#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_NTotCov	i_NVarCov	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	i_dbSNP_AF	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
ZMYND12	84217	hgsc.bcm.edu	37	1	42921631	42921631	+	Missense_Mutation	SNP	C	C	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr1:42921631C>T	ENST00000372565.3	-	1	307	c.38G>A	c.(37-39)cGc>cAc	p.R13H	PPCS_ENST00000372560.3_5'Flank|ZMYND12_ENST00000433602.2_5'UTR|PPCS_ENST00000455780.1_5'Flank|PPCS_ENST00000372562.1_5'Flank|PPCS_ENST00000372561.3_5'Flank|PPCS_ENST00000372556.3_5'Flank	NM_032257.4	NP_115633.3	Q9H0C1	ZMY12_HUMAN	zinc finger, MYND-type containing 12	13						intracellular (GO:0005622)	metal ion binding (GO:0046872)			NS(1)|endometrium(2)|large_intestine(3)|lung(5)|ovary(2)|prostate(2)|skin(2)	17	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				GCAGAGTCTGCGCCCCTTGGG	0.627																																					p.R13H		Atlas-SNP	.											.	ZMYND12	35	.	0			c.G38A						.						54.0	48.0	50.0					1																	42921631		2203	4300	6503	SO:0001583	missense	84217	exon1			AGTCTGCGCCCCT	AK057384	CCDS467.1	1p34.1	2008-02-05			ENSG00000066185	ENSG00000066185		"""Zinc fingers, MYND-type"""	21192	protein-coding gene	gene with protein product						11230166	Standard	NM_032257		Approved	DKFZp434N2435	uc001chj.3	Q9H0C1	OTTHUMG00000007333	ENST00000372565.3:c.38G>A	chr1.hg19:g.42921631C>T	ENSP00000361646:p.Arg13His	52.0	0.0		56.0	10.0	NM_032257	Q5VUS6|Q8TC87|Q96M51	Missense_Mutation	SNP	ENST00000372565.3	hg19	CCDS467.1	.	.	.	.	.	.	.	.	.	.	C	19.18	3.778003	0.70107	.	.	ENSG00000066185	ENST00000372565	T	0.46451	0.87	5.04	5.04	0.67666	.	0.207898	0.41823	D	0.000808	T	0.57095	0.2030	L	0.59436	1.845	0.80722	D	1	D	0.89917	1.0	D	0.71184	0.972	T	0.57329	-0.7830	10	0.56958	D	0.05	-12.7733	10.8881	0.46978	0.1875:0.8125:0.0:0.0	.	13	Q9H0C1	ZMY12_HUMAN	H	13	ENSP00000361646:R13H	ENSP00000361646:R13H	R	-	2	0	ZMYND12	42694218	1.000000	0.71417	1.000000	0.80357	0.522000	0.34438	2.641000	0.46587	2.612000	0.88384	0.563000	0.77884	CGC	.	.		0.627	ZMYND12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019170.1	NM_032257	
MIER1	57708	hgsc.bcm.edu	37	1	67436525	67436525	+	Silent	SNP	T	T	C			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr1:67436525T>C	ENST00000355356.3	+	8	797	c.648T>C	c.(646-648)ccT>ccC	p.P216P	MIER1_ENST00000401042.3_Silent_p.P216P|MIER1_ENST00000355977.6_Silent_p.P153P|MIER1_ENST00000371014.1_Silent_p.P269P|MIER1_ENST00000401041.1_Silent_p.P269P|MIER1_ENST00000371018.3_Silent_p.P233P|MIER1_ENST00000357692.2_Silent_p.P233P|MIER1_ENST00000371016.1_Silent_p.P233P	NM_001077701.2|NM_001077704.2	NP_001071169.1|NP_001071172.1	Q8N108	MIER1_HUMAN	mesoderm induction early response 1, transcriptional regulator	216	ELM2. {ECO:0000255|PROSITE- ProRule:PRU00512}.|Interaction with HDAC1.				positive regulation of chromatin silencing (GO:0031937)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(3)	15						TGTGGGACCCTGAGTACTTAC	0.328																																					p.P269P		Atlas-SNP	.											.	MIER1	86	.	0			c.T807C						.						82.0	77.0	79.0					1																	67436525		1828	4092	5920	SO:0001819	synonymous_variant	57708	exon9			GGACCCTGAGTAC		CCDS41347.1, CCDS41348.1, CCDS53325.1, CCDS53326.1, CCDS53327.1, CCDS53328.1, CCDS53329.1, CCDS53330.1, CCDS60163.1	1p31.2	2013-07-23	2013-07-23		ENSG00000198160	ENSG00000198160			29657	protein-coding gene	gene with protein product			"""mesoderm induction early response 1 homolog (Xenopus laevis)"""			12242014, 12482978	Standard	NM_020948		Approved	hMI-ER1, MI-ER1, KIAA1610	uc001dde.2	Q8N108	OTTHUMG00000009194	ENST00000355356.3:c.648T>C	chr1.hg19:g.67436525T>C		118.0	0.0		126.0	11.0	NM_001077700	C9JFD4|Q08AE0|Q32NC4|Q5T104|Q5TAD1|Q5TAD2|Q5TAD4|Q5TAD5|Q6AHY8|Q86TB4|Q8N156|Q8N161|Q8NC37|Q8NES4|Q8NES5|Q8NES6|Q8WWG2|Q9HCG2	Silent	SNP	ENST00000355356.3	hg19	CCDS41348.1																																																																																			.	.		0.328	MIER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025491.2	NM_020948	
GBP2	2634	hgsc.bcm.edu	37	1	89578243	89578243	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr1:89578243A>T	ENST00000370466.3	-	8	1542	c.1274T>A	c.(1273-1275)tTt>tAt	p.F425Y	GBP2_ENST00000463660.1_5'UTR	NM_004120.3	NP_004111.2	P32456	GBP2_HUMAN	guanylate binding protein 2, interferon-inducible	425					cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(1)	20		Lung NSC(277;0.0908)		all cancers(265;0.0151)|Epithelial(280;0.0284)		TGGTTTAGAAAATGTTCCCTG	0.428																																					p.F425Y		Atlas-SNP	.											.	GBP2	58	.	0			c.T1274A						.						175.0	166.0	169.0					1																	89578243		2203	4300	6503	SO:0001583	missense	2634	exon8			TTAGAAAATGTTC	BC073163	CCDS719.1	1p22.2	2008-02-05			ENSG00000162645	ENSG00000162645			4183	protein-coding gene	gene with protein product		600412				1715024	Standard	NM_004120		Approved		uc001dmz.1	P32456	OTTHUMG00000010662	ENST00000370466.3:c.1274T>A	chr1.hg19:g.89578243A>T	ENSP00000359497:p.Phe425Tyr	233.0	0.0		193.0	25.0	NM_004120	Q6GPH0|Q6IAU2|Q86TB0	Missense_Mutation	SNP	ENST00000370466.3	hg19	CCDS719.1	.	.	.	.	.	.	.	.	.	.	A	6.621	0.482934	0.12581	.	.	ENSG00000162645	ENST00000370466	T	0.02085	4.46	3.56	-2.84	0.05751	Guanylate-binding protein, C-terminal (3);	0.094194	0.42682	U	0.000679	T	0.00412	0.0013	N	0.11756	0.17	0.09310	N	1	B	0.12630	0.006	B	0.20184	0.028	T	0.38394	-0.9663	10	0.17832	T	0.49	-8.5448	8.7717	0.34735	0.3966:0.0:0.0:0.6034	.	425	P32456	GBP2_HUMAN	Y	425	ENSP00000359497:F425Y	ENSP00000359497:F425Y	F	-	2	0	GBP2	89350831	0.001000	0.12720	0.004000	0.12327	0.011000	0.07611	-0.264000	0.08658	-0.714000	0.04975	-0.490000	0.04691	TTT	.	.		0.428	GBP2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029406.2	NM_004120	
HFM1	164045	hgsc.bcm.edu	37	1	91784929	91784929	+	Silent	SNP	T	T	C			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr1:91784929T>C	ENST00000370425.3	-	24	2699	c.2601A>G	c.(2599-2601)ctA>ctG	p.L867L	HFM1_ENST00000294696.5_Silent_p.L99L|HFM1_ENST00000462405.1_5'UTR|HFM1_ENST00000370424.3_Silent_p.L546L	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	867	SEC63.				resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		GAATGCATCCTAGTTGAGCCT	0.383																																					p.L867L		Atlas-SNP	.											.	HFM1	188	.	0			c.A2601G						.						100.0	96.0	97.0					1																	91784929		2203	4300	6503	SO:0001819	synonymous_variant	164045	exon24			GCATCCTAGTTGA	AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"""SEC63 domain containing 1"""	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.2601A>G	chr1.hg19:g.91784929T>C		111.0	0.0		88.0	14.0	NM_001017975	B1B0B6|Q8N9Q0	Silent	SNP	ENST00000370425.3	hg19	CCDS30769.2	.	.	.	.	.	.	.	.	.	.	T	8.633	0.894213	0.17613	.	.	ENSG00000162669	ENST00000430465	.	.	.	5.0	3.79	0.43588	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.8832	0.18866	0.2429:0.0756:0.0:0.6815	.	.	.	.	W	123	.	.	X	-	2	0	HFM1	91557517	0.862000	0.29867	1.000000	0.80357	0.984000	0.73092	-0.066000	0.11598	1.996000	0.58369	0.528000	0.53228	TAG	.	.		0.383	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975	
C1orf146	388649	hgsc.bcm.edu	37	1	92711222	92711222	+	Missense_Mutation	SNP	C	C	A			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr1:92711222C>A	ENST00000370375.3	+	6	682	c.534C>A	c.(532-534)aaC>aaA	p.N178K	C1orf146_ENST00000370373.2_Missense_Mutation_p.N119K	NM_001012425.1	NP_001012425.1	Q5VVC0	CA146_HUMAN	chromosome 1 open reading frame 146	178										breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	8		all_lung(203;0.00528)|Lung NSC(277;0.0193)		all cancers(265;0.00846)|Epithelial(280;0.0952)		ATTCAGTTAACCCAAATTAGA	0.284																																					p.N178K		Atlas-SNP	.											.	C1orf146	21	.	0			c.C534A						.						55.0	59.0	58.0					1																	92711222		2203	4297	6500	SO:0001583	missense	388649	exon6			AGTTAACCCAAAT		CCDS30772.1	1p22.1	2008-02-05			ENSG00000203910	ENSG00000203910			24032	protein-coding gene	gene with protein product						15496913	Standard	NM_001012425		Approved		uc001doq.3	Q5VVC0	OTTHUMG00000010285	ENST00000370375.3:c.534C>A	chr1.hg19:g.92711222C>A	ENSP00000359401:p.Asn178Lys	176.0	0.0		153.0	28.0	NM_001012425	Q5VVC4	Missense_Mutation	SNP	ENST00000370375.3	hg19	CCDS30772.1	.	.	.	.	.	.	.	.	.	.	C	12.00	1.807788	0.31961	.	.	ENSG00000203910	ENST00000370375;ENST00000370373	.	.	.	4.86	-2.77	0.05877	.	0.737577	0.11935	N	0.515324	T	0.11495	0.0280	L	0.27053	0.805	0.09310	N	1	B	0.25609	0.13	B	0.21917	0.037	T	0.30297	-0.9983	9	0.52906	T	0.07	-11.9764	10.2976	0.43633	0.0:0.4187:0.0:0.5813	.	178	Q5VVC0	CA146_HUMAN	K	178;157	.	ENSP00000359399:N157K	N	+	3	2	C1orf146	92483810	0.000000	0.05858	0.001000	0.08648	0.113000	0.19764	-0.721000	0.04963	-0.455000	0.07054	0.655000	0.94253	AAC	.	.		0.284	C1orf146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028364.1	NM_001012425	
PALMD	54873	hgsc.bcm.edu	37	1	100154912	100154912	+	Missense_Mutation	SNP	A	A	C			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr1:100154912A>C	ENST00000263174.4	+	7	1471	c.1096A>C	c.(1096-1098)Aag>Cag	p.K366Q	PALMD_ENST00000605497.1_Missense_Mutation_p.K366Q	NM_017734.4	NP_060204.1	Q9NP74	PALMD_HUMAN	palmdelphin	366					regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|membrane (GO:0016020)				central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(8)|ovary(6)|pancreas(1)|prostate(2)	31		all_epithelial(167;0.000813)|all_lung(203;0.0214)|Lung NSC(277;0.0216)		Epithelial(280;0.067)|all cancers(265;0.117)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)		ACCCTCTCCAAAGCCAAGGCT	0.458																																					p.K366Q		Atlas-SNP	.											.	PALMD	64	.	0			c.A1096C						.						52.0	48.0	49.0					1																	100154912		2203	4300	6503	SO:0001583	missense	54873	exon7			TCTCCAAAGCCAA	AJ312214	CCDS758.1	1p22-p21	2008-07-18			ENSG00000099260	ENSG00000099260			15846	protein-coding gene	gene with protein product		610182		C1orf11		11478809	Standard	NM_017734		Approved	FLJ20271, PALML	uc001dsg.3	Q9NP74	OTTHUMG00000010764	ENST00000263174.4:c.1096A>C	chr1.hg19:g.100154912A>C	ENSP00000263174:p.Lys366Gln	159.0	0.0		126.0	13.0	NM_017734	Q9H7E6|Q9NPM5|Q9NPM6|Q9NPS0	Missense_Mutation	SNP	ENST00000263174.4	hg19	CCDS758.1	.	.	.	.	.	.	.	.	.	.	A	5.985	0.365684	0.11352	.	.	ENSG00000099260	ENST00000263174	T	0.18338	2.22	5.93	3.62	0.41486	.	0.561503	0.20364	N	0.093794	T	0.04272	0.0118	L	0.44542	1.39	0.21325	N	0.999729	B;P	0.34724	0.045;0.465	B;B	0.31101	0.023;0.124	T	0.35674	-0.9779	10	0.31617	T	0.26	-8.0102	6.2561	0.20874	0.729:0.1344:0.1366:0.0	.	366;286	Q9NP74;Q9NP74-2	PALMD_HUMAN;.	Q	366	ENSP00000263174:K366Q	ENSP00000263174:K366Q	K	+	1	0	PALMD	99927500	0.006000	0.16342	0.409000	0.26459	0.134000	0.20937	0.468000	0.22051	0.496000	0.27904	0.460000	0.39030	AAG	.	.		0.458	PALMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029672.1	NM_017734	
SPAG17	200162	hgsc.bcm.edu	37	1	118548101	118548101	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr1:118548101T>A	ENST00000336338.5	-	32	4777	c.4712A>T	c.(4711-4713)tAc>tTc	p.Y1571F		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1571						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		CCTCATGATGTACCTGCCAGC	0.448																																					p.Y1571F		Atlas-SNP	.											.	SPAG17	263	.	0			c.A4712T						.						141.0	136.0	138.0					1																	118548101		2203	4300	6503	SO:0001583	missense	200162	exon32			ATGATGTACCTGC		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.4712A>T	chr1.hg19:g.118548101T>A	ENSP00000337804:p.Tyr1571Phe	104.0	0.0		103.0	8.0	NM_206996	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	hg19	CCDS899.1	.	.	.	.	.	.	.	.	.	.	T	16.87	3.241748	0.58995	.	.	ENSG00000155761	ENST00000336338;ENST00000437255	T	0.68903	-0.36	5.72	5.72	0.89469	.	0.056586	0.64402	D	0.000001	T	0.76343	0.3974	M	0.73962	2.25	0.39965	D	0.974715	D	0.89917	1.0	D	0.66847	0.947	T	0.80777	-0.1231	10	0.87932	D	0	.	14.9829	0.71324	0.0:0.0:0.0:1.0	.	1571	Q6Q759	SPG17_HUMAN	F	1571;51	ENSP00000337804:Y1571F	ENSP00000337804:Y1571F	Y	-	2	0	SPAG17	118349624	1.000000	0.71417	0.998000	0.56505	0.121000	0.20230	5.486000	0.66856	2.177000	0.69029	0.533000	0.62120	TAC	.	.		0.448	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996	
FLG	2312	hgsc.bcm.edu	37	1	152281931	152281931	+	Missense_Mutation	SNP	C	C	A			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr1:152281931C>A	ENST00000368799.1	-	3	5466	c.5431G>T	c.(5431-5433)Gac>Tac	p.D1811Y	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1811	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CGAATGGTGTCCTGACCCTCT	0.597									Ichthyosis																												p.D1811Y		Atlas-SNP	.											FLG,left_upper_lobe,carcinoma,0,1	FLG	900	.	0			c.G5431T						.						344.0	352.0	349.0					1																	152281931		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGGTGTCCTGACC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.5431G>T	chr1.hg19:g.152281931C>A	ENSP00000357789:p.Asp1811Tyr	384.0	1.0		466.0	65.0	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	hg19	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	C	9.802	1.180789	0.21787	.	.	ENSG00000143631	ENST00000368799;ENST00000271820	T	0.01705	4.68	3.72	1.79	0.24919	.	.	.	.	.	T	0.03477	0.0100	M	0.80028	2.48	0.09310	N	1	D	0.76494	0.999	D	0.80764	0.994	T	0.33624	-0.9861	9	0.62326	D	0.03	.	6.2456	0.20815	0.0:0.7607:0.0:0.2393	.	1811	P20930	FILA_HUMAN	Y	1811;46	ENSP00000357789:D1811Y	ENSP00000271820:D46Y	D	-	1	0	FLG	150548555	0.000000	0.05858	0.029000	0.17559	0.111000	0.19643	-1.742000	0.01835	0.366000	0.24427	0.447000	0.29281	GAC	.	.		0.597	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
SPRR2B	6701	hgsc.bcm.edu	37	1	153043186	153043186	+	Missense_Mutation	SNP	G	G	A			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr1:153043186G>A	ENST00000368755.2	-	1	130	c.130C>T	c.(130-132)Ccc>Tcc	p.P44S	SPRR2B_ENST00000341611.2_Missense_Mutation_p.P44S|SPRR2B_ENST00000368752.4_Missense_Mutation_p.P44S			P35325	SPR2B_HUMAN	small proline-rich protein 2B	44	3 X 9 AA tandem repeats of P-K-C-P-[EQ]- P-C-P-P.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)				endometrium(2)|large_intestine(1)|lung(2)	5	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			GGTGGGCAGGGCTGTGGACAC	0.617																																					p.P44S		Atlas-SNP	.											.	SPRR2B	15	.	0			c.C130T						.						95.0	88.0	90.0					1																	153043186		2203	4297	6500	SO:0001583	missense	6701	exon3			GGCAGGGCTGTGG	AF333952	CCDS30865.1	1q21-q22	2008-02-05			ENSG00000196805	ENSG00000196805			11262	protein-coding gene	gene with protein product		182268				8325635	Standard	NM_001017418		Approved		uc001fbg.3	P35325	OTTHUMG00000013863	ENST00000368755.2:c.130C>T	chr1.hg19:g.153043186G>A	ENSP00000357744:p.Pro44Ser	216.0	0.0		207.0	24.0	NM_001017418	Q5T528	Missense_Mutation	SNP	ENST00000368755.2	hg19	CCDS30865.1	.	.	.	.	.	.	.	.	.	.	G	11.06	1.527789	0.27299	.	.	ENSG00000196805	ENST00000368755;ENST00000341611;ENST00000368752	T;T;T	0.29917	1.55;1.55;1.55	3.34	1.12	0.20585	.	0.490293	0.15324	N	0.268362	T	0.09202	0.0227	.	.	.	0.09310	N	1	B	0.27700	0.186	B	0.30855	0.121	T	0.24190	-1.0167	9	0.87932	D	0	.	4.6748	0.12706	0.1334:0.0:0.6562:0.2103	.	44	P35325	SPR2B_HUMAN	S	44	ENSP00000357744:P44S;ENSP00000340703:P44S;ENSP00000357741:P44S	ENSP00000340703:P44S	P	-	1	0	SPRR2B	151309810	0.009000	0.17119	0.001000	0.08648	0.755000	0.42902	0.405000	0.21015	0.478000	0.27488	0.455000	0.32223	CCC	.	.		0.617	SPRR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038905.2		
OR10T2	128360	hgsc.bcm.edu	37	1	158368778	158368778	+	Missense_Mutation	SNP	G	G	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr1:158368778G>T	ENST00000334438.1	-	1	478	c.479C>A	c.(478-480)gCc>gAc	p.A160D		NM_001004475.1	NP_001004475.1	Q8NGX3	O10T2_HUMAN	olfactory receptor, family 10, subfamily T, member 2	160						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_hematologic(112;0.0378)					GAGGTTGGTGGCCACCAAAGC	0.468																																					p.A160D		Atlas-SNP	.											.	OR10T2	76	.	0			c.C479A						.						68.0	66.0	67.0					1																	158368778		2203	4300	6503	SO:0001583	missense	128360	exon1			TTGGTGGCCACCA	AB065643	CCDS30895.1	1q23.1	2012-08-09			ENSG00000186306	ENSG00000186306		"""GPCR / Class A : Olfactory receptors"""	14816	protein-coding gene	gene with protein product							Standard	NM_001004475		Approved		uc010pih.2	Q8NGX3	OTTHUMG00000017521	ENST00000334438.1:c.479C>A	chr1.hg19:g.158368778G>T	ENSP00000334115:p.Ala160Asp	60.0	0.0		85.0	5.0	NM_001004475	Q6IF98	Missense_Mutation	SNP	ENST00000334438.1	hg19	CCDS30895.1	.	.	.	.	.	.	.	.	.	.	G	7.889	0.731896	0.15507	.	.	ENSG00000186306	ENST00000334438	T	0.00130	8.69	4.57	2.7	0.31948	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41823	D	0.000819	T	0.00039	0.0001	N	0.13003	0.285	0.09310	N	1	P	0.47191	0.891	P	0.54889	0.763	T	0.01280	-1.1397	10	0.44086	T	0.13	.	5.6799	0.17769	0.1753:0.0:0.6681:0.1565	.	160	Q8NGX3	O10T2_HUMAN	D	160	ENSP00000334115:A160D	ENSP00000334115:A160D	A	-	2	0	OR10T2	156635402	0.000000	0.05858	0.987000	0.45799	0.799000	0.45148	0.554000	0.23407	0.546000	0.28920	0.655000	0.94253	GCC	.	.		0.468	OR10T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046371.1	NM_001004475	
HSD17B7	51478	hgsc.bcm.edu	37	1	162760596	162760596	+	Silent	SNP	A	A	G			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr1:162760596A>G	ENST00000254521.3	+	1	61	c.6A>G	c.(4-6)cgA>cgG	p.R2R	HSD17B7_ENST00000367917.3_Silent_p.R2R|HSD17B7_ENST00000485405.1_3'UTR|HSD17B7_ENST00000367913.1_Silent_p.R2R|HSD17B7_ENST00000367915.1_Silent_p.R2R	NM_016371.2	NP_057455.1	P56937	DHB7_HUMAN	hydroxysteroid (17-beta) dehydrogenase 7	2					cholesterol biosynthetic process (GO:0006695)|estrogen biosynthetic process (GO:0006703)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	3-keto sterol reductase activity (GO:0000253)|estradiol 17-beta-dehydrogenase activity (GO:0004303)			endometrium(3)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	9	all_hematologic(112;0.115)					CGAAGATGCGAAAGGTGGTTT	0.607																																					p.R2R		Atlas-SNP	.											.	HSD17B7	25	.	0			c.A6G						.						59.0	48.0	51.0					1																	162760596		2203	4300	6503	SO:0001819	synonymous_variant	51478	exon1			GATGCGAAAGGTG	AF098786	CCDS1242.1	1q23	2011-09-14			ENSG00000132196	ENSG00000132196	1.1.1.270	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	5215	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 37C, member 1"""	606756				10544267, 10419022, 19027726	Standard	NM_016371		Approved	PRAP, SDR37C1	uc001gci.3	P56937	OTTHUMG00000034420	ENST00000254521.3:c.6A>G	chr1.hg19:g.162760596A>G		547.0	0.0		671.0	86.0	NM_016371	Q5T246|Q7Z4V9|Q8WWS2|Q9UF00	Silent	SNP	ENST00000254521.3	hg19	CCDS1242.1																																																																																			.	.		0.607	HSD17B7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083207.1	NM_016371	
POGK	57645	hgsc.bcm.edu	37	1	166818288	166818288	+	Missense_Mutation	SNP	A	A	G			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr1:166818288A>G	ENST00000367875.1	+	5	832	c.472A>G	c.(472-474)Atc>Gtc	p.I158V	POGK_ENST00000536514.1_Missense_Mutation_p.I73V|POGK_ENST00000367876.4_Missense_Mutation_p.I158V|POGK_ENST00000537173.1_Missense_Mutation_p.I40V			Q9P215	POGK_HUMAN	pogo transposable element with KRAB domain	158					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|kidney(1)|large_intestine(8)|lung(4)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	22						GCCTCGGGATATCACAGAGCT	0.557																																					p.I158V	GBM(76;192 1530 30153 48742)	Atlas-SNP	.											.	POGK	54	.	0			c.A472G						.						106.0	101.0	103.0					1																	166818288		2203	4300	6503	SO:0001583	missense	57645	exon5			CGGGATATCACAG	AB040946	CCDS1254.1	1q23.2	2013-01-08			ENSG00000143157	ENSG00000143157		"""-"""	18800	protein-coding gene	gene with protein product	"""KRAB box domain containing 2"""						Standard	NM_017542		Approved	KIAA15131, LST003, BASS2, KRBOX2	uc001gdt.1	Q9P215	OTTHUMG00000034325	ENST00000367875.1:c.472A>G	chr1.hg19:g.166818288A>G	ENSP00000356849:p.Ile158Val	304.0	0.0		340.0	63.0	NM_017542	Q5TIJ1|Q8TE07	Missense_Mutation	SNP	ENST00000367875.1	hg19	CCDS1254.1	.	.	.	.	.	.	.	.	.	.	A	9.958	1.222131	0.22457	.	.	ENSG00000143157	ENST00000537173;ENST00000536514;ENST00000449930;ENST00000367876;ENST00000367875	T;T;T;T;T	0.35605	1.33;1.3;4.79;4.71;4.71	5.39	-1.24	0.09435	.	0.634401	0.13847	N	0.358600	T	0.09335	0.0230	N	0.19112	0.55	0.23070	N	0.998344	B;B;B	0.13594	0.004;0.008;0.008	B;B;B	0.15870	0.014;0.006;0.006	T	0.20240	-1.0281	9	0.62326	D	0.03	-18.915	10.1994	0.43073	0.2428:0.6429:0.0:0.1142	.	40;73;158	G3V1P0;B4DS22;Q9P215	.;.;POGK_HUMAN	V	40;73;158;158;158	ENSP00000442763:I40V;ENSP00000441187:I73V;ENSP00000404402:I158V;ENSP00000356850:I158V;ENSP00000356849:I158V	ENSP00000356849:I158V	I	+	1	0	POGK	165084912	0.021000	0.18746	0.086000	0.20670	0.959000	0.62525	-0.176000	0.09811	-0.370000	0.08016	0.533000	0.62120	ATC	.	.		0.557	POGK-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082888.1	NM_017542	
KIAA0040	9674	hgsc.bcm.edu	37	1	175129922	175129922	+	Missense_Mutation	SNP	A	A	C			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr1:175129922A>C	ENST00000423313.1	-	4	764	c.228T>G	c.(226-228)gaT>gaG	p.D76E	KIAA0040_ENST00000567124.1_5'Flank|KIAA0040_ENST00000545251.2_Missense_Mutation_p.D76E|KIAA0040_ENST00000444639.1_Missense_Mutation_p.D76E	NM_001162893.1|NM_001162895.1|NM_014656.2	NP_001156365.1|NP_001156367.1|NP_055471.2	Q15053	K0040_HUMAN	KIAA0040	0																	GGtcttcttcatccttcttct	0.498																																					p.D76E		Atlas-SNP	.											.	KIAA0040	2	.	0			c.T228G						.						123.0	102.0	108.0					1																	175129922		692	1591	2283	SO:0001583	missense	9674	exon3			TTCTTCATCCTTC	D25539		1q24-q25	2012-11-29			ENSG00000235750	ENSG00000235750			28950	protein-coding gene	gene with protein product							Standard	NM_014656		Approved		uc001gkn.3	Q15053	OTTHUMG00000034880	ENST00000423313.1:c.228T>G	chr1.hg19:g.175129922A>C	ENSP00000462172:p.Asp76Glu	91.0	0.0		108.0	6.0	NM_001162895	A8K9H6|Q2NKQ0	Missense_Mutation	SNP	ENST00000423313.1	hg19																																																																																				.	.		0.498	KIAA0040-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000084420.3	NM_014656	
KIAA0040	9674	hgsc.bcm.edu	37	1	175129924	175129924	+	Missense_Mutation	SNP	C	C	T	rs150137790		TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr1:175129924C>T	ENST00000423313.1	-	4	762	c.226G>A	c.(226-228)Gat>Aat	p.D76N	KIAA0040_ENST00000567124.1_5'Flank|KIAA0040_ENST00000545251.2_Missense_Mutation_p.D76N|KIAA0040_ENST00000444639.1_Missense_Mutation_p.D76N	NM_001162893.1|NM_001162895.1|NM_014656.2	NP_001156365.1|NP_001156367.1|NP_055471.2	Q15053	K0040_HUMAN	KIAA0040	0																	tcttcttcatccttcttcttc	0.502																																					p.D76N		Atlas-SNP	.											.	KIAA0040	2	.	0			c.G226A						.						120.0	100.0	106.0					1																	175129924		692	1591	2283	SO:0001583	missense	9674	exon3			CTTCATCCTTCTT	D25539		1q24-q25	2012-11-29			ENSG00000235750	ENSG00000235750			28950	protein-coding gene	gene with protein product							Standard	NM_014656		Approved		uc001gkn.3	Q15053	OTTHUMG00000034880	ENST00000423313.1:c.226G>A	chr1.hg19:g.175129924C>T	ENSP00000462172:p.Asp76Asn	91.0	0.0		105.0	5.0	NM_001162895	A8K9H6|Q2NKQ0	Missense_Mutation	SNP	ENST00000423313.1	hg19																																																																																				.	.		0.502	KIAA0040-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000084420.3	NM_014656	
PTPRC	5788	hgsc.bcm.edu	37	1	198682109	198682109	+	Missense_Mutation	SNP	G	G	A			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr1:198682109G>A	ENST00000367376.2	+	12	1364	c.1193G>A	c.(1192-1194)tGt>tAt	p.C398Y	PTPRC_ENST00000352140.3_Missense_Mutation_p.C350Y|PTPRC_ENST00000442510.2_Missense_Mutation_p.C400Y|PTPRC_ENST00000348564.6_Missense_Mutation_p.C239Y|PTPRC_ENST00000594404.1_Missense_Mutation_p.C237Y	NM_002838.4	NP_002829.3	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	398	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|bone marrow development (GO:0048539)|cell cycle phase transition (GO:0044770)|cell surface receptor signaling pathway (GO:0007166)|defense response to virus (GO:0051607)|dephosphorylation (GO:0016311)|hematopoietic progenitor cell differentiation (GO:0002244)|immunoglobulin biosynthetic process (GO:0002378)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of antigen receptor-mediated signaling pathway (GO:0050857)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of T cell proliferation (GO:0042102)|protein dephosphorylation (GO:0006470)|regulation of cell cycle (GO:0051726)|release of sequestered calcium ion into cytosol (GO:0051209)|stem cell development (GO:0048864)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(7)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(22)|lung(41)|ovary(4)|pancreas(2)|prostate(1)|skin(13)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	111						ATTATTTTTTGTAGAAGTGAA	0.323																																					p.C400Y		Atlas-SNP	.											.	PTPRC	229	.	0			c.G1199A						.						104.0	113.0	110.0					1																	198682109		2203	4300	6503	SO:0001583	missense	5788	exon12			TTTTTTGTAGAAG	Y00062	CCDS1397.1, CCDS1398.1, CCDS44291.1, CCDS1397.2, CCDS1398.2, CCDS44291.2	1q31-q32	2014-09-17			ENSG00000081237	ENSG00000081237		"""CD molecules"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9666	protein-coding gene	gene with protein product		151460		CD45		2169617	Standard	NM_001267798		Approved	LCA, T200, GP180	uc001gur.2	P08575	OTTHUMG00000035702	ENST00000367376.2:c.1193G>A	chr1.hg19:g.198682109G>A	ENSP00000356346:p.Cys398Tyr	110.0	0.0		140.0	9.0	NM_002838	A8K7W6|Q16614|Q9H0Y6	Missense_Mutation	SNP	ENST00000367376.2	hg19		.	.	.	.	.	.	.	.	.	.	G	12.44	1.939446	0.34189	.	.	ENSG00000081237	ENST00000367376;ENST00000367366;ENST00000352140;ENST00000535566;ENST00000530727;ENST00000442510;ENST00000367367;ENST00000348564	T	0.56941	0.43	3.86	2.91	0.33838	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.474926	0.18045	N	0.153479	T	0.66446	0.2790	M	0.65975	2.015	0.09310	N	1	D;D;D;D;D	0.76494	0.998;0.999;0.994;0.999;0.993	D;D;D;D;D	0.76071	0.969;0.987;0.949;0.949;0.93	T	0.54529	-0.8280	10	0.87932	D	0	.	8.7144	0.34403	0.0:0.0:0.7741:0.2259	.	334;334;239;350;398	F5GXZ3;B4DSZ5;B1ALS3;E9PC28;P08575	.;.;.;.;PTPRC_HUMAN	Y	400;334;350;350;284;398;332;237	ENSP00000193532:C350Y	ENSP00000306782:C237Y	C	+	2	0	PTPRC	196948732	0.043000	0.20138	0.002000	0.10522	0.002000	0.02628	1.531000	0.36018	1.158000	0.42547	0.591000	0.81541	TGT	.	.		0.323	PTPRC-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding			
MARK1	4139	hgsc.bcm.edu	37	1	220826560	220826560	+	Silent	SNP	G	G	A			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr1:220826560G>A	ENST00000366917.4	+	16	2120	c.1854G>A	c.(1852-1854)caG>caA	p.Q618Q	MARK1_ENST00000402574.1_Silent_p.Q483Q|MARK1_ENST00000366918.4_Silent_p.Q596Q					MAP/microtubule affinity-regulating kinase 1											central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(12)|lung(22)|ovary(4)|pancreas(1)|skin(3)|stomach(3)|urinary_tract(1)	63				GBM - Glioblastoma multiforme(131;0.0407)		ATGGTGAACAGCTCCGGGAGC	0.562																																					p.Q618Q		Atlas-SNP	.											.	MARK1	161	.	0			c.G1854A						.						95.0	84.0	87.0					1																	220826560		2203	4300	6503	SO:0001819	synonymous_variant	4139	exon16			TGAACAGCTCCGG	AF154845	CCDS31029.2, CCDS65789.1, CCDS73033.1, CCDS73034.1	1q41	2013-06-27			ENSG00000116141	ENSG00000116141			6896	protein-coding gene	gene with protein product		606511				9108484	Standard	NM_018650		Approved	MARK, PAR-1C	uc001hmn.4	Q9P0L2	OTTHUMG00000037351	ENST00000366917.4:c.1854G>A	chr1.hg19:g.220826560G>A		230.0	0.0		237.0	12.0	NM_018650		Silent	SNP	ENST00000366917.4	hg19	CCDS31029.2																																																																																			.	.		0.562	MARK1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090899.1		
OR2M5	127059	hgsc.bcm.edu	37	1	248308834	248308834	+	Missense_Mutation	SNP	C	C	G	rs150844237		TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr1:248308834C>G	ENST00000366476.1	+	1	385	c.385C>G	c.(385-387)Cct>Gct	p.P129A		NM_001004690.1	NP_001004690.1	A3KFT3	OR2M5_HUMAN	olfactory receptor, family 2, subfamily M, member 5	129						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	49	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0388)			CATTTGCCACCCTCTAAGATA	0.443																																					p.P129A		Atlas-SNP	.											.	OR2M5	117	.	0			c.C385G						.						287.0	286.0	287.0					1																	248308834		2203	4300	6503	SO:0001583	missense	127059	exon1			TGCCACCCTCTAA		CCDS31105.1	1q44	2012-08-09		2004-03-10	ENSG00000162727	ENSG00000162727		"""GPCR / Class A : Olfactory receptors"""	19576	protein-coding gene	gene with protein product				OR2M5P			Standard	NM_001004690		Approved		uc010pze.2	A3KFT3	OTTHUMG00000040447	ENST00000366476.1:c.385C>G	chr1.hg19:g.248308834C>G	ENSP00000355432:p.Pro129Ala	400.0	0.0		508.0	26.0	NM_001004690		Missense_Mutation	SNP	ENST00000366476.1	hg19	CCDS31105.1	.	.	.	.	.	.	.	.	.	.	c	13.37	2.217809	0.39201	.	.	ENSG00000162727	ENST00000366476	T	0.01838	4.61	3.28	3.28	0.37604	GPCR, rhodopsin-like superfamily (1);	0.000000	0.31949	U	0.006810	T	0.14227	0.0344	H	0.98314	4.2	0.33242	D	0.557303	D	0.54964	0.969	P	0.48770	0.589	T	0.57046	-0.7878	10	0.87932	D	0	.	14.4562	0.67418	0.0:1.0:0.0:0.0	.	129	A3KFT3	OR2M5_HUMAN	A	129	ENSP00000355432:P129A	ENSP00000355432:P129A	P	+	1	0	OR2M5	246375457	0.996000	0.38824	0.033000	0.17914	0.084000	0.17831	5.640000	0.67875	1.528000	0.49103	0.492000	0.49549	CCT	.	C|1.000;T|0.000		0.443	OR2M5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097343.1	NM_001004690	
OR2T11	127077	hgsc.bcm.edu	37	1	248789769	248789769	+	Missense_Mutation	SNP	T	T	C			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr1:248789769T>C	ENST00000330803.2	-	1	722	c.661A>G	c.(661-663)Acc>Gcc	p.T221A		NM_001001964.1	NP_001001964.1	Q8NH01	O2T11_HUMAN	olfactory receptor, family 2, subfamily T, member 11 (gene/pseudogene)	221						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|large_intestine(5)|lung(20)|skin(2)	28	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CGGTGGATGGTTAACAAGATG	0.488																																					p.T221A		Atlas-SNP	.											.	OR2T11	64	.	0			c.A661G						.						67.0	70.0	69.0					1																	248789769		2053	4233	6286	SO:0001583	missense	127077	exon1			GGATGGTTAACAA	BK004476	CCDS31122.1	1q44	2013-10-10	2013-10-10		ENSG00000183130	ENSG00000183130		"""GPCR / Class A : Olfactory receptors"""	19574	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily T, member 11"""				Standard	NM_001001964		Approved	OR2T11Q	uc001ier.1	Q8NH01	OTTHUMG00000040384	ENST00000330803.2:c.661A>G	chr1.hg19:g.248789769T>C	ENSP00000328934:p.Thr221Ala	198.0	0.0		224.0	18.0	NM_001001964	Q6IEY6	Missense_Mutation	SNP	ENST00000330803.2	hg19	CCDS31122.1	.	.	.	.	.	.	.	.	.	.	.	0.012	-1.652132	0.00785	.	.	ENSG00000183130	ENST00000330803	T	0.00029	8.91	4.23	0.506	0.16961	GPCR, rhodopsin-like superfamily (1);	0.000000	0.43260	D	0.000596	T	0.00073	0.0002	N	0.10945	0.07	0.09310	N	1	B	0.19706	0.038	B	0.31245	0.126	T	0.12967	-1.0527	10	0.07175	T	0.84	.	7.8476	0.29435	0.0:0.3676:0.0:0.6324	.	221	Q8NH01	O2T11_HUMAN	A	221	ENSP00000328934:T221A	ENSP00000328934:T221A	T	-	1	0	OR2T11	246856392	0.008000	0.16893	0.001000	0.08648	0.002000	0.02628	0.367000	0.20382	0.185000	0.20105	0.528000	0.53228	ACC	.	.		0.488	OR2T11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097134.1	NM_001001964	
ZNF638	27332	hgsc.bcm.edu	37	2	71629093	71629093	+	Missense_Mutation	SNP	A	A	G			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr2:71629093A>G	ENST00000409544.1	+	16	3335	c.2705A>G	c.(2704-2706)gAa>gGa	p.E902G	ZNF638_ENST00000355812.3_Missense_Mutation_p.E902G|ZNF638_ENST00000264447.4_Missense_Mutation_p.E902G	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	902					regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						AAGGAAACAGAAGAAATGTGT	0.269																																					p.E902G		Atlas-SNP	.											.	ZNF638	179	.	0			c.A2705G						.						69.0	74.0	72.0					2																	71629093		2203	4297	6500	SO:0001583	missense	27332	exon16			AAACAGAAGAAAT	D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"""RNA binding motif (RRM) containing"""	17894	protein-coding gene	gene with protein product		614349	"""zinc finger, matrin-like"""	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.2705A>G	chr2.hg19:g.71629093A>G	ENSP00000386433:p.Glu902Gly	62.0	0.0		49.0	9.0	NM_014497	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Missense_Mutation	SNP	ENST00000409544.1	hg19	CCDS1917.1	.	.	.	.	.	.	.	.	.	.	A	16.34	3.094463	0.56075	.	.	ENSG00000075292	ENST00000394137;ENST00000355812;ENST00000264447;ENST00000409544	T;T;T	0.59772	0.24;1.24;1.24	5.69	5.69	0.88448	.	0.382752	0.27691	N	0.018253	T	0.54886	0.1886	M	0.61703	1.905	0.80722	D	1	P;P;P;P	0.38827	0.518;0.465;0.649;0.518	B;B;B;B	0.36666	0.115;0.085;0.23;0.115	T	0.56896	-0.7903	10	0.38643	T	0.18	-14.4221	13.8977	0.63783	1.0:0.0:0.0:0.0	.	902;902;902;902	A8K583;Q14966-4;Q14966-3;Q14966	.;.;.;ZN638_HUMAN	G	481;902;902;902	ENSP00000348066:E902G;ENSP00000264447:E902G;ENSP00000386433:E902G	ENSP00000264447:E902G	E	+	2	0	ZNF638	71482601	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	5.314000	0.65804	2.167000	0.68274	0.477000	0.44152	GAA	.	.		0.269	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497	
DNAH6	1768	hgsc.bcm.edu	37	2	84921530	84921530	+	Missense_Mutation	SNP	G	G	A			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr2:84921530G>A	ENST00000237449.6	+	45	7458	c.7450G>A	c.(7450-7452)Gaa>Aaa	p.E2484K	DNAH6_ENST00000398278.2_Missense_Mutation_p.E2435K|DNAH6_ENST00000602588.1_Missense_Mutation_p.E456K|DNAH6_ENST00000389394.3_Missense_Mutation_p.E2484K			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	2484	AAA 4. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						TAGTTTTCATGAAGACCTGAG	0.423																																					p.E2484K		Atlas-SNP	.											.	DNAH6	194	.	0			c.G7450A						.						161.0	145.0	150.0					2																	84921530		692	1591	2283	SO:0001583	missense	1768	exon46			TTTCATGAAGACC	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"""Axonemal dyneins"""	2951	protein-coding gene	gene with protein product		603336	"""dynein, axonemal, heavy polypeptide 6"", ""dynein heavy chain-like 1"""	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.7450G>A	chr2.hg19:g.84921530G>A	ENSP00000237449:p.Glu2484Lys	152.0	0.0		158.0	13.0	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	hg19	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	G	35	5.582390	0.96578	.	.	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	T;T;T	0.41400	1.0;1.2;1.0	5.47	5.47	0.80525	Dynein heavy chain, P-loop containing D4 domain (1);ATPase, AAA+ type, core (1);	.	.	.	.	T	0.72087	0.3417	M	0.93420	3.415	0.58432	D	0.999999	D;D	0.58970	0.966;0.984	P;P	0.61800	0.884;0.894	T	0.80155	-0.1500	9	0.72032	D	0.01	.	18.0925	0.89479	0.0:0.0:1.0:0.0	.	2484;2435	Q9C0G6;Q9C0G6-4	DYH6_HUMAN;.	K	2484;2435;2484	ENSP00000374045:E2484K;ENSP00000381326:E2435K;ENSP00000237449:E2484K	ENSP00000237449:E2484K	E	+	1	0	DNAH6	84775041	1.000000	0.71417	0.996000	0.52242	0.964000	0.63967	8.279000	0.89901	2.565000	0.86533	0.655000	0.94253	GAA	.	.		0.423	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370	
