsc.bcm.edu	37	3	184922367	184922367	+	Silent	SNP	G	G	A	rs149294851		TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr3:184922367G>A	ENST00000231887.3	-	6	822	c.747C>T	c.(745-747)atC>atT	p.I249I	EHHADH_ENST00000456310.1_Silent_p.I153I	NM_001166415.1|NM_001966.3	NP_001159887.1|NP_001957.2	Q08426	ECHP_HUMAN	enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase	249	Enoyl-CoA hydratase / isomerase.				fatty acid beta-oxidation (GO:0006635)|internal protein amino acid acetylation (GO:0006475)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisome (GO:0005777)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|coenzyme binding (GO:0050662)|dodecenoyl-CoA delta-isomerase activity (GO:0004165)|enoyl-CoA hydratase activity (GO:0004300)|enzyme binding (GO:0019899)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(2)|skin(3)	24	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)			CCTCCTTCTTGATGCCCACTT	0.517																																					p.I249I		Atlas-SNP	.											.	EHHADH	73	.	0			c.C747T						PASS	.						131.0	128.0	129.0					3																	184922367		2203	4300	6503	SO:0001819	synonymous_variant	1962	exon6			CTTCTTGATGCCC	L07077	CCDS33901.1, CCDS54694.1	3q26.3-q28	2012-07-13	2010-04-30		ENSG00000113790	ENSG00000113790	4.2.1.17, 1.1.1.35, 5.3.3.8		3247	protein-coding gene	gene with protein product		607037	"""enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase"""	ECHD		8188243	Standard	NM_001966		Approved		uc003fpf.3	Q08426	OTTHUMG00000156698	ENST00000231887.3:c.747C>T	chr3.hg19:g.184922367G>A		234.0	0.0	.		289.0	88.0	.	NM_001966	A8K6Y3|B4DWG3|D3DNU0|Q58EZ5	Silent	SNP	ENST00000231887.3	hg19	CCDS33901.1																																																																																			.	G|1.000;C|0.000	.	alt		0.517	EHHADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345326.1		
MFSD10	10227	hgsc.bcm.edu	37	4	2934901	2934901	+	Missense_Mutation	SNP	G	G	C			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr4:2934901G>C	ENST00000329687.4	-	3	838	c.304C>G	c.(304-306)Ctg>Gtg	p.L102V	MFSD10_ENST00000514800.1_Missense_Mutation_p.L102V|MFSD10_ENST00000355443.4_Missense_Mutation_p.L102V|NOP14-AS1_ENST00000507999.1_RNA|NOP14-AS1_ENST00000505731.1_RNA|MFSD10_ENST00000508221.1_Missense_Mutation_p.L102V|NOP14-AS1_ENST00000515194.1_RNA|NOP14-AS1_ENST00000512712.2_RNA|MFSD10_ENST00000507555.1_Missense_Mutation_p.L102V	NM_001120.4	NP_001111.3	Q14728	MFS10_HUMAN	major facilitator superfamily domain containing 10	102					apoptotic process (GO:0006915)|tetracycline transport (GO:0015904)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)	tetracycline transporter activity (GO:0008493)			breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|skin(1)	7				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		GGCGCACACAGAAACTGCAGG	0.617																																					p.L102V		Atlas-SNP	.											MFSD10,bladder,carcinoma,0,1	MFSD10	22	.	0			c.C304G						PASS	.						53.0	53.0	53.0					4																	2934901		2202	4299	6501	SO:0001583	missense	10227	exon3			CACACAGAAACTG	L11669	CCDS3365.1	4p16.3	2008-03-03			ENSG00000109736	ENSG00000109736			16894	protein-coding gene	gene with protein product	"""tetracycline transporter like protein"""	610977				8353488, 17362938	Standard	NM_001120		Approved	TETRAN, IT10C3	uc003gfz.3	Q14728	OTTHUMG00000122081	ENST00000329687.4:c.304C>G	chr4.hg19:g.2934901G>C	ENSP00000332646:p.Leu102Val	38.0	0.0	.		54.0	9.0	.	NM_001120	Q07706	Missense_Mutation	SNP	ENST00000329687.4	hg19	CCDS3365.1	.	.	.	.	.	.	.	.	.	.	G	5.826	0.336718	0.11013	.	.	ENSG00000109736	ENST00000514800;ENST00000355443;ENST00000329687;ENST00000508221;ENST00000507555	T;T;T;T;T	0.57107	0.42;0.42;0.42;0.42;0.42	4.19	-0.214	0.13161	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.370891	0.28062	N	0.016760	T	0.33585	0.0868	L	0.45422	1.42	0.20307	N	0.999916	B;B;B;B	0.23735	0.012;0.022;0.09;0.007	B;B;B;B	0.29267	0.042;0.078;0.1;0.032	T	0.09796	-1.0658	10	0.14656	T	0.56	-10.5579	0.8156	0.01102	0.2667:0.3381:0.2238:0.1713	.	102;102;102;102	D6RIZ4;D6RE79;D6RA47;Q14728	.;.;.;MFS10_HUMAN	V	102	ENSP00000426907:L102V;ENSP00000347619:L102V;ENSP00000332646:L102V;ENSP00000425757:L102V;ENSP00000423402:L102V	ENSP00000332646:L102V	L	-	1	2	MFSD10	2904699	0.985000	0.35326	0.153000	0.22517	0.211000	0.24417	0.178000	0.16820	0.045000	0.15804	0.561000	0.74099	CTG	.	.	.	none		0.617	MFSD10-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358072.2	NM_001120	
JAKMIP1	152789	hgsc.bcm.edu	37	4	6066676	6066676	+	Silent	SNP	C	C	T			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr4:6066676C>T	ENST00000282924.5	-	9	1847	c.1362G>A	c.(1360-1362)ttG>ttA	p.L454L	JAKMIP1_ENST00000409371.3_Silent_p.L269L|JAKMIP1_ENST00000457227.2_5'UTR|JAKMIP1_ENST00000409831.1_Silent_p.L454L|JAKMIP1_ENST00000410077.2_Silent_p.L289L|JAKMIP1_ENST00000409021.3_Silent_p.L454L	NM_144720.3	NP_653321.1	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein 1	454	Mediates interaction with TYK2 and GABBR1.				cognition (GO:0050890)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|microtubule (GO:0005874)|ribonucleoprotein complex (GO:0030529)	GABA receptor binding (GO:0050811)|RNA binding (GO:0003723)			NS(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						ATGTTTCGGACAACGTTTCTG	0.488																																					p.L454L		Atlas-SNP	.											.	JAKMIP1	250	.	0			c.G1362A						PASS	.						192.0	163.0	173.0					4																	6066676		2203	4300	6503	SO:0001819	synonymous_variant	152789	exon9			TTCGGACAACGTT	AK056126	CCDS3385.1, CCDS47005.1	4p16.1	2013-10-11	2009-08-13		ENSG00000152969	ENSG00000152969			26460	protein-coding gene	gene with protein product		611195				18941173	Standard	NM_144720		Approved	MARLIN1, JAMIP1, Gababrbp, FLJ31564	uc010idb.1	Q96N16	OTTHUMG00000125491	ENST00000282924.5:c.1362G>A	chr4.hg19:g.6066676C>T		125.0	0.0	.		92.0	6.0	.	NM_001099433	A6H2J2|A6H2J3|A6H2J4|A6H2J5|A8MTK6|B4DHZ8|B8ZZR7|D3DVT0|Q86Y69|Q8N7G3	Silent	SNP	ENST00000282924.5	hg19	CCDS3385.1																																																																																			.	.	.	none		0.488	JAKMIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246816.2	NM_144720	
BOD1L1	259282	hgsc.bcm.edu	37	4	13601157	13601157	+	Missense_Mutation	SNP	A	A	G			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr4:13601157A>G	ENST00000040738.5	-	10	7502	c.7367T>C	c.(7366-7368)cTc>cCc	p.L2456P		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	2456						nucleus (GO:0005634)	DNA binding (GO:0003677)										TGCATTTATGAGGTGTAAAGT	0.468											OREG0016115	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L2456P		Atlas-SNP	.											.	.	.	.	0			c.T7367C						PASS	.						164.0	147.0	153.0					4																	13601157		2203	4300	6503	SO:0001583	missense	259282	exon10			TTTATGAGGTGTA	AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"""family with sequence similarity 44, member A"", ""biorientation of chromosomes in cell division 1-like"""	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.7367T>C	chr4.hg19:g.13601157A>G	ENSP00000040738:p.Leu2456Pro	112.0	0.0	.	688	108.0	5.0	.	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	hg19	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	A	13.05	2.120234	0.37436	.	.	ENSG00000038219	ENST00000040738	T	0.09350	2.99	4.17	-0.642	0.11486	.	0.433636	0.16546	N	0.209707	T	0.06781	0.0173	L	0.27053	0.805	0.09310	N	1	B	0.12630	0.006	B	0.08055	0.003	T	0.30937	-0.9961	10	0.40728	T	0.16	.	8.0002	0.30293	0.597:0.0:0.403:0.0	.	2456	Q8NFC6	BOD1L_HUMAN	P	2456	ENSP00000040738:L2456P	ENSP00000040738:L2456P	L	-	2	0	BOD1L	13210255	0.000000	0.05858	0.003000	0.11579	0.018000	0.09664	0.222000	0.17699	-0.013000	0.14199	0.454000	0.30748	CTC	.	.	.	none		0.468	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894	
KIAA0825	285600	hgsc.bcm.edu	37	5	93856481	93856481	+	Missense_Mutation	SNP	A	A	C			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr5:93856481A>C	ENST00000329378.7	-	5	691	c.442T>G	c.(442-444)Tct>Gct	p.S148A	KIAA0825_ENST00000427991.2_Missense_Mutation_p.S148A|KIAA0825_ENST00000513200.3_Missense_Mutation_p.S148A|KIAA0825_ENST00000312498.7_Missense_Mutation_p.S148A	NM_173665.2	NP_775936.1	Q8IV33	K0825_HUMAN	KIAA0825	148										breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|pancreas(1)|prostate(1)|skin(1)	13						TCTTCAACAGAATGAAGAGAC	0.418																																					p.S148A		Atlas-SNP	.											.	KIAA0825	172	.	0			c.T442G						PASS	.						68.0	68.0	68.0					5																	93856481		2203	4299	6502	SO:0001583	missense	285600	exon5			CAACAGAATGAAG	BX648338	CCDS4070.1	5q15	2011-02-23	2011-02-23	2011-02-23	ENSG00000185261	ENSG00000185261			28532	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 36"""	C5orf36		12477932	Standard	NM_173665		Approved	DKFZp686F0372, MGC34713	uc011cuk.2	Q8IV33	OTTHUMG00000131331	ENST00000329378.7:c.442T>G	chr5.hg19:g.93856481A>C	ENSP00000331385:p.Ser148Ala	55.0	0.0	.		60.0	15.0	.	NM_173665	O94914|Q6ZNN2	Missense_Mutation	SNP	ENST00000329378.7	hg19	CCDS4070.1	.	.	.	.	.	.	.	.	.	.	A	0.007	-1.938185	0.00484	.	.	ENSG00000185261	ENST00000513200;ENST00000427991;ENST00000312498;ENST00000329378	T;T;T;T	0.38077	1.18;1.18;1.16;1.18	5.27	4.16	0.48862	.	1.670800	0.02660	N	0.107410	T	0.19644	0.0472	N	0.11560	0.145	0.21445	N	0.999683	B;B	0.11235	0.001;0.004	B;B	0.08055	0.002;0.003	T	0.37197	-0.9716	10	0.05436	T	0.98	.	6.5441	0.22397	0.4544:0.4284:0.0:0.1172	.	148;148	Q8IV33;Q8IV33-2	K0825_HUMAN;.	A	148	ENSP00000424618:S148A;ENSP00000400288:S148A;ENSP00000312205:S148A;ENSP00000331385:S148A	ENSP00000312205:S148A	S	-	1	0	KIAA0825	93882237	1.000000	0.71417	0.939000	0.37840	0.025000	0.11179	2.208000	0.42797	1.984000	0.57885	0.477000	0.44152	TCT	.	.	.	none		0.418	KIAA0825-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371180.2	NM_173665	
HSD17B4	3295	hgsc.bcm.edu	37	5	118824931	118824931	+	Missense_Mutation	SNP	C	C	T			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr5:118824931C>T	ENST00000256216.6	+	9	800	c.667C>T	c.(667-669)Ctt>Ttt	p.L223F	HSD17B4_ENST00000504811.1_Missense_Mutation_p.L248F|HSD17B4_ENST00000515320.1_Missense_Mutation_p.L205F|HSD17B4_ENST00000414835.2_Missense_Mutation_p.L83F|HSD17B4_ENST00000509514.1_5'UTR|HSD17B4_ENST00000513628.1_Missense_Mutation_p.L86F|HSD17B4_ENST00000510025.1_Missense_Mutation_p.L199F	NM_000414.3	NP_000405.1	P51659	DHB4_HUMAN	hydroxysteroid (17-beta) dehydrogenase 4	223	(3R)-hydroxyacyl-CoA dehydrogenase.				alpha-linolenic acid metabolic process (GO:0036109)|androgen metabolic process (GO:0008209)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|estrogen metabolic process (GO:0008210)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|medium-chain fatty-acyl-CoA metabolic process (GO:0036112)|metabolic process (GO:0008152)|osteoblast differentiation (GO:0001649)|oxidation-reduction process (GO:0055114)|Sertoli cell development (GO:0060009)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)|very long-chain fatty-acyl-CoA metabolic process (GO:0036111)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	17-beta-hydroxysteroid dehydrogenase (NAD+) activity (GO:0044594)|3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity (GO:0033989)|isomerase activity (GO:0016853)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(2)	25		all_cancers(142;0.0206)|Prostate(80;0.0322)		OV - Ovarian serous cystadenocarcinoma(64;0.000247)|Epithelial(69;0.000849)|all cancers(49;0.0122)		ACCTCTTGTCCTTTGGCTTTG	0.378																																					p.L248F	Colon(35;490 801 34689 41394 43344)	Atlas-SNP	.											.	HSD17B4	63	.	0			c.C742T						PASS	.						221.0	214.0	217.0					5																	118824931		2202	4300	6502	SO:0001583	missense	3295	exon10			CTTGTCCTTTGGC		CCDS4126.1, CCDS56378.1, CCDS56379.1	5q2	2011-09-20			ENSG00000133835	ENSG00000133835	4.2.1.107, 1.1.1.35	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	5213	protein-coding gene	gene with protein product	"""17beta-estradiol dehydrogenase type IV"", ""peroxisomal multifunctional protein 2"", ""17-beta-HSD IV"", ""17-beta-hydroxysteroid dehydrogenase 4"", ""D-bifunctional protein, peroxisomal"", ""D-3-hydroxyacyl-CoA dehydratase"", ""3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholest-24-enoyl-CoA hydratase"", ""beta-keto-reductase"", ""beta-hydroxyacyl dehydrogenase"", ""short chain dehydrogenase/reductase family 8C, member 1"""	601860				8938456, 19027726	Standard	NM_000414		Approved	MFE-2, DBP, SDR8C1	uc003ksj.3	P51659	OTTHUMG00000128899	ENST00000256216.6:c.667C>T	chr5.hg19:g.118824931C>T	ENSP00000256216:p.Leu223Phe	87.0	0.0	.		186.0	61.0	.	NM_001199291	B4DNV1|B4DVS5|E9PB82|F5HE57	Missense_Mutation	SNP	ENST00000256216.6	hg19	CCDS4126.1	.	.	.	.	.	.	.	.	.	.	C	17.85	3.490542	0.64074	.	.	ENSG00000133835	ENST00000256216;ENST00000515320;ENST00000510025;ENST00000504811;ENST00000414835;ENST00000513628	D;D;D;D;D;D	0.90955	-2.76;-2.76;-2.76;-2.76;-2.76;-2.76	5.97	5.97	0.96955	NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.95262	0.8463	M	0.87381	2.88	0.80722	D	1	D;P;P;P	0.71674	0.998;0.891;0.746;0.891	D;B;B;B	0.71414	0.973;0.266;0.266;0.194	D	0.94345	0.7574	10	0.39692	T	0.17	-19.2226	13.265	0.60128	0.0:0.9271:0.0:0.0729	.	248;205;199;223	F5HE57;E9PB82;E7EWE5;P51659	.;.;.;DHB4_HUMAN	F	223;205;199;248;83;86	ENSP00000256216:L223F;ENSP00000424613:L205F;ENSP00000424940:L199F;ENSP00000420914:L248F;ENSP00000411960:L83F;ENSP00000425993:L86F	ENSP00000256216:L223F	L	+	1	0	HSD17B4	118852830	0.999000	0.42202	1.000000	0.80357	0.393000	0.30537	3.986000	0.56937	2.834000	0.97654	0.650000	0.86243	CTT	.	.	.	none		0.378	HSD17B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250863.3	NM_000414	
ZNF608	57507	hgsc.bcm.edu	37	5	123980011	123980011	+	Missense_Mutation	SNP	G	G	A			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr5:123980011G>A	ENST00000306315.5	-	5	4484	c.4049C>T	c.(4048-4050)cCt>cTt	p.P1350L	ZNF608_ENST00000513985.1_5'UTR|ZNF608_ENST00000504926.1_Missense_Mutation_p.P923L	NM_020747.2	NP_065798.2	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	1350							metal ion binding (GO:0046872)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(12)|ovary(3)|skin(6)|urinary_tract(1)	46		all_cancers(142;0.186)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783)		CTGTGGGTAAGGATAAGCATG	0.502																																					p.P1350L		Atlas-SNP	.											.	ZNF608	117	.	0			c.C4049T						PASS	.						216.0	161.0	179.0					5																	123980011		2203	4300	6503	SO:0001583	missense	57507	exon5			GGGTAAGGATAAG	AB033107	CCDS34219.1	5q23.2	2008-05-02			ENSG00000168916	ENSG00000168916		"""Zinc fingers, C2H2-type"""	29238	protein-coding gene	gene with protein product						10574462, 10508479	Standard	NM_020747		Approved	KIAA1281, DKFZp434M098, NY-REN-36	uc003ktq.1	Q9ULD9	OTTHUMG00000162999	ENST00000306315.5:c.4049C>T	chr5.hg19:g.123980011G>A	ENSP00000307746:p.Pro1350Leu	86.0	0.0	.		105.0	17.0	.	NM_020747	A7E2W9|Q3SYM6|Q68D12|Q8IY05|Q9Y5A1	Missense_Mutation	SNP	ENST00000306315.5	hg19	CCDS34219.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.704307	0.88924	.	.	ENSG00000168916	ENST00000504926;ENST00000306315	T;T	0.50813	0.78;0.73	5.55	5.55	0.83447	.	0.063529	0.64402	D	0.000002	T	0.68961	0.3058	M	0.65498	2.005	0.80722	D	1	D	0.76494	0.999	D	0.74023	0.982	T	0.70439	-0.4871	10	0.87932	D	0	-13.536	19.8645	0.96799	0.0:0.0:1.0:0.0	.	1350	Q9ULD9	ZN608_HUMAN	L	923;1350	ENSP00000427657:P923L;ENSP00000307746:P1350L	ENSP00000307746:P1350L	P	-	2	0	ZNF608	124007910	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.896000	0.87350	2.766000	0.95052	0.643000	0.83706	CCT	.	.	.	none		0.502	ZNF608-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371300.1	XM_114432	