Unknown	0	hgsc.bcm.edu	37	2	97312182	97312182	+	IGR	SNP	T	T	A			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr2:97312182T>A								KANSL3 (8067 upstream) : FER1L5 (23772 downstream)																							TGATCCCGTGTGGAATGAGGT	0.507																																					p.W44R		Atlas-SNP	.											.	FER1L5	113	.	0			c.T130A						.						176.0	150.0	158.0					2																	97312182		692	1591	2283	SO:0001628	intergenic_variant	90342	exon2			CCCGTGTGGAATG																													chr2.hg19:g.97312182T>A		325.0	0.0		273.0	14.0	NM_001113382		Missense_Mutation	SNP		hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.87|13.87	2.367208|2.367208	0.41902|0.41902	.|.	.|.	ENSG00000214272|ENSG00000214272	ENST00000342152|ENST00000414152;ENST00000436930	.|.	.|.	.|.	3.58|3.58	3.58|3.58	0.41010|0.41010	.|C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	1.523470|.	0.04630|.	N|.	0.403585|.	.|T	.|0.72938	.|0.3523	M|M	0.79123|0.79123	2.44|2.44	.|.	.|.	.|.	.|D	.|0.76494	.|0.999	.|D	.|0.87578	.|0.998	.|T	.|0.80469	.|-0.1369	.|7	0.02654|0.87932	T|D	1|0	.|.	8.8311|8.8311	0.35085|0.35085	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|44	.|A0AVI2	.|FR1L5_HUMAN	X|R	4|44	.|.	ENSP00000441631:C4X|ENSP00000444148:W44R	C|W	+|+	3|1	2|0	FER1L5|FER1L5	96675909|96675909	0.993000|0.993000	0.37304|0.37304	0.905000|0.905000	0.35620|0.35620	0.852000|0.852000	0.48524|0.48524	3.479000|3.479000	0.53165|0.53165	1.873000|1.873000	0.54277|0.54277	0.454000|0.454000	0.30748|0.30748	TGT|TGG	.	.	0	0.507								
SCN1A	6323	hgsc.bcm.edu	37	2	166852534	166852534	+	Missense_Mutation	SNP	G	G	T	rs143088184		TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr2:166852534G>T	ENST00000303395.4	-	24	4569	c.4570C>A	c.(4570-4572)Cct>Act	p.P1524T	SCN1A_ENST00000375405.3_Missense_Mutation_p.P1513T|AC010127.3_ENST00000595647.1_RNA|AC010127.3_ENST00000597623.1_RNA|SCN1A_ENST00000409050.1_Missense_Mutation_p.P1496T|SCN1A_ENST00000423058.2_Missense_Mutation_p.P1524T			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	1524					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CCTGGTCGAGGTATAGGCTTT	0.338																																					p.P1524T		Atlas-SNP	.											.	SCN1A	641	.	0			c.C4570A						.	G	THR/PRO,THR/PRO,THR/PRO,THR/PRO	1,4405	2.1+/-5.4	0,1,2202	128.0	123.0	124.0		4570,4486,4570,4537	5.8	1.0	2	dbSNP_134	124	0,8600		0,0,4300	no	missense,missense,missense,missense	SCN1A	NM_001165963.1,NM_001165964.1,NM_001202435.1,NM_006920.4	38,38,38,38	0,1,6502	TT,TG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging	1524/2010,1496/1982,1524/2010,1513/1999	166852534	1,13005	2203	4300	6503	SO:0001583	missense	6323	exon24			GTCGAGGTATAGG	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10585	protein-coding gene	gene with protein product		182389	"""febrile convulsions 3"""	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.4570C>A	chr2.hg19:g.166852534G>T	ENSP00000303540:p.Pro1524Thr	50.0	0.0		50.0	5.0	NM_001165963	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Missense_Mutation	SNP	ENST00000303395.4	hg19	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.038482	0.93630	2.27E-4	0.0	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.97138	-4.26;-4.26;-4.21;-4.18	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	D	0.98912	0.9631	M	0.92367	3.3	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99342	1.0912	10	0.87932	D	0	.	20.1438	0.98071	0.0:0.0:1.0:0.0	.	1513	P35498-2	.	T	1524;1524;1513;1496	ENSP00000407030:P1524T;ENSP00000303540:P1524T;ENSP00000364554:P1513T;ENSP00000386312:P1496T	ENSP00000303540:P1524T	P	-	1	0	SCN1A	166560780	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.810000	0.99221	2.768000	0.95171	0.650000	0.86243	CCT	.	G|1.000;T|0.000		0.338	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920	
ABCB11	8647	hgsc.bcm.edu	37	2	169791714	169791714	+	Silent	SNP	G	G	A			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr2:169791714G>A	ENST00000263817.6	-	23	3160	c.3036C>T	c.(3034-3036)ctC>ctT	p.L1012L		NM_003742.2	NP_003733.2	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 11	1012	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|canalicular bile acid transport (GO:0015722)|small molecule metabolic process (GO:0044281)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical part of cell (GO:0045177)|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)|bile acid-exporting ATPase activity (GO:0015432)|canalicular bile acid transmembrane transporter activity (GO:0015126)|sodium-exporting ATPase activity, phosphorylative mechanism (GO:0008554)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(16)|lung(26)|ovary(3)|stomach(1)	57					Adenosine triphosphate(DB00171)|Bosentan(DB00559)|Chlorpromazine(DB00477)|Cimetidine(DB00501)|Clofazimine(DB00845)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Digoxin(DB00390)|Doxorubicin(DB00997)|Ethinyl Estradiol(DB00977)|Fluorescein(DB00693)|Fusidic Acid(DB02703)|Glyburide(DB01016)|Ketoconazole(DB01026)|Novobiocin(DB01051)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Ponatinib(DB08901)|Pravastatin(DB00175)|Progesterone(DB00396)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Rosuvastatin(DB01098)|Tamoxifen(DB00675)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	AGCTGAAATGGAGCCCCTCAT	0.423																																					p.L1012L		Atlas-SNP	.											.	ABCB11	136	.	0			c.C3036T						.						151.0	142.0	145.0					2																	169791714		1911	4118	6029	SO:0001819	synonymous_variant	8647	exon23			GAAATGGAGCCCC	AF091582	CCDS46444.1	2q24	2012-03-14			ENSG00000073734	ENSG00000073734		"""ATP binding cassette transporters / subfamily B"""	42	protein-coding gene	gene with protein product	"""ABC member 16, MDR/TAP subfamily"""	603201	"""progressive familial intrahepatic cholestasis 2"", ""bile salt export pump"""	BSEP, PFIC2		9806540	Standard	NM_003742		Approved	ABC16, SPGP, PFIC-2, PGY4	uc002ueo.1	O95342	OTTHUMG00000154039	ENST00000263817.6:c.3036C>T	chr2.hg19:g.169791714G>A		174.0	0.0		165.0	16.0	NM_003742	Q53TL2|Q9UNB2	Silent	SNP	ENST00000263817.6	hg19	CCDS46444.1																																																																																			.	.		0.423	ABCB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333616.2	NM_003742	
ASNSD1	54529	hgsc.bcm.edu	37	2	190531503	190531503	+	Silent	SNP	G	G	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr2:190531503G>T	ENST00000260952.4	+	4	1058	c.645G>T	c.(643-645)ctG>ctT	p.L215L	ASNSD1_ENST00000607062.1_Intron	NM_019048.2	NP_061921	Q9NWL6	ASND1_HUMAN	asparagine synthetase domain containing 1	215					asparagine biosynthetic process (GO:0006529)|glutamine metabolic process (GO:0006541)		asparagine synthase (glutamine-hydrolyzing) activity (GO:0004066)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(3)	25			OV - Ovarian serous cystadenocarcinoma(117;0.00318)|Epithelial(96;0.0449)|all cancers(119;0.118)			TTAATAGCCTGAGTCAAATTT	0.333																																					p.L215L		Atlas-SNP	.											.	ASNSD1	63	.	0			c.G645T						.						50.0	55.0	54.0					2																	190531503		2201	4299	6500	SO:0001819	synonymous_variant	54529	exon4			TAGCCTGAGTCAA	AY116969	CCDS2300.1	2q32.2	2012-09-20			ENSG00000138381	ENSG00000138381			24910	protein-coding gene	gene with protein product							Standard	NM_019048		Approved	NS3TP1, FLJ20752, NBLA00058	uc002uqt.3	Q9NWL6	OTTHUMG00000132665	ENST00000260952.4:c.645G>T	chr2.hg19:g.190531503G>T		46.0	0.0		57.0	7.0	NM_019048	D3DPH6|Q3LIC3|Q4ZG45	Silent	SNP	ENST00000260952.4	hg19	CCDS2300.1																																																																																			.	.		0.333	ASNSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255919.3	NM_019048	
ZDBF2	57683	hgsc.bcm.edu	37	2	207175044	207175044	+	Missense_Mutation	SNP	G	G	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr2:207175044G>T	ENST00000374423.3	+	5	6178	c.5792G>T	c.(5791-5793)gGg>gTg	p.G1931V		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	1931							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						AAGCAAAAGGGGCGTGTGGCT	0.433																																					p.G1931V		Atlas-SNP	.											.	ZDBF2	531	.	0			c.G5792T						.						71.0	71.0	71.0					2																	207175044		1958	4153	6111	SO:0001583	missense	57683	exon5			AAAAGGGGCGTGT	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"""Zinc fingers, DBF-type"""	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.5792G>T	chr2.hg19:g.207175044G>T	ENSP00000363545:p.Gly1931Val	217.0	0.0		251.0	31.0	NM_020923	Q6ZNP7|Q6ZSN8	Missense_Mutation	SNP	ENST00000374423.3	hg19	CCDS46501.1	.	.	.	.	.	.	.	.	.	.	G	7.815	0.716570	0.15306	.	.	ENSG00000204186	ENST00000374423	T	0.45276	0.9	5.64	4.76	0.60689	.	.	.	.	.	T	0.31888	0.0811	N	0.19112	0.55	0.20638	N	0.999874	B	0.19583	0.037	B	0.17722	0.019	T	0.25328	-1.0135	9	0.52906	T	0.07	.	14.4819	0.67590	0.0706:0.0:0.9294:0.0	.	1931	Q9HCK1	ZDBF2_HUMAN	V	1931	ENSP00000363545:G1931V	ENSP00000363545:G1931V	G	+	2	0	ZDBF2	206883289	0.974000	0.33945	0.002000	0.10522	0.001000	0.01503	2.264000	0.43302	1.396000	0.46663	0.558000	0.71614	GGG	.	.		0.433	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923	
CAMP	820	hgsc.bcm.edu	37	3	48266103	48266103	+	Missense_Mutation	SNP	G	G	A	rs375338469		TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr3:48266103G>A	ENST00000576243.1	+	3	460	c.320G>A	c.(319-321)cGg>cAg	p.R107Q	CAMP_ENST00000296435.2_Missense_Mutation_p.R110Q			P49913	CAMP_HUMAN	cathelicidin antimicrobial peptide	107					antibacterial humoral response (GO:0019731)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to peptidoglycan (GO:0071224)|cellular response to tumor necrosis factor (GO:0071356)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|killing by host of symbiont cells (GO:0051873)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of growth of symbiont on or near host surface (GO:0044140)|phagosome maturation (GO:0090382)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein phosphorylation (GO:0001934)	cell projection (GO:0042995)|cell wall (GO:0005618)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|specific granule (GO:0042581)				endometrium(2)|large_intestine(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6				BRCA - Breast invasive adenocarcinoma(193;0.000614)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		CTGGTGAAGCGGTGTATGGGG	0.567																																					p.R110Q		Atlas-SNP	.											.	CAMP	12	.	0			c.G329A						.	G	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	144.0	135.0	138.0		320	-6.1	0.0	3		138	0,8600		0,0,4300	no	missense	CAMP	NM_004345.4	43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	107/171	48266103	1,13005	2203	4300	6503	SO:0001583	missense	820	exon3			TGAAGCGGTGTAT	BC055089	CCDS2762.1, CCDS2762.2	3p21.3	2014-01-30			ENSG00000164047	ENSG00000164047		"""Endogenous ligands"""	1472	protein-coding gene	gene with protein product		600474				7624374	Standard	NM_004345		Approved	CAP18, FALL39, FALL-39, LL37	uc003csj.3	P49913	OTTHUMG00000133526	ENST00000576243.1:c.320G>A	chr3.hg19:g.48266103G>A	ENSP00000458149:p.Arg107Gln	231.0	0.0		187.0	27.0	NM_004345	Q71SN9	Missense_Mutation	SNP	ENST00000576243.1	hg19		.	.	.	.	.	.	.	.	.	.	G	2.258	-0.369857	0.05069	2.27E-4	0.0	ENSG00000164047	ENST00000296435	.	.	.	5.49	-6.14	0.02111	.	1.302650	0.04982	N	0.465755	T	0.11067	0.0270	N	0.02334	-0.595	0.09310	N	1	B	0.12013	0.005	B	0.04013	0.001	T	0.36359	-0.9751	9	0.02654	T	1	-12.3855	7.7195	0.28723	0.3798:0.0:0.5027:0.1176	.	107	P49913	CAMP_HUMAN	Q	107	.	ENSP00000296435:R107Q	R	+	2	0	CAMP	48241107	0.000000	0.05858	0.003000	0.11579	0.754000	0.42855	-1.300000	0.02751	-0.947000	0.03673	-0.291000	0.09656	CGG	.	.		0.567	CAMP-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_004345	
APEH	327	hgsc.bcm.edu	37	3	49720037	49720037	+	Missense_Mutation	SNP	T	T	C			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr3:49720037T>C	ENST00000296456.5	+	19	2151	c.1751T>C	c.(1750-1752)aTg>aCg	p.M584T	AC099668.5_ENST00000563780.1_RNA|APEH_ENST00000438011.1_Missense_Mutation_p.M584T	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase	584					beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GTGGCCCTTATGGGTGGTTCC	0.587																																					p.M584T		Atlas-SNP	.											.	APEH	45	.	0			c.T1751C						.						194.0	177.0	183.0					3																	49720037		2203	4300	6503	SO:0001583	missense	327	exon19			CCCTTATGGGTGG	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"""acylaminoacyl-peptidase"""	102645	"""N-acylaminoacyl-peptide hydrolase"""	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882	ENST00000296456.5:c.1751T>C	chr3.hg19:g.49720037T>C	ENSP00000296456:p.Met584Thr	223.0	0.0		193.0	35.0	NM_001640	Q9BQ33|Q9P0Y2	Missense_Mutation	SNP	ENST00000296456.5	hg19	CCDS2801.1	.	.	.	.	.	.	.	.	.	.	T	11.76	1.735959	0.30774	.	.	ENSG00000164062	ENST00000296456;ENST00000438011	T;T	0.42513	0.97;0.97	5.27	5.27	0.74061	Peptidase S9, prolyl oligopeptidase, catalytic domain (1);	0.441047	0.29280	N	0.012613	T	0.26484	0.0647	N	0.20807	0.61	0.31683	N	0.642892	B;B	0.13594	0.002;0.008	B;B	0.19946	0.027;0.027	T	0.24190	-1.0167	10	0.12103	T	0.63	-3.8282	11.2314	0.48914	0.0:0.0:0.1531:0.8469	.	584;584	C9JIF9;P13798	.;ACPH_HUMAN	T	584	ENSP00000296456:M584T;ENSP00000415862:M584T	ENSP00000296456:M584T	M	+	2	0	APEH	49695041	0.998000	0.40836	0.988000	0.46212	0.998000	0.95712	2.997000	0.49457	1.987000	0.57996	0.533000	0.62120	ATG	.	.		0.587	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2		
CISH	1154	hgsc.bcm.edu	37	3	50645332	50645332	+	Missense_Mutation	SNP	C	C	A			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr3:50645332C>A	ENST00000348721.3	-	3	663	c.483G>T	c.(481-483)caG>caT	p.Q161H	CISH_ENST00000443053.2_Missense_Mutation_p.Q178H	NM_145071.2	NP_659508.1	Q9NSE2	CISH_HUMAN	cytokine inducible SH2-containing protein	161	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				intracellular signal transduction (GO:0035556)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of signal transduction (GO:0009968)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein ubiquitination (GO:0016567)|regulation of cell growth (GO:0001558)	cytosol (GO:0005829)|plasma membrane (GO:0005886)				breast(2)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)		CCACATAGTGCTGCACAAGGC	0.607																																					p.Q178H		Atlas-SNP	.											.	CISH	27	.	0			c.G534T						.						55.0	55.0	55.0					3																	50645332		2203	4300	6503	SO:0001583	missense	1154	exon4			ATAGTGCTGCACA	Z77852	CCDS2831.1, CCDS46834.1	3p21.3	2013-02-14			ENSG00000114737	ENSG00000114737		"""Suppressors of cytokine signaling"", ""SH2 domain containing"""	1984	protein-coding gene	gene with protein product		602441				9465889, 7796808	Standard	NM_013324		Approved	CIS, G18, CIS-1, SOCS	uc003dax.3	Q9NSE2	OTTHUMG00000156853	ENST00000348721.3:c.483G>T	chr3.hg19:g.50645332C>A	ENSP00000294173:p.Gln161His	122.0	0.0		101.0	7.0	NM_013324	B2R9N1|G5E9R1|Q9NS38|Q9Y5R1	Missense_Mutation	SNP	ENST00000348721.3	hg19	CCDS2831.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.710738	0.89112	.	.	ENSG00000114737	ENST00000443053;ENST00000348721	D;D	0.89050	-2.46;-2.46	5.8	4.92	0.64577	SH2 motif (5);	0.165822	0.56097	D	0.000033	D	0.87795	0.6267	L	0.37466	1.105	0.80722	D	1	P;P	0.51240	0.929;0.943	P;P	0.53722	0.703;0.733	D	0.85983	0.1484	10	0.38643	T	0.18	-4.7135	11.2134	0.48813	0.0:0.8574:0.0:0.1426	.	178;161	G5E9R1;Q9NSE2	.;CISH_HUMAN	H	178;161	ENSP00000409346:Q178H;ENSP00000294173:Q161H	ENSP00000294173:Q161H	Q	-	3	2	CISH	50620336	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.090000	0.57693	2.730000	0.93505	0.563000	0.77884	CAG	.	.		0.607	CISH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346245.1	NM_145071	
BAP1	8314	hgsc.bcm.edu	37	3	52441262	52441262	+	Missense_Mutation	SNP	A	A	C			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr3:52441262A>C	ENST00000460680.1	-	7	979	c.508T>G	c.(508-510)Ttt>Gtt	p.F170V	BAP1_ENST00000296288.5_Missense_Mutation_p.F170V	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0	Interaction with HIP2.				anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.F170V(2)|p.E166fs*13(1)		NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		TAGCTGACAAAGTGGAACGCC	0.577			"""N, Mis, F, S, O"""		"""uveal melanoma, breast, NSCLC, RCC"""	"""mesothelioma, uveal melanoma"""																															p.F170V	GBM(101;493 1458 7992 21037 25532)	Atlas-SNP	.		Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	BAP1,NS,carcinoma,+1,2	BAP1	371	.	3	Substitution - Missense(2)|Deletion - Frameshift(1)	prostate(1)|eye(1)|kidney(1)	c.T508G						.						83.0	81.0	82.0					3																	52441262		2203	4300	6503	SO:0001583	missense	8314	exon7			TGACAAAGTGGAA	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.508T>G	chr3.hg19:g.52441262A>C	ENSP00000417132:p.Phe170Val	160.0	0.0		148.0	23.0	NM_004656	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Missense_Mutation	SNP	ENST00000460680.1	hg19	CCDS2853.1	.	.	.	.	.	.	.	.	.	.	A	29.8	5.040462	0.93630	.	.	ENSG00000163930	ENST00000460680;ENST00000296288;ENST00000470173	T;T;T	0.75260	-0.92;-0.92;-0.92	5.95	5.95	0.96441	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (3);	0.000000	0.85682	D	0.000000	D	0.90174	0.6929	H	0.94462	3.54	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.92742	0.6209	10	0.87932	D	0	-8.6289	16.4216	0.83760	1.0:0.0:0.0:0.0	.	170	Q92560	BAP1_HUMAN	V	170;170;91	ENSP00000417132:F170V;ENSP00000296288:F170V;ENSP00000417776:F91V	ENSP00000296288:F170V	F	-	1	0	BAP1	52416302	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.297000	0.96120	2.285000	0.76669	0.533000	0.62120	TTT	.	.		0.577	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1		
KBTBD12	166348	hgsc.bcm.edu	37	3	127642469	127642469	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr3:127642469T>A	ENST00000405109.1	+	2	1032	c.565T>A	c.(565-567)Tcc>Acc	p.S189T	KBTBD12_ENST00000407609.3_Intron|KBTBD12_ENST00000405256.1_Missense_Mutation_p.S189T|KBTBD12_ENST00000343941.4_Intron			Q3ZCT8	KBTBC_HUMAN	kelch repeat and BTB (POZ) domain containing 12	189	BACK.									endometrium(1)|large_intestine(6)|lung(5)|ovary(1)	13						TCTTAACATATCCAGAGAAGA	0.363																																					p.S189T		Atlas-SNP	.											.	KBTBD12	41	.	0			c.T565A						.						55.0	50.0	52.0					3																	127642469		1868	4108	5976	SO:0001583	missense	166348	exon1			AACATATCCAGAG		CCDS33848.2	3q21.3	2013-01-08	2009-10-01	2009-10-01	ENSG00000187715	ENSG00000187715		"""BTB/POZ domain containing"""	25731	protein-coding gene	gene with protein product			"""kelch domain containing 6"""	KLHDC6			Standard	NM_207335		Approved	FLJ46299	uc010hsr.3	Q3ZCT8	OTTHUMG00000150508	ENST00000405109.1:c.565T>A	chr3.hg19:g.127642469T>A	ENSP00000385957:p.Ser189Thr	111.0	0.0		105.0	5.0	NM_207335	B5MCC6|Q6ZRK1	Missense_Mutation	SNP	ENST00000405109.1	hg19	CCDS33848.2	.	.	.	.	.	.	.	.	.	.	T	7.720	0.696999	0.15106	.	.	ENSG00000187715	ENST00000405109;ENST00000405256	T;T	0.68903	-0.36;-0.36	5.75	0.194	0.15143	BTB/Kelch-associated (2);	.	.	.	.	T	0.55033	0.1895	L	0.39020	1.185	0.31939	N	0.611124	B	0.11235	0.004	B	0.17098	0.017	T	0.53913	-0.8371	9	0.48119	T	0.1	.	11.4285	0.50025	0.4579:0.0:0.0:0.5421	.	189	Q3ZCT8	KBTBC_HUMAN	T	189	ENSP00000385957:S189T;ENSP00000385879:S189T	ENSP00000385957:S189T	S	+	1	0	KBTBD12	129125159	0.972000	0.33761	0.120000	0.21714	0.962000	0.63368	1.529000	0.35996	-0.183000	0.10585	-0.710000	0.03640	TCC	.	.		0.363	KBTBD12-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318682.1	NM_207335	
NMNAT3	349565	hgsc.bcm.edu	37	3	139292479	139292479	+	Missense_Mutation	SNP	C	C	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr3:139292479C>T	ENST00000296202.7	-	5	718	c.337G>A	c.(337-339)Ggc>Agc	p.G113S	RP11-319G6.1_ENST00000381790.3_RNA|NMNAT3_ENST00000511444.1_Intron|NMNAT3_ENST00000339837.5_Missense_Mutation_p.G76S|NMNAT3_ENST00000512391.1_Intron|RP11-319G6.1_ENST00000515247.1_RNA|NMNAT3_ENST00000406824.1_Missense_Mutation_p.G3S|NMNAT3_ENST00000406164.1_Missense_Mutation_p.G76S|NMNAT3_ENST00000413939.2_Intron|NMNAT3_ENST00000507242.1_5'UTR			Q96T66	NMNA3_HUMAN	nicotinamide nucleotide adenylyltransferase 3	113					NAD biosynthetic process (GO:0009435)|NAD metabolic process (GO:0019674)|response to wounding (GO:0009611)|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)|nicotinamide-nucleotide adenylyltransferase activity (GO:0000309)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)			endometrium(2)|kidney(1)|large_intestine(2)|lung(4)	9						TGGTCTGGGCCTTCCATCTGG	0.532																																					p.G76S		Atlas-SNP	.											.	NMNAT3	29	.	0			c.G226A						.						235.0	189.0	205.0					3																	139292479		2203	4300	6503	SO:0001583	missense	349565	exon4			CTGGGCCTTCCAT	AF345564	CCDS3111.1, CCDS56282.1	3q23	2013-09-20			ENSG00000163864	ENSG00000163864			20989	protein-coding gene	gene with protein product		608702				12574164	Standard	NM_178177		Approved	PNAT3	uc003etk.3	Q96T66	OTTHUMG00000159951	ENST00000296202.7:c.337G>A	chr3.hg19:g.139292479C>T	ENSP00000296202:p.Gly113Ser	253.0	0.0		209.0	22.0	NM_178177	B3KVR6|D3DNF2|D3DNF3|Q8N4G1	Missense_Mutation	SNP	ENST00000296202.7	hg19		.	.	.	.	.	.	.	.	.	.	C	14.12	2.441334	0.43326	.	.	ENSG00000163864	ENST00000406164;ENST00000406824;ENST00000339837;ENST00000296202;ENST00000509291	D;D;D;D;D	0.97688	-4.26;-3.96;-4.26;-4.49;-3.07	4.28	4.28	0.50868	Cytidylyltransferase (1);Rossmann-like alpha/beta/alpha sandwich fold (1);	1.476730	0.03816	N	0.266736	D	0.93939	0.8060	N	0.08118	0	0.31342	N	0.683481	B	0.18863	0.031	B	0.22880	0.042	T	0.81185	-0.1048	10	0.16420	T	0.52	-22.9019	14.5326	0.67936	0.0:1.0:0.0:0.0	.	113	Q96T66	NMNA3_HUMAN	S	76;3;76;113;113	ENSP00000384319:G76S;ENSP00000384684:G3S;ENSP00000340523:G76S;ENSP00000296202:G113S;ENSP00000427634:G113S	ENSP00000296202:G113S	G	-	1	0	NMNAT3	140775169	0.946000	0.32159	0.688000	0.30117	0.561000	0.35649	3.298000	0.51818	2.665000	0.90641	0.563000	0.77884	GGC	.	.		0.532	NMNAT3-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000358469.1	NM_178177	
EPHB3	2049	hgsc.bcm.edu	37	3	184294923	184294923	+	Missense_Mutation	SNP	C	C	A			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr3:184294923C>A	ENST00000330394.2	+	5	1758	c.1306C>A	c.(1306-1308)Cct>Act	p.P436T	EIF2B5_ENST00000444495.1_Intron	NM_004443.3	NP_004434.2	P54753	EPHB3_HUMAN	EPH receptor B3	436	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell migration (GO:0016477)|central nervous system projection neuron axonogenesis (GO:0021952)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|digestive tract morphogenesis (GO:0048546)|ephrin receptor signaling pathway (GO:0048013)|palate development (GO:0060021)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of axonogenesis (GO:0050770)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell-cell adhesion (GO:0022407)|regulation of Rac GTPase activity (GO:0032314)|retinal ganglion cell axon guidance (GO:0031290)|substrate adhesion-dependent cell spreading (GO:0034446)|thymus development (GO:0048538)|urogenital system development (GO:0001655)	cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|ephrin receptor activity (GO:0005003)			breast(5)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_cancers(143;1.89e-10)|Ovarian(172;0.0339)		Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22)			GGGCAAGAGCCCTCTGCCGCC	0.637																																					p.P436T		Atlas-SNP	.											.	EPHB3	114	.	0			c.C1306A						.						40.0	37.0	38.0					3																	184294923		2203	4300	6503	SO:0001583	missense	2049	exon5			AAGAGCCCTCTGC	X75208	CCDS3268.1	3q27.1	2013-09-19	2004-10-28		ENSG00000182580	ENSG00000182580		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3394	protein-coding gene	gene with protein product		601839	"""EphB3"""	ETK2		8397371	Standard	NM_004443		Approved	Hek2, Tyro6	uc003foz.3	P54753	OTTHUMG00000156710	ENST00000330394.2:c.1306C>A	chr3.hg19:g.184294923C>A	ENSP00000332118:p.Pro436Thr	68.0	0.0		60.0	7.0	NM_004443	Q7Z740	Missense_Mutation	SNP	ENST00000330394.2	hg19	CCDS3268.1	.	.	.	.	.	.	.	.	.	.	C	18.31	3.595241	0.66219	.	.	ENSG00000182580	ENST00000330394	T	0.57273	0.41	5.3	5.3	0.74995	Fibronectin, type III (1);Immunoglobulin-like fold (1);	0.058251	0.64402	D	0.000001	T	0.62841	0.2461	M	0.75884	2.315	0.80722	D	1	P	0.44946	0.846	P	0.47118	0.538	T	0.64504	-0.6392	10	0.42905	T	0.14	.	18.305	0.90177	0.0:1.0:0.0:0.0	.	436	P54753	EPHB3_HUMAN	T	436	ENSP00000332118:P436T	ENSP00000332118:P436T	P	+	1	0	EPHB3	185777617	1.000000	0.71417	1.000000	0.80357	0.449000	0.32228	6.045000	0.71020	2.639000	0.89480	0.448000	0.29417	CCT	.	.		0.637	EPHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345413.1	NM_004443	
CLDN1	9076	hgsc.bcm.edu	37	3	190030766	190030766	+	Missense_Mutation	SNP	T	T	C			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr3:190030766T>C	ENST00000295522.3	-	2	551	c.283A>G	c.(283-285)Atc>Gtc	p.I95V		NM_021101.4	NP_066924.1	O95832	CLD1_HUMAN	claudin 1	95					calcium-independent cell-cell adhesion (GO:0016338)|cell adhesion (GO:0007155)|cell-cell junction organization (GO:0045216)|establishment of skin barrier (GO:0061436)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			lung(9)	9	all_cancers(143;2.95e-10)|Ovarian(172;0.0512)		Lung(62;2.23e-05)|LUSC - Lung squamous cell carcinoma(58;3.15e-05)	GBM - Glioblastoma multiforme(93;0.015)		GCCACAAAGATTGCTATCACT	0.468																																					p.I95V		Atlas-SNP	.											.	CLDN1	23	.	0			c.A283G						.						246.0	225.0	232.0					3																	190030766		2203	4300	6503	SO:0001583	missense	9076	exon2			CAAAGATTGCTAT	AF101051	CCDS3295.1	3q28-q29	2008-07-18			ENSG00000163347	ENSG00000163347		"""Claudins"""	2032	protein-coding gene	gene with protein product	"""senescence-associated epithelial membrane protein 1"""	603718				10828592, 9892664	Standard	NM_021101		Approved	SEMP1, ILVASC	uc003fsh.3	O95832	OTTHUMG00000156214	ENST00000295522.3:c.283A>G	chr3.hg19:g.190030766T>C	ENSP00000295522:p.Ile95Val	195.0	0.0		191.0	17.0	NM_021101		Missense_Mutation	SNP	ENST00000295522.3	hg19	CCDS3295.1	.	.	.	.	.	.	.	.	.	.	T	8.296	0.818813	0.16607	.	.	ENSG00000163347	ENST00000295522;ENST00000545382	D	0.87966	-2.32	5.82	5.82	0.92795	.	0.177351	0.64402	D	0.000019	T	0.76751	0.4031	N	0.16790	0.44	0.35587	D	0.806767	B	0.20368	0.044	B	0.28011	0.085	T	0.74090	-0.3777	10	0.14252	T	0.57	.	10.1995	0.43075	0.0:0.0777:0.0:0.9223	.	95	O95832	CLD1_HUMAN	V	95;50	ENSP00000295522:I95V	ENSP00000295522:I95V	I	-	1	0	CLDN1	191513460	0.800000	0.28916	0.993000	0.49108	0.957000	0.61999	1.117000	0.31234	2.225000	0.72522	0.459000	0.35465	ATC	.	.		0.468	CLDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343516.2	NM_021101	
HTT	3064	hgsc.bcm.edu	37	4	3240242	3240242	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr4:3240242T>A	ENST00000355072.5	+	65	9105	c.8960T>A	c.(8959-8961)tTc>tAc	p.F2987Y		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	2987					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		CTAGACGACTTCTTCCCACCC	0.557																																					p.F2987Y		Atlas-SNP	.											.	HTT	221	.	0			c.T8960A						.						69.0	76.0	74.0					4																	3240242		1997	4169	6166	SO:0001583	missense	3064	exon65			ACGACTTCTTCCC	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"""Endogenous ligands"""	4851	protein-coding gene	gene with protein product		613004	"""huntingtin (Huntington disease)"""	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.8960T>A	chr4.hg19:g.3240242T>A	ENSP00000347184:p.Phe2987Tyr	202.0	0.0		197.0	18.0	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	hg19	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	T	28.8	4.955624	0.92726	.	.	ENSG00000197386	ENST00000355072	T	0.67523	-0.27	4.8	4.8	0.61643	.	0.000000	0.85682	D	0.000000	T	0.68988	0.3061	M	0.78049	2.395	0.58432	D	0.999999	D	0.54964	0.969	B	0.43386	0.418	T	0.75861	-0.3168	10	0.72032	D	0.01	.	13.5472	0.61711	0.0:0.0:0.0:1.0	.	2987	P42858	HD_HUMAN	Y	2987	ENSP00000347184:F2987Y	ENSP00000347184:F2987Y	F	+	2	0	HTT	3210040	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.693000	0.84214	1.784000	0.52394	0.455000	0.32223	TTC	.	.		0.557	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
UBE2K	3093	hgsc.bcm.edu	37	4	39780009	39780009	+	Silent	SNP	A	A	G			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr4:39780009A>G	ENST00000261427.5	+	7	842	c.558A>G	c.(556-558)aaA>aaG	p.K186K	UBE2K_ENST00000295963.6_Silent_p.K125K|UBE2K_ENST00000438068.2_3'UTR|UBE2K_ENST00000503368.1_Silent_p.K135K|UBE2K_ENST00000445950.2_Silent_p.K143K	NM_001111112.1|NM_005339.4	NP_001104582.1|NP_005330.1	P61086	UBE2K_HUMAN	ubiquitin-conjugating enzyme E2K	186	UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.				intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|protein K48-linked ubiquitination (GO:0070936)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)			large_intestine(1)|lung(1)|ovary(2)	4						TGTCTTCAAAATCATGGGATG	0.403																																					p.K186K	NSCLC(101;689 1592 16105 29682 31745)	Atlas-SNP	.											.	UBE2K	16	.	0			c.A558G						.						152.0	146.0	148.0					4																	39780009		2203	4300	6503	SO:0001819	synonymous_variant	3093	exon7			TTCAAAATCATGG	U58522	CCDS33976.1, CCDS47043.1, CCDS47044.1	4p14	2011-05-19	2011-05-19	2007-12-04	ENSG00000078140	ENSG00000078140		"""Ubiquitin-conjugating enzymes E2"""	4914	protein-coding gene	gene with protein product		602846	"""huntingtin interacting protein 2"", ""ubiquitin-conjugating enzyme E2K (UBC1 homolog, yeast)"""	HIP2		8702625, 17873885	Standard	NM_005339		Approved	HYPG, UBC1	uc003guu.4	P61086	OTTHUMG00000160543	ENST00000261427.5:c.558A>G	chr4.hg19:g.39780009A>G		63.0	0.0		86.0	6.0	NM_005339	A6NJC1|A8K5Y9|B2RDF8|C9JGP1|O54806|P27924|Q16721|Q9CVV9|Q9Y2D3	Silent	SNP	ENST00000261427.5	hg19	CCDS33976.1																																																																																			.	.		0.403	UBE2K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361061.1	NM_005339	
BMP2K	55589	hgsc.bcm.edu	37	4	79808426	79808426	+	Missense_Mutation	SNP	A	A	G			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr4:79808426A>G	ENST00000335016.5	+	15	2216	c.2050A>G	c.(2050-2052)Att>Gtt	p.I684V	PAQR3_ENST00000295462.3_3'UTR	NM_198892.1	NP_942595.1	Q9NSY1	BMP2K_HUMAN	BMP2 inducible kinase	684					regulation of bone mineralization (GO:0030500)	nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatase regulator activity (GO:0019208)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	13						TGTTCCTTTCATTTCTCATTC	0.393																																					p.I684V		Atlas-SNP	.											.	BMP2K	169	.	0			c.A2050G						.						107.0	100.0	103.0					4																	79808426		1928	4137	6065	SO:0001583	missense	55589	exon15			CCTTTCATTTCTC	AB015331	CCDS34019.1, CCDS47083.1	4q21.21	2008-05-15			ENSG00000138756	ENSG00000138756			18041	protein-coding gene	gene with protein product							Standard	NM_017593		Approved	DKFZp434K0614, BIKe	uc003hlk.3	Q9NSY1	OTTHUMG00000160900	ENST00000335016.5:c.2050A>G	chr4.hg19:g.79808426A>G	ENSP00000334836:p.Ile684Val	97.0	0.0		101.0	12.0	NM_198892	O94791|Q4W5H2|Q8IYF2|Q8N2G7|Q8NHG9|Q9NTG8	Missense_Mutation	SNP	ENST00000335016.5	hg19	CCDS47083.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.65|15.65	2.897736|2.897736	0.52227|0.52227	.|.	.|.	ENSG00000138756|ENSG00000138756	ENST00000502613|ENST00000335016	.|T	.|0.21031	.|2.03	5.79|5.79	5.79|5.79	0.91817|0.91817	.|.	.|1.203230	.|0.05992	.|N	.|0.646188	T|T	0.26810|0.26810	0.0656|0.0656	L|L	0.57536|0.57536	1.79|1.79	0.80722|0.80722	D|D	1|1	.|B	.|0.20459	.|0.045	.|B	.|0.15052	.|0.012	T|T	0.06041|0.06041	-1.0849|-1.0849	5|10	.|0.30078	.|T	.|0.28	-16.3946|-16.3946	12.051|12.051	0.53507|0.53507	0.8563:0.1437:0.0:0.0|0.8563:0.1437:0.0:0.0	.|.	.|684	.|Q9NSY1	.|BMP2K_HUMAN	R|V	376|684	.|ENSP00000334836:I684V	.|ENSP00000334836:I684V	H|I	+|+	2|1	0|0	BMP2K|BMP2K	80027450|80027450	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	1.610000|1.610000	0.36869|0.36869	2.223000|2.223000	0.72356|0.72356	0.455000|0.455000	0.32223|0.32223	CAT|ATT	.	.		0.393	BMP2K-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_017593	
SYNPO2	171024	hgsc.bcm.edu	37	4	119947795	119947795	+	Missense_Mutation	SNP	A	A	G			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr4:119947795A>G	ENST00000429713.2	+	3	453	c.271A>G	c.(271-273)Ata>Gta	p.I91V	SYNPO2_ENST00000448416.2_Intron|SYNPO2_ENST00000307142.4_Missense_Mutation_p.I91V|SYNPO2_ENST00000434046.2_Missense_Mutation_p.I91V	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	91						actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|Z disc (GO:0030018)	14-3-3 protein binding (GO:0071889)|muscle alpha-actinin binding (GO:0051371)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						ATCCAGTGGAATAAGTGAGGC	0.423																																					p.I91V		Atlas-SNP	.											.	SYNPO2	353	.	0			c.A271G						.						96.0	99.0	98.0					4																	119947795		2203	4300	6503	SO:0001583	missense	171024	exon3			AGTGGAATAAGTG	AJ010482	CCDS34054.1, CCDS47128.1, CCDS47129.1, CCDS75185.1, CCDS75186.1	4q26	2008-08-29			ENSG00000172403	ENSG00000172403			17732	protein-coding gene	gene with protein product						11673475, 17828378	Standard	NM_133477		Approved	MYOPODIN	uc010inb.3	Q9UMS6	OTTHUMG00000161165	ENST00000429713.2:c.271A>G	chr4.hg19:g.119947795A>G	ENSP00000395143:p.Ile91Val	95.0	0.0		87.0	9.0	NM_001128934	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Missense_Mutation	SNP	ENST00000429713.2	hg19	CCDS47129.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	4.284|4.284	0.051816|0.051816	0.08291|0.08291	.|.	.|.	ENSG00000172403|ENSG00000172403	ENST00000307142;ENST00000429713;ENST00000434046|ENST00000504178	T;T;T|.	0.07444|.	3.19;3.2;3.19|.	5.63|5.63	3.23|3.23	0.37069|0.37069	PDZ/DHR/GLGF (1);|.	0.562038|.	0.18017|.	N|.	0.154370|.	T|T	0.36908|0.36908	0.0984|0.0984	N|N	0.17474|0.17474	0.49|0.49	0.38950|0.38950	D|D	0.958333|0.958333	B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0|.	B;B;B;B|.	0.04013|.	0.0;0.001;0.001;0.001|.	T|T	0.14615|0.14615	-1.0466|-1.0466	10|5	0.11182|.	T|.	0.66|.	-2.8154|-2.8154	7.3145|7.3145	0.26493|0.26493	0.7515:0.0:0.2485:0.0|0.7515:0.0:0.2485:0.0	.|.	91;91;91;91|.	B9EG60;Q9UMS6-2;E9PEM2;Q9UMS6|.	.;.;.;SYNP2_HUMAN|.	V|S	91|42	ENSP00000306015:I91V;ENSP00000395143:I91V;ENSP00000390965:I91V|.	ENSP00000306015:I91V|.	I|N	+|+	1|2	0|0	SYNPO2|SYNPO2	120167243|120167243	0.998000|0.998000	0.40836|0.40836	0.876000|0.876000	0.34364|0.34364	0.640000|0.640000	0.38277|0.38277	1.416000|1.416000	0.34759|0.34759	0.950000|0.950000	0.37743|0.37743	0.528000|0.528000	0.53228|0.53228	ATA|AAT	.	.		0.423	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1		