GPR116	221395	hgsc.bcm.edu	37	6	46867766	46867766	+	Splice_Site	SNP	C	C	A	rs145334563	byFrequency	TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr6:46867766C>A	ENST00000283296.7	-	3	445	c.157G>T	c.(157-159)Gtt>Ttt	p.V53F	GPR116_ENST00000362015.4_Splice_Site_p.V53F|GPR116_ENST00000265417.7_Splice_Site_p.V53F|GPR116_ENST00000456426.2_Splice_Site_p.V53F	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	53					energy reserve metabolic process (GO:0006112)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|neuropeptide signaling pathway (GO:0007218)|regulation of lipid metabolic process (GO:0019216)|surfactant homeostasis (GO:0043129)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(21)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59			Lung(136;0.192)			GTTTACATACCGGCTCGTTTT	0.383																																					p.V53F	NSCLC(59;410 1274 8751 36715 50546)	Atlas-SNP	.											.	GPR116	133	.	0			c.G157T						PASS	.						109.0	98.0	102.0					6																	46867766		2203	4300	6503	SO:0001630	splice_region_variant	221395	exon3			ACATACCGGCTCG	AB018301	CCDS4919.1	6p12.3	2014-08-08			ENSG00000069122	ENSG00000069122		"""-"", ""GPCR / Class B : Orphans"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	19030	protein-coding gene	gene with protein product						12435584	Standard	NM_001098518		Approved	DKFZp564O1923, KIAA0758	uc003oyo.3	Q8IZF2	OTTHUMG00000014793	ENST00000283296.7:c.157+1G>T	chr6.hg19:g.46867766C>A		119.0	0.0	.		100.0	22.0	.	NM_015234	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	Missense_Mutation	SNP	ENST00000283296.7	hg19	CCDS4919.1	.	.	.	.	.	.	.	.	.	.	C	14.20	2.464871	0.43839	.	.	ENSG00000069122	ENST00000452370;ENST00000283296;ENST00000362015;ENST00000456426;ENST00000265417	T;T;T;T	0.29655	1.62;2.0;1.56;1.62	4.96	4.96	0.65561	.	0.286307	0.24695	N	0.036356	T	0.36082	0.0954	M	0.64997	1.995	0.80722	D	1	P;P;P	0.52842	0.956;0.911;0.956	P;P;P	0.56474	0.632;0.799;0.632	T	0.05468	-1.0883	9	.	.	.	-3.8272	14.057	0.64776	0.0:1.0:0.0:0.0	.	53;53;53	A8K0D8;Q8IZF2-3;Q8IZF2	.;.;GP116_HUMAN	F	53	ENSP00000283296:V53F;ENSP00000354563:V53F;ENSP00000412866:V53F;ENSP00000265417:V53F	.	V	-	1	0	GPR116	46975725	0.983000	0.35010	0.886000	0.34754	0.036000	0.12997	3.364000	0.52328	2.479000	0.83701	0.462000	0.41574	GTT	.	C|0.999;T|0.001	.	alt		0.383	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040806.2	NM_015234	Missense_Mutation
COL9A1	1297	hgsc.bcm.edu	37	6	70944522	70944522	+	Missense_Mutation	SNP	C	C	A			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr6:70944522C>A	ENST00000357250.6	-	34	2392	c.2234G>T	c.(2233-2235)gGc>gTc	p.G745V	RP1-149L1.1_ENST00000522264.1_RNA|COL9A1_ENST00000489611.1_5'UTR|COL9A1_ENST00000370499.4_Missense_Mutation_p.G502V|COL9A1_ENST00000320755.7_Missense_Mutation_p.G502V	NM_001851.4	NP_001842.3	P20849	CO9A1_HUMAN	collagen, type IX, alpha 1	745	Collagen-like 8.|Triple-helical region (COL2).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|organ morphogenesis (GO:0009887)|tissue homeostasis (GO:0001894)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(44)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)	80						ACCAGGCAGGCCGGTGGCACC	0.647																																					p.G745V		Atlas-SNP	.											.	COL9A1	228	.	0			c.G2234T						PASS	.						36.0	38.0	37.0					6																	70944522		2203	4300	6503	SO:0001583	missense	1297	exon34			GGCAGGCCGGTGG		CCDS4971.1, CCDS47447.1	6q13	2013-05-07			ENSG00000112280	ENSG00000112280		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2217	protein-coding gene	gene with protein product		120210				1429648	Standard	NM_001851		Approved		uc003pfg.4	P20849	OTTHUMG00000014988	ENST00000357250.6:c.2234G>T	chr6.hg19:g.70944522C>A	ENSP00000349790:p.Gly745Val	55.0	0.0	.		53.0	5.0	.	NM_001851	Q13699|Q13700|Q5TF52|Q6P467|Q96BM8|Q99225|Q9H151|Q9H152|Q9Y6P2|Q9Y6P3	Missense_Mutation	SNP	ENST00000357250.6	hg19	CCDS4971.1	.	.	.	.	.	.	.	.	.	.	C	19.89	3.911377	0.72983	.	.	ENSG00000112280	ENST00000357250;ENST00000320755;ENST00000370499	D;D;D	0.99637	-6.29;-6.29;-6.29	5.74	5.74	0.90152	.	0.149132	0.64402	D	0.000011	D	0.99846	0.9929	H	0.97758	4.07	0.80722	D	1	D;D;P	0.76494	0.999;0.996;0.918	D;D;P	0.75484	0.986;0.941;0.806	D	0.96911	0.9667	10	0.87932	D	0	.	19.9077	0.97014	0.0:1.0:0.0:0.0	.	745;502;294	P20849;P20849-2;B3KWS8	CO9A1_HUMAN;.;.	V	745;502;502	ENSP00000349790:G745V;ENSP00000315252:G502V;ENSP00000359530:G502V	ENSP00000315252:G502V	G	-	2	0	COL9A1	71001243	1.000000	0.71417	0.988000	0.46212	0.907000	0.53573	7.556000	0.82233	2.714000	0.92807	0.585000	0.79938	GGC	.	.	.	none		0.647	COL9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041131.2		
PMS2	5395	hgsc.bcm.edu	37	7	6035170	6035170	+	Missense_Mutation	SNP	C	C	T			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr7:6035170C>T	ENST00000265849.7	-	8	1003	c.898G>A	c.(898-900)Gca>Aca	p.A300T	PMS2_ENST00000441476.2_Missense_Mutation_p.A194T|PMS2_ENST00000406569.3_Missense_Mutation_p.A300T|PMS2_ENST00000469652.1_Intron|PMS2_ENST00000382321.4_Intron	NM_000535.5	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)	300					ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|single base insertion or deletion binding (GO:0032138)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(11)|lung(13)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)		AATACCTTTGCTGGGTCACAA	0.383			"""Mis, N, F"""			"""colorectal, endometrial, ovarian, medulloblastoma, glioma"""		Direct reversal of damage;Mismatch excision repair (MMR)	Turcot syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												p.A300T		Atlas-SNP	.	yes	Rec		"""Hereditary non-polyposis colorectal cancer, Turcot syndrome"""	7	7p22	5395	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)		E	.	PMS2	88	.	0			c.G898A						PASS	.						89.0	84.0	86.0					7																	6035170		2203	4300	6503	SO:0001583	missense	5395	exon8	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	CCTTTGCTGGGTC		CCDS5343.1	7p22.1	2014-09-17	2001-11-28		ENSG00000122512	ENSG00000122512			9122	protein-coding gene	gene with protein product		600259	"""postmeiotic segregation increased (S. cerevisiae) 2"""	PMSL2		8072530	Standard	NM_000535		Approved	H_DJ0042M02.9, HNPCC4	uc003spl.3	P54278	OTTHUMG00000023135	ENST00000265849.7:c.898G>A	chr7.hg19:g.6035170C>T	ENSP00000265849:p.Ala300Thr	95.0	0.0	.		104.0	31.0	.	NM_000535	B2R610|Q52LH6|Q5FBW9|Q5FBX1|Q5FBX2|Q75MR2	Missense_Mutation	SNP	ENST00000265849.7	hg19	CCDS5343.1	.	.	.	.	.	.	.	.	.	.	c	15.72	2.917497	0.52546	.	.	ENSG00000122512	ENST00000265849;ENST00000382322;ENST00000441476;ENST00000406569	D;D;D	0.83992	-1.79;-1.79;-1.79	5.85	4.96	0.65561	Ribosomal protein S5 domain 2-type fold (1);DNA mismatch repair protein, N-terminal (1);Ribosomal protein S5 domain 2-type fold, subgroup (1);DNA mismatch repair protein, C-terminal (1);	0.410133	0.26345	N	0.024920	T	0.73969	0.3655	L	0.49350	1.555	0.42490	D	0.992891	B;B;B	0.34241	0.012;0.068;0.444	B;B;B	0.27262	0.007;0.013;0.078	T	0.69367	-0.5164	10	0.14656	T	0.56	-8.6094	10.6468	0.45626	0.1337:0.7984:0.0:0.0678	.	300;300;194	P54278-3;P54278;C9J167	.;PMS2_HUMAN;.	T	300;253;194;300	ENSP00000265849:A300T;ENSP00000392843:A194T;ENSP00000384308:A300T	ENSP00000265849:A300T	A	-	1	0	PMS2	6001696	0.544000	0.26441	1.000000	0.80357	0.989000	0.77384	0.265000	0.18515	1.469000	0.48083	0.650000	0.86243	GCA	.	.	.	none		0.383	PMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207353.3	NM_000535	
POU6F2	11281	hgsc.bcm.edu	37	7	39446255	39446255	+	Silent	SNP	C	C	T			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr7:39446255C>T	ENST00000403058.1	+	7	1096	c.942C>T	c.(940-942)tcC>tcT	p.S314S	POU6F2_ENST00000559001.1_Intron|POU6F2_ENST00000518318.2_Silent_p.S314S|POU6F2-AS1_ENST00000433519.1_RNA	NM_001166018.1|NM_007252.3	NP_001159490.1|NP_009183.3	P78424	PO6F2_HUMAN	POU class 6 homeobox 2	314	Gln-rich.				central nervous system development (GO:0007417)|ganglion mother cell fate determination (GO:0007402)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	42						CCATGAGCTCCATAGCAAGCT	0.532																																					p.S314S		Atlas-SNP	.											.	POU6F2	117	.	0			c.C942T						PASS	.						57.0	57.0	57.0					7																	39446255		2203	4300	6503	SO:0001819	synonymous_variant	11281	exon7			GAGCTCCATAGCA	U91934	CCDS34620.2, CCDS55103.1	7p14.1	2011-06-20	2007-07-13		ENSG00000106536	ENSG00000106536		"""Homeoboxes / POU class"""	21694	protein-coding gene	gene with protein product	"""Retina-derived POU-domain factor-1"""	609062	"""POU domain, class 6, transcription factor 2"""			8601806	Standard	NM_007252		Approved	RPF-1	uc003thb.2	P78424	OTTHUMG00000150803	ENST00000403058.1:c.942C>T	chr7.hg19:g.39446255C>T		103.0	0.0	.		99.0	31.0	.	NM_007252	A4D1W2|C4AMB9|P78425|Q75ME8|Q86UM6|Q9UDS7	Silent	SNP	ENST00000403058.1	hg19	CCDS34620.2																																																																																			.	.	.	none		0.532	POU6F2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320146.3	NM_007252	
ZMIZ2	83637	hgsc.bcm.edu	37	7	44805818	44805818	+	Silent	SNP	C	C	G			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr7:44805818C>G	ENST00000309315.4	+	17	2421	c.2298C>G	c.(2296-2298)ccC>ccG	p.P766P	ZMIZ2_ENST00000413916.1_Silent_p.P708P|ZMIZ2_ENST00000433667.1_Silent_p.P734P|ZMIZ2_ENST00000265346.7_Silent_p.P740P|ZMIZ2_ENST00000463931.1_3'UTR|ZMIZ2_ENST00000441627.1_Silent_p.P766P	NM_031449.3	NP_113637.3	Q8NF64	ZMIZ2_HUMAN	zinc finger, MIZ-type containing 2	766	Pro-rich.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|zinc ion binding (GO:0008270)			breast(3)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						CCACCACGCCCAGCACCCCAA	0.632																																					p.P766P	NSCLC(20;604 852 1948 16908 50522)	Atlas-SNP	.											.	ZMIZ2	82	.	0			c.C2298G						PASS	.						58.0	66.0	64.0					7																	44805818		1960	4127	6087	SO:0001819	synonymous_variant	83637	exon17			CACGCCCAGCACC	AK090415	CCDS43576.1, CCDS43577.1, CCDS75591.1	7p13	2009-11-06			ENSG00000122515	ENSG00000122515		"""Zinc fingers, MIZ-type"""	22229	protein-coding gene	gene with protein product		611196					Standard	XM_005249866		Approved	KIAA1886, hZIMP7, ZIMP7, DKFZp761I2123, NET27	uc003tlr.3	Q8NF64	OTTHUMG00000155817	ENST00000309315.4:c.2298C>G	chr7.hg19:g.44805818C>G		113.0	0.0	.		138.0	19.0	.	NM_031449	A4D2K7|D3DVL1|O94790|Q0VGB4|Q659A8|Q6JKL5|Q8WTX8|Q96Q01|Q9BQH7	Silent	SNP	ENST00000309315.4	hg19	CCDS43576.1																																																																																			.	.	.	none		0.632	ZMIZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341790.1	NM_031449	
ABCB4	5244	hgsc.bcm.edu	37	7	87051487	87051487	+	Silent	SNP	A	A	G			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr7:87051487A>G	ENST00000265723.4	-	18	2377	c.2266T>C	c.(2266-2268)Ttg>Ctg	p.L756L	ABCB4_ENST00000359206.3_Silent_p.L756L|ABCB4_ENST00000453593.1_Silent_p.L756L|ABCB4_ENST00000545634.1_Silent_p.L756L|ABCB4_ENST00000358400.3_Silent_p.L756L	NM_000443.3|NM_018849.2	NP_000434.1|NP_061337.1	P21439	MDR3_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 4	756	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular lipid metabolic process (GO:0044255)|lipid metabolic process (GO:0006629)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|xenobiotic-transporting ATPase activity (GO:0008559)			breast(5)|endometrium(7)|kidney(2)|large_intestine(15)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				Colchicine(DB01394)|Etravirine(DB06414)|Silodosin(DB06207)	AAGAAAATCAAAGAGAATATG	0.338																																					p.L756L		Atlas-SNP	.											.	ABCB4	177	.	0			c.T2266C						PASS	.						56.0	56.0	56.0					7																	87051487		2203	4300	6503	SO:0001819	synonymous_variant	5244	exon18			AAATCAAAGAGAA	M23234	CCDS5605.1, CCDS5606.1, CCDS5607.1	7q21	2012-03-14			ENSG00000005471	ENSG00000005471		"""ATP binding cassette transporters / subfamily B"""	45	protein-coding gene	gene with protein product		171060		PGY3, MDR3		2892668, 11313316	Standard	NM_018850		Approved	MDR2, PFIC-3, GBD1	uc003uiv.1	P21439	OTTHUMG00000023396	ENST00000265723.4:c.2266T>C	chr7.hg19:g.87051487A>G		59.0	0.0	.		58.0	4.0	.	NM_018850	A0A2V7|A4D1D3|A4D1D4|A4D1D5|D6W5P3|D6W5P4|Q14813	Silent	SNP	ENST00000265723.4	hg19	CCDS5606.1																																																																																			.	.	.	none		0.338	ABCB4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000336083.1	NM_000443	
CYP3A43	64816	hgsc.bcm.edu	37	7	99454477	99454477	+	Missense_Mutation	SNP	C	C	A			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr7:99454477C>A	ENST00000354829.2	+	9	923	c.820C>A	c.(820-822)Cag>Aag	p.Q274K	CYP3A43_ENST00000415413.1_Missense_Mutation_p.Q63K|CYP3A43_ENST00000477658.1_3'UTR|CYP3A43_ENST00000417625.1_Missense_Mutation_p.Q164K|CYP3A43_ENST00000444905.1_Missense_Mutation_p.Q21K|CYP3A43_ENST00000312017.5_Missense_Mutation_p.Q274K|CYP3A43_ENST00000222382.5_Missense_Mutation_p.Q274K|CYP3A43_ENST00000342499.4_Missense_Mutation_p.Q134K	NM_022820.3|NM_057095.1	NP_073731.1|NP_476436.1	Q9HB55	CP343_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 43	274			Missing (in allele CYP3A43*2).		small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(1)	19	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)				Dexamethasone(DB01234)|Dolutegravir(DB08930)|Ethosuximide(DB00593)|Oxazepam(DB00842)|Phenelzine(DB00780)|Praziquantel(DB01058)|Rifampicin(DB01045)|Rifapentine(DB01201)|Testosterone(DB00624)|Troleandomycin(DB01361)|Zalcitabine(DB00943)	TTTCTTTCAACAGATGATCGA	0.438																																					p.Q274K		Atlas-SNP	.											.	CYP3A43	52	.	0			c.C820A						PASS	.						92.0	99.0	97.0					7																	99454477		2203	4300	6503	SO:0001583	missense	64816	exon9			TTTCAACAGATGA	AF319634	CCDS5675.1, CCDS5676.1, CCDS5677.1, CCDS64723.1	7q21.1	2007-12-14	2003-01-14		ENSG00000021461	ENSG00000021461		"""Cytochrome P450s"""	17450	protein-coding gene	gene with protein product		606534	"""cytochrome P450, subfamily IIIA, polypeptide 43"""			11160876, 11266076	Standard	NM_022820		Approved		uc003ury.1	Q9HB55	OTTHUMG00000156498	ENST00000354829.2:c.820C>A	chr7.hg19:g.99454477C>A	ENSP00000346887:p.Gln274Lys	215.0	0.0	.		188.0	18.0	.	NM_057096	Q495Y1|Q75MK2|Q75MK3|Q9HB52|Q9HB53|Q9HB54|Q9HB57	Missense_Mutation	SNP	ENST00000354829.2	hg19	CCDS5676.1	.	.	.	.	.	.	.	.	.	.	C	11.75	1.731904	0.30684	.	.	ENSG00000021461	ENST00000354829;ENST00000417625;ENST00000342499;ENST00000444905;ENST00000415413;ENST00000312017;ENST00000222382	T;T;T;T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28;-0.23;-0.28;-0.28	2.26	0.94	0.19513	.	0.176318	0.37623	U	0.002017	T	0.55625	0.1932	L	0.37697	1.125	0.20873	N	0.999837	B;P;B;B;B	0.39094	0.048;0.659;0.023;0.029;0.012	B;P;B;B;B	0.44732	0.067;0.459;0.006;0.011;0.011	T	0.50742	-0.8792	10	0.87932	D	0	.	4.1559	0.10260	0.0:0.6974:0.0:0.3026	.	164;134;274;274;274	Q495Y1;F8W6L8;Q9HB55-3;Q75MK2;Q9HB55	.;.;.;.;CP343_HUMAN	K	274;164;134;21;63;274;274	ENSP00000346887:Q274K;ENSP00000416581:Q164K;ENSP00000345351:Q134K;ENSP00000405557:Q21K;ENSP00000401521:Q63K;ENSP00000312110:Q274K;ENSP00000222382:Q274K	ENSP00000222382:Q274K	Q	+	1	0	CYP3A43	99292413	0.985000	0.35326	0.730000	0.30809	0.247000	0.25773	0.188000	0.17018	0.257000	0.21650	0.195000	0.17529	CAG	.	.	.	none		0.438	CYP3A43-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000344379.1		
CPA4	51200	hgsc.bcm.edu	37	7	129962495	129962495	+	Silent	SNP	T	T	C			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr7:129962495T>C	ENST00000222482.4	+	11	1273	c.1245T>C	c.(1243-1245)caT>caC	p.H415H	CPA4_ENST00000493259.1_Silent_p.H311H|CPA4_ENST00000445470.2_Silent_p.H382H	NM_016352.3	NP_057436.2	Q9UI42	CBPA4_HUMAN	carboxypeptidase A4	415					histone acetylation (GO:0016573)	extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Melanoma(18;0.0435)					TCATGGAGCATGTGCGGGACA	0.537																																					p.H415H		Atlas-SNP	.											.	CPA4	47	.	0			c.T1245C						PASS	.						198.0	161.0	173.0					7																	129962495		2203	4300	6503	SO:0001819	synonymous_variant	51200	exon11			GGAGCATGTGCGG	AF095719	CCDS5818.1, CCDS55163.1	7q32	2008-07-18			ENSG00000128510	ENSG00000128510			15740	protein-coding gene	gene with protein product	"""carboxypeptidase A3"""	607635				10383164, 10860668	Standard	NM_016352		Approved	CPA3	uc003vpr.3	Q9UI42	OTTHUMG00000157825	ENST00000222482.4:c.1245T>C	chr7.hg19:g.129962495T>C		159.0	0.0	.		188.0	39.0	.	NM_016352	B7Z576|Q86UY9	Silent	SNP	ENST00000222482.4	hg19	CCDS5818.1																																																																																			.	.	.	none		0.537	CPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349725.1	NM_016352	
CPA4	51200	hgsc.bcm.edu	37	7	129962499	129962499	+	Missense_Mutation	SNP	C	C	T			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr7:129962499C>T	ENST00000222482.4	+	11	1277	c.1249C>T	c.(1249-1251)Cgg>Tgg	p.R417W	CPA4_ENST00000493259.1_Missense_Mutation_p.R313W|CPA4_ENST00000445470.2_Missense_Mutation_p.R384W	NM_016352.3	NP_057436.2	Q9UI42	CBPA4_HUMAN	carboxypeptidase A4	417					histone acetylation (GO:0016573)	extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Melanoma(18;0.0435)					GGAGCATGTGCGGGACAACCT	0.542																																					p.R417W		Atlas-SNP	.											.	CPA4	47	.	0			c.C1249T						PASS	.						193.0	157.0	169.0					7																	129962499		2203	4300	6503	SO:0001583	missense	51200	exon11			CATGTGCGGGACA	AF095719	CCDS5818.1, CCDS55163.1	7q32	2008-07-18			ENSG00000128510	ENSG00000128510			15740	protein-coding gene	gene with protein product	"""carboxypeptidase A3"""	607635				10383164, 10860668	Standard	NM_016352		Approved	CPA3	uc003vpr.3	Q9UI42	OTTHUMG00000157825	ENST00000222482.4:c.1249C>T	chr7.hg19:g.129962499C>T	ENSP00000222482:p.Arg417Trp	154.0	0.0	.		185.0	42.0	.	NM_016352	B7Z576|Q86UY9	Missense_Mutation	SNP	ENST00000222482.4	hg19	CCDS5818.1	.	.	.	.	.	.	.	.	.	.	C	13.60	2.286285	0.40494	.	.	ENSG00000128510	ENST00000445470;ENST00000222482;ENST00000538687;ENST00000493259	T;T;T	0.03468	3.92;3.92;3.92	5.75	2.87	0.33458	.	0.218110	0.40908	D	0.000989	T	0.13970	0.0338	M	0.79475	2.455	0.09310	N	1	D;D	0.89917	0.999;1.0	P;D	0.65443	0.827;0.935	T	0.01956	-1.1240	10	0.56958	D	0.05	.	9.1872	0.37178	0.2596:0.6719:0.0:0.0685	.	384;417	B7Z576;Q9UI42	.;CBPA4_HUMAN	W	384;417;222;313	ENSP00000412947:R384W;ENSP00000222482:R417W;ENSP00000419660:R313W	ENSP00000222482:R417W	R	+	1	2	CPA4	129749735	0.000000	0.05858	0.981000	0.43875	0.111000	0.19643	0.043000	0.13971	0.763000	0.33175	0.563000	0.77884	CGG	.	.	.	none		0.542	CPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349725.1	NM_016352	