NUDT6	11162	hgsc.bcm.edu	37	4	123814211	123814211	+	Silent	SNP	T	T	C			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr4:123814211T>C	ENST00000304430.5	-	5	756	c.723A>G	c.(721-723)gaA>gaG	p.E241E	NUDT6_ENST00000339154.2_Silent_p.E72E|FGF2_ENST00000608478.1_3'UTR|FGF2_ENST00000264498.3_3'UTR|NUDT6_ENST00000502270.1_Silent_p.E72E|NUDT6_ENST00000608639.1_5'Flank	NM_007083.4	NP_009014.2	P53370	NUDT6_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 6	241	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.			E -> Q (in Ref. 4; AAA67062). {ECO:0000305}.		mitochondrion (GO:0005739)|nucleus (GO:0005634)	growth factor activity (GO:0008083)|hydrolase activity (GO:0016787)			endometrium(2)|lung(1)|prostate(1)|skin(1)|stomach(1)	6						TTAAGCATTCTTCCTGGCAAA	0.448																																					p.E241E		Atlas-SNP	.											.	NUDT6	50	.	0			c.A723G						.						126.0	121.0	123.0					4																	123814211		2203	4300	6503	SO:0001819	synonymous_variant	11162	exon5			GCATTCTTCCTGG	AF019632	CCDS3729.1, CCDS43268.1	4q26	2011-02-21			ENSG00000170917	ENSG00000170917		"""Nudix motif containing"""	8053	protein-coding gene	gene with protein product		606261				7984147, 10022609	Standard	NM_198041		Approved	gfg-1, gfg, FGF2AS, FGF-AS	uc003iew.3	P53370	OTTHUMG00000039507	ENST00000304430.5:c.723A>G	chr4.hg19:g.123814211T>C		140.0	0.0		124.0	6.0	NM_007083	A8K756|O95097|Q9UQD9	Silent	SNP	ENST00000304430.5	hg19	CCDS43268.1																																																																																			.	.		0.448	NUDT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095331.3	NM_007083	
SPATA4	132851	hgsc.bcm.edu	37	4	177113883	177113883	+	Missense_Mutation	SNP	A	A	C			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr4:177113883A>C	ENST00000280191.2	-	4	691	c.583T>G	c.(583-585)Tca>Gca	p.S195A	SPATA4_ENST00000515234.1_Missense_Mutation_p.S22A	NM_144644.2	NP_653245.2	Q8NEY3	SPAT4_HUMAN	spermatogenesis associated 4	195						cytoplasm (GO:0005737)				NS(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)	22		Breast(14;0.0011)|Prostate(90;0.0129)|Melanoma(52;0.0133)|Renal(120;0.0376)|all_hematologic(60;0.124)		all cancers(43;2.9e-20)|Epithelial(43;1.99e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.58e-09)|GBM - Glioblastoma multiforme(59;0.000162)|STAD - Stomach adenocarcinoma(60;0.000543)|LUSC - Lung squamous cell carcinoma(193;0.096)		AGTAATTCTGATAACCTAATG	0.378																																					p.S195A		Atlas-SNP	.											.	SPATA4	44	.	0			c.T583G						.						81.0	82.0	82.0					4																	177113883		2203	4300	6503	SO:0001583	missense	132851	exon4			ATTCTGATAACCT	AY040204	CCDS3826.1	4q34.2	2008-02-05			ENSG00000150628	ENSG00000150628			17333	protein-coding gene	gene with protein product		609879					Standard	NM_144644		Approved	TSARG2, SPEF1B	uc003iuo.1	Q8NEY3	OTTHUMG00000160788	ENST00000280191.2:c.583T>G	chr4.hg19:g.177113883A>C	ENSP00000280191:p.Ser195Ala	100.0	0.0		83.0	9.0	NM_144644	Q8NCS5|Q8WW15	Missense_Mutation	SNP	ENST00000280191.2	hg19	CCDS3826.1	.	.	.	.	.	.	.	.	.	.	A	15.03	2.712351	0.48517	.	.	ENSG00000150628	ENST00000280191;ENST00000515234	T	0.23147	1.92	5.27	-4.24	0.03777	.	0.214168	0.37304	N	0.002141	T	0.21881	0.0527	L	0.42245	1.32	0.09310	N	0.999999	P	0.39883	0.693	B	0.43838	0.433	T	0.29088	-1.0023	10	0.42905	T	0.14	-17.5849	12.1759	0.54186	0.2333:0.0:0.0:0.7667	.	195	Q8NEY3	SPAT4_HUMAN	A	195;22	ENSP00000280191:S195A	ENSP00000280191:S195A	S	-	1	0	SPATA4	177350877	0.674000	0.27549	0.187000	0.23214	0.965000	0.64279	1.029000	0.30140	-0.248000	0.09583	-0.327000	0.08410	TCA	.	.		0.378	SPATA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362326.1	NM_144644	
FAM149A	25854	hgsc.bcm.edu	37	4	187073131	187073131	+	Silent	SNP	A	A	G			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr4:187073131A>G	ENST00000356371.5	+	4	891	c.891A>G	c.(889-891)aaA>aaG	p.K297K	FAM149A_ENST00000502970.1_Silent_p.K6K|FAM149A_ENST00000503432.1_Silent_p.K6K|FAM149A_ENST00000389354.5_Silent_p.K6K|FAM149A_ENST00000227065.4_Silent_p.K6K|FAM149A_ENST00000514153.1_Silent_p.K6K|FAM149A_ENST00000514829.1_3'UTR			A5PLN7	F149A_HUMAN	family with sequence similarity 149, member A	297										breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(2)	25		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.19e-10)|BRCA - Breast invasive adenocarcinoma(30;1.22e-05)|GBM - Glioblastoma multiforme(59;0.000122)|STAD - Stomach adenocarcinoma(60;0.000288)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.166)		TTGAAGGGAAAGTGAACCCTC	0.512																																					p.K6K		Atlas-SNP	.											.	FAM149A	52	.	0			c.A18G						.						134.0	117.0	123.0					4																	187073131		2203	4300	6503	SO:0001819	synonymous_variant	25854	exon3			AGGGAAAGTGAAC	AK057166	CCDS34117.1	4q35.1	2012-04-19			ENSG00000109794	ENSG00000109794			24527	protein-coding gene	gene with protein product							Standard	NM_015398		Approved	DKFZP564J102, MST119, MSTP119	uc010isl.3	A5PLN7	OTTHUMG00000160565	ENST00000356371.5:c.891A>G	chr4.hg19:g.187073131A>G		261.0	0.0		252.0	11.0	NM_001006655	B5MDB8|Q2TAN6|Q7Z2S5|Q9Y4T9	Silent	SNP	ENST00000356371.5	hg19																																																																																				.	.		0.512	FAM149A-201	KNOWN	basic	protein_coding	protein_coding		NM_001006655	
MARCH11	441061	hgsc.bcm.edu	37	5	16067841	16067841	+	Missense_Mutation	SNP	A	A	C			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr5:16067841A>C	ENST00000332432.8	-	4	1147	c.948T>G	c.(946-948)aaT>aaG	p.N316K		NM_001102562.1	NP_001096032.1	A6NNE9	MARHB_HUMAN	membrane-associated ring finger (C3HC4) 11	316					protein ubiquitination (GO:0016567)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(14)|urinary_tract(1)	20						CCCAGTGCAAATTCACAGCTC	0.428																																					p.N316K		Atlas-SNP	.											.	MARCH11	50	.	0			c.T948G						.						61.0	60.0	60.0					5																	16067841		1902	4137	6039	SO:0001583	missense	441061	exon4			GTGCAAATTCACA	BC150513	CCDS47192.1	5p15.1	2013-01-09			ENSG00000183654	ENSG00000183654		"""RING-type (C3HC4) zinc fingers"", ""MARCH membrane-associated ring fingers"""	33609	protein-coding gene	gene with protein product		613338				17604280	Standard	NM_001102562		Approved	MARCH-XI	uc003jfo.2	A6NNE9	OTTHUMG00000161789	ENST00000332432.8:c.948T>G	chr5.hg19:g.16067841A>C	ENSP00000333181:p.Asn316Lys	69.0	0.0		75.0	8.0	NM_001102562	A7E2S6	Missense_Mutation	SNP	ENST00000332432.8	hg19	CCDS47192.1	.	.	.	.	.	.	.	.	.	.	A	18.04	3.535515	0.64972	.	.	ENSG00000183654	ENST00000332432	T	0.35789	1.29	5.54	-2.2	0.06994	.	0.000000	0.85682	D	0.000000	T	0.51839	0.1698	M	0.64170	1.965	0.54753	D	0.99998	D	0.89917	1.0	D	0.91635	0.999	T	0.54556	-0.8276	10	0.87932	D	0	-21.0751	13.2983	0.60311	0.5631:0.0:0.4369:0.0	.	316	A6NNE9	MARHB_HUMAN	K	316	ENSP00000333181:N316K	ENSP00000333181:N316K	N	-	3	2	MARCH11	16120841	0.961000	0.32948	0.941000	0.38009	0.979000	0.70002	0.064000	0.14437	-0.359000	0.08150	-0.290000	0.09829	AAT	.	.		0.428	MARCH11-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000366096.2	NM_001102562	
ERAP2	64167	hgsc.bcm.edu	37	5	96215831	96215831	+	Missense_Mutation	SNP	A	A	G			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr5:96215831A>G	ENST00000437043.3	+	2	1153	c.442A>G	c.(442-444)Att>Gtt	p.I148V	ERAP2_ENST00000379904.4_Missense_Mutation_p.I148V|ERAP2_ENST00000510309.1_Missense_Mutation_p.I148V|CTD-2260A17.2_ENST00000501338.1_Intron	NM_001130140.1|NM_022350.3	NP_001123612.1|NP_071745.1	Q6P179	ERAP2_HUMAN	endoplasmic reticulum aminopeptidase 2	148					antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|regulation of blood pressure (GO:0008217)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24		all_cancers(142;0.000311)|all_epithelial(76;1.54e-06)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0596)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0703)		TCATGAACAAATTGCACTGCT	0.418																																					p.I148V		Atlas-SNP	.											.	ERAP2	77	.	0			c.A442G						.						88.0	80.0	83.0					5																	96215831		2203	4300	6503	SO:0001583	missense	64167	exon2			GAACAAATTGCAC	AF191545	CCDS4086.1	5q15	2007-11-21			ENSG00000164308	ENSG00000164308			29499	protein-coding gene	gene with protein product	"""leukocyte-derived arginine aminopeptidase"""	609497				12799365, 15908954	Standard	NM_022350		Approved	L-RAP, LRAP	uc003kmt.3	Q6P179	OTTHUMG00000128718	ENST00000437043.3:c.442A>G	chr5.hg19:g.96215831A>G	ENSP00000400376:p.Ile148Val	205.0	0.0		209.0	24.0	NM_001130140	Q7Z5K1|Q8TD32|Q8WVJ4|Q9HBX2	Missense_Mutation	SNP	ENST00000437043.3	hg19	CCDS4086.1	.	.	.	.	.	.	.	.	.	.	A	14.21	2.468388	0.43839	.	.	ENSG00000164308	ENST00000437043;ENST00000510373;ENST00000513084;ENST00000379904;ENST00000510309	T;T;T;T;T	0.04119	3.7;3.7;3.7;3.7;3.7	4.55	3.38	0.38709	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.147069	0.44285	D	0.000461	T	0.03178	0.0093	N	0.16790	0.44	0.36856	D	0.888169	B;B	0.23937	0.094;0.015	B;B	0.28139	0.051;0.086	T	0.45775	-0.9238	10	0.13470	T	0.59	.	8.8314	0.35087	0.9069:0.0:0.0931:0.0	.	148;148	Q6P179-3;Q6P179	.;ERAP2_HUMAN	V	148	ENSP00000400376:I148V;ENSP00000421175:I148V;ENSP00000421849:I148V;ENSP00000369235:I148V;ENSP00000425758:I148V	ENSP00000369235:I148V	I	+	1	0	ERAP2	96241587	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	2.226000	0.42963	1.825000	0.53177	0.383000	0.25322	ATT	.	.		0.418	ERAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250623.2	NM_022350	
HSPA9	3313	hgsc.bcm.edu	37	5	137893621	137893621	+	Missense_Mutation	SNP	T	T	C			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr5:137893621T>C	ENST00000297185.3	-	13	1695	c.1570A>G	c.(1570-1572)Att>Gtt	p.I524V	SNORD63_ENST00000411005.1_RNA|HSPA9_ENST00000501917.2_Intron	NM_004134.6	NP_004125.3	P38646	GRP75_HUMAN	heat shock 70kDa protein 9 (mortalin)	524					cellular protein metabolic process (GO:0044267)|negative regulation of apoptotic process (GO:0043066)|protein export from nucleus (GO:0006611)|protein folding (GO:0006457)|protein targeting to mitochondrion (GO:0006626)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			breast(2)|endometrium(1)|kidney(4)|large_intestine(8)|lung(12)|upper_aerodigestive_tract(1)	28			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			TTGGCATCAATGTCAAATGTA	0.433																																					p.I524V		Atlas-SNP	.											.	HSPA9	49	.	0			c.A1570G						.						96.0	89.0	91.0					5																	137893621		2203	4300	6503	SO:0001583	missense	3313	exon13			CATCAATGTCAAA	L11066	CCDS4208.1	5q31.1	2011-09-02	2006-10-31	2006-10-31	ENSG00000113013	ENSG00000113013		"""Heat shock proteins / HSP70"""	5244	protein-coding gene	gene with protein product		600548	"""heat shock 70kDa protein 9B (mortalin-2)"""	HSPA9B		7684501	Standard	NM_004134		Approved	GRP75, PBP74, mot-2, mthsp75	uc003ldf.3	P38646	OTTHUMG00000129206	ENST00000297185.3:c.1570A>G	chr5.hg19:g.137893621T>C	ENSP00000297185:p.Ile524Val	224.0	0.0		211.0	34.0	NM_004134	B2RCM1|P30036|P31932|Q1HB43|Q53H23|Q6GU03|Q9BWB7|Q9UC56	Missense_Mutation	SNP	ENST00000297185.3	hg19	CCDS4208.1	.	.	.	.	.	.	.	.	.	.	T	25.1	4.607813	0.87258	.	.	ENSG00000113013	ENST00000297185;ENST00000541333;ENST00000540484	T	0.01051	5.4	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	T	0.06826	0.0174	M	0.73598	2.24	0.80722	D	1	D	0.56746	0.977	D	0.87578	0.998	T	0.03587	-1.1022	10	0.66056	D	0.02	-17.9805	14.9425	0.71006	0.0:0.0:0.0:1.0	.	524	P38646	GRP75_HUMAN	V	524;477;510	ENSP00000297185:I524V	ENSP00000297185:I524V	I	-	1	0	HSPA9	137921520	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.986000	0.88173	2.086000	0.62901	0.533000	0.62120	ATT	.	.		0.433	HSPA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251285.1	NM_004134	
PCDHA5	56143	hgsc.bcm.edu	37	5	140203713	140203713	+	Splice_Site	SNP	G	G	A			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr5:140203713G>A	ENST00000529859.1	+	1	2352		c.e1+1		PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000378126.3_Missense_Mutation_p.V785M|PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529619.1_Splice_Site|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5						cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(3)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TACAGACAACGTGAGTTTTCT	0.423																																					p.V785M		Atlas-SNP	.											.	PCDHA5	361	.	0			c.G2353A						.						69.0	67.0	68.0					5																	140203713		2203	4300	6503	SO:0001630	splice_region_variant	56143	exon1			GACAACGTGAGTT	AF152483	CCDS54917.1	5q31	2010-11-26				ENSG00000204965		"""Cadherins / Protocadherins : Clustered"""	8671	other	complex locus constituent	"""ortholog of mouse CNR6"", ""KIAA0345-like 9"""	606311		CNRS6		10380929, 10662547	Standard	NM_018908		Approved	CNR6, CRNR6, CNRN6, PCDH-ALPHA5		Q9Y5H7		ENST00000529859.1:c.2352+1G>A	chr5.hg19:g.140203713G>A		161.0	0.0		132.0	11.0	NM_031501	O75284|Q8N4R3	Missense_Mutation	SNP	ENST00000529859.1	hg19	CCDS54917.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.467|8.467	0.856611|0.856611	0.17106|0.17106	.|.	.|.	ENSG00000204965|ENSG00000204965	ENST00000529619;ENST00000529859|ENST00000378126	.|T	.|0.50001	.|0.76	3.61|3.61	2.72|2.72	0.32119|0.32119	.|.	.|.	.|.	.|.	.|.	.|T	.|0.26666	.|0.0652	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|P	.|0.36183	.|0.542	.|B	.|0.26770	.|0.073	.|T	.|0.05007	.|-1.0912	.|7	.|.	.|.	.|.	.|.	7.6406|7.6406	0.28292|0.28292	0.2731:0.0:0.7269:0.0|0.2731:0.0:0.7269:0.0	.|.	.|785	.|Q9Y5H7-2	.|.	.|M	-1|785	.|ENSP00000367366:V785M	.|.	.|V	+|+	.|1	.|0	PCDHA5|PCDHA5	140183897|140183897	.|.	.|.	0.671000|0.671000	0.29857|0.29857	0.036000|0.036000	0.12997|0.12997	.|.	.|.	1.961000|1.961000	0.56991|0.56991	0.491000|0.491000	0.48974|0.48974	.|GTG	.	.		0.423	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908	Intron
PCDHB5	26167	hgsc.bcm.edu	37	5	140516630	140516630	+	Silent	SNP	G	G	A			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr5:140516630G>A	ENST00000231134.5	+	1	1831	c.1614G>A	c.(1612-1614)ccG>ccA	p.P538P		NM_015669.2	NP_056484.1	Q9Y5E4	PCDB5_HUMAN	protocadherin beta 5	538	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|kidney(1)|large_intestine(18)|lung(25)|ovary(3)|prostate(6)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	81			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GCGGCTCCCCGGCGCTGAGCA	0.682																																					p.P538P		Atlas-SNP	.											.	PCDHB5	184	.	0			c.G1614A						.						40.0	45.0	43.0					5																	140516630		2202	4299	6501	SO:0001819	synonymous_variant	26167	exon1			CTCCCCGGCGCTG	AF152498	CCDS4247.1	5q31	2010-01-26			ENSG00000113209	ENSG00000113209		"""Cadherins / Protocadherins : Clustered"""	8690	other	protocadherin		606331				10380929	Standard	NM_015669		Approved	DKFZp586B0217, PCDH-BETA5	uc003liq.3	Q9Y5E4	OTTHUMG00000129616	ENST00000231134.5:c.1614G>A	chr5.hg19:g.140516630G>A		15.0	0.0		17.0	6.0	NM_015669	Q549F4|Q9UFU9	Silent	SNP	ENST00000231134.5	hg19	CCDS4247.1																																																																																			.	.		0.682	PCDHB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251811.1	NM_015669	
KIAA0141	9812	hgsc.bcm.edu	37	5	141314143	141314143	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr5:141314143A>T	ENST00000432126.2	+	10	1275	c.1141A>T	c.(1141-1143)Aac>Tac	p.N381Y	KIAA0141_ENST00000194118.4_Missense_Mutation_p.N381Y	NM_001142603.1|NM_014773.3	NP_001136075.1|NP_055588.3	Q14154	DELE_HUMAN	KIAA0141	381					extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)	mitochondrion (GO:0005739)				endometrium(3)|large_intestine(4)|lung(5)|skin(1)|urinary_tract(3)	16		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCTTGCAGCCAACAATGGGGT	0.507																																					p.N381Y		Atlas-SNP	.											.	KIAA0141	44	.	0			c.A1141T						.						116.0	110.0	112.0					5																	141314143		2203	4300	6503	SO:0001583	missense	9812	exon10			GCAGCCAACAATG	BC011269	CCDS4268.1	5q31	2011-05-05			ENSG00000081791	ENSG00000081791			28969	protein-coding gene	gene with protein product	"""death ligand signal enhancer"""	615741				20563667	Standard	XM_005268549		Approved	DELE	uc003llt.3	Q14154	OTTHUMG00000129662	ENST00000432126.2:c.1141A>T	chr5.hg19:g.141314143A>T	ENSP00000396225:p.Asn381Tyr	164.0	0.0		145.0	11.0	NM_001142603	Q969R4|Q96EU9	Missense_Mutation	SNP	ENST00000432126.2	hg19	CCDS4268.1	.	.	.	.	.	.	.	.	.	.	A	19.29	3.798993	0.70567	.	.	ENSG00000081791	ENST00000432126;ENST00000194118	T;T	0.52295	0.67;0.67	5.54	1.8	0.24995	Tetratricopeptide-like helical (1);	0.764793	0.12673	N	0.448617	T	0.52419	0.1733	L	0.55103	1.725	0.25299	N	0.98929	D	0.55385	0.971	P	0.55161	0.77	T	0.40001	-0.9586	10	0.66056	D	0.02	-3.3035	6.8394	0.23955	0.7294:0.0:0.2706:0.0	.	381	Q14154	DELE_HUMAN	Y	381	ENSP00000396225:N381Y;ENSP00000194118:N381Y	ENSP00000194118:N381Y	N	+	1	0	KIAA0141	141294327	0.993000	0.37304	0.987000	0.45799	0.961000	0.63080	2.270000	0.43355	0.358000	0.24211	0.528000	0.53228	AAC	.	.		0.507	KIAA0141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251863.2	NM_014773	
GEMIN5	25929	hgsc.bcm.edu	37	5	154311099	154311099	+	Missense_Mutation	SNP	C	C	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr5:154311099C>T	ENST00000285873.7	-	5	775	c.700G>A	c.(700-702)Gct>Act	p.A234T		NM_001252156.1|NM_015465.4	NP_001239085.1|NP_056280.2	Q8TEQ6	GEMI5_HUMAN	gem (nuclear organelle) associated protein 5	234					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|protein complex assembly (GO:0006461)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)	poly(A) RNA binding (GO:0044822)|snRNA binding (GO:0017069)			breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			GTTACTGGAGCTTGTGCTACA	0.373																																					p.A234T		Atlas-SNP	.											.	GEMIN5	120	.	0			c.G700A						.						154.0	135.0	141.0					5																	154311099		2203	4300	6503	SO:0001583	missense	25929	exon5			CTGGAGCTTGTGC	AK022748	CCDS4330.1	5q34	2013-01-10			ENSG00000082516	ENSG00000082516		"""WD repeat domain containing"""	20043	protein-coding gene	gene with protein product		607005				11714716	Standard	NM_015465		Approved		uc003lvx.3	Q8TEQ6	OTTHUMG00000130189	ENST00000285873.7:c.700G>A	chr5.hg19:g.154311099C>T	ENSP00000285873:p.Ala234Thr	119.0	0.0		140.0	27.0	NM_015465	Q14CV0|Q8WWV4|Q969W4|Q9H9K3|Q9UFI5	Missense_Mutation	SNP	ENST00000285873.7	hg19	CCDS4330.1	.	.	.	.	.	.	.	.	.	.	C	0.035	-1.310998	0.01342	.	.	ENSG00000082516	ENST00000285873	T	0.70282	-0.47	5.43	1.47	0.22746	WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.325766	0.32608	N	0.005870	T	0.37210	0.0995	N	0.11154	0.105	0.23366	N	0.997821	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.21449	-1.0245	10	0.02654	T	1	-5.5997	1.2209	0.01924	0.1481:0.1644:0.154:0.5336	.	233;234	B7ZLC9;Q8TEQ6	.;GEMI5_HUMAN	T	234	ENSP00000285873:A234T	ENSP00000285873:A234T	A	-	1	0	GEMIN5	154291292	0.035000	0.19736	0.998000	0.56505	0.111000	0.19643	0.021000	0.13489	0.352000	0.24053	-0.302000	0.09304	GCT	.	.		0.373	GEMIN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252507.1		
RIPK1	8737	hgsc.bcm.edu	37	6	3106115	3106115	+	Missense_Mutation	SNP	A	A	G	rs377213073		TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr6:3106115A>G	ENST00000259808.4	+	9	1704	c.1406A>G	c.(1405-1407)tAt>tGt	p.Y469C	RIPK1_ENST00000380409.2_Missense_Mutation_p.Y469C|RIPK1_ENST00000479389.1_3'UTR|RIPK1_ENST00000541791.1_Missense_Mutation_p.Y423C			Q13546	RIPK1_HUMAN	receptor (TNFRSF)-interacting serine-threonine kinase 1	469	Interaction with SQSTM1.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of JUN kinase activity (GO:0007257)|amyloid fibril formation (GO:1990000)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular protein catabolic process (GO:0044257)|cellular response to growth factor stimulus (GO:0071363)|cellular response to tumor necrosis factor (GO:0071356)|extrinsic apoptotic signaling pathway (GO:0097191)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|necroptotic signaling pathway (GO:0097527)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|peptidyl-serine autophosphorylation (GO:0036289)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of necroptotic process (GO:0060545)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon production (GO:0032481)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of ATP:ADP antiporter activity (GO:0070926)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to tumor necrosis factor (GO:0034612)|ripoptosome assembly (GO:0097343)|ripoptosome assembly involved in necroptotic process (GO:1901026)|T cell apoptotic process (GO:0070231)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)|ripoptosome (GO:0097342)	ATP binding (GO:0005524)|death domain binding (GO:0070513)|death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|protein complex binding (GO:0032403)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	23	Ovarian(93;0.0386)	all_hematologic(90;0.0895)				AATGGATTATATAGCTCACAT	0.493																																					p.Y469C		Atlas-SNP	.											.	RIPK1	56	.	0			c.A1406G						.	A	CYS/TYR	1,4405	2.1+/-5.4	0,1,2202	71.0	60.0	64.0		1406	-1.0	0.0	6		64	0,8600		0,0,4300	no	missense	RIPK1	NM_003804.3	194	0,1,6502	GG,GA,AA		0.0,0.0227,0.0077	probably-damaging	469/672	3106115	1,13005	2203	4300	6503	SO:0001583	missense	8737	exon8			GATTATATAGCTC	U25994	CCDS4482.1	6p25.2	2008-02-05			ENSG00000137275	ENSG00000137275			10019	protein-coding gene	gene with protein product		603453				7538908, 8612133	Standard	XM_005249458		Approved	RIP	uc003mux.3	Q13546	OTTHUMG00000014134	ENST00000259808.4:c.1406A>G	chr6.hg19:g.3106115A>G	ENSP00000259808:p.Tyr469Cys	212.0	0.0		230.0	10.0	NM_003804	A0AV89|B2RAG1|B4E3F9|Q13180|Q59H33	Missense_Mutation	SNP	ENST00000259808.4	hg19	CCDS4482.1	.	.	.	.	.	.	.	.	.	.	A	12.88	2.069635	0.36470	2.27E-4	0.0	ENSG00000137275	ENST00000259808;ENST00000541791;ENST00000380409;ENST00000453483	T;T;T	0.76968	-1.06;-0.52;-1.06	4.95	-1.05	0.10036	.	1.155410	0.06093	N	0.663997	T	0.64768	0.2628	L	0.55481	1.735	0.09310	N	1	D;D	0.61697	0.99;0.985	P;P	0.56474	0.799;0.527	T	0.52616	-0.8552	10	0.38643	T	0.18	-1.8055	1.2455	0.01972	0.3372:0.2916:0.0873:0.2839	.	423;469	Q13546-2;Q13546	.;RIPK1_HUMAN	C	469;423;469;71	ENSP00000259808:Y469C;ENSP00000442294:Y423C;ENSP00000369773:Y469C	ENSP00000259808:Y469C	Y	+	2	0	RIPK1	3051114	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-0.037000	0.12164	-0.007000	0.14345	0.533000	0.62120	TAT	.	.		0.493	RIPK1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039659.2	NM_003804	
FARS2	10667	hgsc.bcm.edu	37	6	5369076	5369076	+	Silent	SNP	G	G	A			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr6:5369076G>A	ENST00000324331.6	+	2	609	c.273G>A	c.(271-273)gaG>gaA	p.E91E	FARS2_ENST00000274680.4_Silent_p.E91E			O95363	SYFM_HUMAN	phenylalanyl-tRNA synthetase 2, mitochondrial	91					gene expression (GO:0010467)|phenylalanyl-tRNA aminoacylation (GO:0006432)|tRNA aminoacylation for protein translation (GO:0006418)|tRNA processing (GO:0008033)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|phenylalanine-tRNA ligase activity (GO:0004826)|tRNA binding (GO:0000049)			endometrium(3)|kidney(1)|large_intestine(5)|lung(3)|prostate(1)|stomach(2)	15	Ovarian(93;0.11)	all_hematologic(90;0.0104)			L-Phenylalanine(DB00120)	TGATCAAGGAGAGGGTGAAGG	0.577																																					p.E91E		Atlas-SNP	.											.	FARS2	33	.	0			c.G273A						.						71.0	57.0	62.0					6																	5369076		2203	4300	6503	SO:0001819	synonymous_variant	10667	exon2			CAAGGAGAGGGTG	AF097441	CCDS4494.1	6p25.1	2011-07-01	2007-02-23	2004-12-03	ENSG00000145982	ENSG00000145982	6.1.1.20	"""Aminoacyl tRNA synthetases / Class II"""	21062	protein-coding gene	gene with protein product	"""phenylalanine tRNA ligase 2, mitochondrial"""	611592	"""phenylalanine-tRNA synthetase 1 (mitochondrial)"""	FARS1		10329163	Standard	NM_006567		Approved	dJ236A3.1	uc003mwr.2	O95363	OTTHUMG00000014178	ENST00000324331.6:c.273G>A	chr6.hg19:g.5369076G>A		276.0	0.0		275.0	11.0	NM_006567	B2R664|Q53F66|Q5TCS3|Q6FG29|Q9NPY7|Q9P062	Silent	SNP	ENST00000324331.6	hg19	CCDS4494.1																																																																																			.	.		0.577	FARS2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467790.1	NM_006567	
KIAA1244	57221	hgsc.bcm.edu	37	6	138629875	138629875	+	Splice_Site	SNP	G	G	C			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr6:138629875G>C	ENST00000251691.4	+	24	4139		c.e24-1			NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		TCCTCCCTTAGGAAAAGGCCA	0.448																																					.		Atlas-SNP	.											.	KIAA1244	236	.	0			c.3974-1G>C						.						137.0	133.0	134.0					6																	138629875		2203	4300	6503	SO:0001630	splice_region_variant	57221	exon24			CCCTTAGGAAAAG	AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	21213	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 33"""		"""chromosome 6 open reading frame 92"""	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.3974-1G>C	chr6.hg19:g.138629875G>C		161.0	0.0		149.0	9.0	NM_020340		Splice_Site	SNP	ENST00000251691.4	hg19	CCDS5189.2	.	.	.	.	.	.	.	.	.	.	G	18.32	3.597971	0.66332	.	.	ENSG00000112379	ENST00000251691	.	.	.	5.89	5.89	0.94794	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.2617	0.98447	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	KIAA1244	138671568	1.000000	0.71417	0.999000	0.59377	0.517000	0.34286	9.869000	0.99810	2.793000	0.96121	0.655000	0.94253	.	.	.		0.448	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340	Intron
SYNE1	23345	hgsc.bcm.edu	37	6	152638095	152638095	+	Silent	SNP	A	A	G			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr6:152638095A>G	ENST00000367255.5	-	87	17200	c.16599T>C	c.(16597-16599)aaT>aaC	p.N5533N	SYNE1_ENST00000356820.4_Silent_p.N57N|SYNE1_ENST00000423061.1_Silent_p.N5462N|SYNE1_ENST00000448038.1_Silent_p.N5462N|SYNE1_ENST00000265368.4_Silent_p.N5533N|SYNE1_ENST00000341594.5_Silent_p.N5145N	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	5533					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		CAAGCATTTCATTGTATTCTT	0.348										HNSCC(10;0.0054)																											p.N5533N		Atlas-SNP	.											.	SYNE1	3227	.	0			c.T16599C						.						103.0	102.0	102.0					6																	152638095		2203	4300	6503	SO:0001819	synonymous_variant	23345	exon87			CATTTCATTGTAT	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.16599T>C	chr6.hg19:g.152638095A>G		56.0	0.0		63.0	7.0	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	hg19	CCDS5236.2																																																																																			.	.		0.348	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
TAGAP	117289	hgsc.bcm.edu	37	6	159457832	159457832	+	Missense_Mutation	SNP	C	C	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr6:159457832C>T	ENST00000367066.3	-	10	1554	c.1223G>A	c.(1222-1224)cGg>cAg	p.R408Q	RP1-111C20.4_ENST00000607796.1_RNA|RP1-111C20.4_ENST00000606466.1_RNA|RP1-111C20.4_ENST00000607391.1_RNA|TAGAP_ENST00000326965.6_Missense_Mutation_p.R230Q|RP1-111C20.4_ENST00000606470.1_RNA	NM_001278733.1|NM_054114.3	NP_001265662.1|NP_473455.2	Q8N103	TAGAP_HUMAN	T-cell activation RhoGTPase activating protein	408					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|autonomic_ganglia(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(2)|skin(1)	23		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.16e-16)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		AGAGCCTACCCGGGGCACGGG	0.572																																					p.R408Q		Atlas-SNP	.											.	TAGAP	75	.	0			c.G1223A						.						59.0	61.0	60.0					6																	159457832		2203	4300	6503	SO:0001583	missense	117289	exon10			CCTACCCGGGGCA	AF385429	CCDS5261.1, CCDS5262.1, CCDS5263.1	6q25.3	2011-09-07	2008-03-25		ENSG00000164691	ENSG00000164691		"""Rho GTPase activating proteins"""	15669	protein-coding gene	gene with protein product		609667	"""T-cell activation GTPase activating protein"""			16375659, 18311140, 18356936	Standard	NM_152133		Approved	FLJ32631, IDDM21, ARHGAP47	uc003qrz.3	Q8N103	OTTHUMG00000015923	ENST00000367066.3:c.1223G>A	chr6.hg19:g.159457832C>T	ENSP00000356033:p.Arg408Gln	157.0	0.0		146.0	17.0	NM_054114	Q2NKM8|Q8NI40|Q96KZ2|Q96QA2	Missense_Mutation	SNP	ENST00000367066.3	hg19	CCDS5261.1	.	.	.	.	.	.	.	.	.	.	C	5.985	0.365634	0.11352	.	.	ENSG00000164691	ENST00000367066;ENST00000326965;ENST00000539071	T;T	0.16457	2.34;2.63	6.05	-10.3	0.00346	.	1.110370	0.06750	N	0.779814	T	0.01387	0.0045	N	0.02011	-0.69	0.09310	N	0.999999	B	0.12630	0.006	B	0.06405	0.002	T	0.48801	-0.9003	10	0.02654	T	1	-0.7484	21.2762	0.99950	0.0:0.2287:0.0:0.7713	.	408	Q8N103	TAGAP_HUMAN	Q	408;230;73	ENSP00000356033:R408Q;ENSP00000322650:R230Q	ENSP00000322650:R230Q	R	-	2	0	TAGAP	159377820	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.398000	0.01051	-2.181000	0.00765	-0.827000	0.03088	CGG	.	.		0.572	TAGAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042890.1	NM_054114	
CCR6	1235	hgsc.bcm.edu	37	6	167550283	167550283	+	Missense_Mutation	SNP	T	T	C			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr6:167550283T>C	ENST00000341935.5	+	3	1117	c.565T>C	c.(565-567)Tac>Cac	p.Y189H	CCR6_ENST00000349984.4_Missense_Mutation_p.Y189H|CCR6_ENST00000400926.2_Missense_Mutation_p.Y189H|RP11-517H2.6_ENST00000609590.1_RNA	NM_031409.3	NP_113597.2	P51684	CCR6_HUMAN	chemokine (C-C motif) receptor 6	189					cellular component movement (GO:0006928)|cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|humoral immune response (GO:0006959)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)|receptor activity (GO:0004872)			endometrium(3)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)	14		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;8.21e-20)|BRCA - Breast invasive adenocarcinoma(81;4.55e-06)|GBM - Glioblastoma multiforme(31;0.00507)		CAACCAAAAATACAACACCCA	0.517																																					p.Y189H		Atlas-SNP	.											.	CCR6	36	.	0			c.T565C						.						101.0	95.0	97.0					6																	167550283		2203	4300	6503	SO:0001583	missense	1235	exon3			CAAAAATACAACA	U68030	CCDS5298.1	6q27	2012-08-08			ENSG00000112486	ENSG00000112486		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1607	protein-coding gene	gene with protein product		601835		STRL22		8886020	Standard	NM_031409		Approved	CKR-L3, GPR-CY4, CMKBR6, GPR29, DRY-6, DCR2, BN-1, CD196	uc010kkm.3	P51684	OTTHUMG00000016015	ENST00000341935.5:c.565T>C	chr6.hg19:g.167550283T>C	ENSP00000343952:p.Tyr189His	212.0	0.0		215.0	37.0	NM_004367	E1P5C6|P78553|Q92846	Missense_Mutation	SNP	ENST00000341935.5	hg19	CCDS5298.1	.	.	.	.	.	.	.	.	.	.	T	10.97	1.502385	0.26949	.	.	ENSG00000112486	ENST00000400926;ENST00000341935;ENST00000349984	T;T;T	0.72505	-0.66;-0.66;-0.66	4.94	4.94	0.65067	GPCR, rhodopsin-like superfamily (1);	0.985479	0.08239	U	0.976353	T	0.56001	0.1956	L	0.33710	1.025	0.80722	D	1	B	0.29552	0.248	B	0.41135	0.348	T	0.45234	-0.9275	10	0.24483	T	0.36	.	13.7779	0.63066	0.0:0.0:0.0:1.0	.	189	P51684	CCR6_HUMAN	H	189	ENSP00000383715:Y189H;ENSP00000343952:Y189H;ENSP00000339393:Y189H	ENSP00000343952:Y189H	Y	+	1	0	CCR6	167470273	1.000000	0.71417	0.155000	0.22561	0.013000	0.08279	5.417000	0.66423	1.836000	0.53414	0.533000	0.62120	TAC	.	.		0.517	CCR6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043118.1		
PDGFA	5154	hgsc.bcm.edu	37	7	540840	540840	+	Missense_Mutation	SNP	T	T	C			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr7:540840T>C	ENST00000354513.5	-	5	885	c.493A>G	c.(493-495)Aaa>Gaa	p.K165E	PDGFA_ENST00000402802.3_Missense_Mutation_p.K165E	NM_002607.5	NP_002598.4	P04085	PDGFA_HUMAN	platelet-derived growth factor alpha polypeptide	165					actin cytoskeleton organization (GO:0030036)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell activation (GO:0001775)|cell projection assembly (GO:0030031)|cell-cell signaling (GO:0007267)|embryo development (GO:0009790)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|lung alveolus development (GO:0048286)|negative chemotaxis (GO:0050919)|negative regulation of phosphatidylinositol biosynthetic process (GO:0010512)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway (GO:0035793)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of branching involved in salivary gland morphogenesis by epithelial-mesenchymal signaling (GO:0060683)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of smooth muscle cell migration (GO:0014910)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to inorganic substance (GO:0010035)|response to retinoic acid (GO:0032526)|response to wounding (GO:0009611)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi membrane (GO:0000139)|microvillus (GO:0005902)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|growth factor activity (GO:0008083)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	16		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|Epithelial(4;1.1e-17)|OV - Ovarian serous cystadenocarcinoma(56;1.7e-17)|all cancers(6;4.89e-15)		TGGACTTCTTTTAATTTTGGC	0.557																																					p.K165E		Atlas-SNP	.											.	PDGFA	34	.	0			c.A493G						.						285.0	267.0	273.0					7																	540840		2203	4296	6499	SO:0001583	missense	5154	exon5			CTTCTTTTAATTT		CCDS34578.1, CCDS47524.1	7p22	2008-07-18			ENSG00000197461	ENSG00000197461			8799	protein-coding gene	gene with protein product	"""PDGF A-chain"", ""platelet-derived growth factor alpha chain"""	173430				1505216, 2536956	Standard	NM_002607		Approved	PDGF1, PDGF-A	uc003sir.3	P04085	OTTHUMG00000151412	ENST00000354513.5:c.493A>G	chr7.hg19:g.540840T>C	ENSP00000346508:p.Lys165Glu	180.0	0.0		192.0	28.0	NM_002607	B5BU73	Missense_Mutation	SNP	ENST00000354513.5	hg19	CCDS34578.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.82|14.82	2.648079|2.648079	0.47258|0.47258	.|.	.|.	ENSG00000197461|ENSG00000197461	ENST00000402802;ENST00000354513|ENST00000400761	T;T|.	0.47177|.	0.85;0.85|.	4.98|4.98	4.98|4.98	0.66077|0.66077	Platelet-derived growth factor (PDGF) (3);|.	0.149699|0.149699	0.64402|0.64402	N|D	0.000016|0.000016	T|T	0.61311|0.61311	0.2337|0.2337	L|L	0.46885|0.46885	1.475|1.475	0.49299|0.49299	D|D	0.999775|0.999775	D;D;D|.	0.71674|.	0.975;0.998;0.987|.	P;D;P|.	0.72625|.	0.72;0.978;0.895|.	T|T	0.59247|0.59247	-0.7490|-0.7490	10|6	0.18276|.	T|.	0.48|.	-14.308|-14.308	14.3501|14.3501	0.66694|0.66694	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	179;165;165|.	Q32M96;P04085-2;P04085|.	.;.;PDGFA_HUMAN|.	E|R	165|171	ENSP00000383889:K165E;ENSP00000346508:K165E|.	ENSP00000346508:K165E|.	K|K	-|-	1|2	0|0	PDGFA|PDGFA	507366|507366	1.000000|1.000000	0.71417|0.71417	0.989000|0.989000	0.46669|0.46669	0.994000|0.994000	0.84299|0.84299	3.094000|3.094000	0.50227|0.50227	1.859000|1.859000	0.53934|0.53934	0.533000|0.533000	0.62120|0.62120	AAA|AAA	.	.		0.557	PDGFA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322534.1		
HDAC9	9734	hgsc.bcm.edu	37	7	18688120	18688120	+	Silent	SNP	G	G	A			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr7:18688120G>A	ENST00000432645.2	+	10	1272	c.1272G>A	c.(1270-1272)ttG>ttA	p.L424L	HDAC9_ENST00000406072.1_Silent_p.L411L|HDAC9_ENST00000524023.1_Silent_p.L347L|HDAC9_ENST00000417496.2_Silent_p.L422L|HDAC9_ENST00000441542.2_Silent_p.L427L|HDAC9_ENST00000456174.2_Silent_p.L396L|HDAC9_ENST00000428307.2_Silent_p.L380L|HDAC9_ENST00000406451.4_Silent_p.L424L|HDAC9_ENST00000405010.3_Silent_p.L424L|HDAC9_ENST00000401921.1_Silent_p.L383L	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9	424					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|regulation of skeletal muscle fiber development (GO:0048742)|regulation of striated muscle cell differentiation (GO:0051153)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(3)|central_nervous_system(4)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|liver(2)|lung(37)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	82	all_lung(11;0.187)				Valproic Acid(DB00313)	AGTCTCCCTTGGCAACAAAAG	0.463																																					p.L427L		Atlas-SNP	.											.	HDAC9	560	.	0			c.G1281A						.						77.0	76.0	77.0					7																	18688120		1886	4117	6003	SO:0001819	synonymous_variant	9734	exon10			TCCCTTGGCAACA	AF124924	CCDS47553.1, CCDS47554.1, CCDS47555.1, CCDS47557.1, CCDS56465.1, CCDS56466.1, CCDS56467.1, CCDS56468.1, CCDS75565.1	7p21.1	2008-05-15			ENSG00000048052	ENSG00000048052			14065	protein-coding gene	gene with protein product		606543				10523670, 10487760	Standard	NM_178425		Approved	KIAA0744, HDAC, MITR, HD7, HDAC7B	uc003sui.3	Q9UKV0	OTTHUMG00000152487	ENST00000432645.2:c.1272G>A	chr7.hg19:g.18688120G>A		63.0	0.0		65.0	9.0	NM_178425	A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	Silent	SNP	ENST00000432645.2	hg19	CCDS47555.1																																																																																			.	.		0.463	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1		
LGI3	203190	hgsc.bcm.edu	37	8	22006415	22006415	+	Missense_Mutation	SNP	C	C	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr8:22006415C>T	ENST00000306317.2	-	8	1194	c.905G>A	c.(904-906)gGc>gAc	p.G302D	LGI3_ENST00000424267.2_Missense_Mutation_p.G278D	NM_139278.2	NP_644807.1	Q8N145	LGI3_HUMAN	leucine-rich repeat LGI family, member 3	302					exocytosis (GO:0006887)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|extracellular region (GO:0005576)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)	catalytic activity (GO:0003824)			endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	17				Colorectal(74;0.00189)|COAD - Colon adenocarcinoma(73;0.0612)|READ - Rectum adenocarcinoma(644;0.0999)		AATGTAAGAGCCGCCAAACAG	0.612																																					p.G302D		Atlas-SNP	.											.	LGI3	44	.	0			c.G905A						.						62.0	55.0	57.0					8																	22006415		2203	4300	6503	SO:0001583	missense	203190	exon8			TAAGAGCCGCCAA	AJ487518	CCDS6025.1	8p21.2	2008-07-28			ENSG00000168481	ENSG00000168481			18711	protein-coding gene	gene with protein product		608302				12023020, 18628660	Standard	NM_139278		Approved		uc003xav.3	Q8N145	OTTHUMG00000131599	ENST00000306317.2:c.905G>A	chr8.hg19:g.22006415C>T	ENSP00000302297:p.Gly302Asp	228.0	0.0		158.0	29.0	NM_139278	A5PLP2|Q86TL4|Q8N296	Missense_Mutation	SNP	ENST00000306317.2	hg19	CCDS6025.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.473992	0.84640	.	.	ENSG00000168481	ENST00000306317;ENST00000424267	T;T	0.05649	3.41;3.41	4.6	4.6	0.57074	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	T	0.21387	0.0515	L	0.57536	1.79	0.58432	D	0.999999	D;D	0.89917	0.999;1.0	D;D	0.91635	0.975;0.999	T	0.00280	-1.1852	10	0.87932	D	0	-45.5027	14.9741	0.71257	0.0:1.0:0.0:0.0	.	278;302	A5PLP2;Q8N145	.;LGI3_HUMAN	D	302;278	ENSP00000302297:G302D;ENSP00000399121:G278D	ENSP00000302297:G302D	G	-	2	0	LGI3	22062360	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.922000	0.70036	2.366000	0.80165	0.561000	0.74099	GGC	.	.		0.612	LGI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254482.1		
MMP16	4325	hgsc.bcm.edu	37	8	89180168	89180168	+	Nonsense_Mutation	SNP	C	C	A			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr8:89180168C>A	ENST00000286614.6	-	4	720	c.439G>T	c.(439-441)Gag>Tag	p.E147*	MMP16_ENST00000544227.1_5'UTR	NM_005941.4	NP_005932.2	P51512	MMP16_HUMAN	matrix metallopeptidase 16 (membrane-inserted)	147					chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of catalytic activity (GO:0043085)	Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(1)|lung(51)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	81					Marimastat(DB00786)	TTACGAGTCTCAGGGTCTCCT	0.373																																					p.E147X		Atlas-SNP	.											.	MMP16	176	.	0			c.G439T						.						111.0	101.0	105.0					8																	89180168		2203	4300	6503	SO:0001587	stop_gained	4325	exon4			GAGTCTCAGGGTC	D85511	CCDS6246.1	8q21	2009-01-09	2005-08-08		ENSG00000156103	ENSG00000156103			7162	protein-coding gene	gene with protein product		602262	"""matrix metalloproteinase 16 (membrane-inserted)"", ""chromosome 8 open reading frame 57"""	C8orf57		7559440	Standard	NM_005941		Approved	MT3-MMP, DKFZp761D112	uc003yeb.4	P51512	OTTHUMG00000163769	ENST00000286614.6:c.439G>T	chr8.hg19:g.89180168C>A	ENSP00000286614:p.Glu147*	149.0	0.0		142.0	7.0	NM_005941	B2RAN7|Q14824|Q52H48	Nonsense_Mutation	SNP	ENST00000286614.6	hg19	CCDS6246.1	.	.	.	.	.	.	.	.	.	.	C	37	6.147893	0.97324	.	.	ENSG00000156103	ENST00000286614;ENST00000522726	.	.	.	6.16	6.16	0.99307	.	0.042023	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33940	T	0.23	.	20.8598	0.99761	0.0:1.0:0.0:0.0	.	.	.	.	X	147;164	.	ENSP00000286614:E147X	E	-	1	0	MMP16	89249284	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.768000	0.62293	2.937000	0.99478	0.650000	0.86243	GAG	.	.		0.373	MMP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375304.2	NM_005941	
CSMD3	114788	hgsc.bcm.edu	37	8	113348909	113348909	+	Missense_Mutation	SNP	C	C	G			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr8:113348909C>G	ENST00000297405.5	-	44	7235	c.6991G>C	c.(6991-6993)Gaa>Caa	p.E2331Q	CSMD3_ENST00000343508.3_Missense_Mutation_p.E2291Q|CSMD3_ENST00000352409.3_Missense_Mutation_p.E2261Q|CSMD3_ENST00000455883.2_Missense_Mutation_p.E2227Q	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2331	CUB 13. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TATATTGGTTCTGTTTGAAGG	0.318										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.E2331Q		Atlas-SNP	.											.	CSMD3	2325	.	0			c.G6991C						.						110.0	112.0	111.0					8																	113348909		2203	4300	6503	SO:0001583	missense	114788	exon44			TTGGTTCTGTTTG	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.6991G>C	chr8.hg19:g.113348909C>G	ENSP00000297405:p.Glu2331Gln	85.0	0.0		98.0	22.0	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	29.7	5.028607	0.93518	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18;-0.18	5.64	5.64	0.86602	CUB (5);	0.000000	0.64402	D	0.000001	T	0.81408	0.4816	M	0.83312	2.635	0.58432	D	0.999998	D;D;D	0.89917	0.999;0.996;1.0	D;D;D	0.83275	0.996;0.996;0.991	T	0.78610	-0.2137	10	0.34782	T	0.22	.	19.8946	0.96949	0.0:1.0:0.0:0.0	.	2227;2331;2291	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	Q	2291;2331;1601;2227;2261	ENSP00000345799:E2291Q;ENSP00000297405:E2331Q;ENSP00000341558:E1601Q;ENSP00000412263:E2227Q;ENSP00000343124:E2261Q	ENSP00000297405:E2331Q	E	-	1	0	CSMD3	113418085	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.651000	0.83577	2.937000	0.99478	0.650000	0.86243	GAA	.	.		0.318	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
SQLE	6713	hgsc.bcm.edu	37	8	126030343	126030343	+	Missense_Mutation	SNP	T	T	G			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr8:126030343T>G	ENST00000265896.5	+	8	2145	c.1247T>G	c.(1246-1248)cTt>cGt	p.L416R	SQLE_ENST00000523430.1_Missense_Mutation_p.L321R	NM_003129.3	NP_003120.2	Q14534	ERG1_HUMAN	squalene epoxidase	416					cellular aromatic compound metabolic process (GO:0006725)|cholesterol biosynthetic process (GO:0006695)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|squalene monooxygenase activity (GO:0004506)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)	14	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)		Butenafine(DB01091)|Naftifine(DB00735)|Terbinafine(DB00857)	AGGCATCCACTTACTGGTGGA	0.368																																					p.L416R		Atlas-SNP	.											.	SQLE	29	.	0			c.T1247G						.						113.0	109.0	110.0					8																	126030343		1828	4073	5901	SO:0001583	missense	6713	exon8			ATCCACTTACTGG	D78130	CCDS47918.1	8q24.1	2014-06-23			ENSG00000104549	ENSG00000104549	1.14.13.132		11279	protein-coding gene	gene with protein product	"""squalene monooxygenase"""	602019				9286711	Standard	NM_003129		Approved		uc011liq.2	Q14534	OTTHUMG00000164990	ENST00000265896.5:c.1247T>G	chr8.hg19:g.126030343T>G	ENSP00000265896:p.Leu416Arg	40.0	0.0		49.0	7.0	NM_003129	Q9UEK6	Missense_Mutation	SNP	ENST00000265896.5	hg19	CCDS47918.1	.	.	.	.	.	.	.	.	.	.	T	17.27	3.348267	0.61183	.	.	ENSG00000104549	ENST00000523430;ENST00000265896;ENST00000541193;ENST00000518931	T;T;T	0.49139	0.79;0.79;0.79	5.38	5.38	0.77491	Aromatic-ring hydroxylase-like (1);Squalene epoxidase (1);	0.000000	0.85682	D	0.000000	T	0.78027	0.4219	H	0.95574	3.69	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85256	0.1047	10	0.87932	D	0	-20.2226	15.3909	0.74741	0.0:0.0:0.0:1.0	.	416	Q14534	ERG1_HUMAN	R	321;416;221;68	ENSP00000430331:L321R;ENSP00000265896:L416R;ENSP00000429916:L68R	ENSP00000265896:L416R	L	+	2	0	SQLE	126099525	1.000000	0.71417	1.000000	0.80357	0.143000	0.21401	7.831000	0.86748	2.037000	0.60232	0.533000	0.62120	CTT	.	.		0.368	SQLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381362.1	NM_003129	
OR13J1	392309	hgsc.bcm.edu	37	9	35869767	35869767	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr9:35869767A>T	ENST00000377981.2	-	1	694	c.632T>A	c.(631-633)cTg>cAg	p.L211Q		NM_001004487.1	NP_001004487.1	Q8NGT2	O13J1_HUMAN	olfactory receptor, family 13, subfamily J, member 1	211						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|large_intestine(1)|lung(3)|skin(1)	6	all_epithelial(49;0.169)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00494)|STAD - Stomach adenocarcinoma(86;0.194)			GATGAATGCCAGGGGTACAGG	0.622																																					p.L211Q		Atlas-SNP	.											.	OR13J1	37	.	0			c.T632A						.						56.0	45.0	49.0					9																	35869767		2203	4300	6503	SO:0001583	missense	392309	exon1			AATGCCAGGGGTA		CCDS35011.1	9p13.3	2013-09-24			ENSG00000168828	ENSG00000168828		"""GPCR / Class A : Olfactory receptors"""	15108	protein-coding gene	gene with protein product							Standard	NM_001004487		Approved		uc011lph.2	Q8NGT2	OTTHUMG00000019879	ENST00000377981.2:c.632T>A	chr9.hg19:g.35869767A>T	ENSP00000367219:p.Leu211Gln	135.0	0.0		108.0	7.0	NM_001004487	B2RN66|Q6IF20|Q96R40	Missense_Mutation	SNP	ENST00000377981.2	hg19	CCDS35011.1	.	.	.	.	.	.	.	.	.	.	A	8.953	0.968595	0.18659	.	.	ENSG00000168828	ENST00000377981	T	0.49432	0.78	4.5	0.877	0.19145	GPCR, rhodopsin-like superfamily (1);	0.335275	0.21315	N	0.076577	T	0.67618	0.2912	M	0.91249	3.19	0.09310	N	1	D	0.89917	1.0	D	0.74348	0.983	T	0.57124	-0.7865	10	0.87932	D	0	.	4.9583	0.14054	0.6677:0.1581:0.1743:0.0	.	211	Q8NGT2	O13J1_HUMAN	Q	211	ENSP00000367219:L211Q	ENSP00000367219:L211Q	L	-	2	0	OR13J1	35859767	0.000000	0.05858	0.323000	0.25347	0.000000	0.00434	0.461000	0.21940	0.142000	0.18901	-1.133000	0.01973	CTG	.	.		0.622	OR13J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052381.1		
TMEFF1	8577	hgsc.bcm.edu	37	9	103271393	103271393	+	Missense_Mutation	SNP	T	T	C			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr9:103271393T>C	ENST00000374879.4	+	3	845	c.413T>C	c.(412-414)aTa>aCa	p.I138T	TMEFF1_ENST00000334943.6_Missense_Mutation_p.I99T|MSANTD3-TMEFF1_ENST00000502978.1_Silent_p.N101N	NM_003692.4	NP_003683.2	Q8IYR6	TEFF1_HUMAN	transmembrane protein with EGF-like and two follistatin-like domains 1	138	Kazal-like 1. {ECO:0000255|PROSITE- ProRule:PRU00798}.				multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|kidney(1)|large_intestine(7)|lung(9)|stomach(1)	19		Acute lymphoblastic leukemia(62;0.0452)				ATAACAGTAATAGCAAGAGGA	0.373																																					p.I212T		Atlas-SNP	.											.	.	.	.	0			c.T635C						.						100.0	99.0	99.0					9																	103271393		2203	4300	6503	SO:0001583	missense	100526694	exon3			CAGTAATAGCAAG	U19878	CCDS6750.1	9q31	2010-05-04			ENSG00000241697	ENSG00000241697			11866	protein-coding gene	gene with protein product	"""tomoregulin-1"", ""cancer/testis antigen family 120, member 1"""	603421		C9orf2		9730596	Standard	NM_003692		Approved	H7365, CT120.1		Q8IYR6	OTTHUMG00000020367	ENST00000374879.4:c.413T>C	chr9.hg19:g.103271393T>C	ENSP00000364013:p.Ile138Thr	55.0	0.0		63.0	15.0	NM_001198812	Q13086|Q8N3T8	Missense_Mutation	SNP	ENST00000374879.4	hg19	CCDS6750.1	.	.	.	.	.	.	.	.	.	.	T	13.72	2.321581	0.41096	.	.	ENSG00000241697	ENST00000334943;ENST00000374879	T;T	0.04156	3.69;3.69	5.58	5.58	0.84498	Proteinase inhibitor I1, Kazal (1);Protease inhibitor, Kazal-type (1);	0.066028	0.64402	D	0.000010	T	0.05777	0.0151	L	0.35542	1.07	0.20926	N	0.999828	B;B	0.11235	0.004;0.002	B;B	0.16722	0.016;0.0	T	0.26326	-1.0106	10	0.54805	T	0.06	-8.2017	13.6963	0.62582	0.0:0.0:0.0:1.0	.	138;99	Q8IYR6;Q8IYR6-2	TEFF1_HUMAN;.	T	99;138	ENSP00000334447:I99T;ENSP00000364013:I138T	ENSP00000334447:I99T	I	+	2	0	TMEFF1	102311214	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	3.674000	0.54598	2.113000	0.64589	0.528000	0.53228	ATA	.	.		0.373	TMEFF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053418.1	NM_003692	
ORM2	5005	hgsc.bcm.edu	37	9	117093116	117093116	+	Missense_Mutation	SNP	G	G	A			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr9:117093116G>A	ENST00000431067.2	+	3	338	c.302G>A	c.(301-303)cGg>cAg	p.R101Q	ORM2_ENST00000412657.1_3'UTR	NM_000608.2	NP_000599.1	P19652	A1AG2_HUMAN	orosomucoid 2	101					acute-phase response (GO:0006953)|regulation of immune system process (GO:0002682)|transport (GO:0006810)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|large_intestine(1)|lung(1)|skin(2)|urinary_tract(1)	7		Myeloproliferative disorder(63;0.163)			Chlorpromazine(DB00477)|Oxycodone(DB00497)|Thalidomide(DB01041)	AATGTCCAGCGGGAGAATGGG	0.552																																					p.R101Q	NSCLC(65;867 1308 1814 2391 12508)	Atlas-SNP	.											.	ORM2	13	.	0			c.G302A						.						80.0	77.0	78.0					9																	117093116		2203	4300	6503	SO:0001583	missense	5005	exon3			TCCAGCGGGAGAA		CCDS6804.1	9q32	2013-09-19			ENSG00000228278	ENSG00000228278		"""Lipocalins"""	8499	protein-coding gene	gene with protein product	"""alpha-1-acid glycoprotein, type 2"""	138610				4711474, 2970990	Standard	NM_000608		Approved	AGP-B, AGP-B', AGP2		P19652	OTTHUMG00000021014	ENST00000431067.2:c.302G>A	chr9.hg19:g.117093116G>A	ENSP00000394936:p.Arg101Gln	143.0	0.0		167.0	21.0	NM_000608	B2R5L2|Q16571|Q5T538|Q6IB74	Missense_Mutation	SNP	ENST00000431067.2	hg19	CCDS6804.1	.	.	.	.	.	.	.	.	.	.	-	17.22	3.335318	0.60853	.	.	ENSG00000228278	ENST00000431067	T	0.13657	2.57	2.72	2.72	0.32119	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.283482	0.32736	N	0.005715	T	0.33147	0.0853	M	0.79475	2.455	0.24851	N	0.992406	D	0.89917	1.0	D	0.74674	0.984	T	0.02220	-1.1193	10	0.87932	D	0	-13.5568	9.1868	0.37176	0.0:0.0:1.0:0.0	.	101	P19652	A1AG2_HUMAN	Q	101	ENSP00000394936:R101Q	ENSP00000394936:R101Q	R	+	2	0	ORM2	116132937	0.038000	0.19896	0.013000	0.15412	0.012000	0.07955	3.528000	0.53524	1.864000	0.54056	0.500000	0.49745	CGG	.	.		0.552	ORM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055432.1	NM_000608	
CDK5RAP2	55755	hgsc.bcm.edu	37	9	123210343	123210343	+	Missense_Mutation	SNP	T	T	C			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr9:123210343T>C	ENST00000349780.4	-	22	3034	c.2855A>G	c.(2854-2856)tAt>tGt	p.Y952C	CDK5RAP2_ENST00000359309.3_Missense_Mutation_p.Y952C|CDK5RAP2_ENST00000360822.3_Missense_Mutation_p.Y920C|CDK5RAP2_ENST00000360190.4_Missense_Mutation_p.Y952C	NM_018249.4	NP_060719.4	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	952	Interaction with MAPRE1.				brain development (GO:0007420)|centrosome organization (GO:0051297)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of centriole replication (GO:0046600)|negative regulation of neuron differentiation (GO:0045665)|neurogenesis (GO:0022008)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of spindle checkpoint (GO:0090231)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)			breast(6)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	58						AGGGAGACGATACATATTTCC	0.468																																					p.Y952C		Atlas-SNP	.											.	CDK5RAP2	157	.	0			c.A2855G						.						105.0	108.0	107.0					9																	123210343		2203	4300	6503	SO:0001583	missense	55755	exon22			AGACGATACATAT	BK005504	CCDS6823.1, CCDS43871.1, CCDS75888.1	9q33.3	2014-02-21			ENSG00000136861	ENSG00000136861			18672	protein-coding gene	gene with protein product	"""centrosomin"""	608201	"""microcephaly, primary autosomal recessive 3"""	MCPH3		10721722, 17764569, 24466316	Standard	NM_018249		Approved	C48, FLJ10867, CEP215	uc004bkf.4	Q96SN8	OTTHUMG00000021043	ENST00000349780.4:c.2855A>G	chr9.hg19:g.123210343T>C	ENSP00000343818:p.Tyr952Cys	203.0	0.0		189.0	24.0	NM_018249	Q5JV18|Q7Z3L4|Q7Z3U1|Q7Z7I6|Q9BSW0|Q9H6J6|Q9HCD9|Q9NV90|Q9UIW9	Missense_Mutation	SNP	ENST00000349780.4	hg19	CCDS6823.1	.	.	.	.	.	.	.	.	.	.	T	7.260	0.604943	0.14002	.	.	ENSG00000136861	ENST00000360822;ENST00000359309;ENST00000349780;ENST00000360190;ENST00000416449;ENST00000425647;ENST00000345313	T;T;T;T;T;T	0.38887	3.87;3.81;3.88;3.78;2.19;1.11	4.83	2.47	0.30058	.	1.242190	0.05894	N	0.628697	T	0.46347	0.1388	N	0.19112	0.55	0.09310	N	1	B;B;B;B;B;D	0.76494	0.009;0.002;0.009;0.244;0.005;0.999	B;B;B;B;B;D	0.76071	0.007;0.004;0.01;0.141;0.005;0.987	T	0.28808	-1.0032	10	0.49607	T	0.09	.	3.7924	0.08726	0.0:0.2142:0.1874:0.5984	.	3;721;920;952;952;346	Q5JTU8;Q6MZT4;Q96SN8-2;Q96SN8-4;Q96SN8;B1AMJ5	.;.;.;.;CK5P2_HUMAN;.	C	920;952;952;952;346;3;724	ENSP00000354065:Y920C;ENSP00000352258:Y952C;ENSP00000343818:Y952C;ENSP00000353317:Y952C;ENSP00000400395:Y346C;ENSP00000409941:Y3C	ENSP00000341695:Y724C	Y	-	2	0	CDK5RAP2	122250164	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	0.041000	0.13927	0.222000	0.20900	0.383000	0.25322	TAT	.	.		0.468	CDK5RAP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055535.1	NM_018249	
AK8	158067	hgsc.bcm.edu	37	9	135698618	135698618	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr9:135698618A>T	ENST00000298545.3	-	9	1384	c.863T>A	c.(862-864)cTg>cAg	p.L288Q	AK8_ENST00000477396.1_5'UTR	NM_152572.2	NP_689785.1	Q96MA6	KAD8_HUMAN	adenylate kinase 8	288	Adenylate kinase 2.				nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)			NS(1)|kidney(2)|large_intestine(4)|lung(11)|pancreas(2)|prostate(1)|urinary_tract(2)	23						TTTCTGGGCCAGGAGGGCGGC	0.627																																					p.L288Q		Atlas-SNP	.											.	AK8	45	.	0			c.T863A						.						91.0	99.0	96.0					9																	135698618		2203	4300	6503	SO:0001583	missense	158067	exon9			TGGGCCAGGAGGG	AK093446	CCDS6954.1	9q34.13	2013-04-29	2010-12-07	2010-12-07	ENSG00000165695	ENSG00000165695	2.7.4.3	"""Adenylate kinases"""	26526	protein-coding gene	gene with protein product		615365	"""chromosome 9 open reading frame 98"""	C9orf98		21080915	Standard	NM_152572		Approved	FLJ32704	uc004cbu.1	Q96MA6	OTTHUMG00000021009	ENST00000298545.3:c.863T>A	chr9.hg19:g.135698618A>T	ENSP00000298545:p.Leu288Gln	140.0	0.0		121.0	11.0	NM_152572	A8K821|Q8N9W9	Missense_Mutation	SNP	ENST00000298545.3	hg19	CCDS6954.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.047467	0.75846	.	.	ENSG00000165695	ENST00000298545	D	0.81499	-1.5	5.61	4.47	0.54385	.	0.230691	0.36591	N	0.002503	D	0.92378	0.7581	H	0.96943	3.91	0.43385	D	0.995493	D	0.89917	1.0	D	0.91635	0.999	D	0.93217	0.6605	10	0.87932	D	0	-23.719	10.8686	0.46870	0.9267:0.0:0.0733:0.0	.	288	Q96MA6	KAD8_HUMAN	Q	288	ENSP00000298545:L288Q	ENSP00000298545:L288Q	L	-	2	0	AK8	134688439	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.998000	0.76277	1.070000	0.40811	0.533000	0.62120	CTG	.	.		0.627	AK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055413.1	NM_152572	
PMPCA	23203	hgsc.bcm.edu	37	9	139313081	139313081	+	Silent	SNP	C	C	G	rs553050557	byFrequency	TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr9:139313081C>G	ENST00000371717.3	+	9	1074	c.1065C>G	c.(1063-1065)ccC>ccG	p.P355P	PMPCA_ENST00000399219.3_Silent_p.P224P|PMPCA_ENST00000462616.1_3'UTR	NM_001282946.1|NM_015160.1	NP_001269875.1|NP_055975.1	Q10713	MPPA_HUMAN	peptidase (mitochondrial processing) alpha	355					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			endometrium(3)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|urinary_tract(1)	14		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;9.3e-06)|Epithelial(140;1.15e-05)		CTGGTGGGCCCGGCAAGGGCA	0.597																																					p.P355P		Atlas-SNP	.											.	PMPCA	29	.	0			c.C1065G						.						82.0	75.0	77.0					9																	139313081		2203	4300	6503	SO:0001819	synonymous_variant	23203	exon9			TGGGCCCGGCAAG	D21064	CCDS35180.1, CCDS65192.1	9q34.3	2008-02-05	2003-06-13	2003-06-20	ENSG00000165688	ENSG00000165688			18667	protein-coding gene	gene with protein product		613036	"""inositol polyphosphate-5-phosphatase, 72 kD"""	INPP5E		8590280, 7788527	Standard	NM_015160		Approved	KIAA0123, Alpha-MPP	uc004chl.3	Q10713	OTTHUMG00000020926	ENST00000371717.3:c.1065C>G	chr9.hg19:g.139313081C>G		139.0	0.0		137.0	9.0	NM_015160	B4DKL3|E7ET61|Q16639|Q5SXM9|Q8N513	Silent	SNP	ENST00000371717.3	hg19	CCDS35180.1																																																																																			.	.		0.597	PMPCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055054.1	NM_015160	
NRP1	8829	hgsc.bcm.edu	37	10	33515205	33515205	+	Missense_Mutation	SNP	G	G	A			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr10:33515205G>A	ENST00000265371.4	-	8	1519	c.994C>T	c.(994-996)Ctt>Ttt	p.L332F	NRP1_ENST00000374867.2_Missense_Mutation_p.L332F|NRP1_ENST00000374822.4_Missense_Mutation_p.L332F|NRP1_ENST00000374821.5_Missense_Mutation_p.L332F|NRP1_ENST00000374823.5_Missense_Mutation_p.L332F|NRP1_ENST00000374875.1_Missense_Mutation_p.L151F|NRP1_ENST00000432372.2_Missense_Mutation_p.L332F|NRP1_ENST00000374816.3_Missense_Mutation_p.L332F|NRP1_ENST00000395995.1_Missense_Mutation_p.L332F			O14786	NRP1_HUMAN	neuropilin 1	332	F5/8 type C 1. {ECO:0000255|PROSITE- ProRule:PRU00081}.				angiogenesis (GO:0001525)|angiogenesis involved in coronary vascular morphogenesis (GO:0060978)|artery morphogenesis (GO:0048844)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell signaling (GO:0007267)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|commissural neuron axon guidance (GO:0071679)|coronary artery morphogenesis (GO:0060982)|dendrite development (GO:0016358)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell chemotaxis (GO:0035767)|endothelial tip cell fate specification (GO:0097102)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|patterning of blood vessels (GO:0001569)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of cytokine activity (GO:0060301)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of retinal ganglion cell axon guidance (GO:1902336)|positive regulation of smooth muscle cell migration (GO:0014911)|protein localization to early endosome (GO:1902946)|regulation of retinal ganglion cell axon guidance (GO:0090259)|regulation of vesicle-mediated transport (GO:0060627)|renal artery morphogenesis (GO:0061441)|response to wounding (GO:0009611)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal ganglion cell axon guidance (GO:0031290)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|sympathetic ganglion development (GO:0061549)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|VEGF-activated neuropilin signaling pathway (GO:0038190)|VEGF-activated neuropilin signaling pathway involved in axon guidance (GO:1902378)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neurofilament (GO:0005883)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|semaphorin receptor complex (GO:0002116)|sorting endosome (GO:0097443)	coreceptor activity (GO:0015026)|cytokine binding (GO:0019955)|growth factor binding (GO:0019838)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)|semaphorin receptor activity (GO:0017154)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(2)	48					Palifermin(DB00039)|Pegaptanib(DB04895)	AAGCGCAGAAGGCCCAAGTCT	0.498																																					p.L332F	Melanoma(104;886 1489 44640 45944 51153)	Atlas-SNP	.											.	NRP1	126	.	0			c.C994T						.						81.0	69.0	73.0					10																	33515205		2203	4300	6503	SO:0001583	missense	8829	exon7			GCAGAAGGCCCAA	AF016050	CCDS7177.1, CCDS31179.1, CCDS31180.1	10p12	2006-02-23			ENSG00000099250	ENSG00000099250		"""CD molecules"""	8004	protein-coding gene	gene with protein product		602069				9529250, 9331348	Standard	NM_003873		Approved	NRP, VEGF165R, CD304	uc001iwx.4	O14786	OTTHUMG00000019343	ENST00000265371.4:c.994C>T	chr10.hg19:g.33515205G>A	ENSP00000265371:p.Leu332Phe	91.0	0.0		107.0	11.0	NM_001244973	B0LPG9|O60461|Q5T7F1|Q5T7F2|Q5T7F3|Q86T59|Q96I90|Q96IH5	Missense_Mutation	SNP	ENST00000265371.4	hg19	CCDS7177.1	.	.	.	.	.	.	.	.	.	.	G	0.008	-1.896663	0.00522	.	.	ENSG00000099250	ENST00000265371;ENST00000374875;ENST00000374867;ENST00000395995;ENST00000374822;ENST00000374821;ENST00000374823;ENST00000374816;ENST00000432372	D;D;D;D;D;D;D;D;D	0.98178	-4.77;-4.77;-4.77;-4.77;-4.77;-4.77;-4.77;-4.77;-4.77	5.62	1.44	0.22558	Coagulation factor 5/8 C-terminal type domain (4);Galactose-binding domain-like (1);	0.227351	0.44285	D	0.000462	D	0.88566	0.6471	N	0.01048	-1.04	0.41790	D	0.989864	B;B;B;B;P;P;B;B;B	0.43352	0.0;0.004;0.004;0.0;0.766;0.804;0.0;0.0;0.002	B;B;B;B;B;B;B;B;B	0.41917	0.003;0.02;0.009;0.007;0.364;0.37;0.003;0.004;0.003	D	0.87551	0.2465	10	0.02654	T	1	-8.9796	6.1874	0.20506	0.2331:0.1292:0.6377:0.0	.	332;332;332;332;332;332;332;151;332	A8K9V7;E7EX60;Q5T7F0;Q5T7F1;O14786-2;Q68DN3;O14786;Q5JWQ6;E9PEP6	.;.;.;.;.;.;NRP1_HUMAN;.;.	F	332;151;332;332;332;332;332;332;5	ENSP00000265371:L332F;ENSP00000364009:L151F;ENSP00000364001:L332F;ENSP00000379317:L332F;ENSP00000363955:L332F;ENSP00000363954:L332F;ENSP00000363956:L332F;ENSP00000363949:L332F;ENSP00000408911:L5F	ENSP00000265371:L332F	L	-	1	0	NRP1	33555211	0.999000	0.42202	0.928000	0.36995	0.027000	0.11550	1.755000	0.38379	0.248000	0.21435	-0.266000	0.10368	CTT	.	.		0.498	NRP1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051203.2		
ZNF33A	7581	hgsc.bcm.edu	37	10	38345268	38345268	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr10:38345268A>T	ENST00000458705.2	+	5	2371	c.2213A>T	c.(2212-2214)cAt>cTt	p.H738L	ZNF33A_ENST00000469037.2_Intron|ZNF33A_ENST00000374618.3_Missense_Mutation_p.H739L|ZNF33A_ENST00000307441.9_Missense_Mutation_p.H738L|ZNF33A_ENST00000432900.2_Missense_Mutation_p.H745L			Q06730	ZN33A_HUMAN	zinc finger protein 33A	738					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)			cervix(2)|endometrium(2)|large_intestine(8)|liver(2)|lung(27)|ovary(2)|prostate(1)|skin(2)	46						CTTGCTCAACATCAGAGATCA	0.383																																					p.H739L		Atlas-SNP	.											.	ZNF33A	103	.	0			c.A2216T						.						106.0	102.0	103.0					10																	38345268		2203	4300	6503	SO:0001583	missense	7581	exon5			CTCAACATCAGAG	D31763	CCDS31182.1, CCDS60514.1, CCDS73088.1, CCDS73089.1	10p11.2	2013-01-08	2005-03-18		ENSG00000189180	ENSG00000189180		"""Zinc fingers, C2H2-type"", ""-"""	13096	protein-coding gene	gene with protein product	"""zinc finger and ZAK associated protein with KRAB domain"""	194521	"""zinc finger protein 33a (KOX 31)"", ""zinc finger protein 11A"""	ZNF33, ZNF11A		2014798, 8464732	Standard	NM_006974		Approved	KOX5, KOX31, KIAA0065, FLJ23404, ZZAPK	uc031pui.1	Q06730	OTTHUMG00000017983	ENST00000458705.2:c.2213A>T	chr10.hg19:g.38345268A>T	ENSP00000387713:p.His738Leu	131.0	0.0		123.0	21.0	NM_006954	A8K9X9|B4E0M8|F6TH33|F8WAJ5|P17013|Q5VZ86	Missense_Mutation	SNP	ENST00000458705.2	hg19	CCDS31182.1	.	.	.	.	.	.	.	.	.	.	A	11.26	1.585753	0.28268	.	.	ENSG00000189180	ENST00000374618;ENST00000432900;ENST00000458705;ENST00000307441	D;D;D;D	0.86865	-2.18;-2.18;-2.18;-2.18	1.92	1.92	0.25849	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.35096	N	0.003450	D	0.93539	0.7938	H	0.95224	3.64	0.31398	N	0.677078	D;D;D	0.69078	0.964;0.971;0.997	P;P;D	0.63597	0.504;0.637;0.916	D	0.90977	0.4824	10	0.87932	D	0	.	7.4341	0.27145	1.0:0.0:0.0:0.0	.	745;738;739	F6TH33;Q06730;F8WAJ5	.;ZN33A_HUMAN;.	L	739;745;738;738	ENSP00000363747:H739L;ENSP00000402467:H745L;ENSP00000387713:H738L;ENSP00000304268:H738L	ENSP00000304268:H738L	H	+	2	0	ZNF33A	38385274	1.000000	0.71417	0.998000	0.56505	0.374000	0.29953	5.998000	0.70653	0.864000	0.35578	0.260000	0.18958	CAT	.	.		0.383	ZNF33A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047614.1	NM_006974	
ZNF485	220992	hgsc.bcm.edu	37	10	44112662	44112662	+	Missense_Mutation	SNP	T	T	C			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr10:44112662T>C	ENST00000361807.3	+	5	1365	c.1171T>C	c.(1171-1173)Ttt>Ctt	p.F391L	ZNF485_ENST00000374435.3_Missense_Mutation_p.F391L|ZNF485_ENST00000374437.2_Missense_Mutation_p.F300L	NM_145312.3	NP_660355.2	Q8NCK3	ZN485_HUMAN	zinc finger protein 485	391					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	16						TGGGAAAGCCTTTCGGCACAG	0.443																																					p.F391L		Atlas-SNP	.											.	ZNF485	102	.	0			c.T1171C						.						59.0	58.0	58.0					10																	44112662		2203	4300	6503	SO:0001583	missense	220992	exon5			AAAGCCTTTCGGC	AK074679	CCDS7205.2	10q11.21	2013-01-08			ENSG00000198298	ENSG00000198298		"""Zinc fingers, C2H2-type"", ""-"""	23440	protein-coding gene	gene with protein product							Standard	NM_145312		Approved		uc010qfc.2	Q8NCK3	OTTHUMG00000018040	ENST00000361807.3:c.1171T>C	chr10.hg19:g.44112662T>C	ENSP00000354694:p.Phe391Leu	91.0	0.0		90.0	7.0	NM_145312	B4DSE6|Q96CL0	Missense_Mutation	SNP	ENST00000361807.3	hg19	CCDS7205.2	.	.	.	.	.	.	.	.	.	.	T	14.97	2.693663	0.48202	.	.	ENSG00000198298	ENST00000361807;ENST00000374437;ENST00000374435	T;T;T	0.46063	0.88;0.88;0.88	1.59	1.59	0.23543	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.63896	0.2550	M	0.87617	2.895	0.32192	N	0.578896	D	0.89917	1.0	D	0.97110	1.0	T	0.67917	-0.5546	9	0.87932	D	0	.	7.233	0.26053	0.0:0.0:0.0:1.0	.	391	Q8NCK3	ZN485_HUMAN	L	391;300;391	ENSP00000354694:F391L;ENSP00000363560:F300L;ENSP00000363558:F391L	ENSP00000354694:F391L	F	+	1	0	ZNF485	43432668	1.000000	0.71417	0.533000	0.28001	0.985000	0.73830	6.169000	0.71913	0.982000	0.38575	0.260000	0.18958	TTT	.	.		0.443	ZNF485-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047719.2	NM_145312	
DDX50	79009	hgsc.bcm.edu	37	10	70679601	70679601	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr10:70679601A>T	ENST00000373585.3	+	8	1210	c.1103A>T	c.(1102-1104)cAg>cTg	p.Q368L		NM_024045.1	NP_076950.1	Q9BQ39	DDX50_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 50	368						membrane (GO:0016020)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(5)|liver(2)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	29						TTGGCCATCCAGTGTCATTGG	0.358																																					p.Q368L		Atlas-SNP	.											.	DDX50	65	.	0			c.A1103T						.						92.0	92.0	92.0					10																	70679601		2203	4300	6503	SO:0001583	missense	79009	exon8			CCATCCAGTGTCA	AF334103	CCDS7283.1	10q22.2	2010-09-30			ENSG00000107625	ENSG00000107625		"""DEAD-boxes"""	17906	protein-coding gene	gene with protein product		610373				11891046	Standard	NM_024045		Approved	GU2, MGC3199, GUB, RH-II/GuB	uc001jou.3	Q9BQ39	OTTHUMG00000018362	ENST00000373585.3:c.1103A>T	chr10.hg19:g.70679601A>T	ENSP00000362687:p.Gln368Leu	282.0	0.0		219.0	20.0	NM_024045	Q5VX37|Q8WV76|Q9BWI8	Missense_Mutation	SNP	ENST00000373585.3	hg19	CCDS7283.1	.	.	.	.	.	.	.	.	.	.	A	14.41	2.526230	0.44969	.	.	ENSG00000107625	ENST00000373585;ENST00000541832	T	0.04234	3.67	4.94	4.94	0.65067	.	0.158822	0.53938	D	0.000051	T	0.05502	0.0145	L	0.37850	1.14	0.40437	D	0.98	B	0.26445	0.149	B	0.20955	0.032	T	0.39921	-0.9590	10	0.36615	T	0.2	-5.6776	14.8851	0.70560	1.0:0.0:0.0:0.0	.	368	Q9BQ39	DDX50_HUMAN	L	368	ENSP00000362687:Q368L	ENSP00000362687:Q368L	Q	+	2	0	DDX50	70349607	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.343000	0.59348	1.970000	0.57323	0.397000	0.26171	CAG	.	.		0.358	DDX50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048363.1	NM_024045	
MINPP1	9562	hgsc.bcm.edu	37	10	89312033	89312033	+	Missense_Mutation	SNP	A	A	G			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr10:89312033A>G	ENST00000371996.4	+	5	1303	c.1262A>G	c.(1261-1263)cAc>cGc	p.H421R	MINPP1_ENST00000472891.1_3'UTR|MINPP1_ENST00000371994.4_3'UTR|MINPP1_ENST00000536010.1_Missense_Mutation_p.H220R	NM_004897.4	NP_004888.2	Q9UNW1	MINP1_HUMAN	multiple inositol-polyphosphate phosphatase 1	421					bone mineralization (GO:0030282)|dephosphorylation (GO:0016311)|inositol phosphate metabolic process (GO:0043647)|ossification (GO:0001503)|polyphosphate metabolic process (GO:0006797)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	acid phosphatase activity (GO:0003993)|bisphosphoglycerate 3-phosphatase activity (GO:0034417)|inositol hexakisphosphate 2-phosphatase activity (GO:0052826)|phosphohistidine phosphatase activity (GO:0008969)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|urinary_tract(2)	5		Colorectal(252;0.122)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00123)		GTGCTTTACCACTGTGAAAAT	0.383																																					p.H421R		Atlas-SNP	.											.	MINPP1	22	.	0			c.A1262G						.						133.0	128.0	130.0					10																	89312033		2203	4300	6503	SO:0001583	missense	9562	exon5			TTTACCACTGTGA	AF046915	CCDS7384.1, CCDS53551.1, CCDS53552.1	10q23	2010-05-04	2010-05-04		ENSG00000107789	ENSG00000107789	3.1.3.62		7102	protein-coding gene	gene with protein product		605391	"""multiple inositol polyphosphate histidine phosphatase, 1"""			10087200	Standard	NM_004897		Approved	MIPP	uc001keu.3	Q9UNW1	OTTHUMG00000018678	ENST00000371996.4:c.1262A>G	chr10.hg19:g.89312033A>G	ENSP00000361064:p.His421Arg	196.0	0.0		173.0	7.0	NM_004897	F5H683|O95172|O95286|Q59EJ2|Q9UGA3	Missense_Mutation	SNP	ENST00000371996.4	hg19	CCDS7384.1	.	.	.	.	.	.	.	.	.	.	A	12.26	1.885766	0.33255	.	.	ENSG00000107789	ENST00000371996;ENST00000546140;ENST00000536010	T;T	0.26660	1.72;1.72	6.08	6.08	0.98989	.	0.156143	0.64402	D	0.000016	T	0.15132	0.0365	N	0.16098	0.37	0.44168	D	0.996977	B	0.17852	0.024	B	0.24155	0.051	T	0.19257	-1.0311	10	0.17369	T	0.5	-22.4426	10.1859	0.42998	0.9267:0.0:0.0733:0.0	.	421	Q9UNW1	MINP1_HUMAN	R	421;280;220	ENSP00000361064:H421R;ENSP00000437823:H220R	ENSP00000361064:H421R	H	+	2	0	MINPP1	89302013	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	5.130000	0.64745	2.333000	0.79357	0.482000	0.46254	CAC	.	.		0.383	MINPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049221.1		