AKR1B15	441282	hgsc.bcm.edu	37	7	134260620	134260620	+	Silent	SNP	C	C	T	rs267601304		TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr7:134260620C>T	ENST00000457545.2	+	8	944	c.684C>T	c.(682-684)tgC>tgT	p.C228C	AKR1B15_ENST00000423958.1_Silent_p.C200C	NM_001080538.2	NP_001074007.2	C9JRZ8	AK1BF_HUMAN	aldo-keto reductase family 1, member B15	228							oxidoreductase activity (GO:0016491)			endometrium(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|urinary_tract(1)	18						TCCAGTACTGCCACTCCAAGG	0.532																																					p.C228C		Atlas-SNP	.											.	AKR1B15	105	.	0			c.C684T						PASS	.						111.0	88.0	96.0					7																	134260620		2203	4300	6503	SO:0001819	synonymous_variant	441282	exon8			GTACTGCCACTCC		CCDS47715.1, CCDS47715.2	7q33	2009-09-09			ENSG00000227471	ENSG00000227471		"""Aldo-keto reductases"""	37281	protein-coding gene	gene with protein product							Standard	NM_001080538		Approved		uc011kpr.2	C9JRZ8	OTTHUMG00000155376	ENST00000457545.2:c.684C>T	chr7.hg19:g.134260620C>T		129.0	0.0	.		105.0	20.0	.	NM_001080538	C9J3V2	Silent	SNP	ENST00000457545.2	hg19	CCDS47715.2																																																																																			.	.	.	none		0.532	AKR1B15-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339726.2		
SVOPL	136306	hgsc.bcm.edu	37	7	138281232	138281232	+	Missense_Mutation	SNP	G	G	A			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr7:138281232G>A	ENST00000419765.3	-	14	1430	c.1397C>T	c.(1396-1398)tCa>tTa	p.S466L	SVOPL_ENST00000421622.1_Missense_Mutation_p.S346L|SVOPL_ENST00000288513.5_Missense_Mutation_p.S314L|SVOPL_ENST00000463557.1_5'UTR|SVOPL_ENST00000436657.1_Missense_Mutation_p.S314L	NM_001139456.1	NP_001132928.1	Q8N434	SVOPL_HUMAN	SVOP-like	466						integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	19						ACAGACAGATGAGAAGAGACA	0.463																																					p.S466L		Atlas-SNP	.											.	SVOPL	111	.	0			c.C1397T						PASS	.						117.0	111.0	113.0					7																	138281232		2203	4300	6503	SO:0001583	missense	136306	exon14			ACAGATGAGAAGA	BC036796	CCDS5848.1, CCDS47721.1	7q34	2011-07-12	2007-04-04		ENSG00000157703	ENSG00000157703			27034	protein-coding gene	gene with protein product		611700	"""SV2 related protein homolog (rat)-like"""				Standard	NM_001139456		Approved	MGC46715	uc011kqh.2	Q8N434	OTTHUMG00000155870	ENST00000419765.3:c.1397C>T	chr7.hg19:g.138281232G>A	ENSP00000405482:p.Ser466Leu	80.0	0.0	.		107.0	14.0	.	NM_001139456		Missense_Mutation	SNP	ENST00000419765.3	hg19	CCDS47721.1	.	.	.	.	.	.	.	.	.	.	G	12.07	1.826903	0.32329	.	.	ENSG00000157703	ENST00000288513;ENST00000421622;ENST00000436657;ENST00000419765	T;T;T;T	0.58210	0.35;0.35;0.35;0.35	5.48	5.48	0.80851	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.260251	0.37483	N	0.002067	T	0.40145	0.1105	N	0.22421	0.69	0.35878	D	0.828749	B;B	0.33171	0.012;0.4	B;B	0.28011	0.055;0.085	T	0.51317	-0.8721	10	0.45353	T	0.12	-3.3112	17.1313	0.86727	0.0:0.0:1.0:0.0	.	466;314	Q8N434;Q8N434-2	SVOPL_HUMAN;.	L	314;346;314;466	ENSP00000288513:S314L;ENSP00000412830:S346L;ENSP00000417018:S314L;ENSP00000405482:S466L	ENSP00000288513:S314L	S	-	2	0	SVOPL	137931772	1.000000	0.71417	0.821000	0.32701	0.024000	0.10985	5.924000	0.70054	2.563000	0.86464	0.655000	0.94253	TCA	.	.	.	none		0.463	SVOPL-005	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342092.4	NM_174959	
ZNF777	27153	hgsc.bcm.edu	37	7	149152518	149152518	+	Missense_Mutation	SNP	A	A	T			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr7:149152518A>T	ENST00000247930.4	-	2	919	c.596T>A	c.(595-597)cTg>cAg	p.L199Q		NM_015694.2	NP_056509.2	Q9ULD5	ZN777_HUMAN	zinc finger protein 777	199					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(5)|lung(17)|ovary(1)|skin(2)|urinary_tract(1)	26	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			CTGGGCCTCCAGCTTCCTCTC	0.597																																					p.L199Q		Atlas-SNP	.											.	ZNF777	63	.	0			c.T596A						PASS	.						67.0	76.0	73.0					7																	149152518		2188	4291	6479	SO:0001583	missense	27153	exon2			GCCTCCAGCTTCC	AB033111	CCDS43675.1	7q36.1	2013-01-08			ENSG00000196453	ENSG00000196453		"""Zinc fingers, C2H2-type"", ""-"""	22213	protein-coding gene	gene with protein product							Standard	NM_015694		Approved	KIAA1285	uc003wfv.3	Q9ULD5	OTTHUMG00000158967	ENST00000247930.4:c.596T>A	chr7.hg19:g.149152518A>T	ENSP00000247930:p.Leu199Gln	204.0	0.0	.		209.0	46.0	.	NM_015694	Q8N2R2|Q8N659	Missense_Mutation	SNP	ENST00000247930.4	hg19	CCDS43675.1	.	.	.	.	.	.	.	.	.	.	A	19.31	3.802961	0.70682	.	.	ENSG00000196453	ENST00000247930	T	0.06294	3.32	4.93	4.93	0.64822	.	0.234968	0.21936	N	0.066956	T	0.06554	0.0168	N	0.08118	0	0.33892	D	0.637431	D	0.54207	0.965	P	0.51355	0.667	T	0.32322	-0.9911	10	0.72032	D	0.01	-14.7997	11.0022	0.47614	1.0:0.0:0.0:0.0	.	199	Q9ULD5-2	.	Q	199	ENSP00000247930:L199Q	ENSP00000247930:L199Q	L	-	2	0	ZNF777	148783451	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	5.489000	0.66875	1.856000	0.53863	0.533000	0.62120	CTG	.	.	.	none		0.597	ZNF777-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352708.1	NM_015694	
TSNARE1	203062	hgsc.bcm.edu	37	8	143381927	143381927	+	Missense_Mutation	SNP	C	C	G			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr8:143381927C>G	ENST00000307180.3	-	10	1327	c.1210G>C	c.(1210-1212)Gag>Cag	p.E404Q	TSNARE1_ENST00000519651.1_Missense_Mutation_p.E185Q|TSNARE1_ENST00000524325.1_Missense_Mutation_p.E403Q|TSNARE1_ENST00000518928.1_5'UTR|TSNARE1_ENST00000520166.1_Missense_Mutation_p.E404Q	NM_145003.3	NP_659440.2	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1	404					intracellular protein transport (GO:0006886)|synaptic vesicle exocytosis (GO:0016079)	integral component of membrane (GO:0016021)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)			breast(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(6)|ovary(2)|stomach(2)|urinary_tract(1)	20	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					AGCGCCTGCTCCTGGCCCTGC	0.617																																					p.E404Q		Atlas-SNP	.											.	TSNARE1	59	.	0			c.G1210C						PASS	.						73.0	66.0	69.0					8																	143381927		2203	4300	6503	SO:0001583	missense	203062	exon10			CCTGCTCCTGGCC			8q24.3	2005-08-18							26437	protein-coding gene	gene with protein product						14702039	Standard	XM_005250828		Approved	FLJ31164	uc003ywk.3	Q96NA8		ENST00000307180.3:c.1210G>C	chr8.hg19:g.143381927C>G	ENSP00000303437:p.Glu404Gln	109.0	0.0	.		103.0	14.0	.	NM_145003	B7ZLB0|Q14D03	Missense_Mutation	SNP	ENST00000307180.3	hg19	CCDS6384.1	.	.	.	.	.	.	.	.	.	.	C	7.933	0.741084	0.15642	.	.	ENSG00000171045	ENST00000524325;ENST00000307180;ENST00000520166;ENST00000519651	T;T;T;T	0.20463	2.07;2.07;2.07;2.07	4.76	3.89	0.44902	t-SNARE (1);	0.233173	0.21158	U	0.079203	T	0.16214	0.0390	L	0.37630	1.12	0.23254	N	0.998034	P;B;P;P	0.47409	0.895;0.421;0.895;0.895	B;B;B;B	0.41299	0.353;0.058;0.353;0.353	T	0.08351	-1.0726	10	0.27082	T	0.32	-20.6332	10.2182	0.43182	0.0:0.9055:0.0:0.0945	.	403;185;404;405	B7ZLB0;E5RHT3;Q96NA8;A0AVG3	.;.;TSNA1_HUMAN;.	Q	403;404;404;185	ENSP00000428763:E403Q;ENSP00000303437:E404Q;ENSP00000427770:E404Q;ENSP00000429679:E185Q	ENSP00000303437:E404Q	E	-	1	0	TSNARE1	143379834	0.970000	0.33590	0.175000	0.22980	0.206000	0.24218	1.184000	0.32053	1.001000	0.39076	-0.137000	0.14449	GAG	.	.	.	none		0.617	TSNARE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_145003	
TSTD2	158427	hgsc.bcm.edu	37	9	100368460	100368460	+	Missense_Mutation	SNP	G	G	T			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr9:100368460G>T	ENST00000341170.4	-	7	1301	c.919C>A	c.(919-921)Ctt>Att	p.L307I	TSTD2_ENST00000354801.2_Missense_Mutation_p.L47I	NM_139246.4	NP_640339.4	Q5T7W7	TSTD2_HUMAN	thiosulfate sulfurtransferase (rhodanese)-like domain containing 2	307	Rhodanese. {ECO:0000255|PROSITE- ProRule:PRU00173}.							p.L307I(1)		large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	15						CAATCAAGAAGGATAGTATCA	0.353																																					p.L307I		Atlas-SNP	.											TSTD2,NS,carcinoma,0,1	TSTD2	42	.	1	Substitution - Missense(1)	ovary(1)	c.C919A						PASS	.						117.0	116.0	117.0					9																	100368460		2203	4300	6503	SO:0001583	missense	158427	exon7			CAAGAAGGATAGT	AF258575	CCDS6727.2	9q22.33	2013-09-20	2009-08-12	2009-08-12	ENSG00000136925	ENSG00000136925			30087	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 97"""	C9orf97		12477932	Standard	NM_139246		Approved	PP4189	uc004axn.3	Q5T7W7	OTTHUMG00000020328	ENST00000341170.4:c.919C>A	chr9.hg19:g.100368460G>T	ENSP00000342499:p.Leu307Ile	103.0	0.0	.		72.0	9.0	.	NM_139246	A6NMJ4|A8K584|Q6ZQZ6|Q8IYM3|Q8WY73|Q96ML6|Q96MU1	Missense_Mutation	SNP	ENST00000341170.4	hg19	CCDS6727.2	.	.	.	.	.	.	.	.	.	.	G	14.49	2.552202	0.45487	.	.	ENSG00000136925	ENST00000375172;ENST00000341170;ENST00000375165;ENST00000354801	T;T;T	0.27104	1.69;1.69;1.69	5.18	3.31	0.37934	Rhodanese-like (5);	0.066943	0.64402	N	0.000014	T	0.17916	0.0430	L	0.41492	1.28	0.32895	D	0.512421	B;B	0.33477	0.013;0.413	B;B	0.35607	0.032;0.206	T	0.14172	-1.0482	10	0.20046	T	0.44	-5.0176	5.6795	0.17767	0.1448:0.0:0.666:0.1892	.	81;307	B3KVC7;Q5T7W7	.;TSTD2_HUMAN	I	81;307;47;47	ENSP00000342499:L307I;ENSP00000364308:L47I;ENSP00000346856:L47I	ENSP00000342499:L307I	L	-	1	0	TSTD2	99408281	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	1.989000	0.40707	1.490000	0.48466	0.655000	0.94253	CTT	.	.	.	none		0.353	TSTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053325.4	NM_139246	
HSPA5	3309	hgsc.bcm.edu	37	9	128001454	128001454	+	Silent	SNP	A	A	G			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr9:128001454A>G	ENST00000324460.6	-	5	965	c.762T>C	c.(760-762)ggT>ggC	p.G254G	RP11-65N13.8_ENST00000468244.1_RNA	NM_005347.4	NP_005338.1	P11021	GRP78_HUMAN	heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa)	254					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cellular response to antibiotic (GO:0071236)|cellular response to glucose starvation (GO:0042149)|cellular response to interleukin-4 (GO:0071353)|cerebellar Purkinje cell layer development (GO:0021680)|cerebellum structural organization (GO:0021589)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|maintenance of protein localization in endoplasmic reticulum (GO:0035437)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cell migration (GO:0030335)|positive regulation of protein ubiquitination (GO:0031398)|regulation of protein folding in endoplasmic reticulum (GO:0060904)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum chaperone complex (GO:0034663)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|chaperone binding (GO:0051087)|enzyme binding (GO:0019899)|glycoprotein binding (GO:0001948)|misfolded protein binding (GO:0051787)|protein domain specific binding (GO:0019904)|ribosome binding (GO:0043022)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(4)|prostate(2)|skin(1)	23					Acetylsalicylic acid(DB00945)|Antihemophilic Factor(DB00025)	AGTCTTCTCCACCCAGATGAG	0.468										Prostate(1;0.17)																											p.G254G		Atlas-SNP	.											.	HSPA5	41	.	0			c.T762C						PASS	.						58.0	57.0	57.0					9																	128001454		2203	4300	6503	SO:0001819	synonymous_variant	3309	exon5			TTCTCCACCCAGA		CCDS6863.1	9q33.3	2011-09-02	2002-08-29		ENSG00000044574	ENSG00000044574		"""Heat shock proteins / HSP70"""	5238	protein-coding gene	gene with protein product		138120	"""heat shock 70kD protein 5 (glucose-regulated protein, 78kD)"""	GRP78			Standard	NM_005347		Approved	BiP	uc004bpn.3	P11021	OTTHUMG00000020672	ENST00000324460.6:c.762T>C	chr9.hg19:g.128001454A>G		68.0	0.0	.		52.0	7.0	.	NM_005347	B0QZ61|Q2EF78|Q9NPF1|Q9UK02	Silent	SNP	ENST00000324460.6	hg19	CCDS6863.1																																																																																			.	.	.	none		0.468	HSPA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054062.1		
PKN3	29941	hgsc.bcm.edu	37	9	131476565	131476565	+	Missense_Mutation	SNP	C	C	A			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr9:131476565C>A	ENST00000291906.4	+	11	1795	c.1402C>A	c.(1402-1404)Ccg>Acg	p.P468T		NM_013355.3	NP_037487.2	Q6P5Z2	PKN3_HUMAN	protein kinase N3	468	Pro-rich.				epithelial cell migration (GO:0010631)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24						CTGCAGCTCCCCGAGCACAAT	0.647																																					p.P468T		Atlas-SNP	.											.	PKN3	62	.	0			c.C1402A						PASS	.						62.0	70.0	67.0					9																	131476565		2203	4300	6503	SO:0001583	missense	29941	exon11			AGCTCCCCGAGCA	AB019692	CCDS6908.1	9q34.13	2008-02-05			ENSG00000160447	ENSG00000160447			17999	protein-coding gene	gene with protein product		610714				10441506	Standard	NM_013355		Approved	PKNbeta	uc004bvw.3	Q6P5Z2	OTTHUMG00000020757	ENST00000291906.4:c.1402C>A	chr9.hg19:g.131476565C>A	ENSP00000291906:p.Pro468Thr	243.0	0.0	.		240.0	42.0	.	NM_013355	Q9UM03	Missense_Mutation	SNP	ENST00000291906.4	hg19	CCDS6908.1	.	.	.	.	.	.	.	.	.	.	C	6.729	0.503216	0.12822	.	.	ENSG00000160447	ENST00000291906	T	0.27256	1.68	5.3	4.36	0.52297	.	.	.	.	.	T	0.22742	0.0549	L	0.51422	1.61	0.26351	N	0.977203	P	0.42827	0.791	B	0.40901	0.343	T	0.05616	-1.0874	9	0.09590	T	0.72	.	11.1984	0.48726	0.3181:0.6818:0.0:0.0	.	468	Q6P5Z2	PKN3_HUMAN	T	468	ENSP00000291906:P468T	ENSP00000291906:P468T	P	+	1	0	PKN3	130516386	0.031000	0.19500	0.911000	0.35937	0.516000	0.34256	1.330000	0.33781	2.478000	0.83669	0.563000	0.77884	CCG	.	.	.	none		0.647	PKN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054487.1	NM_013355	
ZER1	10444	hgsc.bcm.edu	37	9	131512978	131512978	+	Missense_Mutation	SNP	A	A	G			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr9:131512978A>G	ENST00000291900.2	-	8	1682	c.1276T>C	c.(1276-1278)Tac>Cac	p.Y426H	ZER1_ENST00000494461.1_5'Flank|snoU13_ENST00000459043.1_RNA	NM_006336.2	NP_006327.2	Q7Z7L7	ZER1_HUMAN	zyg-11 related, cell cycle regulator	426					protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein transferase activity (GO:0051438)	Cul2-RING ubiquitin ligase complex (GO:0031462)	ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	15						TCTGAGCGGTACTCGGAATTT	0.562																																					p.Y426H		Atlas-SNP	.											.	ZER1	49	.	0			c.T1276C						PASS	.						102.0	89.0	94.0					9																	131512978		2203	4300	6503	SO:0001583	missense	10444	exon8			AGCGGTACTCGGA	X99802	CCDS6910.1	9q33.3	2013-01-17	2012-12-10	2007-01-04	ENSG00000160445	ENSG00000160445		"""ZYG11 cell cycle regulator family"""	30960	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 60"", ""zyg-11 homolog B (C. elegans)-like"", ""zer-1 homolog (C. elegans)"""	C9orf60, ZYG11BL		11719588	Standard	NM_006336		Approved	ZYG, Hzyg	uc004bwa.2	Q7Z7L7	OTTHUMG00000020759	ENST00000291900.2:c.1276T>C	chr9.hg19:g.131512978A>G	ENSP00000291900:p.Tyr426His	82.0	0.0	.		100.0	16.0	.	NM_006336	O00156|Q5T272|Q5T273	Missense_Mutation	SNP	ENST00000291900.2	hg19	CCDS6910.1	.	.	.	.	.	.	.	.	.	.	A	12.92	2.082101	0.36758	.	.	ENSG00000160445	ENST00000291900	T	0.06218	3.33	4.35	4.35	0.52113	Armadillo-like helical (1);Armadillo-type fold (1);	0.146987	0.47455	D	0.000229	T	0.07234	0.0183	L	0.44542	1.39	0.58432	D	0.999999	B	0.26258	0.145	B	0.31191	0.125	T	0.29181	-1.0020	10	0.15499	T	0.54	-31.0091	12.8828	0.58026	1.0:0.0:0.0:0.0	.	426	Q7Z7L7	ZER1_HUMAN	H	426	ENSP00000291900:Y426H	ENSP00000291900:Y426H	Y	-	1	0	ZER1	130552799	1.000000	0.71417	1.000000	0.80357	0.583000	0.36354	8.478000	0.90428	1.832000	0.53329	0.383000	0.25322	TAC	.	.	.	none		0.562	ZER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054491.1	NM_006336	
AKR1C3	8644	hgsc.bcm.edu	37	10	5139633	5139633	+	Missense_Mutation	SNP	C	C	G			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr10:5139633C>G	ENST00000380554.3	+	3	912	c.260C>G	c.(259-261)tCc>tGc	p.S87C	AKR1C3_ENST00000439082.2_5'UTR|AKR1C3_ENST00000470862.2_3'UTR|AKR1C3_ENST00000605149.1_Missense_Mutation_p.S64C	NM_001253908.1|NM_003739.5	NP_001240837.1|NP_003730.4	P42330	AK1C3_HUMAN	aldo-keto reductase family 1, member C3	87					arachidonic acid metabolic process (GO:0019369)|cellular response to cadmium ion (GO:0071276)|cellular response to calcium ion (GO:0071277)|cellular response to corticosteroid stimulus (GO:0071384)|cellular response to jasmonic acid stimulus (GO:0071395)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to reactive oxygen species (GO:0034614)|cellular response to starvation (GO:0009267)|cyclooxygenase pathway (GO:0019371)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|farnesol catabolic process (GO:0016488)|G-protein coupled receptor signaling pathway (GO:0007186)|keratinocyte differentiation (GO:0030216)|male gonad development (GO:0008584)|multicellular organismal macromolecule metabolic process (GO:0044259)|negative regulation of retinoic acid biosynthetic process (GO:1900053)|oxidation-reduction process (GO:0055114)|phototransduction, visible light (GO:0007603)|positive regulation of cell death (GO:0010942)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|progesterone metabolic process (GO:0042448)|prostaglandin metabolic process (GO:0006693)|protein import into nucleus, translocation (GO:0000060)|regulation of retinoic acid receptor signaling pathway (GO:0048385)|regulation of testosterone biosynthetic process (GO:2000224)|renal absorption (GO:0070293)|response to nutrient (GO:0007584)|response to prostaglandin (GO:0034694)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity (GO:0047020)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|aldo-keto reductase (NADP) activity (GO:0004033)|androsterone dehydrogenase activity (GO:0047023)|delta4-3-oxosteroid 5beta-reductase activity (GO:0047787)|dihydrotestosterone 17-beta-dehydrogenase activity (GO:0035410)|geranylgeranyl reductase activity (GO:0045550)|indanol dehydrogenase activity (GO:0047718)|ketoreductase activity (GO:0045703)|ketosteroid monooxygenase activity (GO:0047086)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|phenanthrene 9,10-monooxygenase activity (GO:0018636)|prostaglandin D2 11-ketoreductase activity (GO:0036131)|prostaglandin F receptor activity (GO:0004958)|prostaglandin-F synthase activity (GO:0047017)|retinal dehydrogenase activity (GO:0001758)|retinol dehydrogenase activity (GO:0004745)|testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)|testosterone dehydrogenase (NAD+) activity (GO:0047035)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|skin(1)	14					Bimatoprost(DB00905)|Doxorubicin(DB00997)	CAGCTTTGGTCCACTTTTCAT	0.393																																					p.S87C		Atlas-SNP	.											.	AKR1C3	21	.	0			c.C260G						PASS	.						134.0	128.0	130.0					10																	5139633		2203	4300	6503	SO:0001583	missense	8644	exon3			TTTGGTCCACTTT	L43839	CCDS7063.1, CCDS73062.1	10p15-p14	2012-12-04	2012-12-04		ENSG00000196139	ENSG00000196139	1.1.1.213, 1.1.1.188	"""Aldo-keto reductases"""	386	protein-coding gene	gene with protein product	"""dihydrodiol dehydrogenase X"", ""prostaglandin F synthase"", ""3-alpha hydroxysteroid dehydrogenase, type II"""	603966	"""hydroxysteroid (17-beta) dehydrogenase 5"", ""aldo-keto reductase family 1, member C3 (3-alpha hydroxysteroid dehydrogenase, type II)"""	HSD17B5		7650035, 9792917	Standard	NM_003739		Approved	KIAA0119, DDX, HAKRB, PGFS	uc021pml.1	P42330	OTTHUMG00000017585	ENST00000380554.3:c.260C>G	chr10.hg19:g.5139633C>G	ENSP00000369927:p.Ser87Cys	137.0	0.0	.		134.0	28.0	.	NM_001253908	A8K2V0|B4DL37|Q5T2L1|Q96DJ1|Q96KI8|Q99530|Q9UCX1|Q9UII3|Q9UKL9	Missense_Mutation	SNP	ENST00000380554.3	hg19	CCDS7063.1	.	.	.	.	.	.	.	.	.	.	C	0.010	-1.788233	0.00628	.	.	ENSG00000196139	ENST00000380554	T	0.26373	1.74	1.93	-3.27	0.05048	NADP-dependent oxidoreductase domain (3);	1.227770	0.05968	N	0.641929	T	0.11153	0.0272	N	0.11651	0.15	0.58432	D	0.999999	B;B	0.15473	0.011;0.013	B;B	0.23852	0.049;0.048	T	0.47045	-0.9147	10	0.05833	T	0.94	.	7.0923	0.25291	0.0:0.392:0.4898:0.1181	.	87;87	B4DKT3;P42330	.;AK1C3_HUMAN	C	87	ENSP00000369927:S87C	ENSP00000369927:S87C	S	+	2	0	AKR1C3	5129633	0.000000	0.05858	0.013000	0.15412	0.934000	0.57294	-1.103000	0.03329	-0.933000	0.03737	-0.458000	0.05436	TCC	.	.	.	none		0.393	AKR1C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046533.2	NM_003739	
IL15RA	3601	hgsc.bcm.edu	37	10	6008174	6008174	+	Missense_Mutation	SNP	T	T	C			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr10:6008174T>C	ENST00000379977.3	-	2	314	c.217A>G	c.(217-219)Acg>Gcg	p.T73A	IL15RA_ENST00000528354.1_Missense_Mutation_p.T73A|IL15RA_ENST00000525219.2_Missense_Mutation_p.T37A|IL15RA_ENST00000397248.2_Missense_Mutation_p.T37A|IL15RA_ENST00000397250.2_Intron|IL15RA_ENST00000534292.1_5'UTR|IL15RA_ENST00000397255.3_Missense_Mutation_p.T73A|IL15RA_ENST00000530685.1_Missense_Mutation_p.T73A|IL15RA_ENST00000397251.3_Intron|IL15RA_ENST00000379971.1_Intron			Q13261	I15RA_HUMAN	interleukin 15 receptor, alpha	73	Sushi. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|JAK-STAT cascade (GO:0007259)|negative regulation of neuron projection development (GO:0010977)|positive regulation of natural killer cell differentiation (GO:0032825)|response to nutrient levels (GO:0031667)|signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|signal transducer activity (GO:0004871)			cervix(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	5						ACGCACTCCGTCAGGCTGGAC	0.557																																					p.T159A		Atlas-SNP	.											.	IL15RA	17	.	0			c.A475G						PASS	.						91.0	78.0	82.0					10																	6008174		2203	4300	6503	SO:0001583	missense	3601	exon3			ACTCCGTCAGGCT	U31628	CCDS7074.1, CCDS7075.1, CCDS7075.2, CCDS58069.1, CCDS73065.1	10p15.1	2012-02-27			ENSG00000134470	ENSG00000134470		"""Interleukins and interleukin receptors"", ""CD molecules"""	5978	protein-coding gene	gene with protein product		601070				8530383	Standard	NM_002189		Approved	CD215, IL-15RA	uc021pmo.1	Q13261	OTTHUMG00000017612	ENST00000379977.3:c.217A>G	chr10.hg19:g.6008174T>C	ENSP00000369312:p.Thr73Ala	65.0	0.0	.		40.0	6.0	.	NM_001256765	B4E2C2|Q3B769|Q5JVA1|Q5JVA2|Q5JVA4|Q6B0J2|Q7LDR4|Q7Z609	Missense_Mutation	SNP	ENST00000379977.3	hg19	CCDS7074.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.76|15.76	2.927337|2.927337	0.52759|0.52759	.|.	.|.	ENSG00000134470|ENSG00000134470	ENST00000397246;ENST00000379977;ENST00000397248;ENST00000319465;ENST00000528354;ENST00000530685;ENST00000397255;ENST00000429135;ENST00000453922|ENST00000532039	T;T;T;T;T;T;T;T|.	0.29397|.	1.92;1.57;1.57;1.92;1.92;1.57;1.92;1.57|.	4.8|4.8	4.8|4.8	0.61643|0.61643	Complement control module (2);Sushi/SCR/CCP (2);|.	0.149436|.	0.43747|.	D|.	0.000539|.	T|.	0.47414|.	0.1444|.	L|L	0.57536|0.57536	1.79|1.79	0.24971|0.24971	N|N	0.991666|0.991666	D;D|.	0.64830|.	0.994;0.994|.	P;P|.	0.61328|.	0.887;0.887|.	T|.	0.38714|.	-0.9648|.	10|.	0.51188|.	T|.	0.08|.	-16.2672|-16.2672	10.7393|10.7393	0.46143|0.46143	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	73;73|.	Q13261-3;Q13261|.	.;I15RA_HUMAN|.	A|W	37;73;37;37;73;73;73;73;37|43	ENSP00000380420:T37A;ENSP00000369312:T73A;ENSP00000380421:T37A;ENSP00000435454:T73A;ENSP00000435995:T73A;ENSP00000380426:T73A;ENSP00000395113:T73A;ENSP00000405107:T37A|.	ENSP00000322245:T37A|.	T|X	-|-	1|3	0|0	IL15RA|IL15RA	6048180|6048180	0.998000|0.998000	0.40836|0.40836	0.968000|0.968000	0.41197|0.41197	0.304000|0.304000	0.27724|0.27724	3.427000|3.427000	0.52785|0.52785	1.783000|1.783000	0.52377|0.52377	0.379000|0.379000	0.24179|0.24179	ACG|TGA	.	.	.	none		0.557	IL15RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046615.2	NM_172200, NM_002189	
VDAC2	7417	hgsc.bcm.edu	37	10	76980587	76980587	+	Missense_Mutation	SNP	C	C	T			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr10:76980587C>T	ENST00000332211.6	+	7	656	c.443C>T	c.(442-444)gCa>gTa	p.A148V	VDAC2_ENST00000313132.4_Missense_Mutation_p.A163V|VDAC2_ENST00000543351.1_Missense_Mutation_p.A148V|VDAC2_ENST00000535553.1_Missense_Mutation_p.A109V|VDAC2_ENST00000472137.1_3'UTR	NM_003375.3	NP_003366.2	P45880	VDAC2_HUMAN	voltage-dependent anion channel 2	148					anion transport (GO:0006820)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of protein polymerization (GO:0032272)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|pore complex (GO:0046930)	nucleotide binding (GO:0000166)|porin activity (GO:0015288)|voltage-gated anion channel activity (GO:0008308)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|lung(1)|ovary(1)|pancreas(2)|prostate(1)|urinary_tract(1)	10	all_cancers(46;0.0642)|all_epithelial(25;0.00604)|Prostate(51;0.0112)|Ovarian(15;0.183)				Dihydroxyaluminium(DB01375)	GCTGGACCTGCAATCCATGGT	0.418																																					p.A163V		Atlas-SNP	.											.	VDAC2	27	.	0			c.C488T						PASS	.						97.0	95.0	95.0					10																	76980587		2203	4297	6500	SO:0001583	missense	7417	exon8			GACCTGCAATCCA	BC000165	CCDS7348.1, CCDS53544.1	10q22	2011-11-15			ENSG00000165637	ENSG00000165637		"""Voltage-dependent anion channels"""	12672	protein-coding gene	gene with protein product		193245				7517385, 10049775	Standard	NM_003375		Approved		uc021ptp.1	P45880	OTTHUMG00000018517	ENST00000332211.6:c.443C>T	chr10.hg19:g.76980587C>T	ENSP00000361686:p.Ala148Val	165.0	0.0	.		129.0	20.0	.	NM_001184783	Q5VWK1|Q5VWK3|Q6IB40|Q7L3J5|Q9BWK8|Q9Y5I6	Missense_Mutation	SNP	ENST00000332211.6	hg19	CCDS7348.1	.	.	.	.	.	.	.	.	.	.	C	14.32	2.501060	0.44455	.	.	ENSG00000165637	ENST00000298468;ENST00000543351;ENST00000344036;ENST00000332211;ENST00000535553;ENST00000313132;ENST00000447677	T;T;T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02;1.02;1.02	5.48	5.48	0.80851	.	0.050056	0.85682	D	0.000000	T	0.26304	0.0642	N	0.05441	-0.05	0.58432	D	0.999999	B;B;B	0.21520	0.025;0.036;0.057	B;B;B	0.22880	0.019;0.036;0.042	T	0.10474	-1.0628	10	0.12766	T	0.61	.	19.3533	0.94401	0.0:1.0:0.0:0.0	.	109;163;148	B4DKM5;P45880-1;P45880	.;.;VDAC2_HUMAN	V	148;148;148;148;109;163;148	ENSP00000298468:A148V;ENSP00000443092:A148V;ENSP00000344876:A148V;ENSP00000361686:A148V;ENSP00000445901:A109V;ENSP00000361635:A163V;ENSP00000401492:A148V	ENSP00000298468:A148V	A	+	2	0	VDAC2	76650593	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.013000	0.70776	2.588000	0.87417	0.563000	0.77884	GCA	.	.	.	none		0.418	VDAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048792.1	NM_003375	
BTAF1	9044	hgsc.bcm.edu	37	10	93773747	93773747	+	Missense_Mutation	SNP	A	A	T			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr10:93773747A>T	ENST00000265990.6	+	32	4853	c.4545A>T	c.(4543-4545)aaA>aaT	p.K1515N	BTAF1_ENST00000544642.1_Missense_Mutation_p.K343N	NM_003972.2	NP_003963.1	O14981	BTAF1_HUMAN	BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170kDa	1515					negative regulation of chromatin binding (GO:0035562)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(2)|urinary_tract(6)	59		Colorectal(252;0.0846)				TTCCACCTAAAATTATTCAAG	0.368																																					p.K1515N		Atlas-SNP	.											.	BTAF1	148	.	0			c.A4545T						PASS	.						134.0	144.0	140.0					10																	93773747		2203	4300	6503	SO:0001583	missense	9044	exon32			ACCTAAAATTATT	AJ001017	CCDS7419.1	10q22-q23	2013-05-01	2013-05-01		ENSG00000095564	ENSG00000095564			17307	protein-coding gene	gene with protein product	"""Mot1 homolog (S. cerevisiae)"""	605191	"""BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170 kD (Mot1 homolog, S. cerevisiae)"""			9342322, 9488487	Standard	NM_003972		Approved	TAFII170, TAF172, MOT1, TAF-172, TAF(II)170	uc001khr.3	O14981	OTTHUMG00000018752	ENST00000265990.6:c.4545A>T	chr10.hg19:g.93773747A>T	ENSP00000265990:p.Lys1515Asn	262.0	0.0	.		184.0	23.0	.	NM_003972	B4E0W6|O43578	Missense_Mutation	SNP	ENST00000265990.6	hg19	CCDS7419.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.299734	0.81136	.	.	ENSG00000095564	ENST00000265990;ENST00000544642;ENST00000538688	D;D	0.94723	-3.5;-3.5	5.8	5.8	0.92144	SNF2-related (1);	0.050554	0.85682	D	0.000000	D	0.98726	0.9572	H	0.99719	4.725	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99525	1.0959	10	0.87932	D	0	-21.227	16.2031	0.82102	1.0:0.0:0.0:0.0	.	1515	O14981	BTAF1_HUMAN	N	1515;343;365	ENSP00000265990:K1515N;ENSP00000439924:K343N	ENSP00000265990:K1515N	K	+	3	2	BTAF1	93763727	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.660000	0.68018	2.231000	0.72958	0.524000	0.50904	AAA	.	.	.	none		0.368	BTAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049380.4	NM_003972	
PSD	5662	hgsc.bcm.edu	37	10	104176443	104176443	+	Missense_Mutation	SNP	G	G	C			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr10:104176443G>C	ENST00000020673.5	-	2	879	c.353C>G	c.(352-354)cCt>cGt	p.P118R	PSD_ENST00000492902.2_5'Flank|PSD_ENST00000406432.1_Missense_Mutation_p.P118R	NM_001270966.1|NM_002779.4	NP_001257895.1|NP_002770.3	A5PKW4	PSD1_HUMAN	pleckstrin and Sec7 domain containing	118	Pro-rich.				neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)|signal transducer activity (GO:0004871)			breast(4)|endometrium(2)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				Epithelial(162;1.27e-08)|all cancers(201;2.85e-07)		CCCTGGAGCAGGTAGCCCATT	0.657																																					p.P118R		Atlas-SNP	.											.	PSD	164	.	0			c.C353G						PASS	.						29.0	33.0	32.0					10																	104176443		2203	4296	6499	SO:0001583	missense	5662	exon3			GGAGCAGGTAGCC	X99688	CCDS31272.1, CCDS73187.1	10q24	2013-01-10	2004-04-28		ENSG00000059915	ENSG00000059915		"""Pleckstrin homology (PH) domain containing"""	9507	protein-coding gene	gene with protein product		602327	"""pleckstrin and Sec7 domain protein"""			9417912	Standard	NM_002779		Approved	KIAA2011, TYL, PSD1	uc009xxd.2	A5PKW4	OTTHUMG00000018954	ENST00000020673.5:c.353C>G	chr10.hg19:g.104176443G>C	ENSP00000020673:p.Pro118Arg	90.0	0.0	.		81.0	17.0	.	NM_001270965	B1AKX7|D3DR87|Q15673|Q8IVG0	Missense_Mutation	SNP	ENST00000020673.5	hg19	CCDS31272.1	.	.	.	.	.	.	.	.	.	.	G	18.29	3.592108	0.66219	.	.	ENSG00000059915	ENST00000020673;ENST00000406432	T;T	0.28666	1.6;1.6	4.36	4.36	0.52297	.	0.109296	0.37483	N	0.002079	T	0.30665	0.0772	N	0.08118	0	0.35207	D	0.774816	D	0.62365	0.991	P	0.58013	0.831	T	0.51068	-0.8752	10	0.66056	D	0.02	.	15.5617	0.76253	0.0:0.0:1.0:0.0	.	118	A5PKW4	PSD1_HUMAN	R	118	ENSP00000020673:P118R;ENSP00000384830:P118R	ENSP00000020673:P118R	P	-	2	0	PSD	104166433	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	2.473000	0.45145	2.375000	0.81037	0.561000	0.74099	CCT	.	.	.	none		0.657	PSD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050041.2		
BRSK2	9024	hgsc.bcm.edu	37	11	1459605	1459605	+	Missense_Mutation	SNP	G	G	A			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr11:1459605G>A	ENST00000528841.1	+	3	640	c.256G>A	c.(256-258)Gaa>Aaa	p.E86K	BRSK2_ENST00000308230.5_Missense_Mutation_p.E86K|BRSK2_ENST00000382179.1_Missense_Mutation_p.E132K|BRSK2_ENST00000531197.1_Missense_Mutation_p.E86K|BRSK2_ENST00000528710.1_Missense_Mutation_p.E26K|BRSK2_ENST00000526678.1_Missense_Mutation_p.E86K|BRSK2_ENST00000308219.9_Missense_Mutation_p.E86K			Q8IWQ3	BRSK2_HUMAN	BR serine/threonine kinase 2	86	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|axonogenesis (GO:0007409)|establishment of cell polarity (GO:0030010)|exocytosis (GO:0006887)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mitotic nuclear division (GO:0007067)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			endometrium(4)|large_intestine(1)|lung(5)	10		all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00144)|Lung(200;0.0713)|LUSC - Lung squamous cell carcinoma(625;0.0842)		CGACGTTTATGAAAACAAAAA	0.567																																					p.E132K		Atlas-SNP	.											.	BRSK2	97	.	0			c.G394A						PASS	.						94.0	104.0	101.0					11																	1459605		2156	4273	6429	SO:0001583	missense	9024	exon3			GTTTATGAAAACA	AF020089	CCDS41590.1, CCDS58106.1, CCDS58107.1, CCDS58108.1, CCDS60696.1	11p15.5	2008-02-05	2003-09-11	2005-01-27	ENSG00000174672	ENSG00000174672			11405	protein-coding gene	gene with protein product	"""serine/threonine kinase 29"""	609236	"""chromsosome 11 open reading frame 7"""	C11orf7, STK29		9852686, 9929968	Standard	NM_001256629		Approved	PEN11B	uc001ltm.4	Q8IWQ3	OTTHUMG00000167089	ENST00000528841.1:c.256G>A	chr11.hg19:g.1459605G>A	ENSP00000432000:p.Glu86Lys	136.0	0.0	.		127.0	15.0	.	NM_001256630	B3KVE9|E9PLM7|O60843|O95099|Q5J5B4|Q6ZMQ4|Q8TB60	Missense_Mutation	SNP	ENST00000528841.1	hg19	CCDS58107.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.766637	0.90020	.	.	ENSG00000174672	ENST00000308219;ENST00000531197;ENST00000308230;ENST00000528841;ENST00000526678;ENST00000528596;ENST00000524702;ENST00000528710;ENST00000382179	T;T;T;T;T;T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21;-0.21;-0.21;-0.21;-0.21;-0.21	2.57	2.57	0.30868	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.063288	0.64402	U	0.000008	T	0.78457	0.4286	M	0.71581	2.175	0.80722	D	1	P;D;B;D;D	0.71674	0.64;0.998;0.411;0.966;0.958	P;D;B;D;P	0.78314	0.602;0.991;0.354;0.923;0.875	T	0.81289	-0.1000	10	0.87932	D	0	.	12.2615	0.54652	0.0:0.0:1.0:0.0	.	86;132;86;86;86	Q8IWQ3-4;Q8IWQ3-5;Q8IWQ3-3;Q8IWQ3;Q8IWQ3-2	.;.;.;BRSK2_HUMAN;.	K	86;86;86;86;86;26;26;26;132	ENSP00000310697:E86K;ENSP00000431152:E86K;ENSP00000310805:E86K;ENSP00000432000:E86K;ENSP00000433370:E86K;ENSP00000434075:E26K;ENSP00000432672:E26K;ENSP00000433235:E26K;ENSP00000371614:E132K	ENSP00000310697:E86K	E	+	1	0	BRSK2	1416181	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.575000	0.74018	1.455000	0.47813	0.313000	0.20887	GAA	.	.	.	none		0.567	BRSK2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393033.1	NM_003957	