FGF8	2253	hgsc.bcm.edu	37	10	103534534	103534534	+	Missense_Mutation	SNP	C	C	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr10:103534534C>T	ENST00000344255.3	-	4	258	c.259G>A	c.(259-261)Gcc>Acc	p.A87T	FGF8_ENST00000347978.2_Missense_Mutation_p.A69T|FGF8_ENST00000485728.1_5'UTR|FGF8_ENST00000346714.3_Missense_Mutation_p.A58T|FGF8_ENST00000320185.2_Missense_Mutation_p.A98T			P55075	FGF8_HUMAN	fibroblast growth factor 8 (androgen-induced)	87					anatomical structure morphogenesis (GO:0009653)|aorta morphogenesis (GO:0035909)|apoptotic process (GO:0006915)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|cell migration involved in mesendoderm migration (GO:0090134)|cell proliferation in forebrain (GO:0021846)|corticotropin hormone secreting cell differentiation (GO:0060128)|dopaminergic neuron differentiation (GO:0071542)|dorsal/ventral axon guidance (GO:0033563)|embryonic hindlimb morphogenesis (GO:0035116)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain morphogenesis (GO:0048853)|forebrain neuron development (GO:0021884)|gastrulation (GO:0007369)|gonad development (GO:0008406)|heart looping (GO:0001947)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|lung morphogenesis (GO:0060425)|male genitalia development (GO:0030539)|MAPK cascade (GO:0000165)|mesodermal cell migration (GO:0008078)|mesonephros development (GO:0001823)|metanephros development (GO:0001656)|midbrain-hindbrain boundary development (GO:0030917)|motor neuron axon guidance (GO:0008045)|negative regulation of cardiac muscle tissue development (GO:0055026)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate morphogenesis (GO:0001839)|neuroepithelial cell differentiation (GO:0060563)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|organ induction (GO:0001759)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|pallium development (GO:0021543)|patterning of blood vessels (GO:0001569)|pharyngeal system development (GO:0060037)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of mitosis (GO:0045840)|positive regulation of organ growth (GO:0046622)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|response to oxidative stress (GO:0006979)|signal transduction involved in regulation of gene expression (GO:0023019)|subpallium development (GO:0021544)|thyroid gland development (GO:0030878)|thyroid-stimulating hormone-secreting cell differentiation (GO:0060129)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|type 1 fibroblast growth factor receptor binding (GO:0005105)|type 2 fibroblast growth factor receptor binding (GO:0005111)			endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(2)	5		Colorectal(252;0.122)		Epithelial(162;3.94e-09)|all cancers(201;2.13e-07)		CGCTTGTTGGCCAGGACCTGC	0.657																																					p.A98T		Atlas-SNP	.											.	FGF8	23	.	0			c.G292A						.						87.0	77.0	80.0					10																	103534534		2203	4300	6503	SO:0001583	missense	2253	exon4			TGTTGGCCAGGAC	D38752	CCDS7515.1, CCDS7516.1, CCDS7517.1, CCDS7518.1, CCDS73185.1	10q25-q26	2014-01-30			ENSG00000107831	ENSG00000107831		"""Endogenous ligands"""	3686	protein-coding gene	gene with protein product		600483				8595889	Standard	NM_033164		Approved	AIGF	uc001ktq.2	P55075	OTTHUMG00000018940	ENST00000344255.3:c.259G>A	chr10.hg19:g.103534534C>T	ENSP00000340039:p.Ala87Thr	96.0	0.0		87.0	4.0	NM_033163	A1A514|Q14915|Q15766	Missense_Mutation	SNP	ENST00000344255.3	hg19	CCDS7517.1	.	.	.	.	.	.	.	.	.	.	C	15.60	2.882909	0.51908	.	.	ENSG00000107831	ENST00000344255;ENST00000320185;ENST00000346714;ENST00000347978	D;D;D;D	0.81579	-1.51;-1.51;-1.51;-1.51	4.52	3.62	0.41486	.	0.412269	0.23536	N	0.047134	T	0.68659	0.3025	L	0.28458	0.855	0.37131	D	0.901278	B;B;B;B	0.31625	0.199;0.093;0.332;0.013	B;B;B;B	0.21708	0.025;0.023;0.036;0.012	T	0.72824	-0.4176	10	0.62326	D	0.03	-11.971	12.8014	0.57588	0.0:0.9198:0.0:0.0802	.	58;69;98;87	P55075-2;P55075-3;P55075-4;P55075	.;.;.;FGF8_HUMAN	T	87;98;58;69	ENSP00000340039:A87T;ENSP00000321797:A98T;ENSP00000344306:A58T;ENSP00000321945:A69T	ENSP00000321797:A98T	A	-	1	0	FGF8	103524524	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.802000	0.47916	1.142000	0.42291	0.486000	0.48141	GCC	.	.		0.657	FGF8-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049999.1	NM_006119, NM_033165	
CFAP58	159686	hgsc.bcm.edu	37	10	106166547	106166547	+	Missense_Mutation	SNP	T	T	G			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr10:106166547T>G	ENST00000369704.3	+	15	2386	c.2252T>G	c.(2251-2253)cTc>cGc	p.L751R		NM_001008723.1	NP_001008723.1	Q5T655	CC147_HUMAN		751						extracellular space (GO:0005615)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	52		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;7.55e-10)|all cancers(201;3.37e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0189)		GAGCTGCTCCTCCAGGTAGCA	0.453																																					p.L751R		Atlas-SNP	.											.	CCDC147	137	.	0			c.T2252G						.						109.0	109.0	109.0					10																	106166547		2203	4300	6503	SO:0001583	missense	159686	exon15			TGCTCCTCCAGGT																												ENST00000369704.3:c.2252T>G	chr10.hg19:g.106166547T>G	ENSP00000358718:p.Leu751Arg	89.0	0.0		121.0	15.0	NM_001008723	D3DRA6|Q8NA27	Missense_Mutation	SNP	ENST00000369704.3	hg19	CCDS31282.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.418241	0.83449	.	.	ENSG00000120051	ENST00000369704	T	0.54675	0.56	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.68357	0.2992	M	0.78637	2.42	0.80722	D	1	D	0.52996	0.957	P	0.55222	0.771	T	0.68614	-0.5362	10	0.39692	T	0.17	-7.9849	16.8061	0.85666	0.0:0.0:0.0:1.0	.	751	Q5T655	CC147_HUMAN	R	751	ENSP00000358718:L751R	ENSP00000358718:L751R	L	+	2	0	CCDC147	106156537	0.993000	0.37304	0.111000	0.21465	0.919000	0.55068	7.394000	0.79862	2.367000	0.80283	0.528000	0.53228	CTC	.	.		0.453	CCDC147-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050216.1		
CSRP3	8048	hgsc.bcm.edu	37	11	19206570	19206570	+	Missense_Mutation	SNP	C	C	T	rs377066670		TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr11:19206570C>T	ENST00000533783.1	-	6	677	c.437G>A	c.(436-438)cGc>cAc	p.R146H	CSRP3_ENST00000265968.3_Missense_Mutation_p.R146H	NM_003476.4	NP_003467.1	P50461	CSRP3_HUMAN	cysteine and glycine-rich protein 3 (cardiac LIM protein)	146	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue development (GO:0048738)|cardiac myofibril assembly (GO:0055003)|cellular calcium ion homeostasis (GO:0006874)|detection of muscle stretch (GO:0035995)|protein localization to organelle (GO:0033365)|regulation of the force of heart contraction (GO:0002026)|skeletal muscle tissue development (GO:0007519)	cytoskeleton (GO:0005856)|nucleus (GO:0005634)|Z disc (GO:0030018)	actinin binding (GO:0042805)|structural constituent of muscle (GO:0008307)|telethonin binding (GO:0031433)|zinc ion binding (GO:0008270)			kidney(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(2)	10						GATGGCACAGCGGAAACAGGT	0.458																																					p.R146H		Atlas-SNP	.											CSRP3,NS,malignant_melanoma,0,1	CSRP3	24	.	0			c.G437A						.	C	HIS/ARG,HIS/ARG	0,4398		0,0,2199	100.0	89.0	93.0		437,437	5.4	1.0	11		93	1,8585	1.2+/-3.3	0,1,4292	no	missense,missense	CSRP3	NM_001127656.1,NM_003476.3	29,29	0,1,6491	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	146/195,146/195	19206570	1,12983	2199	4293	6492	SO:0001583	missense	8048	exon6			GCACAGCGGAAAC	U20324	CCDS7848.1	11p15.1	2014-09-17				ENSG00000129170			2472	protein-coding gene	gene with protein product		600824				7490106	Standard	NM_003476		Approved	CLP, MLP, CMD1M	uc001mpk.3	P50461		ENST00000533783.1:c.437G>A	chr11.hg19:g.19206570C>T	ENSP00000431813:p.Arg146His	160.0	0.0		152.0	17.0	NM_003476	Q9P131	Missense_Mutation	SNP	ENST00000533783.1	hg19	CCDS7848.1	.	.	.	.	.	.	.	.	.	.	C	33	5.246411	0.95305	0.0	1.16E-4	ENSG00000129170	ENST00000265968;ENST00000533783	D;D	0.91295	-2.82;-2.82	5.41	5.41	0.78517	Zinc finger, LIM-type (5);	0.000000	0.85682	D	0.000000	D	0.95430	0.8516	M	0.83384	2.64	0.80722	D	1	D	0.62365	0.991	D	0.64506	0.926	D	0.95733	0.8776	10	0.72032	D	0.01	-7.824	18.7893	0.91966	0.0:1.0:0.0:0.0	.	146	P50461	CSRP3_HUMAN	H	146	ENSP00000265968:R146H;ENSP00000431813:R146H	ENSP00000265968:R146H	R	-	2	0	CSRP3	19163146	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.794000	0.85869	2.552000	0.86080	0.655000	0.94253	CGC	.	.		0.458	CSRP3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394484.1	NM_003476	
NELL1	4745	hgsc.bcm.edu	37	11	20805310	20805310	+	Missense_Mutation	SNP	T	T	C			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr11:20805310T>C	ENST00000357134.5	+	3	421	c.269T>C	c.(268-270)tTg>tCg	p.L90S	NELL1_ENST00000532434.1_Missense_Mutation_p.L90S|NELL1_ENST00000325319.5_Missense_Mutation_p.L90S|NELL1_ENST00000298925.5_Missense_Mutation_p.L118S	NM_006157.3|NM_201551.1	NP_006148.2|NP_963845.1	Q92832	NELL1_HUMAN	NEL-like 1 (chicken)	90	Laminin G-like.				cell differentiation (GO:0030154)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of osteoblast proliferation (GO:0033689)|nervous system development (GO:0007399)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of gene expression (GO:0010468)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(5)|kidney(3)|large_intestine(15)|lung(36)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	70						TTCACCATTTTGGCCACTGTA	0.433																																					p.L90S		Atlas-SNP	.											.	NELL1	179	.	0			c.T269C						.						116.0	105.0	109.0					11																	20805310		2203	4300	6503	SO:0001583	missense	4745	exon3			CCATTTTGGCCAC	AK127805	CCDS7855.1, CCDS44555.1, CCDS73267.1, CCDS73268.1	11p15.1	2008-02-01	2001-11-28		ENSG00000165973	ENSG00000165973			7750	protein-coding gene	gene with protein product		602319	"""nel (chicken)-like 1"""			8975702	Standard	NM_006157		Approved	IDH3GL, FLJ45906	uc001mqe.3	Q92832	OTTHUMG00000166042	ENST00000357134.5:c.269T>C	chr11.hg19:g.20805310T>C	ENSP00000349654:p.Leu90Ser	115.0	0.0		92.0	19.0	NM_006157	B2CKC1|Q4VB90|Q4VB91|Q6NSY8|Q9Y472	Missense_Mutation	SNP	ENST00000357134.5	hg19	CCDS7855.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.403579	0.83230	.	.	ENSG00000165973	ENST00000298925;ENST00000357134;ENST00000325319;ENST00000532434	T;T;T;T	0.02085	4.46;4.46;4.46;4.46	5.9	5.9	0.94986	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);Laminin G, thrombospondin-type, N-terminal (1);	0.174039	0.38959	N	0.001506	T	0.09069	0.0224	L	0.60845	1.875	0.42578	D	0.993207	D;P;D;P	0.55800	0.973;0.954;0.958;0.883	P;P;P;B	0.59546	0.859;0.726;0.844;0.399	T	0.03068	-1.1076	10	0.49607	T	0.09	-0.7057	16.315	0.82915	0.0:0.0:0.0:1.0	.	90;118;90;90	F5H6I3;B3KXR2;Q92832-2;Q92832	.;.;.;NELL1_HUMAN	S	118;90;90;90	ENSP00000298925:L118S;ENSP00000349654:L90S;ENSP00000317837:L90S;ENSP00000437170:L90S	ENSP00000298925:L118S	L	+	2	0	NELL1	20761886	1.000000	0.71417	0.954000	0.39281	0.825000	0.46686	7.780000	0.85658	2.250000	0.74265	0.533000	0.62120	TTG	.	.		0.433	NELL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387588.1	NM_006157	
PRR5L	79899	hgsc.bcm.edu	37	11	36459019	36459019	+	Missense_Mutation	SNP	C	C	A			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr11:36459019C>A	ENST00000378867.3	+	7	792	c.437C>A	c.(436-438)cCa>cAa	p.P146Q	PRR5L_ENST00000389693.3_3'UTR|PRR5L_ENST00000530639.1_Missense_Mutation_p.P146Q|PRR5L_ENST00000311599.5_Missense_Mutation_p.P120Q|PRR5L_ENST00000527487.1_Missense_Mutation_p.P146Q	NM_024841.4	NP_079117.3	Q6MZQ0	PRR5L_HUMAN	proline rich 5 like	146					negative regulation of protein phosphorylation (GO:0001933)|negative regulation of signal transduction (GO:0009968)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|regulation of fibroblast migration (GO:0010762)|TORC2 signaling (GO:0038203)	mitochondrion (GO:0005739)|TORC2 complex (GO:0031932)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(7)|ovary(1)	19						ATATTTTATCCAGTTCAGGTT	0.522																																					p.P146Q		Atlas-SNP	.											.	PRR5L	35	.	0			c.C437A						.						194.0	166.0	175.0					11																	36459019		2202	4298	6500	SO:0001583	missense	79899	exon7			TTTATCCAGTTCA		CCDS31463.1, CCDS53617.1	11p13-p12	2009-07-09				ENSG00000135362			25878	protein-coding gene	gene with protein product	"""protein observed with Rictor-2"""	611728				17461779	Standard	NM_024841		Approved	FLJ14213, PROTOR-2	uc001mwp.3	Q6MZQ0		ENST00000378867.3:c.437C>A	chr11.hg19:g.36459019C>A	ENSP00000368144:p.Pro146Gln	114.0	0.0		124.0	5.0	NM_024841	A4QN22|E9PKY1|Q96H46|Q9H7V4	Missense_Mutation	SNP	ENST00000378867.3	hg19	CCDS31463.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.818956	0.90873	.	.	ENSG00000135362	ENST00000530639;ENST00000311599;ENST00000378867;ENST00000527487	T;T;T;T	0.75938	-0.87;1.68;-0.87;-0.98	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	D	0.86611	0.5974	M	0.75777	2.31	0.80722	D	1	D;D;D	0.89917	0.981;1.0;0.966	P;D;P	0.91635	0.883;0.999;0.883	D	0.87662	0.2535	10	0.87932	D	0	-29.8435	19.0681	0.93122	0.0:1.0:0.0:0.0	.	146;65;146	E9PKY1;Q6MZQ0-3;Q6MZQ0	.;.;PRR5L_HUMAN	Q	146;120;146;146	ENSP00000435050:P146Q;ENSP00000310103:P120Q;ENSP00000368144:P146Q;ENSP00000435241:P146Q	ENSP00000310103:P120Q	P	+	2	0	PRR5L	36415595	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.260000	0.72502	2.659000	0.90383	0.655000	0.94253	CCA	.	.		0.522	PRR5L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389209.1	NM_024841	
C11orf95	65998	hgsc.bcm.edu	37	11	63531074	63531074	+	lincRNA	SNP	T	T	C			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr11:63531074T>C	ENST00000433688.1	-	0	1871							C9JLR9	CK095_HUMAN	chromosome 11 open reading frame 95																		GATGTGGCGCTTGATGGTGCT	0.672																																					p.K618R		Atlas-SNP	.											.	.	.	.	0			c.A1853G						.						45.0	49.0	48.0					11																	63531074		692	1591	2283			65998	exon5			TGGCGCTTGATGG	BC000572, AK096306		11q13	2011-11-24			ENSG00000188070	ENSG00000188070			28449	protein-coding gene	gene with protein product		615699				20607705	Standard	NM_001144936		Approved	MGC3032	uc010rmv.2	C9JLR9			chr11.hg19:g.63531074T>C		75.0	0.0		46.0	6.0	NM_001144936	A6NLS7|Q3C1V4	Missense_Mutation	SNP	ENST00000433688.1	hg19																																																																																				.	.		0.672	C11orf95-201	KNOWN	basic	lincRNA	lincRNA		NM_001144936	
RNF169	254225	hgsc.bcm.edu	37	11	74546763	74546763	+	Missense_Mutation	SNP	A	A	G			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr11:74546763A>G	ENST00000299563.4	+	6	1128	c.1115A>G	c.(1114-1116)aAt>aGt	p.N372S		NM_001098638.1	NP_001092108.1	Q8NCN4	RN169_HUMAN	ring finger protein 169	372					cellular response to DNA damage stimulus (GO:0006974)|negative regulation of double-strand break repair (GO:2000780)|protein ubiquitination (GO:0016567)	intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|site of double-strand break (GO:0035861)	K63-linked polyubiquitin binding (GO:0070530)|ligase activity (GO:0016874)|nucleosome binding (GO:0031491)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|urinary_tract(1)	15						CCTGAGAGCAATGACAGCATC	0.527																																					p.N372S		Atlas-SNP	.											.	RNF169	36	.	0			c.A1115G						.						156.0	161.0	160.0					11																	74546763		2064	4204	6268	SO:0001583	missense	254225	exon6			AGAGCAATGACAG	AB082522	CCDS41691.1	11q13.4	2008-02-05			ENSG00000166439	ENSG00000166439		"""RING-type (C3HC4) zinc fingers"""	26961	protein-coding gene	gene with protein product						12056414	Standard	NM_001098638		Approved	KIAA1991	uc001ovl.4	Q8NCN4	OTTHUMG00000165516	ENST00000299563.4:c.1115A>G	chr11.hg19:g.74546763A>G	ENSP00000299563:p.Asn372Ser	183.0	0.0		155.0	12.0	NM_001098638	Q6N015	Missense_Mutation	SNP	ENST00000299563.4	hg19	CCDS41691.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.218294	0.79464	.	.	ENSG00000166439	ENST00000299563	T	0.52295	0.67	6.05	6.05	0.98169	.	0.000000	0.85682	D	0.000000	T	0.69369	0.3103	M	0.78637	2.42	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.73088	-0.4093	10	0.72032	D	0.01	-30.6562	14.5452	0.68024	1.0:0.0:0.0:0.0	.	372	Q8NCN4	RN169_HUMAN	S	372	ENSP00000299563:N372S	ENSP00000299563:N372S	N	+	2	0	RNF169	74224411	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.730000	0.91510	2.320000	0.78422	0.528000	0.53228	AAT	.	.		0.527	RNF169-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384741.1	XM_495886	
TAF1D	79101	hgsc.bcm.edu	37	11	93472409	93472409	+	Missense_Mutation	SNP	T	T	C			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr11:93472409T>C	ENST00000448108.2	-	2	712	c.62A>G	c.(61-63)aAt>aGt	p.N21S	C11orf54_ENST00000540113.1_5'Flank|C11orf54_ENST00000331239.4_5'Flank|C11orf54_ENST00000528099.1_5'Flank|C11orf54_ENST00000528288.1_5'Flank|C11orf54_ENST00000354421.3_5'Flank	NM_024116.3	NP_077021.1	Q9H5J8	TAF1D_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, D, 41kDa	21					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	microtubule organizing center (GO:0005815)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			large_intestine(1)|lung(3)|prostate(1)|skin(2)	7						TCACCTTCGATTTGCAAGTTC	0.318																																					p.N21S		Atlas-SNP	.											.	TAF1D	18	.	0			c.A62G						.						153.0	142.0	146.0					11																	93472409		2201	4298	6499	SO:0001583	missense	79101	exon2			CTTCGATTTGCAA		CCDS8293.1	11q21	2012-05-30	2008-09-30	2008-09-30	ENSG00000166012	ENSG00000166012			28759	protein-coding gene	gene with protein product		612823	"""Josephin domain containing 3"""	JOSD3		15520167, 17318177	Standard	NM_024116		Approved	MGC5306, TAF(I)41	uc001pec.3	Q9H5J8	OTTHUMG00000167451	ENST00000448108.2:c.62A>G	chr11.hg19:g.93472409T>C	ENSP00000410409:p.Asn21Ser	73.0	0.0		80.0	15.0	NM_024116	Q6I9Y6	Missense_Mutation	SNP	ENST00000448108.2	hg19	CCDS8293.1	.	.	.	.	.	.	.	.	.	.	T	9.351	1.065427	0.20067	.	.	ENSG00000166012	ENST00000448108	.	.	.	3.22	2.08	0.27032	.	0.308799	0.22698	N	0.056729	T	0.20700	0.0498	L	0.27053	0.805	0.21355	N	0.999713	P	0.37500	0.597	B	0.37047	0.24	T	0.08006	-1.0743	9	0.27785	T	0.31	-22.3659	5.1205	0.14858	0.0:0.1378:0.0:0.8622	.	21	Q9H5J8	TAF1D_HUMAN	S	21	.	ENSP00000314971:N21S	N	-	2	0	TAF1D	93112057	0.330000	0.24705	0.544000	0.28141	0.226000	0.24999	0.230000	0.17852	0.617000	0.30160	0.533000	0.62120	AAT	.	.		0.318	TAF1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394662.2	NM_024116	
SIAE	54414	hgsc.bcm.edu	37	11	124517357	124517357	+	Silent	SNP	A	A	G			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr11:124517357A>G	ENST00000263593.3	-	7	1042	c.870T>C	c.(868-870)aaT>aaC	p.N290N	SIAE_ENST00000545756.1_Silent_p.N255N			Q9HAT2	SIAE_HUMAN	sialic acid acetylesterase	290					carbohydrate metabolic process (GO:0005975)|regulation of immune system process (GO:0002682)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	sialate O-acetylesterase activity (GO:0001681)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(2)	15	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.63e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0243)		GGAATGTGCAATTGTACAGAT	0.458																																					p.N290N		Atlas-SNP	.											.	SIAE	37	.	0			c.T870C						.						139.0	124.0	129.0					11																	124517357		2201	4299	6500	SO:0001819	synonymous_variant	54414	exon7			TGTGCAATTGTAC	AF300796	CCDS8449.1, CCDS55795.1	11q24	2005-12-15	2005-12-15	2005-12-15		ENSG00000110013			18187	protein-coding gene	gene with protein product	"""sialic acid-specific acetylesterase II"""	610079	"""Ysg2 homolog (mouse)"""	YSG2		10464298	Standard	NM_001199922		Approved	CSE-C, MGC87009, LSE	uc001qan.3	Q9HAT2		ENST00000263593.3:c.870T>C	chr11.hg19:g.124517357A>G		100.0	0.0		116.0	17.0	NM_170601	B3KPB0|Q8IUT9|Q9HAU7|Q9NT71	Silent	SNP	ENST00000263593.3	hg19	CCDS8449.1																																																																																			.	.		0.458	SIAE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387070.1	NM_170601	
IGSF9B	22997	hgsc.bcm.edu	37	11	133799610	133799610	+	Nonsense_Mutation	SNP	C	C	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr11:133799610C>T	ENST00000321016.8	-	12	1817	c.1587G>A	c.(1585-1587)tgG>tgA	p.W529*	IGSF9B_ENST00000533871.2_Nonsense_Mutation_p.W529*			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	529	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		AGCCTGGTTCCCAGGACACGT	0.592																																					p.W529X		Atlas-SNP	.											.	IGSF9B	290	.	0			c.G1587A						.						126.0	140.0	135.0					11																	133799610		2086	4200	6286	SO:0001587	stop_gained	22997	exon12			TGGTTCCCAGGAC	AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.1587G>A	chr11.hg19:g.133799610C>T	ENSP00000317980:p.Trp529*	154.0	0.0		133.0	14.0	NM_014987	G5EA26	Nonsense_Mutation	SNP	ENST00000321016.8	hg19		.	.	.	.	.	.	.	.	.	.	C	41	9.129628	0.99075	.	.	ENSG00000080854	ENST00000321016;ENST00000533871;ENST00000527648	.	.	.	5.37	5.37	0.77165	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.1228	0.93371	0.0:1.0:0.0:0.0	.	.	.	.	X	529;371;529	.	ENSP00000317980:W529X	W	-	3	0	IGSF9B	133304820	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.757000	0.85209	2.505000	0.84491	0.655000	0.94253	TGG	.	.		0.592	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502	
IQSEC3	440073	hgsc.bcm.edu	37	12	266301	266301	+	Missense_Mutation	SNP	T	T	C			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr12:266301T>C	ENST00000538872.1	+	6	2382	c.2264T>C	c.(2263-2265)aTt>aCt	p.I755T	IQSEC3_ENST00000326261.4_Missense_Mutation_p.I755T|IQSEC3_ENST00000382841.2_Missense_Mutation_p.I452T			Q9UPP2	IQEC3_HUMAN	IQ motif and Sec7 domain 3	755	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)		GAGCGGCTCATTGAGGCCTTC	0.637																																					p.I755T		Atlas-SNP	.											.	IQSEC3	154	.	0			c.T2264C						.						36.0	34.0	35.0					12																	266301		2201	4299	6500	SO:0001583	missense	440073	exon6			GGCTCATTGAGGC	AB029033	CCDS31725.1, CCDS53728.1	12p13.33	2014-03-18			ENSG00000120645	ENSG00000120645			29193	protein-coding gene	gene with protein product		612118				10470851	Standard	NM_001170738		Approved	KIAA1110, MGC30156	uc001qhw.2	Q9UPP2	OTTHUMG00000167975	ENST00000538872.1:c.2264T>C	chr12.hg19:g.266301T>C	ENSP00000437554:p.Ile755Thr	385.0	0.0		315.0	45.0	NM_001170738	A6NIF2|A6NKV9|Q8TB43	Missense_Mutation	SNP	ENST00000538872.1	hg19	CCDS53728.1	.	.	.	.	.	.	.	.	.	.	T	15.84	2.952702	0.53293	.	.	ENSG00000120645	ENST00000538872;ENST00000326261;ENST00000382841	T;T;T	0.78481	-1.18;-1.18;-1.18	3.86	3.86	0.44501	SEC7-like, alpha orthogonal bundle (1);SEC7-like (4);	0.048933	0.85682	D	0.000000	T	0.82015	0.4945	L	0.47016	1.485	0.80722	D	1	D;P	0.56521	0.976;0.928	P;P	0.61940	0.896;0.839	D	0.84001	0.0343	10	0.87932	D	0	.	12.955	0.58421	0.0:0.0:0.0:1.0	.	755;452	Q9UPP2;Q9UPP2-2	IQEC3_HUMAN;.	T	755;755;452	ENSP00000437554:I755T;ENSP00000315662:I755T;ENSP00000372292:I452T	ENSP00000315662:I755T	I	+	2	0	IQSEC3	136562	1.000000	0.71417	0.994000	0.49952	0.230000	0.25150	7.888000	0.87302	1.536000	0.49237	0.260000	0.18958	ATT	.	.		0.637	IQSEC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397382.3	XM_495902	
CACNA1C	775	hgsc.bcm.edu	37	12	2614096	2614096	+	Missense_Mutation	SNP	T	T	C			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr12:2614096T>C	ENST00000347598.4	+	8	1202	c.1202T>C	c.(1201-1203)cTc>cCc	p.L401P	CACNA1C_ENST00000480911.1_Missense_Mutation_p.L401P|CACNA1C_ENST00000399591.1_Missense_Mutation_p.L401P|CACNA1C_ENST00000399638.1_Missense_Mutation_p.L401P|CACNA1C_ENST00000399641.1_Intron|CACNA1C_ENST00000399637.1_Missense_Mutation_p.L401P|CACNA1C_ENST00000399601.1_Missense_Mutation_p.L401P|CACNA1C_ENST00000399597.1_Missense_Mutation_p.L401P|CACNA1C_ENST00000399629.1_Missense_Mutation_p.L401P|CACNA1C_ENST00000335762.5_Missense_Mutation_p.L401P|CACNA1C_ENST00000402845.3_Missense_Mutation_p.L401P|CACNA1C_ENST00000399617.1_Intron|CACNA1C_ENST00000399603.1_Intron|CACNA1C_ENST00000399634.1_Intron|CACNA1C_ENST00000327702.7_Missense_Mutation_p.L401P|CACNA1C_ENST00000399649.1_Missense_Mutation_p.L401P|CACNA1C_ENST00000399595.1_Missense_Mutation_p.L401P|CACNA1C_ENST00000399644.1_Missense_Mutation_p.L401P|CACNA1C_ENST00000399606.1_Missense_Mutation_p.L401P|CACNA1C_ENST00000344100.3_Missense_Mutation_p.L401P|CACNA1C_ENST00000399655.1_Missense_Mutation_p.L401P|CACNA1C_ENST00000491104.1_Intron|CACNA1C_ENST00000399621.1_Missense_Mutation_p.L401P|CACNA1C_ENST00000406454.3_Intron	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	401					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	AACTTGGTTCTCGGTGTGCTT	0.398																																					p.L401P		Atlas-SNP	.											.	CACNA1C	1023	.	0			c.T1202C						.						109.0	102.0	104.0					12																	2614096		1884	4133	6017	SO:0001583	missense	775	exon8			TGGTTCTCGGTGT	AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.1202T>C	chr12.hg19:g.2614096T>C	ENSP00000266376:p.Leu401Pro	176.0	0.0		156.0	17.0	NM_001129831	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Missense_Mutation	SNP	ENST00000347598.4	hg19	CCDS44788.1	.	.	.	.	.	.	.	.	.	.	T	19.06	3.753376	0.69648	.	.	ENSG00000151067	ENST00000335762;ENST00000399655;ENST00000480911;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399595	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.98926	-5.24;-5.24;-5.24;-5.24;-5.24;-5.24;-5.24;-5.24;-5.24;-5.24;-5.24;-5.24;-5.24;-5.24;-5.24;-5.24;-5.24;-5.24	5.27	5.27	0.74061	Ion transport (1);	.	.	.	.	D	0.99441	0.9802	H	0.96633	3.855	0.80722	D	1	D;D;D;D;D;D;D;B;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;0.987;0.999;1.0;1.0;1.0;0.3;1.0;1.0;0.999;0.994;1.0;0.994;0.999;1.0;1.0;0.999;1.0	D;D;P;D;D;D;D;P;D;D;D;P;D;P;D;D;D;D;D	0.97110	0.998;0.999;0.859;0.998;0.999;0.999;0.999;0.673;1.0;0.999;0.999;0.843;0.999;0.843;0.996;0.999;0.999;0.996;0.999	D	0.98310	1.0523	9	0.87932	D	0	.	15.3726	0.74577	0.0:0.0:0.0:1.0	.	401;398;401;401;401;401;401;401;401;401;401;401;401;401;401;401;401;401;401	Q13936-14;Q13936-35;Q13936;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-11;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;Q13936-12	.;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	P	401	ENSP00000336982:L401P;ENSP00000382563:L401P;ENSP00000437936:L401P;ENSP00000382552:L401P;ENSP00000382547:L401P;ENSP00000382506:L401P;ENSP00000382530:L401P;ENSP00000382546:L401P;ENSP00000382500:L401P;ENSP00000266376:L401P;ENSP00000382515:L401P;ENSP00000382510:L401P;ENSP00000341092:L401P;ENSP00000382537:L401P;ENSP00000329877:L401P;ENSP00000382557:L401P;ENSP00000385724:L401P;ENSP00000382504:L401P	ENSP00000329877:L401P	L	+	2	0	CACNA1C	2484357	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.868000	0.87116	2.209000	0.71365	0.533000	0.62120	CTC	.	.		0.398	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719	
AKAP3	10566	hgsc.bcm.edu	37	12	4737905	4737905	+	Missense_Mutation	SNP	C	C	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr12:4737905C>T	ENST00000545990.2	-	5	687	c.163G>A	c.(163-165)Gag>Aag	p.E55K	AKAP3_ENST00000228850.1_Missense_Mutation_p.E55K|RP11-500M8.7_ENST00000536588.1_Intron	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	55					acrosome reaction (GO:0007340)|cellular component movement (GO:0006928)|protein localization (GO:0008104)|single fertilization (GO:0007338)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	acrosomal vesicle (GO:0001669)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	protein kinase A binding (GO:0051018)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|liver(1)|lung(17)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	51						TCTTGGAACTCTGCTGTACTC	0.478																																					p.E55K		Atlas-SNP	.											.	AKAP3	212	.	0			c.G163A						.						69.0	61.0	64.0					12																	4737905		2203	4300	6503	SO:0001583	missense	10566	exon4			GGAACTCTGCTGT	U85715	CCDS8531.1	12p13.3	2009-03-12				ENSG00000111254		"""A-kinase anchor proteins"""	373	protein-coding gene	gene with protein product	"""Fibrous Sheath Protein of 95 kDa"", ""cancer/testis antigen 82"""	604689				10334916, 10319321	Standard	NM_001278309		Approved	FSP95, SOB1, AKAP110, CT82	uc001qnb.4	O75969		ENST00000545990.2:c.163G>A	chr12.hg19:g.4737905C>T	ENSP00000440994:p.Glu55Lys	191.0	0.0		181.0	37.0	NM_006422	O75945|Q86X01|Q9UM61	Missense_Mutation	SNP	ENST00000545990.2	hg19	CCDS8531.1	.	.	.	.	.	.	.	.	.	.	C	18.58	3.655085	0.67472	.	.	ENSG00000111254	ENST00000228850;ENST00000545990;ENST00000540967;ENST00000536414	T;T;T;T	0.30981	1.51;1.51;1.51;1.51	4.78	4.78	0.61160	.	0.430236	0.22055	N	0.065249	T	0.18882	0.0453	N	0.08118	0	0.27525	N	0.951278	B	0.30482	0.281	B	0.30029	0.11	T	0.22836	-1.0205	10	0.72032	D	0.01	-5.2182	15.174	0.72896	0.0:1.0:0.0:0.0	.	55	O75969	AKAP3_HUMAN	K	55	ENSP00000228850:E55K;ENSP00000440994:E55K;ENSP00000442376:E55K;ENSP00000439382:E55K	ENSP00000228850:E55K	E	-	1	0	AKAP3	4608166	0.900000	0.30661	0.885000	0.34714	0.893000	0.52053	2.616000	0.46376	2.631000	0.89168	0.655000	0.94253	GAG	.	.		0.478	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2	NM_006422	
LEMD3	23592	hgsc.bcm.edu	37	12	65633985	65633985	+	Missense_Mutation	SNP	A	A	G			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr12:65633985A>G	ENST00000308330.2	+	8	2119	c.2093A>G	c.(2092-2094)cAt>cGt	p.H698R		NM_001167614.1|NM_014319.4	NP_001161086.1|NP_055134.2	Q9Y2U8	MAN1_HUMAN	LEM domain containing 3	698					negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of cell cycle (GO:0051726)|skeletal muscle cell differentiation (GO:0035914)	integral component of membrane (GO:0016021)|integral component of nuclear inner membrane (GO:0005639)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	36			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0104)		CCTATTCCACATGTACGCGAT	0.323																																					p.H698R		Atlas-SNP	.											.	LEMD3	68	.	0			c.A2093G						.						135.0	128.0	131.0					12																	65633985		2203	4300	6503	SO:0001583	missense	23592	exon8			TTCCACATGTACG	AF263918	CCDS8972.1	12q14	2008-02-05			ENSG00000174106	ENSG00000174106			28887	protein-coding gene	gene with protein product		607844				10671519, 15489854	Standard	NM_014319		Approved	MAN1	uc001ssl.2	Q9Y2U8	OTTHUMG00000168840	ENST00000308330.2:c.2093A>G	chr12.hg19:g.65633985A>G	ENSP00000308369:p.His698Arg	113.0	0.0		131.0	8.0	NM_014319	Q9NT47|Q9NYA5	Missense_Mutation	SNP	ENST00000308330.2	hg19	CCDS8972.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.117937	0.77323	.	.	ENSG00000174106	ENST00000308330	T	0.57752	0.38	5.03	5.03	0.67393	Inner nuclear membrane protein MAN1 (1);	0.000000	0.85682	D	0.000000	T	0.70386	0.3218	M	0.71581	2.175	0.80722	D	1	D	0.58268	0.982	D	0.70227	0.968	T	0.71560	-0.4556	9	.	.	.	-14.0796	15.4702	0.75434	1.0:0.0:0.0:0.0	.	698	Q9Y2U8	MAN1_HUMAN	R	698	ENSP00000308369:H698R	.	H	+	2	0	LEMD3	63920252	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	8.440000	0.90311	2.185000	0.69588	0.482000	0.46254	CAT	.	.		0.323	LEMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401312.2		
OTOGL	283310	hgsc.bcm.edu	37	12	80746178	80746178	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr12:80746178T>A	ENST00000547103.1	+	44	5312	c.5306T>A	c.(5305-5307)tTt>tAt	p.F1769Y	OTOGL_ENST00000458043.2_Missense_Mutation_p.F1781Y			Q3ZCN5	OTOGL_HUMAN	otogelin-like	1769					L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						TGCAACAAGTTTGATATCTGT	0.348																																					p.F1781Y		Atlas-SNP	.											.	OTOGL	235	.	0			c.T5342A						.						127.0	118.0	121.0					12																	80746178		1886	4113	5999	SO:0001583	missense	283310	exon44			ACAAGTTTGATAT	AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"""chromosome 12 open reading frame 64"""	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.5306T>A	chr12.hg19:g.80746178T>A	ENSP00000447211:p.Phe1769Tyr	80.0	0.0		96.0	8.0	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Missense_Mutation	SNP	ENST00000547103.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.53|16.53	3.148777|3.148777	0.57151|0.57151	.|.	.|.	ENSG00000165899|ENSG00000165899	ENST00000547103;ENST00000458043|ENST00000298820	D;D|.	0.86030|.	-2.06;-2.06|.	6.04|6.04	4.86|4.86	0.63082|0.63082	.|.	.|.	.|.	.|.	.|.	T|T	0.39655|0.39655	0.1086|0.1086	L|L	0.41492|0.41492	1.28|1.28	0.28928|0.28928	N|N	0.891723|0.891723	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.29852|0.29852	-0.9998|-0.9998	7|5	0.02654|.	T|.	1|.	.|.	8.8769|8.8769	0.35352|0.35352	0.3644:0.0:0.0:0.6356|0.3644:0.0:0.0:0.6356	.|.	.|.	.|.	.|.	Y|M	1769;1781|224	ENSP00000447211:F1769Y;ENSP00000400895:F1781Y|.	ENSP00000400895:F1781Y|.	F|L	+|+	2|1	0|2	OTOGL|OTOGL	79270309|79270309	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.793000|0.793000	0.44817|0.44817	4.240000|4.240000	0.58701|0.58701	2.317000|2.317000	0.78254|0.78254	0.460000|0.460000	0.39030|0.39030	TTT|TTG	.	.		0.348	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591	
COX6A1	1337	hgsc.bcm.edu	37	12	120878337	120878337	+	Silent	SNP	A	A	G			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr12:120878337A>G	ENST00000229379.2	+	3	364	c.327A>G	c.(325-327)gaA>gaG	p.E109E	AL021546.6_ENST00000551806.1_Intron	NM_004373.3	NP_004364.2	P12074	CX6A1_HUMAN	cytochrome c oxidase subunit VIa polypeptide 1	109					cellular metabolic process (GO:0044237)|generation of precursor metabolites and energy (GO:0006091)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex IV (GO:0005751)	cytochrome-c oxidase activity (GO:0004129)					all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					ACGAAGATGAATAAAGAGAAT	0.493																																					p.E109E		Atlas-SNP	.											.	COX6A1	5	.	0			c.A327G						.						50.0	42.0	45.0					12																	120878337		2203	4297	6500	SO:0001819	synonymous_variant	1337	exon3			AGATGAATAAAGA	X15341	CCDS9197.1	12q24	2011-07-04			ENSG00000111775	ENSG00000111775	1.9.3.1	"""Mitochondrial respiratory chain complex / Complex IV"""	2277	protein-coding gene	gene with protein product		602072		COX6A		9284905	Standard	NM_004373		Approved		uc001tyf.2	P12074	OTTHUMG00000047791	ENST00000229379.2:c.327A>G	chr12.hg19:g.120878337A>G		252.0	0.0		221.0	28.0	NM_004373	B2R500|O43714|Q32Q37	Silent	SNP	ENST00000229379.2	hg19	CCDS9197.1																																																																																			.	.		0.493	COX6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108984.3	NM_004373	
PCDH9	5101	hgsc.bcm.edu	37	13	67801110	67801110	+	Nonsense_Mutation	SNP	A	A	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr13:67801110A>T	ENST00000377865.2	-	1	1597	c.1463T>A	c.(1462-1464)tTa>tAa	p.L488*	PCDH9_ENST00000328454.5_Nonsense_Mutation_p.L488*|PCDH9_ENST00000377861.3_Nonsense_Mutation_p.L488*|PCDH9_ENST00000544246.1_Nonsense_Mutation_p.L488*|PCDH9_ENST00000456367.1_Nonsense_Mutation_p.L488*			Q9HC56	PCDH9_HUMAN	protocadherin 9	488	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				forebrain development (GO:0030900)|homophilic cell adhesion (GO:0007156)	cell-cell contact zone (GO:0044291)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(33)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	103		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		AATAGTTGTTAAGTATAACCC	0.418																																					p.L488X		Atlas-SNP	.											.	PCDH9	252	.	0			c.T1463A						.						104.0	105.0	105.0					13																	67801110		2203	4300	6503	SO:0001587	stop_gained	5101	exon2			GTTGTTAAGTATA	AF169692	CCDS9443.1, CCDS9444.1	13q21.32	2010-02-22			ENSG00000184226	ENSG00000184226		"""Cadherins / Protocadherins : Non-clustered"""	8661	protein-coding gene	gene with protein product		603581				9787079	Standard	NM_020403		Approved		uc001vik.3	Q9HC56	OTTHUMG00000017040	ENST00000377865.2:c.1463T>A	chr13.hg19:g.67801110A>T	ENSP00000367096:p.Leu488*	170.0	0.0		202.0	33.0	NM_203487	A2A6U1|Q5VT83|Q7Z3U0|Q8N3K7	Nonsense_Mutation	SNP	ENST00000377865.2	hg19	CCDS9444.1	.	.	.	.	.	.	.	.	.	.	A	35	5.468908	0.96274	.	.	ENSG00000184226	ENST00000544246;ENST00000377865;ENST00000456367;ENST00000328454;ENST00000377861	.	.	.	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.6438	0.85155	1.0:0.0:0.0:0.0	.	.	.	.	X	488	.	ENSP00000332060:L488X	L	-	2	0	PCDH9	66699111	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.333000	0.79357	0.533000	0.62120	TTA	.	.		0.418	PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276387.1	NM_203487	
NALCN	259232	hgsc.bcm.edu	37	13	101726938	101726938	+	Missense_Mutation	SNP	G	G	C			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr13:101726938G>C	ENST00000251127.6	-	36	4111	c.4030C>G	c.(4030-4032)Ctc>Gtc	p.L1344V		NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	1344					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					AGCAGCAAGAGAAACATGCCT	0.433																																					p.L1344V		Atlas-SNP	.											NALCN,NS,malignant_melanoma,0,1	NALCN	431	.	0			c.C4030G						.						118.0	116.0	117.0					13																	101726938		2203	4300	6503	SO:0001583	missense	259232	exon36			GCAAGAGAAACAT	AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"""Ion channels / Sodium leak channels, non-selective"""	19082	protein-coding gene	gene with protein product		611549	"""voltage gated channel like 1"""	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.4030C>G	chr13.hg19:g.101726938G>C	ENSP00000251127:p.Leu1344Val	38.0	0.0		43.0	7.0	NM_052867	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Missense_Mutation	SNP	ENST00000251127.6	hg19	CCDS9498.1	.	.	.	.	.	.	.	.	.	.	G	17.53	3.413265	0.62511	.	.	ENSG00000102452	ENST00000251127	D	0.98701	-5.08	5.8	3.8	0.43715	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98710	0.9567	M	0.74467	2.265	0.80722	D	1	D	0.62365	0.991	D	0.70016	0.967	D	0.99232	1.0882	10	0.87932	D	0	.	9.7274	0.40339	0.2412:0.0:0.7588:0.0	.	1344	Q8IZF0	NALCN_HUMAN	V	1344	ENSP00000251127:L1344V	ENSP00000251127:L1344V	L	-	1	0	NALCN	100524939	1.000000	0.71417	0.973000	0.42090	0.944000	0.59088	1.980000	0.40618	1.467000	0.48044	0.585000	0.79938	CTC	.	.		0.433	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867	
NALCN	259232	hgsc.bcm.edu	37	13	101759941	101759941	+	Missense_Mutation	SNP	G	G	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr13:101759941G>T	ENST00000251127.6	-	22	2557	c.2476C>A	c.(2476-2478)Ctc>Atc	p.L826I		NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	826					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					TTCTCTCTGAGTTCCTCTTCT	0.493																																					p.L826I		Atlas-SNP	.											.	NALCN	431	.	0			c.C2476A						.						174.0	154.0	161.0					13																	101759941		2203	4300	6503	SO:0001583	missense	259232	exon22			CTCTGAGTTCCTC	AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"""Ion channels / Sodium leak channels, non-selective"""	19082	protein-coding gene	gene with protein product		611549	"""voltage gated channel like 1"""	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.2476C>A	chr13.hg19:g.101759941G>T	ENSP00000251127:p.Leu826Ile	133.0	0.0		141.0	24.0	NM_052867	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Missense_Mutation	SNP	ENST00000251127.6	hg19	CCDS9498.1	.	.	.	.	.	.	.	.	.	.	G	17.30	3.355229	0.61293	.	.	ENSG00000102452	ENST00000251127	D	0.98135	-4.74	5.52	4.49	0.54785	.	0.000000	0.64402	D	0.000001	D	0.97176	0.9077	M	0.64997	1.995	0.80722	D	1	D	0.55800	0.973	P	0.51945	0.685	D	0.96490	0.9363	10	0.54805	T	0.06	.	11.7106	0.51623	0.1515:0.0:0.8485:0.0	.	826	Q8IZF0	NALCN_HUMAN	I	826	ENSP00000251127:L826I	ENSP00000251127:L826I	L	-	1	0	NALCN	100557942	1.000000	0.71417	0.368000	0.25939	0.865000	0.49528	3.850000	0.55918	2.583000	0.87209	0.650000	0.86243	CTC	.	.		0.493	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867	
LINC00283	100874057	hgsc.bcm.edu	37	13	103396874	103396874	+	RNA	SNP	T	T	A			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr13:103396874T>A	ENST00000430111.1	+	0	1247									long intergenic non-protein coding RNA 283																		TTTCATCATGTATCCAGAAAT	0.358																																					p.Y2058F		Atlas-SNP	.											.	.	.	.	0			c.A6173T						.						143.0	123.0	129.0					13																	103396874		692	1591	2283			643677	exon4			ATCATGTATCCAG			13q33.1	2012-10-12	2011-08-10	2011-08-10	ENSG00000231633	ENSG00000231633		"""Long non-coding RNAs"""	38809	non-coding RNA	RNA, long non-coding			"""non-protein coding RNA 283"""	NCRNA00283			Standard			Approved				OTTHUMG00000017311		chr13.hg19:g.103396874T>A		83.0	0.0		80.0	4.0	NM_001146197		Missense_Mutation	SNP	ENST00000430111.1	hg19																																																																																				.	.		0.358	LINC00283-001	KNOWN	not_organism_supported|basic	antisense	antisense	OTTHUMT00000045714.1		
CHAMP1	283489	hgsc.bcm.edu	37	13	115090198	115090198	+	Missense_Mutation	SNP	C	C	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr13:115090198C>T	ENST00000361283.1	+	3	1190	c.881C>T	c.(880-882)cCt>cTt	p.P294L		NM_001164144.1|NM_001164145.1|NM_032436.2	NP_001157616.1|NP_001157617.1|NP_115812.1	Q96JM3	CHAP1_HUMAN	chromosome alignment maintaining phosphoprotein 1	294	Mediates interaction with MAD2L2.|Pro-rich.				attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation (GO:0051315)|protein localization to kinetochore (GO:0034501)|protein localization to microtubule (GO:0035372)|sister chromatid biorientation (GO:0031134)	condensed chromosome (GO:0000793)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)										AAGCCGTTCCCTGCTGTCTCC	0.607																																					p.P294L		Atlas-SNP	.											.	.	.	.	0			c.C881T						.						50.0	58.0	55.0					13																	115090198		2203	4300	6503	SO:0001583	missense	283489	exon3			CGTTCCCTGCTGT	AK074894	CCDS9545.1	13q34	2013-01-07	2011-10-07	2011-10-07	ENSG00000198824	ENSG00000198824		"""Zinc fingers, C2H2-type"""	20311	protein-coding gene	gene with protein product	"""chromosome alignment-maintaining phosphoprotein"""		"""chromosome 13 open reading frame 8"", ""zinc finger protein 828"""	C13orf8, ZNF828		21063390	Standard	NM_032436		Approved	CAMP, CHAMP	uc010ahb.3	Q96JM3	OTTHUMG00000017404	ENST00000361283.1:c.881C>T	chr13.hg19:g.115090198C>T	ENSP00000354730:p.Pro294Leu	79.0	0.0		67.0	4.0	NM_001164144	B3KU06|Q6P181|Q8NC88|Q9BST0	Missense_Mutation	SNP	ENST00000361283.1	hg19	CCDS9545.1	.	.	.	.	.	.	.	.	.	.	C	14.14	2.446661	0.43429	.	.	ENSG00000198824	ENST00000361283	T	0.01438	4.89	5.92	5.92	0.95590	.	0.108147	0.41500	D	0.000868	T	0.02533	0.0077	L	0.49126	1.545	0.45183	D	0.998199	B	0.33171	0.4	B	0.30782	0.12	T	0.63883	-0.6536	9	.	.	.	-5.2128	20.3325	0.98724	0.0:1.0:0.0:0.0	.	294	Q96JM3	ZN828_HUMAN	L	294	ENSP00000354730:P294L	.	P	+	2	0	ZNF828	114108300	0.494000	0.26043	0.996000	0.52242	0.991000	0.79684	5.310000	0.65780	2.805000	0.96524	0.655000	0.94253	CCT	.	.		0.607	CHAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045977.2	NM_032436	
NUBPL	80224	hgsc.bcm.edu	37	14	32031297	32031297	+	Silent	SNP	C	C	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr14:32031297C>T	ENST00000281081.7	+	2	177	c.132C>T	c.(130-132)acC>acT	p.T44T	CTD-2213F21.3_ENST00000548096.1_RNA	NM_001201573.1|NM_001201574.1|NM_025152.2	NP_001188502.1|NP_001188503.1|NP_079428.2	Q8TB37	NUBPL_HUMAN	nucleotide binding protein-like	44					mitochondrial respiratory chain complex I assembly (GO:0032981)|mitochondrion morphogenesis (GO:0070584)	mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			endometrium(1)|lung(2)|prostate(1)|skin(1)	5	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.214)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0677)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0102)		GGAGTGAGACCCTAAAACAAA	0.383																																					p.T44T		Atlas-SNP	.											.	NUBPL	21	.	0			c.C132T						.						51.0	48.0	49.0					14																	32031297		1817	4067	5884	SO:0001819	synonymous_variant	80224	exon2			TGAGACCCTAAAA	AK022722	CCDS41940.1	14q12	2012-10-12	2005-01-07	2005-01-07	ENSG00000151413	ENSG00000151413		"""Mitochondrial respiratory chain complex assembly factors"""	20278	protein-coding gene	gene with protein product	"""iron-sulfur protein required for NADH dehydrogenase"""	613621	"""chromosome 14 open reading frame 127"""	C14orf127			Standard	NM_025152		Approved	FLJ12660, IND1, huInd1	uc001wrk.4	Q8TB37	OTTHUMG00000170521	ENST00000281081.7:c.132C>T	chr14.hg19:g.32031297C>T		67.0	0.0		62.0	11.0	NM_025152	B4DHZ1|Q86TZ4|Q9H9M2	Silent	SNP	ENST00000281081.7	hg19	CCDS41940.1																																																																																			.	.		0.383	NUBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409519.1	NM_025152	
ARHGAP5	394	hgsc.bcm.edu	37	14	32563379	32563379	+	Nonsense_Mutation	SNP	T	T	A			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr14:32563379T>A	ENST00000345122.3	+	2	3819	c.3504T>A	c.(3502-3504)taT>taA	p.Y1168*	ARHGAP5_ENST00000539826.2_Nonsense_Mutation_p.Y1168*|ARHGAP5_ENST00000433497.1_Intron|ARHGAP5_ENST00000556611.1_Nonsense_Mutation_p.Y1168*|ARHGAP5_ENST00000396582.2_Intron|ARHGAP5_ENST00000432921.1_Nonsense_Mutation_p.Y1168*	NM_001030055.1	NP_001025226.1	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5	1168					cell adhesion (GO:0007155)|GTP catabolic process (GO:0006184)|mammary gland development (GO:0030879)|positive regulation of cell migration (GO:0030335)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell size (GO:0008361)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(10)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(12)|ovary(4)|skin(1)|stomach(1)|urinary_tract(4)	55	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)		AGTCATACTATAGAAGAACAC	0.368																																					p.Y1168X	NSCLC(9;77 350 3443 29227 41353)	Atlas-SNP	.											.	ARHGAP5	166	.	0			c.T3504A						.						82.0	86.0	85.0					14																	32563379		2203	4300	6503	SO:0001587	stop_gained	394	exon2			ATACTATAGAAGA	U17032	CCDS32062.1, CCDS45095.1	14q12	2010-02-05						"""Rho GTPase activating proteins"""	675	protein-coding gene	gene with protein product		602680	"""growth factor independent 2"""	GFI2		8537347	Standard	XM_005267635		Approved	RhoGAP5, p190-B, p190BRhoGAP	uc001wrn.3	Q13017		ENST00000345122.3:c.3504T>A	chr14.hg19:g.32563379T>A	ENSP00000371897:p.Tyr1168*	163.0	0.0		141.0	11.0	NM_001173	A1L375|A1L376|A8KAA1|D3DS89|D3DS90|Q05BE8|Q05BU8|Q59ER0|Q6DHZ3	Nonsense_Mutation	SNP	ENST00000345122.3	hg19	CCDS32062.1	.	.	.	.	.	.	.	.	.	.	T	44	10.934715	0.99491	.	.	ENSG00000100852	ENST00000556611;ENST00000539826;ENST00000345122;ENST00000432921	.	.	.	5.39	1.36	0.22044	.	0.384990	0.30043	N	0.010548	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11485	T	0.65	.	10.1991	0.43073	0.0:0.2792:0.0:0.7208	.	.	.	.	X	1168	.	ENSP00000371897:Y1168X	Y	+	3	2	ARHGAP5	31633130	0.712000	0.27916	0.999000	0.59377	0.984000	0.73092	-0.194000	0.09559	0.044000	0.15775	0.460000	0.39030	TAT	.	.		0.368	ARHGAP5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409735.1	NM_001030055	
MAGEL2	54551	hgsc.bcm.edu	37	15	23890789	23890789	+	Missense_Mutation	SNP	C	C	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr15:23890789C>T	ENST00000532292.1	-	1	386	c.292G>A	c.(292-294)Gta>Ata	p.V98I		NM_019066.4	NP_061939.3	Q9UJ55	MAGL2_HUMAN	MAGE-like 2	0					Arp2/3 complex-mediated actin nucleation (GO:0034314)|protein K63-linked ubiquitination (GO:0070534)|retrograde transport, endosome to Golgi (GO:0042147)	endosome (GO:0005768)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;1.84e-06)|Epithelial(43;1.2e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)		GCCGCTGCTACCGGGGGTCCG	0.632																																					p.V701I		Atlas-SNP	.											.	MAGEL2	108	.	0			c.G2101A						.						11.0	12.0	12.0					15																	23890789		1848	4076	5924	SO:0001583	missense	54551	exon1			CTGCTACCGGGGG	AJ243531	CCDS73700.1	15q11-q12	2008-07-18				ENSG00000254585			6814	protein-coding gene	gene with protein product		605283		NDNL1		10556298	Standard	NM_019066		Approved	nM15	uc001ywj.4	Q9UJ55		ENST00000532292.1:c.292G>A	chr15.hg19:g.23890789C>T	ENSP00000433433:p.Val98Ile	100.0	0.0		76.0	21.0	NM_019066		Missense_Mutation	SNP	ENST00000532292.1	hg19																																																																																				.	.		0.632	MAGEL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395182.2	NM_019066	
UBR1	197131	hgsc.bcm.edu	37	15	43318859	43318859	+	Missense_Mutation	SNP	T	T	G			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr15:43318859T>G	ENST00000290650.4	-	23	2513	c.2435A>C	c.(2434-2436)aAa>aCa	p.K812T	UBR1_ENST00000382177.2_Missense_Mutation_p.E794D	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1	812					cellular response to leucine (GO:0071233)|negative regulation of TOR signaling (GO:0032007)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|proteasome complex (GO:0000502)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(7)|large_intestine(12)|lung(25)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	58		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		TACACCTGGTTTCCTAAATAG	0.308																																					p.K812T		Atlas-SNP	.											.	UBR1	124	.	0			c.A2435C						.						115.0	116.0	116.0					15																	43318859		2202	4298	6500	SO:0001583	missense	197131	exon23			CCTGGTTTCCTAA		CCDS10091.1	15q13	2008-06-23			ENSG00000159459	ENSG00000159459		"""Ubiquitin protein ligase E3 component n-recognins"""	16808	protein-coding gene	gene with protein product		605981				9653112	Standard	NM_174916		Approved		uc001zqq.3	Q8IWV7	OTTHUMG00000130702	ENST00000290650.4:c.2435A>C	chr15.hg19:g.43318859T>G	ENSP00000290650:p.Lys812Thr	47.0	0.0		52.0	12.0	NM_174916	O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Missense_Mutation	SNP	ENST00000290650.4	hg19	CCDS10091.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.0|25.0	4.597318|4.597318	0.87055|0.87055	.|.	.|.	ENSG00000159459|ENSG00000159459	ENST00000382177|ENST00000290650;ENST00000546274	T|T	0.50001|0.59906	0.76|0.23	4.81|4.81	4.81|4.81	0.61882|0.61882	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.75817|0.75817	0.3901|0.3901	M|M	0.84082|0.84082	2.675|2.675	0.58432|0.58432	D|D	0.999999|0.999999	.|D;D	.|0.89917	.|0.999;1.0	.|D;D	.|0.85130	.|0.968;0.997	T|T	0.74965|0.74965	-0.3484|-0.3484	7|10	0.33940|0.23891	T|T	0.23|0.37	-18.0994|-18.0994	14.8176|14.8176	0.70048|0.70048	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|812;812	.|B4DYL2;Q8IWV7	.|.;UBR1_HUMAN	D|T	794|812	ENSP00000371612:E794D|ENSP00000290650:K812T	ENSP00000371612:E794D|ENSP00000290650:K812T	E|K	-|-	3|2	2|0	UBR1|UBR1	41106151|41106151	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	7.341000|7.341000	0.79300|0.79300	2.141000|2.141000	0.66446|0.66446	0.455000|0.455000	0.32223|0.32223	GAA|AAA	.	.		0.308	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1	NM_174916	
DENND4A	10260	hgsc.bcm.edu	37	15	65994749	65994749	+	Missense_Mutation	SNP	C	C	A			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr15:65994749C>A	ENST00000431932.2	-	17	2532	c.2324G>T	c.(2323-2325)tGt>tTt	p.C775F	DENND4A_ENST00000443035.3_Missense_Mutation_p.C775F	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	775					positive regulation of Rab GTPase activity (GO:0032851)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(11)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	51						AGCTGGGAGACAAATAAACCA	0.413																																					p.C775F		Atlas-SNP	.											.	DENND4A	217	.	0			c.G2324T						.						70.0	61.0	64.0					15																	65994749		1855	4102	5957	SO:0001583	missense	10260	exon17			GGGAGACAAATAA	AF534403	CCDS45285.1, CCDS53949.1	15q22.31	2012-10-03	2006-01-27	2006-01-27				"""DENN/MADD domain containing"""	24321	protein-coding gene	gene with protein product		600382	"""c-myc promoter binding protein"""	MYCPBP		8056341, 12906859	Standard	NM_005848		Approved	IRLB	uc002api.3	Q7Z401		ENST00000431932.2:c.2324G>T	chr15.hg19:g.65994749C>A	ENSP00000396830:p.Cys775Phe	189.0	0.0		190.0	9.0	NM_001144823	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Missense_Mutation	SNP	ENST00000431932.2	hg19	CCDS45285.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.584304	0.86748	.	.	ENSG00000174485	ENST00000443035;ENST00000431932	T;T	0.05382	3.45;3.46	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.30008	0.0751	M	0.80847	2.515	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.996	T	0.00626	-1.1638	10	0.54805	T	0.06	.	19.9918	0.97368	0.0:1.0:0.0:0.0	.	775;775	E7EPL3;Q7Z401	.;MYCPP_HUMAN	F	775	ENSP00000391167:C775F;ENSP00000396830:C775F	ENSP00000396830:C775F	C	-	2	0	DENND4A	63781803	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.728000	0.93425	0.585000	0.79938	TGT	.	.		0.413	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848	
CT62	196993	hgsc.bcm.edu	37	15	71404534	71404534	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr15:71404534T>A	ENST00000449977.2	-	3	594	c.88A>T	c.(88-90)Agc>Tgc	p.S30C	THSD4_ENST00000355327.3_Intron|CT62_ENST00000566432.1_Missense_Mutation_p.S30C	NM_001102658.1	NP_001096128.1	P0C5K7	CT62_HUMAN	cancer/testis antigen 62	30										NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(2)	6						GAGAAATGGCTGAATGTTCTG	0.522																																					p.S30C		Atlas-SNP	.											.	CT62	7	.	0			c.A88T						.						97.0	116.0	110.0					15																	71404534		2067	4216	6283	SO:0001583	missense	196993	exon3			AATGGCTGAATGT	BC039359, AL080151	CCDS45295.1	15q23	2011-03-09			ENSG00000225362	ENSG00000225362			27286	protein-coding gene	gene with protein product						15905330	Standard	NM_001102658		Approved		uc002ata.2	P0C5K7		ENST00000449977.2:c.88A>T	chr15.hg19:g.71404534T>A	ENSP00000399356:p.Ser30Cys	110.0	0.0		102.0	12.0	NM_001102658		Missense_Mutation	SNP	ENST00000449977.2	hg19	CCDS45295.1	.	.	.	.	.	.	.	.	.	.	T	9.590	1.125872	0.20959	.	.	ENSG00000225362	ENST00000449977	.	.	.	1.88	0.689	0.18033	.	.	.	.	.	T	0.32526	0.0832	N	0.08118	0	0.09310	N	1	D	0.71674	0.998	D	0.70716	0.97	T	0.14008	-1.0488	8	0.87932	D	0	.	4.7512	0.13061	0.0:0.0:0.3315:0.6685	.	30	P0C5K7	CT62_HUMAN	C	30	.	ENSP00000399356:S30C	S	-	1	0	CT62	69191588	0.000000	0.05858	0.001000	0.08648	0.047000	0.14425	-0.661000	0.05311	0.173000	0.19788	0.528000	0.53228	AGC	.	.		0.522	CT62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420810.1	NM_001102658	
THSD4	79875	hgsc.bcm.edu	37	15	71548960	71548960	+	Silent	SNP	A	A	G			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr15:71548960A>G	ENST00000355327.3	+	6	1055	c.921A>G	c.(919-921)ccA>ccG	p.P307P	THSD4_ENST00000261862.6_Silent_p.P307P			Q6ZMP0	THSD4_HUMAN	thrombospondin, type I, domain containing 4	307	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				elastic fiber assembly (GO:0048251)	extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)	metalloendopeptidase activity (GO:0004222)			breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(20)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						AGGTATGTCCAGAAAGCAGTA	0.408																																					p.P307P		Atlas-SNP	.											.	THSD4	75	.	0			c.A921G						.						137.0	138.0	137.0					15																	71548960		1852	4102	5954	SO:0001819	synonymous_variant	79875	exon5			ATGTCCAGAAAGC	AK023772	CCDS10238.2, CCDS66817.1	15q23	2009-11-09			ENSG00000187720	ENSG00000187720			25835	protein-coding gene	gene with protein product		614476				19734141	Standard	NM_001286429		Approved	FVSY9334, PRO34005, FLJ13710, ADAMTSL6	uc002atb.1	Q6ZMP0	OTTHUMG00000133389	ENST00000355327.3:c.921A>G	chr15.hg19:g.71548960A>G		115.0	0.0		106.0	11.0	NM_024817	B2RTY3|B4DR13|Q6MZI3|Q6UXZ8|Q9H8E4	Silent	SNP	ENST00000355327.3	hg19	CCDS10238.2																																																																																			.	.		0.408	THSD4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257253.2	NM_024817	
BLM	641	hgsc.bcm.edu	37	15	91354495	91354495	+	Missense_Mutation	SNP	C	C	A			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr15:91354495C>A	ENST00000355112.3	+	21	4053	c.3935C>A	c.(3934-3936)gCt>gAt	p.A1312D	BLM_ENST00000560509.1_Missense_Mutation_p.A1181D|BLM_ENST00000560136.1_3'UTR	NM_000057.2	NP_000048.1	P54132	BLM_HUMAN	Bloom syndrome, RecQ helicase-like	1312					alpha-beta T cell differentiation (GO:0046632)|ATP catabolic process (GO:0006200)|cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA strand renaturation (GO:0000733)|double-strand break repair via homologous recombination (GO:0000724)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell division (GO:0051782)|negative regulation of DNA recombination (GO:0045910)|negative regulation of mitotic recombination (GO:0045950)|negative regulation of thymocyte apoptotic process (GO:0070244)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of transcription, DNA-templated (GO:0045893)|protein oligomerization (GO:0051259)|regulation of binding (GO:0051098)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to X-ray (GO:0010165)|telomere maintenance (GO:0000723)	cytoplasm (GO:0005737)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|nuclear chromosome (GO:0000228)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|pronucleus (GO:0045120)|replication fork (GO:0005657)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent helicase activity (GO:0008026)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|p53 binding (GO:0002039)|single-stranded DNA binding (GO:0003697)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(11)|liver(4)|lung(9)|ovary(6)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)			AGAAGTGCCGCTGAGGAGCTC	0.498			"""Mis, N, F"""			"""leukemia, lymphoma, skin squamous cell , other cancers"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Bloom syndrome																												p.A1312D		Atlas-SNP	.	yes	Rec		Bloom Syndrome	15	15q26.1	641	Bloom Syndrome		"""L, E"""	.	BLM	122	.	0			c.C3935A						.						77.0	78.0	77.0					15																	91354495		2198	4298	6496	SO:0001583	missense	641	exon21	Familial Cancer Database		GTGCCGCTGAGGA	U39817	CCDS10363.1, CCDS73782.1	15q26.1	2014-09-17	2009-03-19		ENSG00000197299	ENSG00000197299			1058	protein-coding gene	gene with protein product		604610	"""Bloom syndrome"""			9388193	Standard	NM_000057		Approved	BS, RECQL3, RECQ2	uc002bpr.3	P54132	OTTHUMG00000149834	ENST00000355112.3:c.3935C>A	chr15.hg19:g.91354495C>A	ENSP00000347232:p.Ala1312Asp	81.0	0.0		87.0	4.0	NM_000057	Q52M96	Missense_Mutation	SNP	ENST00000355112.3	hg19	CCDS10363.1	.	.	.	.	.	.	.	.	.	.	C	12.14	1.847823	0.32606	.	.	ENSG00000197299	ENST00000355112;ENST00000536925;ENST00000543977	T	0.41758	0.99	5.87	1.71	0.24356	.	1.049400	0.07467	N	0.901657	T	0.19446	0.0467	N	0.08118	0	0.09310	N	1	B;B	0.13145	0.007;0.007	B;B	0.11329	0.006;0.006	T	0.28554	-1.0040	10	0.15499	T	0.54	-4.528	3.3163	0.07034	0.3083:0.4584:0.1494:0.0839	.	1312;1312	B2RAN0;P54132	.;BLM_HUMAN	D	1312;942;499	ENSP00000347232:A1312D	ENSP00000347232:A1312D	A	+	2	0	BLM	89155499	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	0.973000	0.29422	0.934000	0.37316	-0.169000	0.13324	GCT	.	.		0.498	BLM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313495.1		
KDM8	79831	hgsc.bcm.edu	37	16	27232040	27232040	+	Missense_Mutation	SNP	T	T	C			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr16:27232040T>C	ENST00000286096.4	+	8	1413	c.1240T>C	c.(1240-1242)Tgg>Cgg	p.W414R	KDM8_ENST00000567785.1_3'UTR|KDM8_ENST00000441782.2_Missense_Mutation_p.W452R|KDM8_ENST00000380948.2_Missense_Mutation_p.W218R|KDM8_ENST00000568965.1_Missense_Mutation_p.W218R	NM_024773.2	NP_079049.2	Q8N371	KDM8_HUMAN	lysine (K)-specific demethylase 8	414	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				G2/M transition of mitotic cell cycle (GO:0000086)|histone H3-K36 demethylation (GO:0070544)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone demethylase activity (H3-K36 specific) (GO:0051864)|metal ion binding (GO:0046872)										GGTCAGCTTCTGGTGGTCGTA	0.512																																					p.W452R		Atlas-SNP	.											.	.	.	.	0			c.T1354C						.						99.0	96.0	97.0					16																	27232040		2197	4300	6497	SO:0001583	missense	79831	exon8			AGCTTCTGGTGGT	AK023860	CCDS10627.1, CCDS45448.1	16p12.1	2012-03-28	2012-03-28	2012-03-28	ENSG00000155666	ENSG00000155666		"""Chromatin-modifying enzymes / K-demethylases"""	25840	protein-coding gene	gene with protein product		611917	"""jumonji domain containing 5"""	JMJD5		20457893	Standard	NM_024773		Approved	FLJ13798	uc010vcn.1	Q8N371	OTTHUMG00000131677	ENST00000286096.4:c.1240T>C	chr16.hg19:g.27232040T>C	ENSP00000286096:p.Trp414Arg	192.0	0.0		207.0	23.0	NM_001145348	B4DLU9|Q6VAK5|Q9H8B1	Missense_Mutation	SNP	ENST00000286096.4	hg19	CCDS10627.1	.	.	.	.	.	.	.	.	.	.	T	16.75	3.209437	0.58343	.	.	ENSG00000155666	ENST00000380948;ENST00000286096;ENST00000441782	T;T;T	0.34859	1.34;1.34;1.34	5.28	5.28	0.74379	Transcription factor jumonji/aspartyl beta-hydroxylase (2);	0.167364	0.56097	D	0.000023	T	0.60235	0.2253	M	0.75264	2.295	0.51012	D	0.999909	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.65125	-0.6244	10	0.87932	D	0	-21.331	14.0533	0.64751	0.0:0.0:0.0:1.0	.	452;218;414	Q8N371-3;Q8N371-2;Q8N371	.;.;KDM8_HUMAN	R	218;414;452	ENSP00000370335:W218R;ENSP00000286096:W414R;ENSP00000398410:W452R	ENSP00000286096:W414R	W	+	1	0	JMJD5	27139541	1.000000	0.71417	1.000000	0.80357	0.188000	0.23474	7.946000	0.87746	2.000000	0.58554	0.460000	0.39030	TGG	.	.		0.512	KDM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254580.3	NM_024773	
ATXN2L	11273	hgsc.bcm.edu	37	16	28846411	28846411	+	Silent	SNP	A	A	G			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr16:28846411A>G	ENST00000336783.4	+	19	2633	c.2466A>G	c.(2464-2466)ccA>ccG	p.P822P	RP11-24N18.1_ENST00000563565.1_RNA|ATXN2L_ENST00000570200.1_Silent_p.P822P|ATXN2L_ENST00000565845.1_3'UTR|ATXN2L_ENST00000382686.4_Silent_p.P822P|ATXN2L_ENST00000325215.6_Silent_p.P822P|ATXN2L_ENST00000340394.8_Silent_p.P822P|ATXN2L_ENST00000564304.1_Silent_p.P828P|ATXN2L_ENST00000395547.2_Silent_p.P822P	NM_007245.3	NP_009176.2	Q8WWM7	ATX2L_HUMAN	ataxin 2-like	822					regulation of cytoplasmic mRNA processing body assembly (GO:0010603)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|membrane (GO:0016020)|nuclear speck (GO:0016607)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36						AGAGCAACCCACGCATGCTGA	0.627																																					p.P822P		Atlas-SNP	.											.	ATXN2L	159	.	0			c.A2466G						.						103.0	90.0	94.0					16																	28846411		2197	4299	6496	SO:0001819	synonymous_variant	11273	exon19			CAACCCACGCATG		CCDS10639.1, CCDS10640.1, CCDS10641.1, CCDS32423.1, CCDS45451.1, CCDS58443.1	16p11	2008-02-05			ENSG00000168488	ENSG00000168488			31326	protein-coding gene	gene with protein product		607931				11784712, 14769358	Standard	NM_007245		Approved	A2lp, A2D	uc002dqy.4	Q8WWM7	OTTHUMG00000097038	ENST00000336783.4:c.2466A>G	chr16.hg19:g.28846411A>G		200.0	0.0		168.0	22.0	NM_148414	A8K1R6|B9EGM2|E9PAR9|O95135|Q63ZY4|Q6NVJ8|Q6PJW6|Q8IU61|Q8IU95|Q8WWM3|Q8WWM4|Q8WWM5|Q8WWM6|Q99703	Silent	SNP	ENST00000336783.4	hg19	CCDS10641.1																																																																																			.	.		0.627	ATXN2L-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214139.1	NM_007245	
ZNF646	9726	hgsc.bcm.edu	37	16	31088438	31088438	+	Missense_Mutation	SNP	A	A	G			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr16:31088438A>G	ENST00000394979.2	+	1	1216	c.793A>G	c.(793-795)Atc>Gtc	p.I265V	ZNF668_ENST00000564456.1_5'Flank|ZNF646_ENST00000300850.5_Missense_Mutation_p.I265V|ZNF668_ENST00000300849.4_5'Flank			O15015	ZN646_HUMAN	zinc finger protein 646	265					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(1)|lung(21)|ovary(1)|prostate(4)|skin(3)	49						CACGCTGGGCATCTACCCCTG	0.577																																					p.I265V		Atlas-SNP	.											.	ZNF646	133	.	0			c.A793G						.						94.0	85.0	88.0					16																	31088438		2197	4300	6497	SO:0001583	missense	9726	exon2			CTGGGCATCTACC	AB002294	CCDS10702.1	16p11.2	2013-01-08			ENSG00000167395	ENSG00000167395		"""Zinc fingers, C2H2-type"""	29004	protein-coding gene	gene with protein product							Standard	NM_014699		Approved	KIAA0296	uc002eap.3	O15015	OTTHUMG00000047355	ENST00000394979.2:c.793A>G	chr16.hg19:g.31088438A>G	ENSP00000378429:p.Ile265Val	179.0	0.0		151.0	16.0	NM_014699	Q8IVD8	Missense_Mutation	SNP	ENST00000394979.2	hg19		.	.	.	.	.	.	.	.	.	.	A	4.702	0.130532	0.08981	.	.	ENSG00000167395	ENST00000300850;ENST00000394979;ENST00000439353	T;T	0.27557	1.66;1.66	5.51	-2.02	0.07388	.	.	.	.	.	T	0.10981	0.0268	N	0.03016	-0.435	0.09310	N	1	B	0.09022	0.002	B	0.12837	0.008	T	0.35126	-0.9801	9	0.02654	T	1	-4.9644	13.236	0.59969	0.3109:0.0:0.6891:0.0	.	265	O15015-2	.	V	265;265;30	ENSP00000300850:I265V;ENSP00000378429:I265V	ENSP00000300850:I265V	I	+	1	0	ZNF646	30995939	0.000000	0.05858	0.814000	0.32528	0.760000	0.43138	-1.108000	0.03313	-0.152000	0.11156	-0.290000	0.09829	ATC	.	.		0.577	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699	
NOD2	64127	hgsc.bcm.edu	37	16	50744637	50744637	+	Missense_Mutation	SNP	G	G	A			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr16:50744637G>A	ENST00000300589.2	+	4	920	c.815G>A	c.(814-816)aGc>aAc	p.S272N	RP11-327F22.6_ENST00000602304.1_RNA|NOD2_ENST00000526417.2_3'UTR	NM_022162.1	NP_071445.1	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain containing 2	272					activation of MAPK activity (GO:0000187)|activation of MAPK activity involved in innate immune response (GO:0035419)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to peptidoglycan (GO:0071224)|cytokine production involved in immune response (GO:0002367)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|detection of biotic stimulus (GO:0009595)|detection of muramyl dipeptide (GO:0032498)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|innate immune response (GO:0045087)|innate immune response in mucosa (GO:0002227)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|macrophage inflammatory protein-1 alpha production (GO:0071608)|maintenance of gastrointestinal epithelium (GO:0030277)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-18 production (GO:0032701)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of macrophage apoptotic process (GO:2000110)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell mediated immunity (GO:0002710)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of tumor necrosis factor production (GO:0032720)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of B cell activation (GO:0050871)|positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria (GO:0006965)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of dendritic cell cytokine production (GO:0002732)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gamma-delta T cell activation (GO:0046645)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of prostaglandin-E synthase activity (GO:2000363)|positive regulation of prostaglandin-endoperoxide synthase activity (GO:0060585)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type 2 immune response (GO:0002830)|protein oligomerization (GO:0051259)|regulation of inflammatory response (GO:0050727)|regulation of neutrophil chemotaxis (GO:0090022)|response to exogenous dsRNA (GO:0043330)|response to lipopolysaccharide (GO:0032496)|response to muramyl dipeptide (GO:0032495)|response to nutrient (GO:0007584)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|enzyme binding (GO:0019899)|muramyl dipeptide binding (GO:0032500)|peptidoglycan binding (GO:0042834)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(30)|ovary(3)|skin(3)	52		all_cancers(37;0.0156)				CCGCAGAAGAGCCCAGCCACC	0.622																																					p.S272N		Atlas-SNP	.											.	NOD2	118	.	0			c.G815A						.						38.0	39.0	38.0					16																	50744637		2198	4300	6498	SO:0001583	missense	64127	exon4			AGAAGAGCCCAGC	AF178930	CCDS10746.1	16q12	2014-09-17	2006-12-08	2006-12-08	ENSG00000167207	ENSG00000167207		"""Nucleotide-binding domain and leucine rich repeat containing"""	5331	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 2"", ""NOD-like receptor C2"", ""NLR family, CARD domain containing 2"""	605956	"""caspase recruitment domain family, member 15"""	IBD1, CARD15		7809109, 8587604	Standard	XM_005256084		Approved	BLAU, CD, PSORAS1, CLR16.3, NLRC2	uc002egm.1	Q9HC29	OTTHUMG00000133171	ENST00000300589.2:c.815G>A	chr16.hg19:g.50744637G>A	ENSP00000300589:p.Ser272Asn	125.0	0.0		105.0	10.0	NM_022162	E2JEQ6|Q96RH5|Q96RH6|Q96RH8	Missense_Mutation	SNP	ENST00000300589.2	hg19	CCDS10746.1	.	.	.	.	.	.	.	.	.	.	G	7.690	0.690817	0.15039	.	.	ENSG00000167207	ENST00000526417;ENST00000300589	T	0.70399	-0.48	5.63	5.63	0.86233	.	0.078343	0.56097	D	0.000026	T	0.68054	0.2959	M	0.66939	2.045	0.22996	N	0.998451	B;B;B	0.13145	0.007;0.007;0.004	B;B;B	0.11329	0.004;0.006;0.004	T	0.54662	-0.8260	10	0.21014	T	0.42	.	15.1771	0.72920	0.0:0.0:1.0:0.0	.	56;245;272	D6CHF9;Q9HC29-2;Q9HC29	.;.;NOD2_HUMAN	N	245;272	ENSP00000300589:S272N	ENSP00000300589:S272N	S	+	2	0	NOD2	49302138	0.001000	0.12720	0.985000	0.45067	0.248000	0.25809	0.945000	0.29056	2.655000	0.90218	0.462000	0.41574	AGC	.	.		0.622	NOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256876.2	NM_022162	