FBXO3	26273	hgsc.bcm.edu	37	11	33770334	33770334	+	Missense_Mutation	SNP	G	G	T			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr11:33770334G>T	ENST00000265651.3	-	9	1055	c.1037C>A	c.(1036-1038)cCt>cAt	p.P346H	FBXO3_ENST00000534136.1_Missense_Mutation_p.P346H|FBXO3_ENST00000448981.2_Missense_Mutation_p.P346H|FBXO3_ENST00000531080.1_Missense_Mutation_p.P33H|FBXO3_ENST00000532057.1_Missense_Mutation_p.P33H|FBXO3_ENST00000526785.1_Missense_Mutation_p.P233H|FBXO3_ENST00000530401.1_Missense_Mutation_p.P341H	NM_012175.3	NP_036307.2	Q9UK99	FBX3_HUMAN	F-box protein 3	346	ApaG. {ECO:0000255|PROSITE- ProRule:PRU00412}.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|pancreas(1)|stomach(1)	13		Lung NSC(402;0.0804)		BRCA - Breast invasive adenocarcinoma(625;0.00315)|Lung(977;0.00488)|LUSC - Lung squamous cell carcinoma(625;0.008)		AACTACTCCAGGTCCTTGAAC	0.368																																					p.P346H		Atlas-SNP	.											.	FBXO3	37	.	0			c.C1037A						PASS	.						103.0	102.0	102.0					11																	33770334		2202	4298	6500	SO:0001583	missense	26273	exon9			ACTCCAGGTCCTT	AK001943	CCDS7887.1, CCDS44566.1	11p13	2006-07-07	2004-06-15		ENSG00000110429	ENSG00000110429		"""F-boxes /  ""other"""""	13582	protein-coding gene	gene with protein product		609089	"""F-box only protein 3"""			10531037	Standard	NM_033406		Approved	FBX3, FBA	uc001muz.3	Q9UK99	OTTHUMG00000166244	ENST00000265651.3:c.1037C>A	chr11.hg19:g.33770334G>T	ENSP00000265651:p.Pro346His	103.0	0.0	.		79.0	17.0	.	NM_012175	B3KY16|D3DR05|Q86X90|Q9H0V2|Q9NUX2	Missense_Mutation	SNP	ENST00000265651.3	hg19	CCDS7887.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.768020	0.90020	.	.	ENSG00000110429	ENST00000526785;ENST00000265651;ENST00000530401;ENST00000531080;ENST00000532057;ENST00000534136;ENST00000448981	T;T;T;T;T	0.47869	0.84;0.83;0.86;0.86;0.87	5.61	5.61	0.85477	ApaG domain (4);	0.000000	0.85682	D	0.000000	T	0.70859	0.3272	M	0.77486	2.375	0.80722	D	1	P;P;D	0.89917	0.936;0.936;1.0	P;P;D	0.77004	0.64;0.64;0.989	T	0.69636	-0.5092	10	0.41790	T	0.15	-16.4467	19.6304	0.95699	0.0:0.0:1.0:0.0	.	341;346;346	Q9UK99-3;Q9UK99-2;Q9UK99	.;.;FBX3_HUMAN	H	233;346;341;33;33;346;346	ENSP00000435680:P233H;ENSP00000265651:P346H;ENSP00000433781:P341H;ENSP00000431745:P346H;ENSP00000408836:P346H	ENSP00000265651:P346H	P	-	2	0	FBXO3	33726910	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.230000	0.95299	2.663000	0.90544	0.491000	0.48974	CCT	.	.	.	none		0.368	FBXO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388665.1	NM_012175	
USP5	8078	hgsc.bcm.edu	37	12	6968684	6968684	+	Missense_Mutation	SNP	C	C	T			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr12:6968684C>T	ENST00000229268.8	+	9	1161	c.1109C>T	c.(1108-1110)aCc>aTc	p.T370I	USP5_ENST00000389231.5_Missense_Mutation_p.T370I	NM_001098536.1	NP_001092006.1	P45974	UBP5_HUMAN	ubiquitin specific peptidase 5 (isopeptidase T)	370	USP.				positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)	lysosome (GO:0005764)	cysteine-type endopeptidase activity (GO:0004197)|omega peptidase activity (GO:0008242)|ubiquitin thiolesterase activity (GO:0004221)|zinc ion binding (GO:0008270)			breast(6)|endometrium(4)|kidney(2)|large_intestine(6)|lung(14)|skin(2)|urinary_tract(2)	36						ACGGACCCTACCCAGGATTTC	0.562																																					p.T370I		Atlas-SNP	.											.	USP5	124	.	0			c.C1109T						PASS	.						91.0	83.0	86.0					12																	6968684		2203	4300	6503	SO:0001583	missense	8078	exon9			ACCCTACCCAGGA	U35116	CCDS31733.1, CCDS41743.1	12p13	2007-03-02	2005-08-08		ENSG00000111667	ENSG00000111667		"""Ubiquitin-specific peptidases"""	12628	protein-coding gene	gene with protein product		601447	"""ubiquitin specific protease 5 (isopeptidase T)"""			12838346, 8723724	Standard	NM_003481		Approved	IsoT	uc001qri.4	P45974	OTTHUMG00000169233	ENST00000229268.8:c.1109C>T	chr12.hg19:g.6968684C>T	ENSP00000229268:p.Thr370Ile	124.0	0.0	.		116.0	27.0	.	NM_003481	D3DUS7|D3DUS8|Q96J22	Missense_Mutation	SNP	ENST00000229268.8	hg19	CCDS41743.1	.	.	.	.	.	.	.	.	.	.	C	31	5.072808	0.93950	.	.	ENSG00000111667	ENST00000229268;ENST00000389231	T;T	0.29655	1.56;1.56	5.38	5.38	0.77491	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.046637	0.85682	D	0.000000	T	0.56232	0.1971	M	0.74546	2.27	0.80722	D	1	D;P	0.57899	0.981;0.534	D;P	0.66497	0.944;0.454	T	0.51560	-0.8690	10	0.39692	T	0.17	-8.4151	19.3333	0.94303	0.0:1.0:0.0:0.0	.	370;370	P45974;P45974-2	UBP5_HUMAN;.	I	370	ENSP00000229268:T370I;ENSP00000373883:T370I	ENSP00000229268:T370I	T	+	2	0	USP5	6838945	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.609000	0.82925	2.793000	0.96121	0.655000	0.94253	ACC	.	.	.	none		0.562	USP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402982.1		
CGRRF1	10668	hgsc.bcm.edu	37	14	55005042	55005042	+	Missense_Mutation	SNP	G	G	C			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr14:55005042G>C	ENST00000216420.7	+	6	1072	c.940G>C	c.(940-942)Gaa>Caa	p.E314Q		NM_006568.2	NP_006559.1	Q99675	CGRF1_HUMAN	cell growth regulator with ring finger domain 1	314					cell cycle arrest (GO:0007050)|negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|lung(5)|ovary(2)|stomach(1)	13						GTTTGTTCAGGAATCTTTTGC	0.423																																					p.E314Q		Atlas-SNP	.											.	CGRRF1	30	.	0			c.G940C						PASS	.						97.0	89.0	92.0					14																	55005042		2203	4300	6503	SO:0001583	missense	10668	exon6			GTTCAGGAATCTT	BC015063	CCDS9719.1	14q22.2	2013-09-20			ENSG00000100532	ENSG00000100532		"""RING-type (C3HC4) zinc fingers"""	15528	protein-coding gene	gene with protein product		606138				8968090	Standard	NM_006568		Approved	CGR19, RNF197	uc001xay.3	Q99675	OTTHUMG00000140308	ENST00000216420.7:c.940G>C	chr14.hg19:g.55005042G>C	ENSP00000216420:p.Glu314Gln	82.0	0.0	.		89.0	4.0	.	NM_006568	Q96BX2	Missense_Mutation	SNP	ENST00000216420.7	hg19	CCDS9719.1	.	.	.	.	.	.	.	.	.	.	G	19.56	3.850667	0.71719	.	.	ENSG00000100532	ENST00000216420	T	0.67523	-0.27	5.23	3.42	0.39159	Zinc finger, RING/FYVE/PHD-type (1);	0.046947	0.85682	D	0.000000	T	0.60064	0.2240	N	0.25094	0.71	0.43088	D	0.994752	D	0.54601	0.967	P	0.52159	0.691	T	0.57329	-0.7830	10	0.33141	T	0.24	-14.1511	11.656	0.51318	0.143:0.0:0.857:0.0	.	314	Q99675	CGRF1_HUMAN	Q	314	ENSP00000216420:E314Q	ENSP00000216420:E314Q	E	+	1	0	CGRRF1	54074792	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	7.236000	0.78154	0.794000	0.33899	0.462000	0.41574	GAA	.	.	.	none		0.423	CGRRF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276905.2	NM_006568	
CLMN	79789	hgsc.bcm.edu	37	14	95670344	95670344	+	Missense_Mutation	SNP	C	C	T			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr14:95670344C>T	ENST00000298912.4	-	9	1455	c.1342G>A	c.(1342-1344)Ggg>Agg	p.G448R		NM_024734.3	NP_079010.2	Q96JQ2	CLMN_HUMAN	calmin (calponin-like, transmembrane)	448					negative regulation of cell proliferation (GO:0008285)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(17)|prostate(3)|skin(3)	44				Epithelial(152;0.193)		CTTGGGCTCCCTTCAAAGCAA	0.483																																					p.G448R		Atlas-SNP	.											.	CLMN	103	.	0			c.G1342A						PASS	.						87.0	82.0	84.0					14																	95670344		2203	4300	6503	SO:0001583	missense	79789	exon9			GGCTCCCTTCAAA	AB033014	CCDS9933.1	14q32.13	2012-10-02			ENSG00000165959	ENSG00000165959			19972	protein-coding gene	gene with protein product		611121				11386753	Standard	NM_024734		Approved	FLJ12383, KIAA1188, KIAA0500	uc001yef.2	Q96JQ2	OTTHUMG00000171629	ENST00000298912.4:c.1342G>A	chr14.hg19:g.95670344C>T	ENSP00000298912:p.Gly448Arg	109.0	0.0	.		102.0	22.0	.	NM_024734	B2RAR7|Q9H713|Q9HA23|Q9HA57|Q9UFP4|Q9ULN2	Missense_Mutation	SNP	ENST00000298912.4	hg19	CCDS9933.1	.	.	.	.	.	.	.	.	.	.	C	11.56	1.673672	0.29693	.	.	ENSG00000165959	ENST00000298912	D	0.94537	-3.45	5.63	3.66	0.41972	.	0.000000	0.38837	N	0.001556	D	0.90896	0.7139	M	0.66939	2.045	0.18873	N	0.999986	P	0.37122	0.583	B	0.32342	0.144	D	0.86083	0.1545	10	0.87932	D	0	.	5.9466	0.19221	0.3449:0.5687:0.0:0.0864	.	448	Q96JQ2	CLMN_HUMAN	R	448	ENSP00000298912:G448R	ENSP00000298912:G448R	G	-	1	0	CLMN	94740097	0.137000	0.22531	0.209000	0.23619	0.021000	0.10359	0.357000	0.20199	1.337000	0.45525	0.655000	0.94253	GGG	.	.	.	none		0.483	CLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414518.2		
SPTBN5	51332	hgsc.bcm.edu	37	15	42149779	42149779	+	Missense_Mutation	SNP	C	C	G			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr15:42149779C>G	ENST00000320955.6	-	50	8583	c.8356G>C	c.(8356-8358)Gcc>Ccc	p.A2786P		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	2786					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		ACCTCACAGGCCTTCTGGAGC	0.652																																					p.A2751P		Atlas-SNP	.											.	SPTBN5	171	.	0			c.G8251C						PASS	.						28.0	34.0	32.0					15																	42149779		2004	4170	6174	SO:0001583	missense	51332	exon50			CACAGGCCTTCTG	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"""beta V spectrin"""	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.8356G>C	chr15.hg19:g.42149779C>G	ENSP00000317790:p.Ala2786Pro	21.0	0.0	.		23.0	8.0	.	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	hg19		.	.	.	.	.	.	.	.	.	.	.	15.93	2.979532	0.53827	.	.	ENSG00000137877	ENST00000320955	T	0.39787	1.06	4.2	3.28	0.37604	.	0.000000	0.56097	D	0.000023	T	0.62720	0.2451	M	0.78049	2.395	0.19300	N	0.99998	D	0.89917	1.0	D	0.77004	0.989	T	0.56463	-0.7975	10	0.72032	D	0.01	.	12.048	0.53491	0.0:0.916:0.0:0.084	.	2786	Q9NRC6	SPTN5_HUMAN	P	2786	ENSP00000317790:A2786P	ENSP00000317790:A2786P	A	-	1	0	SPTBN5	39937071	0.983000	0.35010	0.020000	0.16555	0.009000	0.06853	2.620000	0.46410	0.977000	0.38444	0.467000	0.42956	GCC	.	.	.	none		0.652	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
SALL1	6299	hgsc.bcm.edu	37	16	51172851	51172851	+	Silent	SNP	A	A	G			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr16:51172851A>G	ENST00000251020.4	-	2	3315	c.3282T>C	c.(3280-3282)caT>caC	p.H1094H	SALL1_ENST00000541611.1_Intron|SALL1_ENST00000566102.1_Intron|SALL1_ENST00000440970.1_Silent_p.H997H	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	1094					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			GAGGAGAAACATGCACGAAGC	0.572																																					p.H1094H	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											.	SALL1	301	.	0			c.T3282C						PASS	.						116.0	104.0	108.0					16																	51172851		2198	4300	6498	SO:0001819	synonymous_variant	6299	exon2			AGAAACATGCACG	X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"""Zinc fingers, C2H2-type"""	10524	protein-coding gene	gene with protein product		602218	"""sal (Drosophila)-like 1"", ""sal-like 1 (Drosophila)"""	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.3282T>C	chr16.hg19:g.51172851A>G		96.0	0.0	.		123.0	18.0	.	NM_002968	Q99881|Q9NSC3|Q9P1R0	Silent	SNP	ENST00000251020.4	hg19	CCDS10747.1																																																																																			.	.	.	none		0.572	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968	
FAM65A	79567	hgsc.bcm.edu	37	16	67577079	67577079	+	Missense_Mutation	SNP	T	T	A			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr16:67577079T>A	ENST00000379312.3	+	13	2523	c.2402T>A	c.(2401-2403)cTa>cAa	p.L801Q	FAM65A_ENST00000042381.4_Missense_Mutation_p.L797Q|FAM65A_ENST00000540839.3_Missense_Mutation_p.L817Q|CTD-2012K14.4_ENST00000564717.1_RNA|FAM65A_ENST00000422602.2_Missense_Mutation_p.L817Q|FAM65A_ENST00000428437.2_Missense_Mutation_p.L811Q|CTD-2012K14.3_ENST00000563083.1_RNA	NM_001193522.1|NM_024519.3	NP_001180451.1|NP_078795.2	Q6ZS17	FA65A_HUMAN	family with sequence similarity 65, member A	801						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(12)|lung(12)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	39		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0474)|Epithelial(162;0.117)		CTGGGGGCCCTAATGGCTGCC	0.642																																					p.L817Q		Atlas-SNP	.											.	FAM65A	104	.	0			c.T2450A						PASS	.						17.0	16.0	17.0					16																	67577079		2198	4298	6496	SO:0001583	missense	79567	exon13			GGGCCCTAATGGC	AK127792	CCDS10840.1, CCDS54026.1, CCDS54027.1, CCDS54028.1	16q22.1	2008-02-05			ENSG00000039523	ENSG00000039523			25836	protein-coding gene	gene with protein product						11572484	Standard	NM_001193522		Approved	FLJ13725	uc010vjp.2	Q6ZS17	OTTHUMG00000137536	ENST00000379312.3:c.2402T>A	chr16.hg19:g.67577079T>A	ENSP00000368614:p.Leu801Gln	39.0	0.0	.		40.0	14.0	.	NM_001193523	B4DEQ9|B4DIM2|E9PBS3|Q4G0A4|Q7Z5R7|Q8NDA4|Q96J39|Q96PV8|Q9H8D9	Missense_Mutation	SNP	ENST00000379312.3	hg19	CCDS54028.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.237952	0.79800	.	.	ENSG00000039523	ENST00000379312;ENST00000042381;ENST00000422602;ENST00000540839	T;T;T	0.49432	0.78;0.78;0.78	5.52	5.52	0.82312	.	0.070064	0.56097	D	0.000022	T	0.67258	0.2874	M	0.72894	2.215	0.09310	N	0.999991	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.68765	0.96;0.96;0.96;0.96	T	0.63664	-0.6586	10	0.87932	D	0	-9.5432	15.6534	0.77115	0.0:0.0:0.0:1.0	.	811;817;801;817	B4DIM2;E9PBS3;Q6ZS17;B4DEQ9	.;.;FA65A_HUMAN;.	Q	801;797;817;811	ENSP00000368614:L801Q;ENSP00000042381:L797Q;ENSP00000400099:L817Q	ENSP00000042381:L797Q	L	+	2	0	FAM65A	66134580	0.901000	0.30685	0.994000	0.49952	0.920000	0.55202	4.728000	0.62000	2.120000	0.65058	0.454000	0.30748	CTA	.	.	.	none		0.642	FAM65A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268866.3	NM_024519	
ZFHX3	463	hgsc.bcm.edu	37	16	72821615	72821615	+	Silent	SNP	G	G	A			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr16:72821615G>A	ENST00000268489.5	-	10	11232	c.10560C>T	c.(10558-10560)ggC>ggT	p.G3520G	RP5-991G20.1_ENST00000563328.2_RNA|ZFHX3_ENST00000397992.5_Silent_p.G2606G|AC004943.1_ENST00000584072.1_RNA|RP5-991G20.4_ENST00000569195.1_RNA	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	3520	Poly-Gly.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				cgccgccgccgccaccgccgc	0.706																																					p.G3520G		Atlas-SNP	.											ZFHX3,NS,carcinoma,0,1	ZFHX3	404	.	0			c.C10560T						PASS	.						10.0	14.0	12.0					16																	72821615		1455	3158	4613	SO:0001819	synonymous_variant	463	exon10			GCCGCCGCCACCG	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.10560C>T	chr16.hg19:g.72821615G>A		53.0	1.0	.		70.0	7.0	.	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	hg19	CCDS10908.1																																																																																			.	.	.	none		0.706	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
ZZEF1	23140	hgsc.bcm.edu	37	17	3919676	3919676	+	Nonsense_Mutation	SNP	C	C	A			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr17:3919676C>A	ENST00000381638.2	-	49	8210	c.8086G>T	c.(8086-8088)Gga>Tga	p.G2696*		NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	2696							calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	84						ACCTCCATTCCTGGCTCCTCC	0.597																																					p.G2696X		Atlas-SNP	.											.	ZZEF1	195	.	0			c.G8086T						PASS	.						154.0	114.0	127.0					17																	3919676		2203	4300	6503	SO:0001587	stop_gained	23140	exon49			CCATTCCTGGCTC	BC035319	CCDS11043.1	17p13.3	2013-01-10	2004-11-03		ENSG00000074755	ENSG00000074755		"""Zinc fingers, ZZ-type"", ""EF-hand domain containing"""	29027	protein-coding gene	gene with protein product			"""zinc finger, ZZ-type with EF hand domain 1"""			9455477	Standard	XM_005256560		Approved	KIAA0399, ZZZ4, FLJ10821	uc002fxe.3	O43149	OTTHUMG00000090741	ENST00000381638.2:c.8086G>T	chr17.hg19:g.3919676C>A	ENSP00000371051:p.Gly2696*	154.0	0.0	.		162.0	39.0	.	NM_015113	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Nonsense_Mutation	SNP	ENST00000381638.2	hg19	CCDS11043.1	.	.	.	.	.	.	.	.	.	.	C	50	17.192008	0.99881	.	.	ENSG00000074755	ENST00000381638	.	.	.	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-14.3127	20.0271	0.97525	0.0:1.0:0.0:0.0	.	.	.	.	X	2696	.	ENSP00000371051:G2696X	G	-	1	0	ZZEF1	3866425	1.000000	0.71417	0.961000	0.40146	0.948000	0.59901	7.487000	0.81328	2.744000	0.94065	0.650000	0.86243	GGA	.	.	.	none		0.597	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113	