CDH11	1009	hgsc.bcm.edu	37	16	64981642	64981642	+	Missense_Mutation	SNP	G	G	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr16:64981642G>T	ENST00000268603.4	-	13	2870	c.2255C>A	c.(2254-2256)gCc>gAc	p.A752D	CDH11_ENST00000566827.1_Missense_Mutation_p.A626D|CDH11_ENST00000394156.3_3'UTR	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	752					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A752V(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		CAGGGACCCGGCCACTGAGCC	0.502			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)																											p.A752D		Atlas-SNP	.		Dom	yes		16	16q22.1	1009	"""cadherin 11, type 2, OB-cadherin (osteoblast)"""		M	CDH11,colon,carcinoma,0,1	CDH11	260	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2255A						.						78.0	81.0	80.0					16																	64981642		2203	4300	6503	SO:0001583	missense	1009	exon13			GACCCGGCCACTG	D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"""Cadherins / Major cadherins"""	1750	protein-coding gene	gene with protein product	"""OB-Cadherin"""	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.2255C>A	chr16.hg19:g.64981642G>T	ENSP00000268603:p.Ala752Asp	161.0	0.0		130.0	8.0	NM_001797	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Missense_Mutation	SNP	ENST00000268603.4	hg19	CCDS10803.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.243198	0.79912	.	.	ENSG00000140937	ENST00000268603;ENST00000538390	D	0.82526	-1.62	6.17	6.17	0.99709	Cadherin, cytoplasmic domain (1);	0.000000	0.85682	D	0.000000	D	0.92724	0.7687	M	0.90252	3.1	0.80722	D	1	D	0.54207	0.965	D	0.63381	0.914	D	0.93033	0.6450	10	0.87932	D	0	.	19.8676	0.96824	0.0:0.0:1.0:0.0	.	752	P55287	CAD11_HUMAN	D	752;735	ENSP00000268603:A752D	ENSP00000268603:A752D	A	-	2	0	CDH11	63539143	1.000000	0.71417	0.985000	0.45067	0.984000	0.73092	9.869000	0.99810	2.941000	0.99782	0.655000	0.94253	GCC	.	.		0.502	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664	
ITGAE	3682	hgsc.bcm.edu	37	17	3680880	3680880	+	Missense_Mutation	SNP	C	C	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr17:3680880C>T	ENST00000263087.4	-	2	207	c.109G>A	c.(109-111)Gtg>Atg	p.V37M		NM_002208.4	NP_002199.3	P38570	ITAE_HUMAN	integrin, alpha E (antigen CD103, human mucosal lymphocyte antigen 1; alpha polypeptide)	37					cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	external side of plasma membrane (GO:0009897)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	41				UCEC - Uterine corpus endometrioid carcinoma (3;0.0813)		GAGCTGAGCACGAAAGGGGCA	0.622																																					p.V37M	NSCLC(182;635 2928 8995 38788)	Atlas-SNP	.											.	ITGAE	96	.	0			c.G109A						.						76.0	70.0	72.0					17																	3680880		2203	4300	6503	SO:0001583	missense	3682	exon2			TGAGCACGAAAGG	L25851	CCDS32531.1	17p13	2010-03-23				ENSG00000083457		"""CD molecules"", ""Integrins"""	6147	protein-coding gene	gene with protein product		604682				8119947	Standard	NM_002208		Approved	CD103, HUMINAE	uc002fwo.4	P38570		ENST00000263087.4:c.109G>A	chr17.hg19:g.3680880C>T	ENSP00000263087:p.Val37Met	140.0	0.0		147.0	20.0	NM_002208	Q17RS6|Q9NZU9	Missense_Mutation	SNP	ENST00000263087.4	hg19	CCDS32531.1	.	.	.	.	.	.	.	.	.	.	C	17.53	3.412563	0.62511	.	.	ENSG00000083457	ENST00000263087	D	0.95554	-3.74	4.37	4.37	0.52481	.	.	.	.	.	D	0.95778	0.8626	L	0.46157	1.445	0.32342	N	0.559569	D	0.89917	1.0	P	0.60609	0.877	D	0.95088	0.8219	9	0.56958	D	0.05	.	12.7158	0.57113	0.0:1.0:0.0:0.0	.	37	P38570	ITAE_HUMAN	M	37	ENSP00000263087:V37M	ENSP00000263087:V37M	V	-	1	0	ITGAE	3627629	0.725000	0.28048	0.963000	0.40424	0.489000	0.33432	0.967000	0.29344	2.732000	0.93576	0.609000	0.83330	GTG	.	.		0.622	ITGAE-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438169.1	NM_002208	
CAMTA2	23125	hgsc.bcm.edu	37	17	4876952	4876952	+	Missense_Mutation	SNP	C	C	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr17:4876952C>T	ENST00000348066.3	-	13	2252	c.2129G>A	c.(2128-2130)cGg>cAg	p.R710Q	CAMTA2_ENST00000414043.3_Missense_Mutation_p.R733Q|CAMTA2_ENST00000361571.5_Missense_Mutation_p.R709Q|RP5-1050D4.2_ENST00000430920.1_RNA|CAMTA2_ENST00000381311.5_Missense_Mutation_p.R712Q|CAMTA2_ENST00000358183.4_Missense_Mutation_p.R710Q|CAMTA2_ENST00000572543.1_Missense_Mutation_p.R715Q	NM_015099.3	NP_055914.2	O94983	CMTA2_HUMAN	calmodulin binding transcription activator 2	710					cardiac muscle hypertrophy in response to stress (GO:0014898)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	31						GCTCATGCCCCGGAAGGGGCT	0.647																																					p.R733Q		Atlas-SNP	.											.	CAMTA2	93	.	0			c.G2198A						.						51.0	52.0	51.0					17																	4876952		2203	4300	6503	SO:0001583	missense	23125	exon13			ATGCCCCGGAAGG	AB020716	CCDS11063.1, CCDS54071.1, CCDS54072.1, CCDS54073.1	17p13.3	2004-09-01			ENSG00000108509	ENSG00000108509			18807	protein-coding gene	gene with protein product		611508				11925432	Standard	NM_015099		Approved	KIAA0909	uc010cku.2	O94983	OTTHUMG00000099417	ENST00000348066.3:c.2129G>A	chr17.hg19:g.4876952C>T	ENSP00000321813:p.Arg710Gln	105.0	0.0		90.0	11.0	NM_001171167	B9EGL0|D3DTL5|E7EWU5|Q7Z6M8|Q8N3V0|Q8NDG4|Q96G17	Missense_Mutation	SNP	ENST00000348066.3	hg19	CCDS11063.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.542269	0.85917	.	.	ENSG00000108509	ENST00000414043;ENST00000381311;ENST00000361571;ENST00000358183;ENST00000348066	T;T;T;T;T	0.71222	-0.55;-0.55;-0.55;-0.55;-0.55	4.85	4.85	0.62838	Ankyrin repeat-containing domain (2);	0.079635	0.49305	D	0.000147	T	0.77558	0.4148	L	0.38649	1.16	0.50313	D	0.999866	P;D;D;D;D	0.89917	0.595;0.99;0.984;0.972;1.0	B;P;P;B;D	0.81914	0.082;0.604;0.455;0.267;0.995	T	0.79284	-0.1867	10	0.62326	D	0.03	-19.2077	15.5004	0.75695	0.0:1.0:0.0:0.0	.	686;733;712;710;709	B7ZM30;E7EWU5;O94983-3;O94983;O94983-4	.;.;.;CMTA2_HUMAN;.	Q	733;712;709;710;710	ENSP00000412886:R733Q;ENSP00000370712:R712Q;ENSP00000354828:R709Q;ENSP00000350910:R710Q;ENSP00000321813:R710Q	ENSP00000321813:R710Q	R	-	2	0	CAMTA2	4817676	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.596000	0.82721	2.528000	0.85240	0.655000	0.94253	CGG	.	.		0.647	CAMTA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216876.1	NM_015099	
SLC5A10	125206	hgsc.bcm.edu	37	17	18872410	18872410	+	Missense_Mutation	SNP	T	T	G			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr17:18872410T>G	ENST00000395645.3	+	6	517	c.499T>G	c.(499-501)Tgg>Ggg	p.W167G	SLC5A10_ENST00000395643.2_Missense_Mutation_p.W167G|SLC5A10_ENST00000395642.1_Missense_Mutation_p.W111G|SLC5A10_ENST00000317977.6_Missense_Mutation_p.W111G|SLC5A10_ENST00000417251.2_Missense_Mutation_p.W167G|FAM83G_ENST00000388995.6_3'UTR|SLC5A10_ENST00000395647.2_Missense_Mutation_p.W167G	NM_001042450.2	NP_001035915.1	A0PJK1	SC5AA_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 10	167					sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(3)|ovary(3)|prostate(3)|skin(3)	24						CTGCCTGGGCTGGAACTTCTA	0.622																																					p.W167G		Atlas-SNP	.											.	SLC5A10	55	.	0			c.T499G						.						156.0	118.0	131.0					17																	18872410		2203	4300	6503	SO:0001583	missense	125206	exon6			CTGGGCTGGAACT		CCDS11201.2, CCDS42275.1, CCDS59277.1, CCDS59278.1, CCDS74008.1	17p11.2	2013-07-19	2013-07-19		ENSG00000154025	ENSG00000154025		"""Solute carriers"""	23155	protein-coding gene	gene with protein product			"""solute carrier family 5 (sodium/glucose cotransporter), member 10"""				Standard	NM_152351		Approved	SGLT5	uc002gut.2	A0PJK1	OTTHUMG00000178143	ENST00000395645.3:c.499T>G	chr17.hg19:g.18872410T>G	ENSP00000379007:p.Trp167Gly	209.0	0.0		156.0	12.0	NM_001042450	A8MUC9|B4DPI0|B7WPR4|Q6P5X0|Q8IXM4|Q96LQ1	Missense_Mutation	SNP	ENST00000395645.3	hg19	CCDS42275.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.207991	0.79240	.	.	ENSG00000154025	ENST00000317977;ENST00000395647;ENST00000395642;ENST00000417251;ENST00000395645;ENST00000395643	D;D;D;D;D;D	0.92149	-2.98;-2.36;-2.98;-2.36;-2.36;-2.35	4.82	3.73	0.42828	.	0.000000	0.85682	D	0.000000	D	0.95294	0.8473	M	0.86740	2.835	0.80722	D	1	D;D;D;D;D	0.67145	0.993;0.991;0.993;0.991;0.996	P;P;P;P;P	0.61533	0.842;0.864;0.842;0.864;0.89	D	0.94685	0.7869	10	0.66056	D	0.02	.	10.3686	0.44039	0.0:0.0795:0.0:0.9205	.	167;167;167;167;111	B4DPI0;A0PJK1-2;A0PJK1;A0PJK1-4;A0PJK1-3	.;.;SC5AA_HUMAN;.;.	G	111;167;111;167;167;167	ENSP00000324346:W111G;ENSP00000379008:W167G;ENSP00000379004:W111G;ENSP00000401875:W167G;ENSP00000379007:W167G;ENSP00000379005:W167G	ENSP00000324346:W111G	W	+	1	0	SLC5A10	18813135	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.663000	0.83820	0.796000	0.33947	0.379000	0.24179	TGG	.	.		0.622	SLC5A10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132129.2	NM_152351	
CCL13	6357	hgsc.bcm.edu	37	17	32685070	32685070	+	Missense_Mutation	SNP	A	A	G			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr17:32685070A>G	ENST00000225844.2	+	3	292	c.217A>G	c.(217-219)Atc>Gtc	p.I73V		NM_005408.2	NP_005399.1	Q99616	CCL13_HUMAN	chemokine (C-C motif) ligand 13	73					cell-cell signaling (GO:0007267)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|cytoskeleton organization (GO:0007010)|eosinophil chemotaxis (GO:0048245)|immune response (GO:0006955)|inflammatory response (GO:0006954)|regulation of cell shape (GO:0008360)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	chemokine activity (GO:0008009)|receptor binding (GO:0005102)			large_intestine(1)|prostate(1)	2		Ovarian(249;0.0443)|Breast(31;0.151)				GGGCAAGGAGATCTGTGCTGA	0.507																																					p.I73V		Atlas-SNP	.											.	CCL13	17	.	0			c.A217G						.						68.0	66.0	67.0					17																	32685070		2203	4300	6503	SO:0001583	missense	6357	exon3			AAGGAGATCTGTG	AJ001634	CCDS11281.1	17q11.2	2013-02-25	2002-08-22	2002-08-23	ENSG00000181374	ENSG00000181374		"""Chemokine ligands"", ""Endogenous ligands"""	10611	protein-coding gene	gene with protein product		601391	"""small inducible cytokine subfamily A (Cys-Cys), member 13"""	SCYA13		8661057	Standard	NM_005408		Approved	MCP-4, NCC-1, SCYL1, CKb10, MGC17134	uc002hic.3	Q99616	OTTHUMG00000132890	ENST00000225844.2:c.217A>G	chr17.hg19:g.32685070A>G	ENSP00000225844:p.Ile73Val	104.0	0.0		146.0	13.0	NM_005408	O95689|Q6ICQ6	Missense_Mutation	SNP	ENST00000225844.2	hg19	CCDS11281.1	.	.	.	.	.	.	.	.	.	.	A	9.344	1.063655	0.20067	.	.	ENSG00000181374	ENST00000225844	T	0.03831	3.79	4.74	-6.44	0.01920	CC chemokine, conserved site (1);Chemokine interleukin-8-like domain (3);	.	.	.	.	T	0.01558	0.0050	.	.	.	0.21802	N	0.999538	B	0.02656	0.0	B	0.26517	0.07	T	0.44081	-0.9351	8	0.05721	T	0.95	.	0.2509	0.00205	0.2607:0.2515:0.2422:0.2456	.	73	Q99616	CCL13_HUMAN	V	73	ENSP00000225844:I73V	ENSP00000225844:I73V	I	+	1	0	CCL13	29709183	0.000000	0.05858	0.190000	0.23270	0.063000	0.16089	-0.938000	0.03938	-1.973000	0.00999	-0.379000	0.06801	ATC	.	.		0.507	CCL13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256389.1	NM_005408	
SPAG9	9043	hgsc.bcm.edu	37	17	49048126	49048126	+	Silent	SNP	C	C	A	rs112947211		TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr17:49048126C>A	ENST00000262013.7	-	29	4000	c.3792G>T	c.(3790-3792)acG>acT	p.T1264T	SPAG9_ENST00000505279.1_Silent_p.T1254T|SPAG9_ENST00000357122.4_Silent_p.T1250T|SPAG9_ENST00000510283.1_Silent_p.T1120T	NM_001130528.2	NP_001124000.1	O60271	JIP4_HUMAN	sperm associated antigen 9	1264					activation of JUN kinase activity (GO:0007257)|muscle cell differentiation (GO:0042692)|negative regulation of protein homodimerization activity (GO:0090074)|positive regulation of cell migration (GO:0030335)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron differentiation (GO:0045666)|protein homooligomerization (GO:0051260)|retrograde transport, endosome to Golgi (GO:0042147)|spermatogenesis (GO:0007283)|striated muscle cell differentiation (GO:0051146)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)				NS(1)|breast(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)			ACTTCAAGGGCGTCTGACTAC	0.517																																					p.T1264T		Atlas-SNP	.											.	SPAG9	151	.	0			c.G3792T						.						142.0	113.0	123.0					17																	49048126		2203	4300	6503	SO:0001819	synonymous_variant	9043	exon29			CAAGGGCGTCTGA	AB011088	CCDS11577.1, CCDS45740.1, CCDS58577.1, CCDS58578.1	17q21.33	2013-09-23			ENSG00000008294	ENSG00000008294			14524	protein-coding gene	gene with protein product	"""sperm surface protein"", ""JNK/SAPK-associated protein"", ""JNK interacting protein"", ""sperm specific protein"", ""c-Jun NH2-terminal kinase-associated leucine zipper protein"", ""Max-binding protein"", ""JNK-associated leucine-zipper protein"", ""HLC-4 protein"", ""lung cancer oncogene 4"", ""proliferation-inducing gene 6"", ""cancer/testis antigen 89"""	605430				9480848, 11106729	Standard	NM_003971		Approved	HSS, SYD1, KIAA0516, MGC14967, MGC74461, MGC117291, JLP, PHET, HLC4, PIG6, FLJ13450, FLJ14006, FLJ26141, FLJ34602, CT89	uc002itc.3	O60271	OTTHUMG00000162316	ENST00000262013.7:c.3792G>T	chr17.hg19:g.49048126C>A		198.0	0.0		143.0	17.0	NM_001130528	A6H8U5|A8MSX0|B4DHH2|O60905|Q3KQU8|Q3MKM7|Q86WC7|Q86WC8|Q8IZX7|Q96II0|Q9H811	Silent	SNP	ENST00000262013.7	hg19	CCDS45740.1																																																																																			.	C|0.999;T|0.001		0.517	SPAG9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368543.2	NM_003971	
KIF2B	84643	hgsc.bcm.edu	37	17	51901391	51901391	+	Missense_Mutation	SNP	G	G	A			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr17:51901391G>A	ENST00000268919.4	+	1	1153	c.997G>A	c.(997-999)Gca>Aca	p.A333T		NM_032559.4	NP_115948.4	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	333	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|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)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(15)|lung(58)|ovary(5)|prostate(4)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						TGCTCTGGTGGCACAGGATGT	0.483																																					p.A333T		Atlas-SNP	.											.	KIF2B	254	.	0			c.G997A						.						107.0	109.0	108.0					17																	51901391		2203	4300	6503	SO:0001583	missense	84643	exon1			CTGGTGGCACAGG	AF333335	CCDS32685.1	17q22	2014-08-12			ENSG00000141200	ENSG00000141200		"""Kinesins"""	29443	protein-coding gene	gene with protein product		615142				11416179	Standard	NM_032559		Approved		uc002iua.2	Q8N4N8	OTTHUMG00000177756	ENST00000268919.4:c.997G>A	chr17.hg19:g.51901391G>A	ENSP00000268919:p.Ala333Thr	117.0	0.0		121.0	18.0	NM_032559	Q96MA2|Q9BXG6	Missense_Mutation	SNP	ENST00000268919.4	hg19	CCDS32685.1	.	.	.	.	.	.	.	.	.	.	G	18.37	3.608153	0.66558	.	.	ENSG00000141200	ENST00000268919;ENST00000416491	T	0.74737	-0.87	5.63	4.67	0.58626	Kinesin, motor domain (4);	0.115539	0.38326	N	0.001727	T	0.76870	0.4048	M	0.64676	1.99	0.50813	D	0.999891	P	0.46706	0.883	P	0.48089	0.566	T	0.78663	-0.2116	10	0.52906	T	0.07	.	13.7237	0.62745	0.0751:0.0:0.9249:0.0	.	333	Q8N4N8	KIF2B_HUMAN	T	333;221	ENSP00000268919:A333T	ENSP00000268919:A333T	A	+	1	0	KIF2B	49256390	1.000000	0.71417	0.303000	0.25071	0.618000	0.37518	9.680000	0.98651	1.507000	0.48752	0.655000	0.94253	GCA	.	.		0.483	KIF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438854.1	NM_032559	
KCNH6	81033	hgsc.bcm.edu	37	17	61613399	61613399	+	Missense_Mutation	SNP	G	G	A			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr17:61613399G>A	ENST00000583023.1	+	6	1482	c.1471G>A	c.(1471-1473)Gtc>Atc	p.V491I	KCNH6_ENST00000581784.1_Missense_Mutation_p.V438I|KCNH6_ENST00000314672.5_Missense_Mutation_p.V491I|KCNH6_ENST00000456941.2_Missense_Mutation_p.V438I|KCNH6_ENST00000580652.1_Missense_Mutation_p.V491I	NM_030779.2	NP_110406.1	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 6	491					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(4)|large_intestine(6)|lung(20)|ovary(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	54					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	CTCCGAGAAGGTCTTCTCCAT	0.532																																					p.V491I		Atlas-SNP	.											.	KCNH6	122	.	0			c.G1471A						.						89.0	73.0	79.0					17																	61613399		2203	4300	6503	SO:0001583	missense	81033	exon6			GAGAAGGTCTTCT	AF311913	CCDS11638.1, CCDS11639.1, CCDS62290.1	17q23.3	2012-07-05				ENSG00000173826		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18862	protein-coding gene	gene with protein product		608168				16382104	Standard	NM_030779		Approved	Kv11.2, erg2, HERG2	uc002jay.3	Q9H252		ENST00000583023.1:c.1471G>A	chr17.hg19:g.61613399G>A	ENSP00000463533:p.Val491Ile	151.0	0.0		145.0	16.0	NM_030779	Q9BRD7	Missense_Mutation	SNP	ENST00000583023.1	hg19	CCDS11638.1	.	.	.	.	.	.	.	.	.	.	G	12.79	2.043710	0.36085	.	.	ENSG00000173826	ENST00000314672;ENST00000456941	D;D	0.97976	-4.64;-4.33	4.36	3.31	0.37934	Ion transport (1);	0.121467	0.53938	D	0.000055	D	0.89171	0.6639	N	0.04043	-0.29	0.25427	N	0.988218	B;B;B;B;B	0.15719	0.014;0.004;0.012;0.003;0.0	B;B;B;B;B	0.27076	0.076;0.023;0.007;0.015;0.003	T	0.79024	-0.1972	10	0.02654	T	1	.	3.5223	0.07747	0.3663:0.0:0.6337:0.0	.	368;491;438;491;491	B4DPJ3;B4DKC0;Q9H252-2;Q9H252;Q9H252-3	.;.;.;KCNH6_HUMAN;.	I	491;438	ENSP00000318212:V491I;ENSP00000396900:V438I	ENSP00000318212:V491I	V	+	1	0	KCNH6	58967131	1.000000	0.71417	1.000000	0.80357	0.703000	0.40648	7.478000	0.81082	2.244000	0.73946	0.313000	0.20887	GTC	.	.		0.532	KCNH6-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443853.1	NM_030779	
NPLOC4	55666	hgsc.bcm.edu	37	17	79589216	79589216	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr17:79589216T>A	ENST00000331134.6	-	3	400	c.185A>T	c.(184-186)aAa>aTa	p.K62I	NPLOC4_ENST00000374747.5_Missense_Mutation_p.K62I|NPLOC4_ENST00000539314.1_5'UTR	NM_017921.2	NP_060391.2	Q8TAT6	NPL4_HUMAN	nuclear protein localization 4 homolog (S. cerevisiae)	62					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|Golgi organization (GO:0007030)|membrane fusion (GO:0061025)	endoplasmic reticulum (GO:0005783)|nuclear outer membrane-endoplasmic reticulum membrane network (GO:0042175)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	11	all_neural(118;0.0878)|Melanoma(429;0.242)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			GTTGAGGGATTTGTTGGAGGA	0.468																																					p.K62I		Atlas-SNP	.											.	NPLOC4	27	.	0			c.A185T						.						116.0	110.0	112.0					17																	79589216		1870	4117	5987	SO:0001583	missense	55666	exon3			AGGGATTTGTTGG	AB040932	CCDS45812.1	17q25.3	2012-09-20			ENSG00000182446	ENSG00000182446			18261	protein-coding gene	gene with protein product		606590				11574150, 10811609	Standard	NM_017921		Approved	NPL4, FLJ20657, KIAA1499	uc002kas.3	Q8TAT6	OTTHUMG00000177990	ENST00000331134.6:c.185A>T	chr17.hg19:g.79589216T>A	ENSP00000331487:p.Lys62Ile	93.0	0.0		89.0	9.0	NM_017921	Q8N3J1|Q9H8V2|Q9H964|Q9NWR5|Q9P229	Missense_Mutation	SNP	ENST00000331134.6	hg19	CCDS45812.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.818320	0.90790	.	.	ENSG00000182446	ENST00000331134;ENST00000374747	.	.	.	5.21	5.21	0.72293	Nuclear pore localisation protein Npl4, ubiquitin-like domain (1);	0.000000	0.85682	D	0.000000	T	0.74351	0.3705	M	0.68952	2.095	0.80722	D	1	D;D	0.62365	0.981;0.991	P;P	0.62184	0.838;0.899	T	0.73994	-0.3807	9	0.36615	T	0.2	-22.3983	15.038	0.71764	0.0:0.0:0.0:1.0	.	62;62	Q8TAT6-2;Q8TAT6	.;NPL4_HUMAN	I	62;61	.	ENSP00000331487:K62I	K	-	2	0	NPLOC4	77199621	1.000000	0.71417	0.987000	0.45799	0.992000	0.81027	6.911000	0.75746	2.088000	0.63022	0.482000	0.46254	AAA	.	.		0.468	NPLOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440140.1		
MYOM1	8736	hgsc.bcm.edu	37	18	3155037	3155037	+	Silent	SNP	C	C	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr18:3155037C>T	ENST00000356443.4	-	11	1884	c.1551G>A	c.(1549-1551)aaG>aaA	p.K517K	MYOM1_ENST00000261606.7_Silent_p.K517K|MYOM1_ENST00000400569.3_Silent_p.K517K	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	517	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						CCTCCAAGCACTTCACATCCA	0.478																																					p.K517K		Atlas-SNP	.											.	MYOM1	192	.	0			c.G1551A						.						58.0	59.0	58.0					18																	3155037		1967	4163	6130	SO:0001819	synonymous_variant	8736	exon11			CAAGCACTTCACA	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.1551G>A	chr18.hg19:g.3155037C>T		78.0	0.0		72.0	9.0	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Silent	SNP	ENST00000356443.4	hg19	CCDS45824.1																																																																																			.	.		0.478	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
NDUFV2	4729	hgsc.bcm.edu	37	18	9119504	9119504	+	Silent	SNP	A	A	G			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr18:9119504A>G	ENST00000318388.6	+	4	330	c.216A>G	c.(214-216)gaA>gaG	p.E72E	NDUFV2_ENST00000400033.1_Silent_p.E75E|RP11-21J18.1_ENST00000579126.1_RNA|RP11-143J12.2_ENST00000582375.1_RNA|NDUFV2_ENST00000465096.1_3'UTR|RP11-143J12.2_ENST00000583081.1_RNA	NM_021074.4	NP_066552.2	P19404	NDUV2_HUMAN	NADH dehydrogenase (ubiquinone) flavoprotein 2, 24kDa	72					cardiac muscle tissue development (GO:0048738)|cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|nervous system development (GO:0007399)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|lung(4)|ovary(1)|stomach(1)	7						ACTATCCAGAAGGCCATAAAG	0.358																																					p.E72E		Atlas-SNP	.											.	NDUFV2	17	.	0			c.A216G						.						53.0	53.0	53.0					18																	9119504		2203	4299	6502	SO:0001819	synonymous_variant	4729	exon4			TCCAGAAGGCCAT	X84421	CCDS11842.1	18p11.22	2011-07-04	2002-08-29		ENSG00000178127	ENSG00000178127	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7717	protein-coding gene	gene with protein product	"""complex I 24kDa subunit"", ""NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial"""	600532	"""NADH dehydrogenase (ubiquinone) flavoprotein 2 (24kD)"""			9763677, 7607668	Standard	NM_021074		Approved	CI-24k	uc002knu.3	P19404	OTTHUMG00000131593	ENST00000318388.6:c.216A>G	chr18.hg19:g.9119504A>G		118.0	0.0		113.0	11.0	NM_021074	Q9BV41	Silent	SNP	ENST00000318388.6	hg19	CCDS11842.1																																																																																			.	.		0.358	NDUFV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254475.2	NM_021074	
MOCOS	55034	hgsc.bcm.edu	37	18	33778679	33778679	+	Missense_Mutation	SNP	A	A	G			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr18:33778679A>G	ENST00000261326.5	+	3	280	c.259A>G	c.(259-261)Agc>Ggc	p.S87G		NM_017947.2	NP_060417.2			molybdenum cofactor sulfurase											breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|liver(1)|lung(15)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						GAACATCAGCAGCAAGCTCAC	0.522																																					p.S87G		Atlas-SNP	.											.	MOCOS	84	.	0			c.A259G						.						157.0	122.0	134.0					18																	33778679		2203	4300	6503	SO:0001583	missense	55034	exon3			ATCAGCAGCAAGC	AK000740	CCDS11919.1	18q12	2003-12-18			ENSG00000075643	ENSG00000075643			18234	protein-coding gene	gene with protein product		613274				11302742	Standard	NM_017947		Approved	HMCS, FLJ20733, MOS	uc002kzq.4	Q96EN8	OTTHUMG00000132590	ENST00000261326.5:c.259A>G	chr18.hg19:g.33778679A>G	ENSP00000261326:p.Ser87Gly	222.0	0.0		237.0	12.0	NM_017947		Missense_Mutation	SNP	ENST00000261326.5	hg19	CCDS11919.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.549254	0.86127	.	.	ENSG00000075643	ENST00000261326	D	0.86432	-2.12	5.58	5.58	0.84498	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);	0.000000	0.85682	D	0.000000	D	0.89818	0.6825	M	0.67625	2.065	0.40017	D	0.97536	P	0.49447	0.924	P	0.53760	0.734	D	0.90666	0.4594	10	0.56958	D	0.05	-26.102	12.1284	0.53930	1.0:0.0:0.0:0.0	.	87	Q96EN8	MOCOS_HUMAN	G	87	ENSP00000261326:S87G	ENSP00000261326:S87G	S	+	1	0	MOCOS	32032677	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.476000	0.81055	2.126000	0.65437	0.460000	0.39030	AGC	.	.		0.522	MOCOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255801.1		
SERPINB3	6317	hgsc.bcm.edu	37	18	61325772	61325772	+	Missense_Mutation	SNP	G	G	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr18:61325772G>T	ENST00000283752.5	-	5	587	c.444C>A	c.(442-444)aaC>aaA	p.N148K	SERPINB11_ENST00000489748.1_RNA|SERPINB3_ENST00000332821.8_Missense_Mutation_p.N148K	NM_006919.2	NP_008850.1	P29508	SPB3_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 3	148					negative regulation of catalytic activity (GO:0043086)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)|virus receptor activity (GO:0001618)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	36						CCACCCAGGAGTTAATCTTCT	0.418																																					p.N148K		Atlas-SNP	.											.	SERPINB3	90	.	0			c.C444A						.						109.0	98.0	102.0					18																	61325772		2203	4298	6501	SO:0001583	missense	6317	exon5			CCAGGAGTTAATC	U19568	CCDS11987.1	18q21.3	2014-02-18	2005-08-18		ENSG00000057149	ENSG00000057149		"""Serine (or cysteine) peptidase inhibitors"""	10569	protein-coding gene	gene with protein product		600517	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 3"""	SCC, SCCA1		7724531, 24172014	Standard	NM_006919		Approved	T4-A, HsT1196	uc002lji.3	P29508	OTTHUMG00000060403	ENST00000283752.5:c.444C>A	chr18.hg19:g.61325772G>T	ENSP00000283752:p.Asn148Lys	105.0	0.0		103.0	12.0	NM_006919	A6NDM2|B2RBT5|B3W5Y6|Q53H28|Q53YB5|Q86VF3|Q86W04|Q8IWL4|Q8IXI3|Q96J21|Q9BYF8	Missense_Mutation	SNP	ENST00000283752.5	hg19	CCDS11987.1	.	.	.	.	.	.	.	.	.	.	G	14.75	2.629054	0.46944	.	.	ENSG00000057149	ENST00000283752;ENST00000332821	D;D	0.92348	-3.02;-3.02	2.97	-0.434	0.12283	Serpin domain (3);	0.000000	0.41194	D	0.000924	D	0.97420	0.9156	H	0.99834	4.825	0.34867	D	0.743223	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.95192	0.8309	10	0.87932	D	0	.	7.7049	0.28644	0.6339:0.0:0.3661:0.0	.	148;148;148	P29508-2;P29508;Q5K684	.;SPB3_HUMAN;.	K	148	ENSP00000283752:N148K;ENSP00000329498:N148K	ENSP00000283752:N148K	N	-	3	2	SERPINB3	59476752	0.004000	0.15560	0.995000	0.50966	0.841000	0.47740	-0.228000	0.09114	-0.091000	0.12440	-0.463000	0.05309	AAC	.	.		0.418	SERPINB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133791.1	NM_006919	
ADNP2	22850	hgsc.bcm.edu	37	18	77895740	77895740	+	Missense_Mutation	SNP	A	A	T	rs113879497	byFrequency	TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr18:77895740A>T	ENST00000262198.4	+	4	2899	c.2444A>T	c.(2443-2445)aAt>aTt	p.N815I		NM_014913.3	NP_055728.1	Q6IQ32	ADNP2_HUMAN	ADNP homeobox 2	815					cellular response to oxidative stress (GO:0034599)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell death (GO:0060548)|neuron differentiation (GO:0030182)|positive regulation of cell growth (GO:0030307)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(9)|liver(1)|lung(15)|ovary(5)|prostate(2)	42		all_cancers(4;1.06e-15)|all_epithelial(4;2.36e-10)|all_lung(4;0.000302)|Lung NSC(4;0.000518)|Esophageal squamous(42;0.0212)|Ovarian(4;0.0256)|all_hematologic(56;0.15)|Melanoma(33;0.2)		Epithelial(2;1.1e-11)|OV - Ovarian serous cystadenocarcinoma(15;7.54e-09)|BRCA - Breast invasive adenocarcinoma(31;0.00247)|STAD - Stomach adenocarcinoma(84;0.164)		GTCGATGCCAATGGCAACCTG	0.478																																					p.N815I		Atlas-SNP	.											.	ADNP2	102	.	0			c.A2444T						.						95.0	94.0	94.0					18																	77895740		2203	4300	6503	SO:0001583	missense	22850	exon4			ATGCCAATGGCAA	AB020670	CCDS32853.1	18q23	2013-01-07	2007-07-17	2007-07-17	ENSG00000101544	ENSG00000101544		"""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	23803	protein-coding gene	gene with protein product			"""zinc finger protein 508"""	ZNF508			Standard	NM_014913		Approved	KIAA0863	uc002lnw.3	Q6IQ32	OTTHUMG00000172535	ENST00000262198.4:c.2444A>T	chr18.hg19:g.77895740A>T	ENSP00000262198:p.Asn815Ile	91.0	0.0		94.0	16.0	NM_014913	A8K951|O94943|Q9H9P3	Missense_Mutation	SNP	ENST00000262198.4	hg19	CCDS32853.1	.	.	.	.	.	.	.	.	.	.	A	13.66	2.303087	0.40795	.	.	ENSG00000101544	ENST00000262198	.	.	.	5.18	2.77	0.32553	.	0.326264	0.28895	N	0.013794	T	0.37972	0.1023	M	0.61703	1.905	0.09310	N	1	B	0.30973	0.302	B	0.33042	0.157	T	0.21999	-1.0229	8	.	.	.	-16.8291	8.4314	0.32759	0.8287:0.0:0.1713:0.0	.	815	Q6IQ32	ADNP2_HUMAN	I	815	.	.	N	+	2	0	ADNP2	75996731	0.000000	0.05858	0.514000	0.27761	0.909000	0.53808	0.670000	0.25157	0.416000	0.25844	0.533000	0.62120	AAT	.	A|0.999;G|0.001		0.478	ADNP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418979.1	NM_014913	
CD70	970	hgsc.bcm.edu	37	19	6586092	6586092	+	Missense_Mutation	SNP	G	G	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr19:6586092G>T	ENST00000245903.3	-	3	670	c.521C>A	c.(520-522)aCa>aAa	p.T174K	CD70_ENST00000423145.3_Intron	NM_001252.3	NP_001243.1	P32970	CD70_HUMAN	CD70 molecule	174					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|extrinsic apoptotic signaling pathway (GO:0097191)|immune response (GO:0006955)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	protease binding (GO:0002020)|receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|skin(1)	11						AGGCAAAAGTGTCCCAGTGAG	0.542																																					p.T174K	Pancreas(183;2617 2876 10173 34193)	Atlas-SNP	.											.	CD70	24	.	0			c.C521A						.						68.0	55.0	59.0					19																	6586092		2203	4300	6503	SO:0001583	missense	970	exon3			AAAAGTGTCCCAG	L08096	CCDS12170.1	19p13	2013-05-22	2006-10-27	2006-10-27		ENSG00000125726		"""Tumor necrosis factor (ligand) superfamily"", ""CD molecules"""	11937	protein-coding gene	gene with protein product		602840	"""tumor necrosis factor (ligand) superfamily, member 7"""	CD27LG, TNFSF7		8387892, 8120384	Standard	NM_001252		Approved	CD27L	uc002mfi.3	P32970		ENST00000245903.3:c.521C>A	chr19.hg19:g.6586092G>T	ENSP00000245903:p.Thr174Lys	93.0	0.0		102.0	16.0	NM_001252	B4DPR8|Q53XX4|Q96J57	Missense_Mutation	SNP	ENST00000245903.3	hg19	CCDS12170.1	.	.	.	.	.	.	.	.	.	.	G	13.69	2.312654	0.40895	.	.	ENSG00000125726	ENST00000245903	D	0.94330	-3.4	4.42	4.42	0.53409	Tumour necrosis factor (3);Tumour necrosis factor-like (2);	0.278703	0.25848	N	0.027906	D	0.86640	0.5981	N	0.14661	0.345	0.09310	N	1	P	0.37914	0.611	B	0.37015	0.239	T	0.82220	-0.0565	10	0.66056	D	0.02	.	12.8622	0.57920	0.0:0.0:1.0:0.0	.	174	P32970	CD70_HUMAN	K	174	ENSP00000245903:T174K	ENSP00000245903:T174K	T	-	2	0	CD70	6537092	0.410000	0.25376	0.017000	0.16124	0.002000	0.02628	2.532000	0.45659	2.184000	0.69523	0.556000	0.70494	ACA	.	.		0.542	CD70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457860.1		
MUC16	94025	hgsc.bcm.edu	37	19	9059729	9059729	+	Silent	SNP	G	G	C			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr19:9059729G>C	ENST00000397910.4	-	3	27920	c.27717C>G	c.(27715-27717)tcC>tcG	p.S9239S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9241	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTAGGACAGAGGAAGGAGATT	0.463																																					p.S9239S		Atlas-SNP	.											.	MUC16	4315	.	0			c.C27717G						.						96.0	96.0	96.0					19																	9059729		2069	4228	6297	SO:0001819	synonymous_variant	94025	exon3			GACAGAGGAAGGA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.27717C>G	chr19.hg19:g.9059729G>C		367.0	0.0		281.0	26.0	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	hg19	CCDS54212.1																																																																																			.	.		0.463	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
KEAP1	9817	hgsc.bcm.edu	37	19	10600002	10600002	+	Missense_Mutation	SNP	T	T	C			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr19:10600002T>C	ENST00000171111.5	-	5	2121	c.1574A>G	c.(1573-1575)tAt>tGt	p.Y525C	CTC-429L19.3_ENST00000592671.1_RNA|KEAP1_ENST00000588024.1_5'Flank|KEAP1_ENST00000393623.2_Missense_Mutation_p.Y525C	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	525					cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)				breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	CTGACCATCATAGCCCCCAGC	0.597																																					p.Y525C		Atlas-SNP	.											.	KEAP1	182	.	0			c.A1574G						.						76.0	58.0	64.0					19																	10600002		2203	4300	6503	SO:0001583	missense	9817	exon5			CCATCATAGCCCC	AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999		"""Kelch-like"", ""BTB/POZ domain containing"""	23177	protein-coding gene	gene with protein product	"""kelch-like family member 19"""	606016					Standard	NM_012289		Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.1574A>G	chr19.hg19:g.10600002T>C	ENSP00000171111:p.Tyr525Cys	197.0	0.0		152.0	9.0	NM_012289	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Missense_Mutation	SNP	ENST00000171111.5	hg19	CCDS12239.1	.	.	.	.	.	.	.	.	.	.	T	17.50	3.405638	0.62288	.	.	ENSG00000079999	ENST00000171111;ENST00000393623	T;T	0.77229	-1.08;-1.08	5.73	5.73	0.89815	Kelch-type beta propeller (1);	0.123265	0.56097	D	0.000026	D	0.85957	0.5818	M	0.64170	1.965	0.51012	D	0.999904	D	0.89917	1.0	D	0.97110	1.0	D	0.86649	0.1897	10	0.56958	D	0.05	.	14.01	0.64490	0.0:0.0:0.0:1.0	.	525	Q14145	KEAP1_HUMAN	C	525	ENSP00000171111:Y525C;ENSP00000377245:Y525C	ENSP00000171111:Y525C	Y	-	2	0	KEAP1	10461002	1.000000	0.71417	0.997000	0.53966	0.580000	0.36256	5.540000	0.67205	2.200000	0.70718	0.477000	0.44152	TAT	.	.		0.597	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289	
ZNF254	9534	hgsc.bcm.edu	37	19	24309164	24309164	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr19:24309164A>T	ENST00000357002.4	+	4	477	c.362A>T	c.(361-363)cAg>cTg	p.Q121L	ZNF254_ENST00000342944.6_Missense_Mutation_p.Q36L	NM_001278661.1|NM_001278662.1|NM_001278664.1|NM_001278677.1|NM_001278678.1|NM_203282.2	NP_001265590.1|NP_001265591.1|NP_001265593.1|NP_001265606.1|NP_001265607.1|NP_975011.3	O75437	ZN254_HUMAN	zinc finger protein 254	121					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)						all_cancers(12;0.086)|all_lung(12;0.00528)|Lung NSC(12;0.00731)|all_epithelial(12;0.0186)				GAGAATTTACAGTTAAGAAAA	0.378																																					p.Q121L		Atlas-SNP	.											.	ZNF254	88	.	0			c.A362T						.						64.0	67.0	66.0					19																	24309164		2203	4299	6502	SO:0001583	missense	9534	exon4			ATTTACAGTTAAG	AF054180	CCDS32983.1, CCDS62622.1, CCDS62623.1, CCDS74323.1, CCDS74324.1	19p13	2013-01-08				ENSG00000213096		"""Zinc fingers, C2H2-type"", ""-"""	13047	protein-coding gene	gene with protein product		604768	"""zinc finger protein 539"""	ZNF91L, ZNF539		9653160	Standard	NM_001278661		Approved	HD-ZNF1, BMZF-5	uc002nru.3	O75437		ENST00000357002.4:c.362A>T	chr19.hg19:g.24309164A>T	ENSP00000349494:p.Gln121Leu	91.0	0.0		120.0	6.0	NM_203282	A4QPC0|Q86XL7	Missense_Mutation	SNP	ENST00000357002.4	hg19	CCDS32983.1	.	.	.	.	.	.	.	.	.	.	A	11.17	1.558381	0.27827	.	.	ENSG00000213096	ENST00000342944;ENST00000357002;ENST00000392281	T;T	0.08008	3.14;3.36	1.3	1.3	0.21679	.	.	.	.	.	T	0.11665	0.0284	M	0.79258	2.445	0.09310	N	1	B	0.18610	0.029	B	0.21151	0.033	T	0.20739	-1.0266	9	0.49607	T	0.09	.	6.3276	0.21253	1.0:0.0:0.0:0.0	.	121	O75437	ZN254_HUMAN	L	36;121;121	ENSP00000445527:Q36L;ENSP00000349494:Q121L	ENSP00000445527:Q36L	Q	+	2	0	ZNF254	24101004	0.001000	0.12720	0.005000	0.12908	0.034000	0.12701	0.386000	0.20702	0.565000	0.29255	0.260000	0.18958	CAG	.	.		0.378	ZNF254-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466453.1	NM_004876	