ZFP3	124961	hgsc.bcm.edu	37	17	4995909	4995909	+	Silent	SNP	T	T	C			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr17:4995909T>C	ENST00000318833.3	+	2	1446	c.1110T>C	c.(1108-1110)tgT>tgC	p.C370C		NM_153018.2	NP_694563.1	Q96NJ6	ZFP3_HUMAN	ZFP3 zinc finger protein	370					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(3)|prostate(1)	20						GTAAGGAATGTGGGAAGGCCT	0.413																																					p.C370C		Atlas-SNP	.											.	ZFP3	54	.	0			c.T1110C						PASS	.						46.0	48.0	48.0					17																	4995909		2203	4300	6503	SO:0001819	synonymous_variant	124961	exon2			GGAATGTGGGAAG	BX647638	CCDS11067.1	17p13.2	2013-01-08	2012-11-27		ENSG00000180787	ENSG00000180787		"""Zinc fingers, C2H2-type"""	12861	protein-coding gene	gene with protein product		194480	"""zinc finger protein homologous to Zfp-3 in mouse"", ""zinc finger protein 3 homolog (mouse)"""				Standard	NM_153018		Approved	FLJ30726, ZNF752	uc002gaq.3	Q96NJ6		ENST00000318833.3:c.1110T>C	chr17.hg19:g.4995909T>C		85.0	0.0	.		72.0	4.0	.	NM_153018	A5PLL4	Silent	SNP	ENST00000318833.3	hg19	CCDS11067.1																																																																																			.	.	.	none		0.413	ZFP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438979.1	NM_153018	
WIPF2	147179	hgsc.bcm.edu	37	17	38420806	38420806	+	Silent	SNP	A	A	G	rs139121244		TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr17:38420806A>G	ENST00000323571.4	+	5	618	c.378A>G	c.(376-378)ccA>ccG	p.P126P	WIPF2_ENST00000394103.3_Intron|WIPF2_ENST00000494757.1_3'UTR|WIPF2_ENST00000585043.1_Silent_p.P126P|WIPF2_ENST00000536600.1_Intron|WIPF2_ENST00000583130.1_Silent_p.P126P	NM_133264.4	NP_573571.1	Q8TF74	WIPF2_HUMAN	WAS/WASL interacting protein family, member 2	126					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)				NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	30						CAAGGCCTCCAGTATCTGCCG	0.582										HNSCC(43;0.11)																											p.P126P		Atlas-SNP	.											.	WIPF2	55	.	0			c.A378G						PASS	.			1,4405	2.1+/-5.4	0,1,2202	60.0	69.0	66.0		378	-5.5	0.3	17	dbSNP_134	66	0,8600		0,0,4300	no	coding-synonymous	WIPF2	NM_133264.4		0,1,6502	GG,GA,AA		0.0,0.0227,0.0077		126/441	38420806	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	147179	exon5			GCCTCCAGTATCT	BC025965	CCDS11364.1	17q21.2	2006-10-12			ENSG00000171475	ENSG00000171475			30923	protein-coding gene	gene with protein product		609692				12213210, 11829459	Standard	XM_005257083		Approved	WICH, WIRE	uc002hug.1	Q8TF74	OTTHUMG00000133331	ENST00000323571.4:c.378A>G	chr17.hg19:g.38420806A>G		168.0	0.0	.		151.0	35.0	.	NM_133264	A8K0L3|Q658J8|Q71RE1|Q8TE44	Silent	SNP	ENST00000323571.4	hg19	CCDS11364.1																																																																																			.	A|1.000;G|0.000	0.000	weak		0.582	WIPF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257157.2	NM_133264	
KRT37	8688	hgsc.bcm.edu	37	17	39577782	39577782	+	Missense_Mutation	SNP	C	C	G			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr17:39577782C>G	ENST00000225550.3	-	6	1077	c.1078G>C	c.(1078-1080)Gcc>Ccc	p.A360P	AC003958.2_ENST00000432258.1_RNA	NM_003770.4	NP_003761.3	O76014	KRT37_HUMAN	keratin 37	360	Coil 2.|Rod.					extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	25		Breast(137;0.000496)				TGCATCTGGGCCAGCTCTGTG	0.567																																					p.A360P		Atlas-SNP	.											.	KRT37	61	.	0			c.G1078C						PASS	.						66.0	63.0	64.0					17																	39577782		2203	4300	6503	SO:0001583	missense	8688	exon6			TCTGGGCCAGCTC	Y16793	CCDS32653.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000108417	ENSG00000108417		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6455	protein-coding gene	gene with protein product		604541	"""keratin, hair, acidic, 7"""	KRTHA7		9756910, 16831889	Standard	NM_003770		Approved		uc002hwp.1	O76014	OTTHUMG00000133606	ENST00000225550.3:c.1078G>C	chr17.hg19:g.39577782C>G	ENSP00000225550:p.Ala360Pro	89.0	0.0	.		101.0	13.0	.	NM_003770		Missense_Mutation	SNP	ENST00000225550.3	hg19	CCDS32653.1	.	.	.	.	.	.	.	.	.	.	C	16.14	3.037494	0.54896	.	.	ENSG00000108417	ENST00000225550	T	0.14640	2.49	5.44	2.17	0.27698	Filament (1);	0.000000	0.49305	D	0.000155	T	0.32763	0.0840	H	0.96861	3.895	0.28206	N	0.92715	B	0.34349	0.45	B	0.37239	0.244	T	0.42582	-0.9443	10	0.66056	D	0.02	.	13.3764	0.60741	0.5453:0.4547:0.0:0.0	.	360	O76014	KRT37_HUMAN	P	360	ENSP00000225550:A360P	ENSP00000225550:A360P	A	-	1	0	KRT37	36831308	0.000000	0.05858	1.000000	0.80357	0.990000	0.78478	-0.196000	0.09532	0.197000	0.20387	0.655000	0.94253	GCC	.	.	.	none		0.567	KRT37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257714.2	NM_003770	
MED13	9969	hgsc.bcm.edu	37	17	60023946	60023946	+	Missense_Mutation	SNP	C	C	G			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr17:60023946C>G	ENST00000397786.2	-	30	6484	c.6408G>C	c.(6406-6408)caG>caC	p.Q2136H		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	2136					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						GTGCATTGTACTGTTCCAAAA	0.378																																					p.Q2136H		Atlas-SNP	.											.	MED13	181	.	0			c.G6408C						PASS	.						79.0	74.0	76.0					17																	60023946		1866	4104	5970	SO:0001583	missense	9969	exon30			ATTGTACTGTTCC	AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"""thyroid hormone receptor associated protein 1"""	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.6408G>C	chr17.hg19:g.60023946C>G	ENSP00000380888:p.Gln2136His	49.0	0.0	.		77.0	24.0	.	NM_005121	B2RU05|O60334	Missense_Mutation	SNP	ENST00000397786.2	hg19	CCDS42366.1	.	.	.	.	.	.	.	.	.	.	C	14.58	2.576706	0.45902	.	.	ENSG00000108510	ENST00000397786;ENST00000262436	D	0.83837	-1.77	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	D	0.90748	0.7096	M	0.75447	2.3	0.80722	D	1	D	0.67145	0.996	D	0.81914	0.995	D	0.90884	0.4756	10	0.48119	T	0.1	-4.4995	18.2754	0.90081	0.0:1.0:0.0:0.0	.	2136	Q9UHV7	MED13_HUMAN	H	2136;2135	ENSP00000380888:Q2136H	ENSP00000262436:Q2135H	Q	-	3	2	MED13	57378728	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.403000	0.79983	2.315000	0.78130	0.591000	0.81541	CAG	.	.	.	none		0.378	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121	
RNF157	114804	hgsc.bcm.edu	37	17	74163165	74163165	+	Missense_Mutation	SNP	C	C	A			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr17:74163165C>A	ENST00000269391.6	-	5	618	c.486G>T	c.(484-486)caG>caT	p.Q162H	RNF157_ENST00000319945.6_Missense_Mutation_p.Q162H	NM_052916.2	NP_443148.1	Q96PX1	RN157_HUMAN	ring finger protein 157	162							zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	25			LUSC - Lung squamous cell carcinoma(166;0.187)			CTCGCTTGTACTGCACAGTCT	0.567																																					p.Q162H	GBM(186;507 2120 27388 27773 52994)	Atlas-SNP	.											.	RNF157	66	.	0			c.G486T						PASS	.						127.0	114.0	118.0					17																	74163165		2203	4300	6503	SO:0001583	missense	114804	exon5			CTTGTACTGCACA	AK091467	CCDS32740.1	17q25.3	2004-02-27			ENSG00000141576	ENSG00000141576		"""RING-type (C3HC4) zinc fingers"""	29402	protein-coding gene	gene with protein product						11572484	Standard	NM_052916		Approved	KIAA1917	uc002jqz.3	Q96PX1	OTTHUMG00000132627	ENST00000269391.6:c.486G>T	chr17.hg19:g.74163165C>A	ENSP00000269391:p.Gln162His	215.0	0.0	.		219.0	29.0	.	NM_052916	Q8NB72|Q96N56	Missense_Mutation	SNP	ENST00000269391.6	hg19	CCDS32740.1	.	.	.	.	.	.	.	.	.	.	C	4.577	0.107271	0.08780	.	.	ENSG00000141576	ENST00000269391;ENST00000319945;ENST00000301610	T;T	0.27890	1.64;1.64	5.43	2.38	0.29361	.	0.131468	0.64402	N	0.000001	T	0.05593	0.0147	N	0.00152	-1.975	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40757	-0.9546	10	0.02654	T	1	-4.6639	10.0104	0.41984	0.0971:0.1243:0.7785:0.0	.	162;162	Q96PX1-2;Q96PX1	.;RN157_HUMAN	H	162;162;124	ENSP00000269391:Q162H;ENSP00000321837:Q162H	ENSP00000269391:Q162H	Q	-	3	2	RNF157	71674760	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	0.577000	0.23758	0.271000	0.22005	-0.128000	0.14901	CAG	.	.	.	none		0.567	RNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255874.2	XM_290732	
BIRC5	332	hgsc.bcm.edu	37	17	76212806	76212806	+	Missense_Mutation	SNP	G	G	A			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr17:76212806G>A	ENST00000350051.3	+	3	402	c.283G>A	c.(283-285)Gaa>Aaa	p.E95K	AC087645.1_ENST00000600484.1_Missense_Mutation_p.S264F|BIRC5_ENST00000301633.4_Missense_Mutation_p.E118K|BIRC5_ENST00000592734.1_Intron|BIRC5_ENST00000374948.2_Intron|BIRC5_ENST00000589892.1_3'UTR	NM_001168.2	NP_001159.2	O15392	BIRC5_HUMAN	baculoviral IAP repeat containing 5	95					apoptotic process (GO:0006915)|cell division (GO:0051301)|chromosome segregation (GO:0007059)|cytokinesis (GO:0000910)|establishment of chromosome localization (GO:0051303)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|positive regulation of exit from mitosis (GO:0031536)|positive regulation of mitotic cell cycle (GO:0045931)|protein complex localization (GO:0031503)|protein phosphorylation (GO:0006468)|spindle checkpoint (GO:0031577)|transcription, DNA-templated (GO:0006351)	centriole (GO:0005814)|chromosome passenger complex (GO:0032133)|chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|interphase microtubule organizing center (GO:0031021)|microtubule (GO:0005874)|midbody (GO:0030496)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	chaperone binding (GO:0051087)|cobalt ion binding (GO:0050897)|cofactor binding (GO:0048037)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|microtubule binding (GO:0008017)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|Ran GTPase binding (GO:0008536)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			kidney(1)|urinary_tract(1)	2			BRCA - Breast invasive adenocarcinoma(99;0.00269)|OV - Ovarian serous cystadenocarcinoma(97;0.153)			GCAGTTTGAAGAATTAACCCT	0.398																																					p.E118K		Atlas-SNP	.											.	BIRC5	32	.	0			c.G352A						PASS	.						72.0	79.0	77.0					17																	76212806		2203	4300	6503	SO:0001583	missense	332	exon4			TTTGAAGAATTAA	U75285	CCDS11755.1, CCDS32751.1, CCDS32752.1	17q25.3	2013-01-17	2011-01-25		ENSG00000089685	ENSG00000089685		"""Baculoviral IAP repeat containing"""	593	protein-coding gene	gene with protein product	"""survivin variant 3 alpha"""	603352	"""apoptosis inhibitor 4"", ""baculoviral IAP repeat-containing 5"""	API4		8106347, 7947793	Standard	XR_243654		Approved	EPR-1, survivin	uc002jvf.3	O15392		ENST00000350051.3:c.283G>A	chr17.hg19:g.76212806G>A	ENSP00000324180:p.Glu95Lys	126.0	0.0	.		117.0	29.0	.	NM_001012271	A2SUH6|B2R4R1|Q2I3N8|Q4VGX0|Q53F61|Q5MGC6|Q6FHL2|Q75SP2|Q9P2W8	Missense_Mutation	SNP	ENST00000350051.3	hg19	CCDS11755.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.456362	0.84317	.	.	ENSG00000089685	ENST00000301633;ENST00000350051;ENST00000432014	T;T	0.03920	3.76;3.76	5.62	5.62	0.85841	Baculoviral inhibition of apoptosis protein repeat (1);	0.384181	0.30762	N	0.008935	T	0.07728	0.0194	L	0.59436	1.845	0.80722	D	1	B;B;B;P	0.50617	0.18;0.118;0.415;0.937	B;B;B;B	0.39590	0.053;0.036;0.202;0.304	T	0.18335	-1.0340	10	0.40728	T	0.16	-19.2617	17.1223	0.86705	0.0:0.0:1.0:0.0	.	95;95;118;95	O15392-4;O15392;O15392-2;A3E0Z5	.;BIRC5_HUMAN;.;.	K	118;95;118	ENSP00000301633:E118K;ENSP00000324180:E95K	ENSP00000301633:E118K	E	+	1	0	BIRC5	73724401	1.000000	0.71417	0.995000	0.50966	0.987000	0.75469	4.796000	0.62496	2.648000	0.89879	0.462000	0.41574	GAA	.	.	.	none		0.398	BIRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437231.2	NM_001168	
APCDD1	147495	hgsc.bcm.edu	37	18	10471914	10471914	+	Silent	SNP	G	G	A			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr18:10471914G>A	ENST00000355285.5	+	3	984	c.630G>A	c.(628-630)caG>caA	p.Q210Q	APCDD1_ENST00000578882.1_Intron	NM_153000.4	NP_694545.1			adenomatosis polyposis coli down-regulated 1											NS(1)|breast(1)|endometrium(3)|large_intestine(5)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22				READ - Rectum adenocarcinoma(15;0.08)		ATGAACTTCAGCTCATCCGGG	0.582																																					p.Q210Q		Atlas-SNP	.											.	APCDD1	57	.	0			c.G630A						PASS	.						145.0	132.0	136.0					18																	10471914		2203	4300	6503	SO:0001819	synonymous_variant	147495	exon3			ACTTCAGCTCATC	AB056722	CCDS11849.1	18p11.21	2006-07-07			ENSG00000154856	ENSG00000154856			15718	protein-coding gene	gene with protein product		607479				12384519	Standard	NM_153000		Approved	B7323	uc002kom.4	Q8J025	OTTHUMG00000131635	ENST00000355285.5:c.630G>A	chr18.hg19:g.10471914G>A		271.0	0.0	.		219.0	38.0	.	NM_153000		Silent	SNP	ENST00000355285.5	hg19	CCDS11849.1																																																																																			.	.	.	none		0.582	APCDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254529.2	NM_153000	
CEP192	55125	hgsc.bcm.edu	37	18	13071144	13071144	+	Missense_Mutation	SNP	G	G	T			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr18:13071144G>T	ENST00000325971.8	+	26	5086	c.3493G>T	c.(3493-3495)Gat>Tat	p.D1165Y	CEP192_ENST00000506447.1_Missense_Mutation_p.D1761Y|CEP192_ENST00000430049.2_Missense_Mutation_p.D1286Y			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	1165					centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						ACCTTGCTTAGATATTCCATC	0.423																																					p.D1761Y		Atlas-SNP	.											.	CEP192	340	.	0			c.G5281T						PASS	.						110.0	110.0	110.0					18																	13071144		2203	4300	6503	SO:0001583	missense	55125	exon28			TGCTTAGATATTC	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25515	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 62"""					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.3493G>T	chr18.hg19:g.13071144G>T	ENSP00000317156:p.Asp1165Tyr	56.0	0.0	.		61.0	14.0	.	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	hg19		.	.	.	.	.	.	.	.	.	.	G	17.34	3.365339	0.61513	.	.	ENSG00000101639	ENST00000506447;ENST00000325971;ENST00000399863;ENST00000430049	T;T;T	0.47869	0.83;0.83;0.83	5.35	3.54	0.40534	.	0.121003	0.53938	D	0.000055	T	0.64875	0.2638	M	0.73962	2.25	0.58432	D	0.999998	B;D;B	0.89917	0.368;1.0;0.328	B;D;B	0.79108	0.091;0.992;0.104	T	0.67692	-0.5605	10	0.87932	D	0	-11.9129	9.8383	0.40982	0.0725:0.0:0.7869:0.1406	.	1286;1761;363	C9JT09;E9PF99;Q9HCK3	.;.;.	Y	1761;1165;1165;1286	ENSP00000427550:D1761Y;ENSP00000317156:D1165Y;ENSP00000389190:D1286Y	ENSP00000317156:D1165Y	D	+	1	0	CEP192	13061144	1.000000	0.71417	0.650000	0.29550	0.606000	0.37113	3.512000	0.53407	1.230000	0.43646	0.650000	0.86243	GAT	.	.	.	none		0.423	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142	
ZNF519	162655	hgsc.bcm.edu	37	18	14105675	14105675	+	Silent	SNP	T	T	C			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr18:14105675T>C	ENST00000590202.1	-	3	1016	c.864A>G	c.(862-864)ggA>ggG	p.G288G	RP11-411B10.3_ENST00000592926.1_RNA|ZNF519_ENST00000589203.1_Intron|ZNF519_ENST00000589498.1_Intron	NM_145287.3	NP_660330.2	Q8TB69	ZN519_HUMAN	zinc finger protein 519	288					negative regulation of transcription during meiosis (GO:0051038)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|urinary_tract(1)	18						AAGGTTTCTCTCCAGTATGAA	0.363																																					p.G288G		Atlas-SNP	.											.	ZNF519	53	.	0			c.A864G						PASS	.						49.0	53.0	52.0					18																	14105675		2203	4299	6502	SO:0001819	synonymous_variant	162655	exon3			TTTCTCTCCAGTA	BC024227	CCDS32797.1	18p11.21	2014-06-18			ENSG00000175322	ENSG00000175322		"""Zinc fingers, C2H2-type"", ""-"""	30574	protein-coding gene	gene with protein product	"""similar to Zinc finger protein 85 (Zinc finger protein HPF4) (HTF1)"""					12477932	Standard	NM_145287		Approved	HsT2362, FLJ36809	uc002kst.2	Q8TB69	OTTHUMG00000182055	ENST00000590202.1:c.864A>G	chr18.hg19:g.14105675T>C		78.0	0.0	.		83.0	18.0	.	NM_145287		Silent	SNP	ENST00000590202.1	hg19	CCDS32797.1																																																																																			.	.	.	none		0.363	ZNF519-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459037.1	NM_145287	
LAMA3	3909	hgsc.bcm.edu	37	18	21451430	21451430	+	Silent	SNP	G	G	T			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr18:21451430G>T	ENST00000313654.9	+	38	5044	c.4803G>T	c.(4801-4803)gtG>gtT	p.V1601V	LAMA3_ENST00000399516.3_Silent_p.V1601V|LAMA3_ENST00000587184.1_5'Flank|LAMA3_ENST00000269217.6_5'Flank	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	1601	Laminin IV type A. {ECO:0000255|PROSITE- ProRule:PRU00458}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					GTGCCCCAGTGTCTAGGGAGG	0.552																																					p.V1601V		Atlas-SNP	.											.	LAMA3	397	.	0			c.G4803T						PASS	.						66.0	69.0	68.0					18																	21451430		2040	4193	6233	SO:0001819	synonymous_variant	3909	exon38			CCCAGTGTCTAGG	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"""Laminins"""	6483	protein-coding gene	gene with protein product		600805	"""laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"""	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.4803G>T	chr18.hg19:g.21451430G>T		112.0	0.0	.		85.0	14.0	.	NM_001127717	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Silent	SNP	ENST00000313654.9	hg19	CCDS42419.1																																																																																			.	.	.	none		0.552	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129	
ZNF521	25925	hgsc.bcm.edu	37	18	22805629	22805629	+	Silent	SNP	G	G	C			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr18:22805629G>C	ENST00000361524.3	-	4	2401	c.2253C>G	c.(2251-2253)gtC>gtG	p.V751V	ZNF521_ENST00000579111.1_5'Flank|ZNF521_ENST00000584787.1_Silent_p.V531V|ZNF521_ENST00000538137.2_Silent_p.V751V	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	751					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					TGCACCTATAGACTTTCTTTT	0.468			T	PAX5	ALL																																p.V751V		Atlas-SNP	.		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	.	ZNF521	269	.	0			c.C2253G						PASS	.						75.0	71.0	72.0					18																	22805629		2203	4300	6503	SO:0001819	synonymous_variant	25925	exon4			CCTATAGACTTTC	AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"""Zinc fingers, C2H2-type"""	24605	protein-coding gene	gene with protein product	"""early hematopoietic zinc finger"""	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.2253C>G	chr18.hg19:g.22805629G>C		79.0	0.0	.		83.0	16.0	.	NM_015461	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Silent	SNP	ENST00000361524.3	hg19	CCDS32806.1																																																																																			.	.	.	none		0.468	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461	
ZNF844	284391	hgsc.bcm.edu	37	19	12187475	12187475	+	Missense_Mutation	SNP	C	C	G			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr19:12187475C>G	ENST00000439326.3	+	4	1715	c.1540C>G	c.(1540-1542)Cat>Gat	p.H514D	ZNF844_ENST00000441304.2_3'UTR	NM_001136501.1	NP_001129973.1	Q08AG5	ZN844_HUMAN	zinc finger protein 844	514					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.H514D(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(1)|prostate(1)	10						AAAGCCTTCACATCTGCCTCA	0.408																																					p.H514D		Atlas-SNP	.											ZNF844,NS,carcinoma,0,6	ZNF844	69	.	1	Substitution - Missense(1)	endometrium(1)	c.C1540G						PASS	.						87.0	81.0	83.0					19																	12187475		692	1591	2283	SO:0001583	missense	284391	exon4			CCTTCACATCTGC	AL832297	CCDS45985.1	19p13.2	2013-01-08			ENSG00000223547	ENSG00000223547		"""Zinc fingers, C2H2-type"", ""-"""	25932	protein-coding gene	gene with protein product							Standard	NM_001136501		Approved	FLJ14959	uc002mtb.2	Q08AG5	OTTHUMG00000156405	ENST00000439326.3:c.1540C>G	chr19.hg19:g.12187475C>G	ENSP00000392024:p.His514Asp	68.0	0.0	.		70.0	6.0	.	NM_001136501	Q5JPI8	Missense_Mutation	SNP	ENST00000439326.3	hg19	CCDS45985.1	.	.	.	.	.	.	.	.	.	.	c	0.059	-1.227642	0.01518	.	.	ENSG00000223547	ENST00000439326;ENST00000541708	T	0.06371	3.31	2.45	-4.91	0.03085	.	.	.	.	.	T	0.02649	0.0080	N	0.04387	-0.21	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.44019	-0.9355	9	0.25106	T	0.35	.	9.0916	0.36614	0.0:0.4133:0.4132:0.1735	.	514	Q08AG5	ZN844_HUMAN	D	514	ENSP00000392024:H514D	ENSP00000392024:H514D	H	+	1	0	ZNF844	12048475	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-4.066000	0.00302	-2.826000	0.00341	-1.839000	0.00587	CAT	.	.	.	none		0.408	ZNF844-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344086.2		
ZNF844	284391	hgsc.bcm.edu	37	19	12187502	12187502	+	Missense_Mutation	SNP	A	A	G			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr19:12187502A>G	ENST00000439326.3	+	4	1742	c.1567A>G	c.(1567-1569)Aaa>Gaa	p.K523E	ZNF844_ENST00000441304.2_3'UTR	NM_001136501.1	NP_001129973.1	Q08AG5	ZN844_HUMAN	zinc finger protein 844	523					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K523E(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(1)|prostate(1)	10						CAAATGCATGAAAGGACTCAC	0.413																																					p.K523E		Atlas-SNP	.											ZNF844,bladder,carcinoma,0,3	ZNF844	69	.	1	Substitution - Missense(1)	endometrium(1)	c.A1567G						PASS	.						94.0	85.0	88.0					19																	12187502		692	1591	2283	SO:0001583	missense	284391	exon4			TGCATGAAAGGAC	AL832297	CCDS45985.1	19p13.2	2013-01-08			ENSG00000223547	ENSG00000223547		"""Zinc fingers, C2H2-type"", ""-"""	25932	protein-coding gene	gene with protein product							Standard	NM_001136501		Approved	FLJ14959	uc002mtb.2	Q08AG5	OTTHUMG00000156405	ENST00000439326.3:c.1567A>G	chr19.hg19:g.12187502A>G	ENSP00000392024:p.Lys523Glu	45.0	0.0	.		44.0	6.0	.	NM_001136501	Q5JPI8	Missense_Mutation	SNP	ENST00000439326.3	hg19	CCDS45985.1	.	.	.	.	.	.	.	.	.	.	a	8.659	0.899999	0.17686	.	.	ENSG00000223547	ENST00000439326;ENST00000541708	T	0.05786	3.39	2.31	-0.0571	0.13803	.	.	.	.	.	T	0.04452	0.0122	L	0.53617	1.68	0.09310	N	1	B	0.26081	0.141	B	0.15052	0.012	T	0.46638	-0.9177	9	0.05833	T	0.94	.	2.4497	0.04515	0.525:0.0:0.2647:0.2102	.	523	Q08AG5	ZN844_HUMAN	E	523	ENSP00000392024:K523E	ENSP00000392024:K523E	K	+	1	0	ZNF844	12048502	0.000000	0.05858	0.000000	0.03702	0.438000	0.31896	-0.320000	0.08028	-0.243000	0.09653	0.166000	0.16787	AAA	.	.	.	none		0.413	ZNF844-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344086.2		
ZNF430	80264	hgsc.bcm.edu	37	19	21240780	21240780	+	Missense_Mutation	SNP	C	C	G			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr19:21240780C>G	ENST00000261560.5	+	5	1847	c.1666C>G	c.(1666-1668)Ctt>Gtt	p.L556V	AC012627.1_ENST00000578233.1_RNA	NM_001172671.1|NM_025189.3	NP_001166142.1|NP_079465.3	Q9H8G1	ZN430_HUMAN	zinc finger protein 430	556					regulation of transcription, DNA-templated (GO:0006355)|substantia nigra development (GO:0021762)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	23						GTCCTCAAACCTTATTGAACA	0.383																																					p.L556V		Atlas-SNP	.											.	ZNF430	59	.	0			c.C1666G						PASS	.						36.0	41.0	40.0					19																	21240780		2182	4285	6467	SO:0001583	missense	80264	exon5			TCAAACCTTATTG	AK023721	CCDS32978.1	19p12	2013-01-08				ENSG00000118620		"""Zinc fingers, C2H2-type"", ""-"""	20808	protein-coding gene	gene with protein product							Standard	NM_025189		Approved	FLJ13659	uc002npj.3	Q9H8G1		ENST00000261560.5:c.1666C>G	chr19.hg19:g.21240780C>G	ENSP00000261560:p.Leu556Val	49.0	0.0	.		39.0	10.0	.	NM_025189	Q86V70	Missense_Mutation	SNP	ENST00000261560.5	hg19	CCDS32978.1	.	.	.	.	.	.	.	.	.	.	.	7.976	0.750166	0.15778	.	.	ENSG00000118620	ENST00000261560	T	0.68331	-0.32	1.01	1.01	0.19927	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.81341	0.4802	M	0.88105	2.93	0.09310	N	1	D;P	0.57571	0.98;0.457	D;B	0.68353	0.957;0.329	T	0.68685	-0.5343	9	0.87932	D	0	.	8.8921	0.35441	0.0:1.0:0.0:0.0	.	555;556	Q2NKJ9;Q9H8G1	.;ZN430_HUMAN	V	556	ENSP00000261560:L556V	ENSP00000261560:L556V	L	+	1	0	ZNF430	21032620	0.000000	0.05858	0.014000	0.15608	0.014000	0.08584	-0.502000	0.06390	0.453000	0.26858	0.456000	0.33151	CTT	.	.	.	none		0.383	ZNF430-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463539.1	NM_025189	
DPY19L3	147991	hgsc.bcm.edu	37	19	32930113	32930113	+	Missense_Mutation	SNP	T	T	G			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr19:32930113T>G	ENST00000342179.5	+	7	907	c.692T>G	c.(691-693)cTg>cGg	p.L231R	DPY19L3_ENST00000392250.2_Missense_Mutation_p.L231R|DPY19L3_ENST00000586987.1_Missense_Mutation_p.L231R	NM_207325.2	NP_997208.2	Q6ZPD9	D19L3_HUMAN	dpy-19-like 3 (C. elegans)	231						integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(17)|ovary(4)|pancreas(1)	32	Esophageal squamous(110;0.162)					ACATATTTCCTGAGACCAAAC	0.363																																					p.L231R		Atlas-SNP	.											.	DPY19L3	70	.	0			c.T692G						PASS	.						133.0	131.0	132.0					19																	32930113		2203	4300	6503	SO:0001583	missense	147991	exon7			ATTTCCTGAGACC		CCDS12422.1	19q13.11	2008-02-05				ENSG00000178904			27120	protein-coding gene	gene with protein product		613894					Standard	NM_207325		Approved		uc002ntg.3	Q6ZPD9		ENST00000342179.5:c.692T>G	chr19.hg19:g.32930113T>G	ENSP00000344937:p.Leu231Arg	124.0	0.0	.		80.0	15.0	.	NM_001172774	Q68DC7|Q6ZTB7|Q6ZTS2	Missense_Mutation	SNP	ENST00000342179.5	hg19	CCDS12422.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.333525	0.81801	.	.	ENSG00000178904	ENST00000392250;ENST00000319326;ENST00000342179	T;T	0.65549	-0.16;-0.16	5.66	5.66	0.87406	.	0.075638	0.53938	D	0.000041	T	0.81331	0.4800	M	0.84683	2.71	0.53005	D	0.99996	D	0.76494	0.999	D	0.76575	0.988	D	0.84659	0.0705	10	0.87932	D	0	-8.1242	15.8965	0.79338	0.0:0.0:0.0:1.0	.	231	Q6ZPD9	D19L3_HUMAN	R	231	ENSP00000376081:L231R;ENSP00000344937:L231R	ENSP00000315672:L231R	L	+	2	0	DPY19L3	37621953	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.816000	0.86201	2.163000	0.67991	0.460000	0.39030	CTG	.	.	.	none		0.363	DPY19L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450311.1	NM_207325	
ATP1A3	478	hgsc.bcm.edu	37	19	42485703	42485703	+	Missense_Mutation	SNP	C	C	A			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr19:42485703C>A	ENST00000302102.5	-	11	1538	c.1388G>T	c.(1387-1389)cGc>cTc	p.R463L	ATP1A3_ENST00000545399.1_Missense_Mutation_p.R476L|ATP1A3_ENST00000602133.1_Missense_Mutation_p.R433L|ATP1A3_ENST00000543770.1_Missense_Mutation_p.R474L	NM_152296.4	NP_689509.1	P13637	AT1A3_HUMAN	ATPase, Na+/K+ transporting, alpha 3 polypeptide	463					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|memory (GO:0007613)|potassium ion import (GO:0010107)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	axon (GO:0030424)|dendritic spine head (GO:0044327)|dendritic spine neck (GO:0044326)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(19)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	52						TTTCTTGTTGCGTTCACGCAT	0.552																																					p.R476L		Atlas-SNP	.											.	ATP1A3	117	.	0			c.G1427T						PASS	.						111.0	95.0	100.0					19																	42485703		2203	4300	6503	SO:0001583	missense	478	exon11			TTGTTGCGTTCAC		CCDS12594.1, CCDS58663.1, CCDS58664.1	19q13.2	2012-10-22			ENSG00000105409	ENSG00000105409	3.6.3.9	"""ATPases / P-type"""	801	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit alpha-3"", ""sodium pump subunit alpha-3"", ""sodium-potassium ATPase catalytic subunit alpha-3"""	182350	"""dystonia 12"""	DYT12		17282997	Standard	NM_152296		Approved		uc002osh.4	P13637	OTTHUMG00000137384	ENST00000302102.5:c.1388G>T	chr19.hg19:g.42485703C>A	ENSP00000302397:p.Arg463Leu	111.0	0.0	.		76.0	4.0	.	NM_001256214	B7Z2T0|B7Z401|F5H6J6|Q16732|Q16735|Q969K5	Missense_Mutation	SNP	ENST00000302102.5	hg19	CCDS12594.1	.	.	.	.	.	.	.	.	.	.	C	15.60	2.882720	0.51908	.	.	ENSG00000105409	ENST00000302102;ENST00000441343;ENST00000545399;ENST00000368080;ENST00000535899;ENST00000543770	D;D;D;D	0.95377	-3.69;-3.69;-3.69;-3.69	3.88	3.88	0.44766	ATPase, cation-transporting, domain N (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.240845	0.39834	N	0.001256	D	0.89760	0.6808	N	0.20483	0.58	0.45108	D	0.998124	B;B;B;B	0.29136	0.004;0.002;0.234;0.003	B;B;B;B	0.31869	0.025;0.022;0.137;0.038	D	0.87571	0.2478	10	0.72032	D	0.01	.	7.5742	0.27926	0.0:0.8868:0.0:0.1132	.	476;474;463;463	B7Z2T0;F5H6J6;E9PC51;P13637	.;.;.;AT1A3_HUMAN	L	463;463;476;433;207;474	ENSP00000302397:R463L;ENSP00000411503:R463L;ENSP00000444688:R476L;ENSP00000437577:R474L	ENSP00000302397:R463L	R	-	2	0	ATP1A3	47177543	0.261000	0.24063	0.961000	0.40146	0.992000	0.81027	1.374000	0.34283	2.449000	0.82847	0.561000	0.74099	CGC	.	.	.	none		0.552	ATP1A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268107.1	NM_152296	
ZNF473	25888	hgsc.bcm.edu	37	19	50550199	50550199	+	Silent	SNP	G	G	T			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr19:50550199G>T	ENST00000595661.1	+	6	2994	c.2499G>T	c.(2497-2499)ctG>ctT	p.L833L	ZNF473_ENST00000445728.3_Silent_p.L821L|CTD-2126E3.3_ENST00000599914.1_RNA|ZNF473_ENST00000270617.3_Silent_p.L833L|ZNF473_ENST00000391821.2_Silent_p.L833L|CTD-2126E3.3_ENST00000599410.1_RNA|ZNF473_ENST00000601364.1_Intron			Q8WTR7	ZN473_HUMAN	zinc finger protein 473	833					gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(9)|liver(2)|lung(12)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37		all_neural(266;0.0459)|Ovarian(192;0.0728)		GBM - Glioblastoma multiforme(134;0.00111)|OV - Ovarian serous cystadenocarcinoma(262;0.0058)		ACCAGCACCTGAGAGTTCACA	0.517											OREG0025632	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L833L		Atlas-SNP	.											.	ZNF473	86	.	0			c.G2499T						PASS	.						68.0	71.0	70.0					19																	50550199		2203	4300	6503	SO:0001819	synonymous_variant	25888	exon5			GCACCTGAGAGTT	AB032967	CCDS33077.1	19q13.33	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	23239	protein-coding gene	gene with protein product						11782445	Standard	NM_015428		Approved	KIAA1141, DKFZP434N043, HZFP100	uc002prn.3	Q8WTR7		ENST00000595661.1:c.2499G>T	chr19.hg19:g.50550199G>T		77.0	0.0	.	970	79.0	18.0	.	NM_015428	A8K8T7|Q9ULS9|Q9Y4Q7	Silent	SNP	ENST00000595661.1	hg19	CCDS33077.1																																																																																			.	.	.	none		0.517	ZNF473-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464833.1	XM_046390	
ZNF28	7576	hgsc.bcm.edu	37	19	53303801	53303801	+	Missense_Mutation	SNP	G	G	C			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr19:53303801G>C	ENST00000457749.2	-	4	1416	c.1297C>G	c.(1297-1299)Cac>Gac	p.H433D	ZNF28_ENST00000360272.4_Missense_Mutation_p.H380D|ZNF28_ENST00000414252.2_Missense_Mutation_p.H380D|ZNF28_ENST00000438150.2_Missense_Mutation_p.H380D	NM_006969.3	NP_008900.3	P17035	ZNF28_HUMAN	zinc finger protein 28	433					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.H380Y(2)|p.H433Y(1)		breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|liver(1)|lung(10)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(134;0.0386)|Lung(386;0.145)		TCTCCAGTGTGAATTATACTA	0.373																																					p.H433D		Atlas-SNP	.											ZNF28_ENST00000457749,NS,carcinoma,0,3	ZNF28	191	.	3	Substitution - Missense(3)	breast(3)	c.C1297G						PASS	.						113.0	120.0	118.0					19																	53303801		2203	4300	6503	SO:0001583	missense	7576	exon4			CAGTGTGAATTAT	X52355	CCDS33093.1, CCDS33093.2	19q13.41	2013-01-08	2006-05-10		ENSG00000198538	ENSG00000198538		"""Zinc fingers, C2H2-type"", ""-"""	13073	protein-coding gene	gene with protein product			"""zinc finger protein 28 (KOX 24)"""				Standard	NR_036599		Approved	KOX24, DKFZp781D0275	uc002qad.3	P17035	OTTHUMG00000154564	ENST00000457749.2:c.1297C>G	chr19.hg19:g.53303801G>C	ENSP00000397693:p.His433Asp	289.0	0.0	.		200.0	30.0	.	NM_006969	A8KAK9|B4E3G0|B9EIK7|Q5H9V1|Q5HYM9|Q6ZML9|Q6ZN56	Missense_Mutation	SNP	ENST00000457749.2	hg19	CCDS33093.2	.	.	.	.	.	.	.	.	.	.	-	14.52	2.559448	0.45590	.	.	ENSG00000198538	ENST00000438150;ENST00000457749;ENST00000360272;ENST00000414252;ENST00000391783	T;T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28;-0.28	1.74	0.624	0.17659	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.84433	0.5471	H	0.96460	3.825	0.27520	N	0.951416	D	0.63880	0.993	D	0.79784	0.993	T	0.73257	-0.4040	9	0.87932	D	0	.	6.9561	0.24572	0.1616:0.0:0.8384:0.0	.	433	P17035	ZNF28_HUMAN	D	380;433;380;380;380	ENSP00000412143:H380D;ENSP00000397693:H433D;ENSP00000353410:H380D;ENSP00000444965:H380D;ENSP00000375661:H380D	ENSP00000353410:H380D	H	-	1	0	ZNF28	57995613	1.000000	0.71417	0.003000	0.11579	0.128000	0.20619	4.471000	0.60182	0.072000	0.16694	0.186000	0.17326	CAC	.	.	.	none		0.373	ZNF28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336038.2	NM_006969	
FCAR	2204	hgsc.bcm.edu	37	19	55401195	55401196	+	Missense_Mutation	DNP	TG	TG	GT			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T|G	T|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr19:55401195_55401196TG>GT	ENST00000355524.3	+	5	840_841	c.830_831TG>GT	c.(829-831)tTG>tGT	p.L277C	FCAR_ENST00000353758.4_Missense_Mutation_p.L168C|FCAR_ENST00000391723.3_3'UTR|FCAR_ENST00000345937.4_Missense_Mutation_p.L181C|FCAR_ENST00000391725.3_Missense_Mutation_p.L255C|FCAR_ENST00000482092.2_3'UTR|FCAR_ENST00000391724.3_Missense_Mutation_p.L243C|CTB-61M7.2_ENST00000594721.1_lincRNA|FCAR_ENST00000359272.4_Missense_Mutation_p.L265C|FCAR_ENST00000391726.3_Missense_Mutation_p.L169C	NM_002000.2	NP_001991.1	P24071	FCAR_HUMAN	Fc fragment of IgA, receptor for	277					immune response (GO:0006955)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|skin(2)	24				GBM - Glioblastoma multiforme(193;0.0443)		CAGCCAGGATTGACCTTTGCAC	0.525																																					p.L277W|p.L277F		Atlas-SNP	.											.|FCAR,NS,malignant_melanoma,0,2	FCAR	110	.	0			c.T830G|c.G831T						PASS	.																																			SO:0001583	missense	2204	exon5			CAGGATTGACCTT|AGGATTGACCTTT	X54150	CCDS12907.1, CCDS12908.1, CCDS12909.1, CCDS12910.1, CCDS42622.1, CCDS42623.1, CCDS42624.1, CCDS42625.1, CCDS46180.1	19q13.42	2013-01-29			ENSG00000186431	ENSG00000186431		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3608	protein-coding gene	gene with protein product		147045				1577457	Standard	NM_133269		Approved	CD89	uc002qhr.1	P24071	OTTHUMG00000065936	Exception_encountered	chr19.hg19:g.55401195_55401196delinsGT	ENSP00000347714:p.Leu277Cys	209.0|207.0	0.0	.		233.0|228.0	36.0	.	NM_002000	Q13603|Q13604|Q15727|Q15728|Q1AJL7|Q1AJL8|Q1AJL9|Q53X38|Q53X39|Q92587|Q92588|Q92590|Q92592|Q92593|Q9UEK0	Missense_Mutation	SNP	ENST00000355524.3	hg19	CCDS12907.1																																																																																			.	.	.	none		0.525	FCAR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000141243.1	NM_002000	