ZFP82	284406	hgsc.bcm.edu	37	19	36884090	36884090	+	Missense_Mutation	SNP	A	A	C			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr19:36884090A>C	ENST00000392161.3	-	5	1394	c.1152T>G	c.(1150-1152)caT>caG	p.H384Q	ZFP82_ENST00000392171.1_Missense_Mutation_p.H384Q	NM_133466.2	NP_597723.1	Q8N141	ZFP82_HUMAN	ZFP82 zinc finger protein	384					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)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						GAATTCTGTGATGGAGAATAA	0.378																																					p.H384Q		Atlas-SNP	.											.	ZFP82	71	.	0			c.T1152G						.						114.0	113.0	113.0					19																	36884090		2203	4300	6503	SO:0001583	missense	284406	exon5			TCTGTGATGGAGA	AL834267	CCDS12493.1	19q13.13	2013-01-08	2012-11-27	2008-07-01		ENSG00000181007		"""Zinc fingers, C2H2-type"", ""-"""	28682	protein-coding gene	gene with protein product			"""zinc finger protein 545"", ""zinc finger protein 82 homolog (mouse)"", ""zinc finger protein 82"""	ZNF545		11853319	Standard	NM_133466		Approved	MGC45380, KIAA1948	uc002ody.1	Q8N141		ENST00000392161.3:c.1152T>G	chr19.hg19:g.36884090A>C	ENSP00000431265:p.His384Gln	101.0	0.0		114.0	11.0	NM_133466	Q8NC63|Q8TF53	Missense_Mutation	SNP	ENST00000392161.3	hg19	CCDS12493.1	.	.	.	.	.	.	.	.	.	.	A	14.93	2.683835	0.47991	.	.	ENSG00000181007	ENST00000392161;ENST00000392171	D;D	0.86865	-2.18;-2.18	4.53	2.44	0.29823	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.42964	D	0.000627	D	0.94377	0.8192	H	0.96430	3.82	0.31754	N	0.634165	D	0.89917	1.0	D	0.97110	1.0	D	0.92064	0.5659	10	0.87932	D	0	.	7.1164	0.25418	0.8075:0.0:0.1925:0.0	.	384	Q8N141	ZFP82_HUMAN	Q	384	ENSP00000431265:H384Q;ENSP00000446080:H384Q	ENSP00000431265:H384Q	H	-	3	2	ZFP82	41575930	0.997000	0.39634	1.000000	0.80357	0.993000	0.82548	2.095000	0.41729	0.279000	0.22186	0.482000	0.46254	CAT	.	.		0.378	ZFP82-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109552.2	NM_133466	
CIC	23152	hgsc.bcm.edu	37	19	42798805	42798805	+	Silent	SNP	A	A	G			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr19:42798805A>G	ENST00000575354.2	+	19	4417	c.4377A>G	c.(4375-4377)ccA>ccG	p.P1459P	CIC_ENST00000160740.3_Silent_p.P1457P|CIC_ENST00000572681.2_Silent_p.P2365P	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	1459					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				ACAAGGTGCCATACTCCTCCC	0.637			"""Mis, F, S"""		oligodendroglioma																																p.P1459P		Atlas-SNP	.		Rec	yes		19	19q13.2	23152	capicua homolog		O	.	CIC	249	.	0			c.A4377G						.						79.0	72.0	75.0					19																	42798805		2203	4300	6503	SO:0001819	synonymous_variant	23152	exon19			GGTGCCATACTCC	AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"""capicua (Drosophila) homolog"", ""capicua homolog (Drosophila)"""			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.4377A>G	chr19.hg19:g.42798805A>G		148.0	0.0		114.0	18.0	NM_015125	Q7LGI1|Q9UEG5|Q9Y6T1	Silent	SNP	ENST00000575354.2	hg19	CCDS12601.1																																																																																			.	.		0.637	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2		
SCAF1	58506	hgsc.bcm.edu	37	19	50156751	50156751	+	Silent	SNP	A	A	G			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr19:50156751A>G	ENST00000360565.3	+	7	3229	c.3105A>G	c.(3103-3105)gaA>gaG	p.E1035E		NM_021228.2	NP_067051.2	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	1035	Glu-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	20		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00113)|GBM - Glioblastoma multiforme(134;0.0204)		aggaagaggaagaggaggagg	0.682																																					p.E1035E		Atlas-SNP	.											.	SCAF1	78	.	0			c.A3105G						.						9.0	12.0	11.0					19																	50156751		2196	4287	6483	SO:0001819	synonymous_variant	58506	exon7			AGAGGAAGAGGAG	AK024444	CCDS33074.1	19q13.3-q13.4	2011-01-10			ENSG00000126461	ENSG00000126461			30403	protein-coding gene	gene with protein product						11461075	Standard	NM_021228		Approved	SR-A1, FLJ00034	uc002poq.3	Q9H7N4		ENST00000360565.3:c.3105A>G	chr19.hg19:g.50156751A>G		23.0	0.0		19.0	6.0	NM_021228	Q7Z5V7|Q8WVA1|Q9NR59	Silent	SNP	ENST00000360565.3	hg19	CCDS33074.1																																																																																			.	.		0.682	SCAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465764.1	NM_021228	
NLRP12	91662	hgsc.bcm.edu	37	19	54310856	54310856	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr19:54310856A>T	ENST00000324134.6	-	4	2304	c.2136T>A	c.(2134-2136)aaT>aaA	p.N712K	NLRP12_ENST00000345770.5_Missense_Mutation_p.N713K|NLRP12_ENST00000391772.1_Missense_Mutation_p.N713K|NLRP12_ENST00000351894.4_Missense_Mutation_p.N712K|NLRP12_ENST00000354278.3_Missense_Mutation_p.N712K|NLRP12_ENST00000391773.1_Missense_Mutation_p.N713K|NLRP12_ENST00000535162.1_Missense_Mutation_p.N712K|NLRP12_ENST00000391775.3_Missense_Mutation_p.N712K	NM_001277126.1|NM_144687.2	NP_001264055.1|NP_653288.1	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12	712					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to cytokine stimulus (GO:0071345)|dendritic cell migration (GO:0036336)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of signal transduction (GO:0009968)|negative regulation of Toll signaling pathway (GO:0045751)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of MHC class I biosynthetic process (GO:0045345)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of interleukin-18 biosynthetic process (GO:0045381)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)			NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(36)|ovary(5)|pancreas(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	80	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)		TCAGGTTTGGATTGGTGCACA	0.562																																					p.L712L		Atlas-SNP	.											.	NLRP12	236	.	0			c.G2136A						.						101.0	88.0	92.0					19																	54310856		2203	4300	6503	SO:0001583	missense	91662	exon4			GTTTGGATTGGTG	AY095146	CCDS12864.1, CCDS62784.1, CCDS62785.1	19q13.42	2014-09-17	2006-12-08	2006-12-08	ENSG00000142405	ENSG00000142405		"""Nucleotide-binding domain and leucine rich repeat containing"""	22938	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 12"""	609648	"""NACHT, leucine rich repeat and PYD containing 12"""	NALP12		12563287, 12019269	Standard	NM_001277129		Approved	RNO2, PYPAF7, Monarch1, PAN6, CLR19.3	uc002qcj.5	P59046	OTTHUMG00000060776	ENST00000324134.6:c.2136T>A	chr19.hg19:g.54310856A>T	ENSP00000319377:p.Asn712Lys	158.0	0.0		133.0	6.0	NM_144687	A8MTQ2|B3KTE7|Q8NEU4|Q9BY26	Silent	SNP	ENST00000324134.6	hg19	CCDS12864.1	.	.	.	.	.	.	.	.	.	.	A	15.26	2.780015	0.49891	.	.	ENSG00000142405	ENST00000324134;ENST00000535162;ENST00000351894;ENST00000354278;ENST00000391775;ENST00000391773;ENST00000345770;ENST00000391772	D;D;D;D;D;D;D	0.90385	-2.66;-2.66;-2.66;-2.66;-2.66;-2.33;-2.33	3.85	-4.67	0.03319	.	0.652514	0.12395	U	0.472677	D	0.92658	0.7667	M	0.80847	2.515	0.09310	N	0.999996	D;P;P;D	0.60575	0.988;0.65;0.931;0.961	P;P;P;P	0.60541	0.876;0.515;0.742;0.864	D	0.87435	0.2391	10	0.66056	D	0.02	.	9.3022	0.37853	0.5708:0.0:0.4292:0.0	.	713;712;712;712	F2Z321;A8K407;A8MTQ2;P59046	.;.;.;NAL12_HUMAN	K	712;712;712;712;712;713;713;713	ENSP00000319377:N712K;ENSP00000438030:N712K;ENSP00000340473:N712K;ENSP00000346231:N712K;ENSP00000375655:N712K;ENSP00000375653:N713K;ENSP00000375652:N713K	ENSP00000319377:N712K	N	-	3	2	NLRP12	59002668	0.000000	0.05858	0.001000	0.08648	0.024000	0.10985	-4.163000	0.00282	-0.852000	0.04141	-0.384000	0.06662	AAT	.	.		0.562	NLRP12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000134340.1	NM_144687	
CHMP2A	27243	hgsc.bcm.edu	37	19	59063031	59063031	+	Missense_Mutation	SNP	G	G	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr19:59063031G>T	ENST00000600118.1	-	5	1079	c.654C>A	c.(652-654)aaC>aaA	p.N218K	CHMP2A_ENST00000312547.2_Missense_Mutation_p.N218K|CHMP2A_ENST00000601220.1_Missense_Mutation_p.N218K			O43633	CHM2A_HUMAN	charged multivesicular body protein 2A	218	Interaction with VPS4B.|Interaction with VTA1.				endosomal transport (GO:0016197)|establishment of protein localization (GO:0045184)|membrane organization (GO:0061024)|positive regulation of viral release from host cell (GO:1902188)|protein transport (GO:0015031)|regulation of viral process (GO:0050792)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	protein domain specific binding (GO:0019904)			endometrium(1)|kidney(1)|large_intestine(3)|lung(2)	7		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179)		CCCTCCGCAGGTTCTTAAGCC	0.552																																					p.N218K		Atlas-SNP	.											.	CHMP2A	25	.	0			c.C654A						.						60.0	65.0	63.0					19																	59063031		2203	4300	6503	SO:0001583	missense	27243	exon6			CCGCAGGTTCTTA	AF042384	CCDS12986.1	19q13.43	2014-09-04	2011-09-21		ENSG00000130724	ENSG00000130724		"""Charged multivesicular body proteins"""	30216	protein-coding gene	gene with protein product	"""putative breast adenocarcinoma marker (32kD)"", ""VPS2 homolog A (S. cerevisiae)"""	610893	"""chromatin modifying protein 2A"""			15173323, 11559748	Standard	XM_005258746		Approved	BC-2, CHMP2, VPS2, VPS2A	uc002qtk.3	O43633	OTTHUMG00000183547	ENST00000600118.1:c.654C>A	chr19.hg19:g.59063031G>T	ENSP00000469240:p.Asn218Lys	76.0	0.0		69.0	5.0	NM_198426	B2R4W6|Q3ZTT0	Missense_Mutation	SNP	ENST00000600118.1	hg19	CCDS12986.1	.	.	.	.	.	.	.	.	.	.	G	9.989	1.230373	0.22542	.	.	ENSG00000130724	ENST00000312547	T	0.77489	-1.1	4.83	2.65	0.31530	.	0.000000	0.85682	D	0.000000	T	0.50548	0.1622	N	0.08118	0	0.58432	D	0.999999	B	0.25904	0.137	B	0.12156	0.007	T	0.39165	-0.9627	10	0.07813	T	0.8	.	8.6462	0.34007	0.196:0.0:0.804:0.0	.	218	O43633	CHM2A_HUMAN	K	218	ENSP00000310440:N218K	ENSP00000310440:N218K	N	-	3	2	CHMP2A	63754843	1.000000	0.71417	0.996000	0.52242	0.372000	0.29890	3.644000	0.54381	0.710000	0.31997	0.650000	0.86243	AAC	.	.		0.552	CHMP2A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467088.1	NM_014453	
KIZ	55857	hgsc.bcm.edu	37	20	21213370	21213370	+	RNA	SNP	A	A	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr20:21213370A>T	ENST00000457464.1	+	0	1380																											CGCTTATCACAGGTTTGAATA	0.433																																					.		Atlas-SNP	.											.	.	.	.	0			c.1384-2A>T						.						51.0	52.0	52.0					20																	21213370		1986	4174	6160			55857	exon9			TATCACAGGTTTG																													chr20.hg19:g.21213370A>T		113.0	0.0		132.0	7.0	NM_001163023		Splice_Site	SNP	ENST00000457464.1	hg19																																																																																				.	.		0.433	PLK1S1-003	KNOWN	not_organism_supported|sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000078262.2		
DIDO1	11083	hgsc.bcm.edu	37	20	61511821	61511821	+	Silent	SNP	A	A	G			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr20:61511821A>G	ENST00000266070.4	-	16	5812	c.5487T>C	c.(5485-5487)tcT>tcC	p.S1829S	DIDO1_ENST00000395343.1_Silent_p.S1829S	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	1829	Pro-rich.				apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					CACCAAGGTAAGAGGGTGAGG	0.602																																					p.S1829S	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											.	DIDO1	321	.	0			c.T5487C						.						66.0	74.0	72.0					20																	61511821		2203	4300	6503	SO:0001819	synonymous_variant	11083	exon16			AAGGTAAGAGGGT	AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"""Zinc fingers, PHD-type"""	2680	protein-coding gene	gene with protein product		604140	"""chromosome 20 open reading frame 158"", ""death associated transcription factor 1"""	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.5487T>C	chr20.hg19:g.61511821A>G		156.0	0.0		129.0	14.0	NM_001193369	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Silent	SNP	ENST00000266070.4	hg19	CCDS33506.1																																																																																			.	.		0.602	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796	
KRTAP13-3	337960	hgsc.bcm.edu	37	21	31797785	31797785	+	Missense_Mutation	SNP	G	G	A			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr21:31797785G>A	ENST00000390690.2	-	1	501	c.446C>T	c.(445-447)cCa>cTa	p.P149L		NM_181622.1	NP_853653.1	Q3SY46	KR133_HUMAN	keratin associated protein 13-3	149						intermediate filament (GO:0005882)				endometrium(1)|large_intestine(1)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	14						AAAATAGATTGGATGGCAGAA	0.428																																					p.P149L		Atlas-SNP	.											.	KRTAP13-3	47	.	0			c.C446T						.						57.0	55.0	56.0					21																	31797785		1925	4161	6086	SO:0001583	missense	337960	exon1			TAGATTGGATGGC	AP001708	CCDS13591.1	21q22.1	2006-03-13			ENSG00000240432	ENSG00000240432		"""Keratin associated proteins"""	18925	protein-coding gene	gene with protein product						12359730	Standard	NM_181622		Approved	KAP13.3	uc002yob.1	Q3SY46	OTTHUMG00000057776	ENST00000390690.2:c.446C>T	chr21.hg19:g.31797785G>A	ENSP00000375109:p.Pro149Leu	103.0	0.0		72.0	7.0	NM_181622	Q3LI78	Missense_Mutation	SNP	ENST00000390690.2	hg19	CCDS13591.1	.	.	.	.	.	.	.	.	.	.	g	15.25	2.779012	0.49891	.	.	ENSG00000240432	ENST00000390690;ENST00000448917	T	0.09445	2.98	4.03	4.03	0.46877	.	0.175309	0.26742	U	0.022739	T	0.31389	0.0795	M	0.82132	2.575	0.09310	N	1	D	0.71674	0.998	D	0.66847	0.947	T	0.03597	-1.1021	10	0.66056	D	0.02	0.0569	12.1568	0.54081	0.0:0.0:1.0:0.0	.	149	Q3SY46	KR133_HUMAN	L	149;139	ENSP00000375109:P149L	ENSP00000375109:P149L	P	-	2	0	KRTAP13-3	30719656	0.287000	0.24315	0.008000	0.14137	0.002000	0.02628	2.354000	0.44098	2.570000	0.86706	0.568000	0.79292	CCA	.	.		0.428	KRTAP13-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128228.2		
CSTB	1476	hgsc.bcm.edu	37	21	45194153	45194153	+	Missense_Mutation	SNP	T	T	C			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr21:45194153T>C	ENST00000291568.5	-	3	402	c.227A>G	c.(226-228)gAa>gGa	p.E76G		NM_000100.3	NP_000091.1	P04080	CYTB_HUMAN	cystatin B (stefin B)	76					adult locomotory behavior (GO:0008344)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|endopeptidase inhibitor activity (GO:0004866)|poly(A) RNA binding (GO:0044822)|protease binding (GO:0002020)			lung(1)|prostate(1)	2				STAD - Stomach adenocarcinoma(101;0.168)		GGGCTTGTTTTCATGAGGGAG	0.527																																					p.E76G	Esophageal Squamous(58;831 1093 17019 29789 35147)	Atlas-SNP	.											.	CSTB	3	.	0			c.A227G						.						246.0	212.0	224.0					21																	45194153		2203	4300	6503	SO:0001583	missense	1476	exon3			TTGTTTTCATGAG	L03558	CCDS13701.1	21q22.3	2014-09-17			ENSG00000160213	ENSG00000160213			2482	protein-coding gene	gene with protein product		601145		EPM1, STFB		8596935	Standard	NM_000100		Approved	CST6, PME	uc002zdr.4	P04080	OTTHUMG00000086886	ENST00000291568.5:c.227A>G	chr21.hg19:g.45194153T>C	ENSP00000291568:p.Glu76Gly	335.0	0.0		341.0	26.0	NM_000100		Missense_Mutation	SNP	ENST00000291568.5	hg19	CCDS13701.1	.	.	.	.	.	.	.	.	.	.	T	18.52	3.641191	0.67244	.	.	ENSG00000160213	ENST00000291568	T	0.77098	-1.07	5.46	5.46	0.80206	Proteinase inhibitor I25, cystatin (2);	0.237197	0.42053	D	0.000767	D	0.82462	0.5042	.	.	.	0.28066	N	0.932773	D	0.57571	0.98	P	0.57679	0.825	T	0.77351	-0.2620	9	0.40728	T	0.16	-13.3196	11.9348	0.52868	0.0:0.0:0.0:1.0	.	76	P04080	CYTB_HUMAN	G	76	ENSP00000291568:E76G	ENSP00000291568:E76G	E	-	2	0	CSTB	44018581	0.993000	0.37304	0.149000	0.22428	0.589000	0.36550	4.155000	0.58131	2.074000	0.62210	0.459000	0.35465	GAA	.	.		0.527	CSTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195689.1	NM_000100	
RASD2	23551	hgsc.bcm.edu	37	22	35942929	35942929	+	Missense_Mutation	SNP	C	C	G			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr22:35942929C>G	ENST00000216127.4	+	2	715	c.73C>G	c.(73-75)Ctg>Gtg	p.L25V		NM_014310.3	NP_055125.2	Q96D21	RHES_HUMAN	RASD family, member 2	25					locomotory behavior (GO:0007626)|negative regulation of protein ubiquitination (GO:0031397)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein sumoylation (GO:0033235)|regulation of cAMP-mediated signaling (GO:0043949)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission, dopaminergic (GO:0001963)	plasma membrane (GO:0005886)	G-protein beta-subunit binding (GO:0031681)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(2)|large_intestine(1)|lung(8)|prostate(1)|skin(1)	13						CATGGTGGTGCTGGGTGCCTC	0.577																																					p.L25V		Atlas-SNP	.											.	RASD2	34	.	0			c.C73G						.						100.0	75.0	84.0					22																	35942929		2203	4300	6503	SO:0001583	missense	23551	exon2			GTGGTGCTGGGTG	AF279143	CCDS13916.1	22q13.1	2014-05-09			ENSG00000100302	ENSG00000100302			18229	protein-coding gene	gene with protein product	"""tumor endothelial marker 2"", ""Ras homolog enriched in striatum"""	612842				10947988, 10467249, 14724584	Standard	NM_014310		Approved	TEM2, Rhes, MGC:4834	uc003anx.3	Q96D21	OTTHUMG00000150607	ENST00000216127.4:c.73C>G	chr22.hg19:g.35942929C>G	ENSP00000216127:p.Leu25Val	150.0	0.0		129.0	15.0	NM_014310	O95520|Q5THY8	Missense_Mutation	SNP	ENST00000216127.4	hg19	CCDS13916.1	.	.	.	.	.	.	.	.	.	.	C	18.56	3.651205	0.67472	.	.	ENSG00000100302	ENST00000216127	T	0.76448	-1.02	5.3	4.07	0.47477	Small GTP-binding protein domain (1);	0.000000	0.64402	D	0.000001	D	0.83801	0.5333	L	0.49256	1.55	0.44110	D	0.996881	D	0.76494	0.999	D	0.74674	0.984	D	0.84290	0.0499	10	0.51188	T	0.08	.	14.8621	0.70389	0.0:0.9189:0.0:0.0811	.	25	Q96D21	RHES_HUMAN	V	25	ENSP00000216127:L25V	ENSP00000216127:L25V	L	+	1	2	RASD2	34272875	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	2.019000	0.41001	2.499000	0.84300	0.558000	0.71614	CTG	.	.		0.577	RASD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319063.1	NM_014310	
GRAP2	9402	hgsc.bcm.edu	37	22	40351828	40351828	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr22:40351828A>T	ENST00000344138.4	+	3	347	c.84A>T	c.(82-84)ttA>ttT	p.L28F	GRAP2_ENST00000540310.1_Intron|GRAP2_ENST00000543252.1_Missense_Mutation_p.L28F|GRAP2_ENST00000407075.3_Missense_Mutation_p.L28F|GRAP2_ENST00000399090.2_Intron|GRAP2_ENST00000478445.1_3'UTR|GRAP2_ENST00000544756.1_Intron	NM_004810.2	NP_004801.1	O75791	GRAP2_HUMAN	GRB2-related adaptor protein 2	28	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cell-cell signaling (GO:0007267)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of signal transduction (GO:0009967)|Ras protein signal transduction (GO:0007265)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|nucleus (GO:0005634)	SH3/SH2 adaptor activity (GO:0005070)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	14						TGTAGATTTTAAGTAACCAAG	0.453																																					p.L28F		Atlas-SNP	.											.	GRAP2	29	.	0			c.A84T						.						77.0	72.0	73.0					22																	40351828		2203	4300	6503	SO:0001583	missense	9402	exon3			GATTTTAAGTAAC	AF102694	CCDS13999.1	22q13.2	2013-02-14			ENSG00000100351	ENSG00000100351		"""SH2 domain containing"""	4563	protein-coding gene	gene with protein product		604518				9878555, 10224278	Standard	XM_005261836		Approved	Grf40, GrbX, GRBLG, GADS, Mona	uc003ayh.2	O75791	OTTHUMG00000151097	ENST00000344138.4:c.84A>T	chr22.hg19:g.40351828A>T	ENSP00000339186:p.Leu28Phe	109.0	0.0		100.0	4.0	NM_004810	B7Z8I3|O43726|Q9NRB7	Missense_Mutation	SNP	ENST00000344138.4	hg19	CCDS13999.1	.	.	.	.	.	.	.	.	.	.	A	16.65	3.183080	0.57800	.	.	ENSG00000100351	ENST00000344138;ENST00000543252;ENST00000420971;ENST00000407075	T;T;T;T	0.58652	0.32;0.32;0.32;0.32	5.46	0.272	0.15645	Src homology-3 domain (4);	0.234859	0.34110	N	0.004247	T	0.69584	0.3127	M	0.75085	2.285	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.66756	-0.5843	10	0.87932	D	0	-10.2871	7.3065	0.26451	0.5728:0.2186:0.2086:0.0	.	28;28	Q6FI14;O75791	.;GRAP2_HUMAN	F	28	ENSP00000339186:L28F;ENSP00000446350:L28F;ENSP00000396355:L28F;ENSP00000385607:L28F	ENSP00000339186:L28F	L	+	3	2	GRAP2	38681774	0.998000	0.40836	0.993000	0.49108	0.878000	0.50629	0.618000	0.24373	-0.175000	0.10725	-1.139000	0.01908	TTA	.	.		0.453	GRAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321295.1	NM_004810	
ARSA	410	hgsc.bcm.edu	37	22	51064685	51064685	+	Silent	SNP	G	G	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr22:51064685G>T	ENST00000547307.1	-	5	1275	c.870C>A	c.(868-870)tcC>tcA	p.S290S	ARSA_ENST00000216124.5_Silent_p.S292S|ARSA_ENST00000356098.5_Silent_p.S292S|ARSA_ENST00000453344.2_Silent_p.S206S|ARSA_ENST00000395619.3_Silent_p.S292S|ARSA_ENST00000547805.1_Silent_p.S290S|ARSA_ENST00000610191.1_5'Flank|ARSA_ENST00000395621.3_Silent_p.S292S			P15289	ARSA_HUMAN	arylsulfatase A	290				S -> P (in Ref. 5; AK098659). {ECO:0000305}.	autophagy (GO:0006914)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|central nervous system development (GO:0007417)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to methylmercury (GO:0051597)|response to nutrient (GO:0007584)|response to pH (GO:0009268)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum lumen (GO:0005788)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|cerebroside-sulfatase activity (GO:0004098)|sulfuric ester hydrolase activity (GO:0008484)			endometrium(1)|large_intestine(1)|lung(5)|pancreas(1)|skin(1)	9		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)	Micafungin(DB01141)|Suramin(DB04786)	AGCCGCCTCGGGACATACGCA	0.642																																					p.S292S		Atlas-SNP	.											.	ARSA	19	.	0			c.C876A						.						47.0	42.0	44.0					22																	51064685		2203	4300	6503	SO:0001819	synonymous_variant	410	exon6			GCCTCGGGACATA	X52150	CCDS14100.1, CCDS46736.1, CCDS14100.2	22q13.33	2013-09-19			ENSG00000100299	ENSG00000100299	3.1.6.8	"""Arylsulfatase family"""	713	protein-coding gene	gene with protein product	"""metachromatic leucodystrophy"""	607574				15772092	Standard	NM_000487		Approved		uc003bmz.5	P15289	OTTHUMG00000150180	ENST00000547307.1:c.870C>A	chr22.hg19:g.51064685G>T		133.0	0.0		99.0	4.0	NM_001085426	B2RCA6|B7XD04|F8WCC8|Q6ICI5|Q96CJ0	Silent	SNP	ENST00000547307.1	hg19																																																																																				.	.		0.642	ARSA-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000487	
NXF3	56000	hgsc.bcm.edu	37	X	102334164	102334164	+	Missense_Mutation	SNP	C	C	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chrX:102334164C>T	ENST00000395065.3	-	16	1464	c.1363G>A	c.(1363-1365)Ggg>Agg	p.G455R	NXF3_ENST00000425644.1_Missense_Mutation_p.G127R	NM_022052.1	NP_071335.1	Q9H4D5	NXF3_HUMAN	nuclear RNA export factor 3	455	NTF2. {ECO:0000255|PROSITE- ProRule:PRU00137}.				mRNA export from nucleus (GO:0006406)|poly(A)+ mRNA export from nucleus (GO:0016973)	cytoplasm (GO:0005737)|nuclear RNA export factor complex (GO:0042272)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)	p.G455W(1)		NS(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(15)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26						TTGAACACCCCGTTGACAGAA	0.587																																					p.G455R		Atlas-SNP	.											.	NXF3	81	.	1	Substitution - Missense(1)	lung(1)	c.G1363A						.						251.0	223.0	233.0					X																	102334164		2203	4300	6503	SO:0001583	missense	56000	exon16			ACACCCCGTTGAC	AJ277527	CCDS14503.1	Xq22	2008-02-05			ENSG00000147206	ENSG00000147206			8073	protein-coding gene	gene with protein product		300316				11073998	Standard	NM_022052		Approved		uc004eju.3	Q9H4D5	OTTHUMG00000022088	ENST00000395065.3:c.1363G>A	chrX.hg19:g.102334164C>T	ENSP00000378504:p.Gly455Arg	270.0	0.0		275.0	87.0	NM_022052	B4DYS7|Q5H9I1|Q9H1A9	Missense_Mutation	SNP	ENST00000395065.3	hg19	CCDS14503.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	14.37|14.37	2.514215|2.514215	0.44763|0.44763	.|.	.|.	ENSG00000147206|ENSG00000147206	ENST00000395065;ENST00000425644|ENST00000427570	T;T|.	0.63580|.	-0.05;-0.05|.	4.22|4.22	3.35|3.35	0.38373|0.38373	Nuclear transport factor 2, Eukaryote (1);Nuclear transport factor 2 (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.84665|0.84665	0.5522|0.5522	H|H	0.96239|0.96239	3.79|3.79	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.87578|.	0.975;0.998|.	D|D	0.86659|0.86659	0.1903|0.1903	10|5	0.87932|.	D|.	0|.	-4.1391|-4.1391	9.8204|9.8204	0.40878|0.40878	0.0:0.8909:0.0:0.1091|0.0:0.8909:0.0:0.1091	.|.	351;455|.	E9PEY7;Q9H4D5|.	.;NXF3_HUMAN|.	R|Q	455;127|331	ENSP00000378504:G455R;ENSP00000401026:G127R|.	ENSP00000378504:G455R|.	G|R	-|-	1|2	0|0	NXF3|NXF3	102220820|102220820	0.996000|0.996000	0.38824|0.38824	0.015000|0.015000	0.15790|0.15790	0.327000|0.327000	0.28475|0.28475	5.633000|5.633000	0.67825|0.67825	0.898000|0.898000	0.36418|0.36418	0.593000|0.593000	0.82588|0.82588	GGG|CGG	.	.		0.587	NXF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057684.1	NM_022052	
TEX13A	56157	hgsc.bcm.edu	37	X	104464383	104464383	+	Silent	SNP	G	G	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chrX:104464383G>T	ENST00000413579.1	-	3	606	c.495C>A	c.(493-495)gcC>gcA	p.A165A	IL1RAPL2_ENST00000344799.4_Intron|IL1RAPL2_ENST00000372582.1_Intron|TEX13A_ENST00000372578.3_Silent_p.A165A|TEX13A_ENST00000372575.1_Silent_p.A165A			Q9BXU3	TX13A_HUMAN	testis expressed 13A	165							zinc ion binding (GO:0008270)			large_intestine(5)|ovary(2)|upper_aerodigestive_tract(1)	8						AAACCCCTCCGGCAGTGGCCA	0.647																																					p.A165A		Atlas-SNP	.											.	TEX13A	55	.	0			c.C495A						.						23.0	27.0	26.0					X																	104464383		2079	4102	6181	SO:0001819	synonymous_variant	56157	exon3			CCCTCCGGCAGTG	AF285597	CCDS76005.1	Xq28	2012-04-20	2007-03-13		ENSG00000133149	ENSG00000268629			11735	protein-coding gene	gene with protein product		300312	"""testis expressed sequence 13A"""			11279525	Standard	NM_031274		Approved		uc004ema.3	Q9BXU3	OTTHUMG00000022133	ENST00000413579.1:c.495C>A	chrX.hg19:g.104464383G>T		15.0	0.0		7.0	4.0	NM_031274	B1B1G8|Q32NB6	Silent	SNP	ENST00000413579.1	hg19																																																																																				.	.		0.647	TEX13A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_031274	
MAGEA4	4103	hgsc.bcm.edu	37	X	151093077	151093077	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chrX:151093077A>T	ENST00000360243.2	+	3	1208	c.941A>T	c.(940-942)gAa>gTa	p.E314V	MAGEA4_ENST00000276344.2_Missense_Mutation_p.E314V|MAGEA4_ENST00000370337.4_Missense_Mutation_p.E314V|MAGEA4_ENST00000393920.1_Missense_Mutation_p.E314V|MAGEA4_ENST00000370335.1_Missense_Mutation_p.E314V|MAGEA4_ENST00000370340.3_Missense_Mutation_p.E314V|MAGEA4_ENST00000393921.1_Missense_Mutation_p.E314V	NM_001011550.1	NP_001011550.1	P43358	MAGA4_HUMAN	melanoma antigen family A, 4	314										breast(2)|central_nervous_system(4)|endometrium(1)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)	27	Acute lymphoblastic leukemia(192;6.56e-05)					TTAGAGGAGGAAGAGGGAGTC	0.572																																					p.E314V		Atlas-SNP	.											.	MAGEA4	68	.	0			c.A941T						.						67.0	66.0	67.0					X																	151093077		2203	4300	6503	SO:0001583	missense	4103	exon3			AGGAGGAAGAGGG		CCDS14702.1	Xq28	2009-03-13			ENSG00000147381	ENSG00000147381			6802	protein-coding gene	gene with protein product	"""melanoma-associated antigen 4"", ""cancer/testis antigen family 1, member 4"""	300175		MAGE4		8575766	Standard	XM_005274677		Approved	MAGE4A, MAGE4B, MAGE-41, MAGE-X2, MGC21336, CT1.4	uc004ffa.3	P43358	OTTHUMG00000024174	ENST00000360243.2:c.941A>T	chrX.hg19:g.151093077A>T	ENSP00000353379:p.Glu314Val	132.0	0.0		103.0	8.0	NM_001011548	Q14798	Missense_Mutation	SNP	ENST00000360243.2	hg19	CCDS14702.1	.	.	.	.	.	.	.	.	.	.	A	7.227	0.598562	0.13939	.	.	ENSG00000147381	ENST00000276344;ENST00000393921;ENST00000370337;ENST00000393920;ENST00000370340;ENST00000370335;ENST00000360243	T;T;T;T;T;T;T	0.02050	4.48;4.48;4.48;4.48;4.48;4.48;4.48	1.74	-2.88	0.05682	.	1.413460	0.04436	N	0.370110	T	0.02267	0.0070	M	0.67569	2.06	0.09310	N	1	P	0.37663	0.604	B	0.24269	0.052	T	0.38845	-0.9642	9	.	.	.	.	0.1052	0.00052	0.3372:0.2417:0.1811:0.24	.	314	P43358	MAGA4_HUMAN	V	314	ENSP00000276344:E314V;ENSP00000377498:E314V;ENSP00000359362:E314V;ENSP00000377497:E314V;ENSP00000359365:E314V;ENSP00000359360:E314V;ENSP00000353379:E314V	.	E	+	2	0	MAGEA4	150843733	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-0.830000	0.04410	-0.905000	0.03871	-0.915000	0.02750	GAA	.	.		0.572	MAGEA4-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060898.1	NM_002362	
CNOT4	4850	hgsc.bcm.edu	37	7	135122994	135122994	+	Frame_Shift_Del	DEL	A	A	-			TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr7:135122994delA	ENST00000315544.5	-	2	365	c.86delT	c.(85-87)ttcfs	p.F29fs	CNOT4_ENST00000541284.1_Frame_Shift_Del_p.F29fs|CNOT4_ENST00000356162.4_Frame_Shift_Del_p.F29fs|CNOT4_ENST00000361528.4_Frame_Shift_Del_p.F29fs|CNOT4_ENST00000414802.1_Frame_Shift_Del_p.F29fs|CNOT4_ENST00000428680.2_Frame_Shift_Del_p.F29fs|CNOT4_ENST00000451834.1_Frame_Shift_Del_p.F29fs|CNOT4_ENST00000423368.2_Frame_Shift_Del_p.F29fs	NM_001190848.1	NP_001177777.1	O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4	29					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|protein autoubiquitination (GO:0051865)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)	22						GGTGCAAGGGAAAAAGTTGAT	0.453																																					p.F29fs	Ovarian(51;766 1130 5502 35047 50875)	Atlas-Indel,Pindel	.											.	CNOT4	146	.	0			c.87delC						.						85.0	81.0	82.0					7																	135122994		1924	4134	6058	SO:0001589	frameshift_variant	4850	exon2			.	AF180475	CCDS43650.1, CCDS47719.1, CCDS55164.1, CCDS55165.1, CCDS55166.1, CCDS55167.1	7q33	2013-09-19			ENSG00000080802	ENSG00000080802		"""RNA binding motif (RRM) containing"""	7880	protein-coding gene	gene with protein product		604911		NOT4		10637334	Standard	NM_013316		Approved	CLONE243, NOT4H	uc011kpy.2	O95628	OTTHUMG00000155568	ENST00000315544.5:c.86delT	chr7.hg19:g.135122994delA	ENSP00000326731:p.Phe29fs	248.0	0.0		221.0	35.0	NM_001190847	B7Z6I4|E7ET38|F8VQP3|O95339|O95627|Q8IYM7|Q8NCL0|Q9NPQ1|Q9NZN6	Frame_Shift_Del	DEL	ENST00000315544.5	hg19	CCDS55166.1																																																																																			.	.		0.453	CNOT4-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_013316	
NCOR1	9611	hgsc.bcm.edu	37	17	15942894	15942923	+	In_Frame_Del	DEL	CCTTCCTGATAATGTCTTCCAGCCCAAGAT	CCTTCCTGATAATGTCTTCCAGCCCAAGAT	-	rs3205089|rs371002943		TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	CCTTCCTGATAATGTCTTCCAGCCCAAGAT	CCTTCCTGATAATGTCTTCCAGCCCAAGAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr17:15942894_15942923delCCTTCCTGATAATGTCTTCCAGCCCAAGAT	ENST00000268712.3	-	44	7036_7065	c.6779_6808delATCTTGGGCTGGAAGACATTATCAGGAAGG	c.(6778-6810)aatcttgggctggaagacattatcaggaaggct>act	p.2260_2270NLGLEDIIRKA>T	AC002553.1_ENST00000442828.1_5'Flank|NCOR1_ENST00000395851.1_In_Frame_Del_p.2157_2167NLGLEDIIRKA>T|NCOR1_ENST00000395857.3_In_Frame_Del_p.844_854NLGLEDIIRKA>T	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	2260	ID2. {ECO:0000250}.|Interaction with C1D. {ECO:0000250}.				CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		CCCATGAGAGCCTTCCTGATAATGTCTTCCAGCCCAAGATTACTGGCAGG	0.457																																					p.2260_2270del		Pindel	.											.	NCOR1	240	.	0			c.6780_6809del						.																																			SO:0001651	inframe_deletion	9611	exon44			.	AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"""thyroid hormone- and retinoic acid receptor-associated corepressor 1"", ""protein phosphatase 1, regulatory subunit 109"""	600849	"""nuclear receptor co-repressor 1"""			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.6779_6808delATCTTGGGCTGGAAGACATTATCAGGAAGG	chr17.hg19:g.15942894_15942923delCCTTCCTGATAATGTCTTCCAGCCCAAGAT	ENSP00000268712:p.Asn2260_Ala2270delinsThr	181.0	0.0		178.0	11.0	NM_006311	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	In_Frame_Del	DEL	ENST00000268712.3	hg19	CCDS11175.1																																																																																			.	.		0.457	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311	
FBXO31	79791	hgsc.bcm.edu	37	16	87376481	87376503	+	Splice_Site	DEL	GCCGGCTGGTGGGCTCACCTCCT	GCCGGCTGGTGGGCTCACCTCCT	-	rs140641305	byFrequency	TCGA-ED-A4XI-01A-11D-A25V-10	TCGA-ED-A4XI-10A-01D-A25V-10	GCCGGCTGGTGGGCTCACCTCCT	GCCGGCTGGTGGGCTCACCTCCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	670f971f-a525-4ef8-91ba-610cfbaeb914	72f5179f-1c32-4e78-8f77-027a5400e7fd	g.chr16:87376481_87376503delGCCGGCTGGTGGGCTCACCTCCT	ENST00000311635.7	-	5	724_745	c.712_733delAGGAGGTGAGCCCACCAGCCGGC	c.(712-735)aggaggtgagcccaccagccggca>ca	p.RR*AHQPA238fs		NM_001282683.1|NM_024735.3	NP_001269612.1|NP_079011.3	Q5XUX0	FBX31_HUMAN	F-box protein 31	238					cellular response to DNA damage stimulus (GO:0006974)|cyclin catabolic process (GO:0008054)|mitotic G1 DNA damage checkpoint (GO:0031571)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)	p.G68G(1)|p.G240G(1)|p.S67S(1)|p.S239S(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)	17				BRCA - Breast invasive adenocarcinoma(80;0.0272)		TGGTGGGCTCACCTCCTGCCTCCCGCCGGACATCCTGTGGTGG	0.561																																					p.243_244del		Pindel	.											.	FBXO31	82	.	4	Substitution - coding silent(4)	endometrium(4)	c.729_732del						.																																			SO:0001630	splice_region_variant	79791	exon5			.	BC002985	CCDS32501.1, CCDS73922.1	16q24	2008-12-18	2004-05-27			ENSG00000103264		"""F-boxes /  ""other"""""	16510	protein-coding gene	gene with protein product		609102	"""F-box only protein 31"""				Standard	NM_024735		Approved	FBX14, FBXO14, Fbx31, MGC15419	uc002fjw.3	Q5XUX0		ENST00000311635.7:c.732+1AGGAGGTGAGCCCACCAGCCGGC>-	chr16.hg19:g.87376481_87376503delGCCGGCTGGTGGGCTCACCTCCT		201.0	0.0		151.0	11.0	NM_024735	Q5K680|Q8WYV1|Q96D73|Q9UFV4	Frame_Shift_Del	DEL	ENST00000311635.7	hg19	CCDS32501.1																																																																																			.	.		0.561	FBXO31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430799.2	NM_024735	Frame_Shift_Del