HIRA	7290	hgsc.bcm.edu	37	22	19393327	19393327	+	Missense_Mutation	SNP	G	G	T			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr22:19393327G>T	ENST00000263208.5	-	5	635	c.379C>A	c.(379-381)Ctc>Atc	p.L127I	HIRA_ENST00000546308.1_Missense_Mutation_p.L83I|HIRA_ENST00000340170.4_Missense_Mutation_p.L127I|HIRA_ENST00000464189.1_5'UTR|HIRA_ENST00000541063.1_Missense_Mutation_p.L83I	NM_003325.3	NP_003316.3	P54198	HIRA_HUMAN	histone cell cycle regulator	127					anatomical structure morphogenesis (GO:0009653)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|gastrulation (GO:0007369)|muscle cell differentiation (GO:0042692)|osteoblast differentiation (GO:0001649)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(2)|prostate(1)|skin(1)	37	Colorectal(54;0.0993)					TGATTCCGGAGGATAGAGACA	0.612																																					p.L127I		Atlas-SNP	.											.	HIRA	100	.	0			c.C379A						PASS	.						86.0	70.0	76.0					22																	19393327		2203	4300	6503	SO:0001583	missense	7290	exon5			TCCGGAGGATAGA	X75296	CCDS13759.1	22q11.2	2013-05-03	2013-05-03		ENSG00000100084	ENSG00000100084		"""WD repeat domain containing"""	4916	protein-coding gene	gene with protein product	"""DiGeorge critical region gene 1"""	600237	"""HIR (histone cell cycle regulation defective) homolog A (S. cerevisiae)"", ""HIR histone cell cycle regulation defective homolog A (S. cerevisiae)"""	TUPLE1		8111380, 7633437, 9731536	Standard	NM_003325		Approved	DGCR1, TUP1	uc002zpf.1	P54198	OTTHUMG00000150134	ENST00000263208.5:c.379C>A	chr22.hg19:g.19393327G>T	ENSP00000263208:p.Leu127Ile	63.0	0.0	.		97.0	4.0	.	NM_003325	Q05BU9|Q8IXN2	Missense_Mutation	SNP	ENST00000263208.5	hg19	CCDS13759.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.907418	0.92107	.	.	ENSG00000100084	ENST00000340170;ENST00000263208;ENST00000541063;ENST00000546308	T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.26	4.86	4.86	0.63082	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.80502	0.4635	M	0.63843	1.955	0.80722	D	1	D;D	0.89917	0.996;1.0	D;D	0.97110	0.986;1.0	T	0.82592	-0.0381	10	0.87932	D	0	-14.4293	18.1731	0.89753	0.0:0.0:1.0:0.0	.	127;127	P54198-2;P54198	.;HIRA_HUMAN	I	127;127;83;83	ENSP00000345350:L127I;ENSP00000263208:L127I;ENSP00000446073:L83I;ENSP00000441870:L83I	ENSP00000263208:L127I	L	-	1	0	HIRA	17773327	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.187000	0.77730	2.519000	0.84933	0.563000	0.77884	CTC	.	.	.	none		0.612	HIRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316488.2	NM_003325	
PAK3	5063	hgsc.bcm.edu	37	X	110366494	110366494	+	Missense_Mutation	SNP	G	G	A			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chrX:110366494G>A	ENST00000372010.1	+	5	605	c.163G>A	c.(163-165)Gga>Aga	p.G55R	PAK3_ENST00000262836.4_Missense_Mutation_p.G55R|PAK3_ENST00000518291.1_Missense_Mutation_p.G55R|PAK3_ENST00000446737.1_Missense_Mutation_p.G55R|PAK3_ENST00000417227.1_Missense_Mutation_p.G55R|PAK3_ENST00000360648.4_Missense_Mutation_p.G55R|PAK3_ENST00000425146.1_Missense_Mutation_p.G55R|PAK3_ENST00000519681.1_Missense_Mutation_p.G55R|PAK3_ENST00000372007.5_Missense_Mutation_p.G55R			O75914	PAK3_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 3	55					activation of MAPK activity (GO:0000187)|axonogenesis (GO:0007409)|dendrite development (GO:0016358)|dendritic spine morphogenesis (GO:0060997)|MAPK cascade (GO:0000165)|regulation of actin filament polymerization (GO:0030833)|synapse organization (GO:0050808)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(15)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	41						CTTCCCAGGAGGAGGGGATAA	0.448										TSP Lung(19;0.15)																											p.G55R		Atlas-SNP	.											.	PAK3	179	.	0			c.G163A						PASS	.						70.0	69.0	70.0					X																	110366494		2203	4300	6503	SO:0001583	missense	5063	exon3			CCAGGAGGAGGGG	AF068864	CCDS14554.1, CCDS48151.1, CCDS48152.1, CCDS48153.1	Xq22.3	2008-06-17	2008-06-17		ENSG00000077264	ENSG00000077264			8592	protein-coding gene	gene with protein product		300142	"""mental retardation, X-linked 47"", ""p21 (CDKN1A)-activated kinase 3"""	MRX30, MRX47		8826460, 9731525	Standard	NM_002578		Approved	hPAK3, bPAK	uc010npv.1	O75914	OTTHUMG00000022202	ENST00000372010.1:c.163G>A	chrX.hg19:g.110366494G>A	ENSP00000361080:p.Gly55Arg	50.0	0.0	.		47.0	15.0	.	NM_001128166	A8K389|B1GX77|B1GX78|B1GX79|Q5JWX1|Q5JWX2|Q7Z2D6|Q7Z2E4|Q7Z3Z8|Q8WWK5|Q8WX23|Q9P0J8	Missense_Mutation	SNP	ENST00000372010.1	hg19	CCDS48153.1	.	.	.	.	.	.	.	.	.	.	G	16.93	3.257186	0.59321	.	.	ENSG00000077264	ENST00000446737;ENST00000425146;ENST00000372010;ENST00000519681;ENST00000372007;ENST00000518291;ENST00000429193;ENST00000360648;ENST00000417227;ENST00000262836	T;T;T;T;T;T;T;T;T	0.71461	-0.55;-0.55;-0.57;-0.56;-0.55;-0.54;-0.54;-0.56;-0.57	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	T	0.68284	0.2984	L	0.29908	0.895	0.80722	D	1	P;P;B;B	0.43607	0.801;0.812;0.399;0.037	P;P;B;B	0.48454	0.578;0.578;0.194;0.049	T	0.64322	-0.6435	10	0.22706	T	0.39	.	18.4314	0.90627	0.0:0.0:1.0:0.0	.	55;55;55;55	O75914-4;O75914-3;O75914;O75914-2	.;.;PAK3_HUMAN;.	R	55	ENSP00000410853:G55R;ENSP00000401982:G55R;ENSP00000361080:G55R;ENSP00000429113:G55R;ENSP00000361077:G55R;ENSP00000428921:G55R;ENSP00000353864:G55R;ENSP00000389172:G55R;ENSP00000262836:G55R	ENSP00000262836:G55R	G	+	1	0	PAK3	110253150	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.143000	0.94623	2.380000	0.81148	0.600000	0.82982	GGA	.	.	.	none		0.448	PAK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057918.1	NM_002578	
GPR98	84059	hgsc.bcm.edu	37	5	89953910	89953915	+	In_Frame_Del	DEL	AAATCA	AAATCA	-			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	AAATCA	AAATCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr5:89953910_89953915delAAATCA	ENST00000405460.2	+	21	4663_4668	c.4567_4572delAAATCA	c.(4567-4572)aaatcadel	p.KS1523del		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	1523	Calx-beta 10. {ECO:0000305|PubMed:11606593}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		AGAAACTAACAAATCATTCATTATTT	0.374																																					p.1522_1524del		Atlas-INDEL	.											.	GPR98	605	.	0			c.4566_4571del						PASS	.																																			SO:0001651	inframe_deletion	84059	exon21			.	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.4567_4572delAAATCA	chr5.hg19:g.89953910_89953915delAAATCA	ENSP00000384582:p.Lys1523_Ser1524del	124.0	0.0	0		126.0	30.0	0.238095	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	In_Frame_Del	DEL	ENST00000405460.2	hg19	CCDS47246.1																																																																																			.	.	.	none		0.374	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
DMTF1	9988	hgsc.bcm.edu	37	7	86808890	86808890	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr7:86808890delC	ENST00000394703.5	+	10	1112	c.549delC	c.(547-549)atcfs	p.I184fs	DMTF1_ENST00000411766.2_Frame_Shift_Del_p.I143fs|DMTF1_ENST00000331242.7_Frame_Shift_Del_p.I184fs|DMTF1_ENST00000413276.2_Frame_Shift_Del_p.I184fs|DMTF1_ENST00000432937.2_Frame_Shift_Del_p.I96fs|DMTF1_ENST00000394702.3_Frame_Shift_Del_p.I184fs|DMTF1_ENST00000414194.2_5'UTR	NM_021145.3	NP_066968.3	Q9Y222	DMTF1_HUMAN	cyclin D binding myb-like transcription factor 1	184	Interaction with CCND1, CCND2 and CCND3. {ECO:0000250}.|Interaction with CCND2. {ECO:0000250}.|Required for DNA-binding. {ECO:0000250}.				cell cycle (GO:0007049)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)	16	Esophageal squamous(14;0.0058)					CTACAGAAATCATCTTTGAGA	0.363																																					p.I183fs		Atlas-INDEL	.											.	DMTF1	48	.	0			c.548delT						PASS	.						63.0	58.0	60.0					7																	86808890		2203	4300	6503	SO:0001589	frameshift_variant	9988	exon10			.	AF084530	CCDS5601.1, CCDS47633.1	7q21	2014-06-25			ENSG00000135164	ENSG00000135164			14603	protein-coding gene	gene with protein product	"""cyclin D-binding Myb-like protein"""	608491				10095122, 24958102	Standard	NR_024549		Approved	DMP1, DMTF, hDMP1, MRUL	uc003uih.3	Q9Y222	OTTHUMG00000154135	ENST00000394703.5:c.549delC	chr7.hg19:g.86808890delC	ENSP00000378193:p.Ile184fs	39.0	0.0	0		51.0	10.0	0.196078	NM_021145	B2RBE1|B4DJS5|Q05C48|Q59G79|Q6IS13|Q969T2|Q9H2Z2|Q9H2Z3	Frame_Shift_Del	DEL	ENST00000394703.5	hg19	CCDS5601.1																																																																																			.	.	.	none		0.363	DMTF1-002	KNOWN	alternative_5_UTR|non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334025.5	NM_021145	
WDR47	22911	hgsc.bcm.edu	37	1	109554105	109554105	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr1:109554105delT	ENST00000369962.3	-	5	785	c.563delA	c.(562-564)aagfs	p.K188fs	WDR47_ENST00000369965.4_Frame_Shift_Del_p.K188fs|WDR47_ENST00000357672.3_Frame_Shift_Del_p.K160fs|WDR47_ENST00000361054.3_Frame_Shift_Del_p.K160fs|WDR47_ENST00000400794.3_Frame_Shift_Del_p.K195fs			O94967	WDR47_HUMAN	WD repeat domain 47	188					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20		all_lung(203;0.00519)|all_epithelial(167;0.00611)|Lung NSC(277;0.00822)		Colorectal(144;0.0165)|Lung(183;0.0484)|COAD - Colon adenocarcinoma(174;0.128)|Epithelial(280;0.168)|all cancers(265;0.201)|LUSC - Lung squamous cell carcinoma(189;0.244)		GTTACTAGCCTTAAAACCAGC	0.413																																					p.K195fs		Atlas-INDEL	.											.	WDR47	56	.	0			c.585delG						PASS	.						206.0	212.0	210.0					1																	109554105		2203	4296	6499	SO:0001589	frameshift_variant	22911	exon5			.	AB020700	CCDS30787.1, CCDS44186.1, CCDS44187.1	1p13.3	2013-01-09			ENSG00000085433	ENSG00000085433		"""WD repeat domain containing"""	29141	protein-coding gene	gene with protein product		615734				10048485	Standard	NM_014969		Approved	KIAA0893	uc001dwl.3	O94967	OTTHUMG00000011734	ENST00000369962.3:c.563delA	chr1.hg19:g.109554105delT	ENSP00000358979:p.Lys188fs	435.0	0.0	0		342.0	55.0	0.160819	NM_001142550	A8MX09|Q5TYV7|Q5TYV8|Q5TYV9|Q8IXT7|Q8IYU9	Frame_Shift_Del	DEL	ENST00000369962.3	hg19	CCDS44187.1																																																																																			.	.	.	none		0.413	WDR47-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000032414.2	NM_014969	
SLC31A1	1317	hgsc.bcm.edu	37	9	116018468	116018469	+	Frame_Shift_Ins	INS	-	-	C			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr9:116018468_116018469insC	ENST00000374212.4	+	2	192_193	c.40_41insC	c.(40-42)tccfs	p.S14fs	CDC26_ENST00000490408.1_Intron|SLC31A1_ENST00000374210.6_Frame_Shift_Ins_p.S14fs	NM_001859.3	NP_001850.1	O15431	COPT1_HUMAN	solute carrier family 31 (copper transporter), member 1	14					cellular copper ion homeostasis (GO:0006878)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	copper ion transmembrane transporter activity (GO:0005375)|copper uptake transmembrane transporter activity (GO:0015088)			breast(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)	7					Bortezomib(DB00188)|Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	CTATATGGACTCCAACAGTACC	0.436																																					p.S14fs	Ovarian(135;1049 1799 4519 17564 28677)	Atlas-INDEL	.											.	SLC31A1	12	.	0			c.40_41insC						PASS	.																																			SO:0001589	frameshift_variant	1317	exon2			.	U83460	CCDS6789.1	9q32	2013-07-17	2013-07-17		ENSG00000136868	ENSG00000136868		"""Solute carriers"""	11016	protein-coding gene	gene with protein product	copper transport 1 homolog (S. cerevisiae)	603085		COPT1		9207117	Standard	NM_001859		Approved	hCTR1, CTR1	uc004bgu.3	O15431	OTTHUMG00000020519	ENST00000374212.4:c.42dupC	chr9.hg19:g.116018470_116018470dupC	ENSP00000363329:p.Ser14fs	134.0	0.0	0		118.0	18.0	0.152542	NM_001859	A8K8Z6|Q53GR5|Q5T1M4	Frame_Shift_Ins	INS	ENST00000374212.4	hg19	CCDS6789.1																																																																																			.	.	.	none		0.436	SLC31A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053715.1	NM_001859	
C16orf92	146378	hgsc.bcm.edu	37	16	30035201	30035219	+	Splice_Site	DEL	ACTCAGGTATGAACCAGCT	ACTCAGGTATGAACCAGCT	-			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	ACTCAGGTATGAACCAGCT	ACTCAGGTATGAACCAGCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr16:30035201_30035219delACTCAGGTATGAACCAGCT	ENST00000300575.2	+	2	305_310	c.284_289delACTCAGGTATGAACCAGCT	c.(283-291)aactcaggt>agt	p.NSG95fs	DOC2A_ENST00000567824.1_5'Flank	NM_001109659.1|NM_001109660.1	NP_001103129.1|NP_001103130.1	Q96LL3	CP092_HUMAN	chromosome 16 open reading frame 92	95						integral component of membrane (GO:0016021)				breast(3)|lung(3)	6						GTGTTCATTAACTCAGGTATGAACCAGCTTGAGAAGGGA	0.543																																					p.95_97del		Atlas-INDEL	.											.	C16orf92	11	.	0			c.283_289del						PASS	.																																			SO:0001630	splice_region_variant	146378	exon2			.	AK058133	CCDS42146.1	16p11.2	2012-05-30			ENSG00000167194	ENSG00000167194			26346	protein-coding gene	gene with protein product							Standard	NM_001109659		Approved	FLJ25404	uc002dvs.2	Q96LL3	OTTHUMG00000177107	ENST00000300575.2:c.289+1ACTCAGGTATGAACCAGCT>-	chr16.hg19:g.30035201_30035219delACTCAGGTATGAACCAGCT		81.0	0.0	0		62.0	10.0	0.16129	NM_001109660	Q494R8	Frame_Shift_Del	DEL	ENST00000300575.2	hg19	CCDS42146.1																																																																																			.	.	.	none		0.543	C16orf92-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435351.1	NM_001109659	Frame_Shift_Del
OR1N2	138882	hgsc.bcm.edu	37	9	125316283	125316283	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr9:125316283delC	ENST00000373688.2	+	1	893	c.835delC	c.(835-837)cctfs	p.P280fs		NM_001004457.1	NP_001004457.1	Q8NGR9	OR1N2_HUMAN	olfactory receptor, family 1, subfamily N, member 2	280						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(3)	26						GTATTTACTTCCTCCATCAAC	0.463																																					p.L278fs		Atlas-INDEL	.											.	OR1N2	51	.	0			c.834delT						PASS	.						196.0	199.0	198.0					9																	125316283		2203	4300	6503	SO:0001589	frameshift_variant	138882	exon1			.		CCDS35123.1	9q33.2	2013-09-20			ENSG00000171501	ENSG00000171501		"""GPCR / Class A : Olfactory receptors"""	15111	protein-coding gene	gene with protein product							Standard	NM_001004457		Approved		uc011lyx.2	Q8NGR9	OTTHUMG00000020607	ENST00000373688.2:c.835delC	chr9.hg19:g.125316283delC	ENSP00000362792:p.Pro280fs	115.0	0.0	0		140.0	21.0	0.15	NM_001004457	A3KFM2|B2RNY4|Q6IF17|Q96RA3	Frame_Shift_Del	DEL	ENST00000373688.2	hg19	CCDS35123.1																																																																																			.	.	.	none		0.463	OR1N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053937.2		
WIPF2	147179	hgsc.bcm.edu	37	17	38420795	38420800	+	In_Frame_Del	DEL	CCAAGG	CCAAGG	-			TCGA-DW-7838-01A-11D-2136-08	TCGA-DW-7838-10A-01D-2136-08	CCAAGG	CCAAGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c7897a3f-6f47-41e8-b9b6-29bceb9d3c54	a0033479-cc47-403c-a95a-2fca2634ddbf	g.chr17:38420795_38420800delCCAAGG	ENST00000323571.4	+	5	607_612	c.367_372delCCAAGG	c.(367-372)ccaaggdel	p.PR123del	WIPF2_ENST00000394103.3_Intron|WIPF2_ENST00000494757.1_3'UTR|WIPF2_ENST00000585043.1_In_Frame_Del_p.PR123del|WIPF2_ENST00000536600.1_Intron|WIPF2_ENST00000583130.1_In_Frame_Del_p.PR123del	NM_133264.4	NP_573571.1	Q8TF74	WIPF2_HUMAN	WAS/WASL interacting protein family, member 2	123					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)		p.R124G(1)		NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	30						AGCTGCTGCCCCAAGGCCTCCAGTAT	0.573										HNSCC(43;0.11)																											p.122_124del		Atlas-INDEL	.											.	WIPF2	55	.	1	Substitution - Missense(1)	kidney(1)	c.366_371del						PASS	.																																			SO:0001651	inframe_deletion	147179	exon5			.	BC025965	CCDS11364.1	17q21.2	2006-10-12			ENSG00000171475	ENSG00000171475			30923	protein-coding gene	gene with protein product		609692				12213210, 11829459	Standard	XM_005257083		Approved	WICH, WIRE	uc002hug.1	Q8TF74	OTTHUMG00000133331	ENST00000323571.4:c.367_372delCCAAGG	chr17.hg19:g.38420795_38420800delCCAAGG	ENSP00000320924:p.Pro123_Arg124del	163.0	0.0	0		141.0	24.0	0.170213	NM_133264	A8K0L3|Q658J8|Q71RE1|Q8TE44	In_Frame_Del	DEL	ENST00000323571.4	hg19	CCDS11364.1																																																																																			.	.	.	none		0.573	WIPF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257157.2	NM_133264	
