#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
ANGPTL7	10218	hgsc.bcm.edu	37	1	11249872	11249872	+	Missense_Mutation	SNP	T	T	C			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr1:11249872T>C	ENST00000376819.3	+	1	475	c.236T>C	c.(235-237)aTg>aCg	p.M79T	MTOR_ENST00000361445.4_Intron	NM_021146.2	NP_066969.1	O43827	ANGL7_HUMAN	angiopoietin-like 7	79					response to oxidative stress (GO:0006979)	extracellular region (GO:0005576)				endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|skin(2)|stomach(1)	10	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.000818)|all_lung(284;0.00105)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;1.39e-06)|COAD - Colon adenocarcinoma(227;0.000244)|BRCA - Breast invasive adenocarcinoma(304;0.000294)|Kidney(185;0.000728)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0487)		AGCGTGGTCATGCAGGTGATG	0.542																																					p.M79T		Atlas-SNP	.											.	ANGPTL7	23	.	0			c.T236C						.						107.0	100.0	103.0					1																	11249872		2203	4300	6503	SO:0001583	missense	10218	exon1			TGGTCATGCAGGT	Y16132	CCDS128.1	1p36	2013-02-06			ENSG00000171819	ENSG00000171819		"""Fibrinogen C domain containing"""	24078	protein-coding gene	gene with protein product						9727400, 11682471	Standard	NM_021146		Approved	CDT6, AngX	uc001ase.4	O43827	OTTHUMG00000002002	ENST00000376819.3:c.236T>C	chr1.hg19:g.11249872T>C	ENSP00000366015:p.Met79Thr	187.0	0.0		178.0	10.0	NM_021146	B2R9B2|F1T0A6|Q4ZGK4	Missense_Mutation	SNP	ENST00000376819.3	hg19	CCDS128.1	.	.	.	.	.	.	.	.	.	.	T	13.15	2.151799	0.38021	.	.	ENSG00000171819	ENST00000376819	T	0.53640	0.61	5.07	5.07	0.68467	.	0.136234	0.64402	D	0.000001	T	0.33818	0.0876	L	0.29908	0.895	0.50313	D	0.999865	B	0.29716	0.255	B	0.24394	0.053	T	0.12760	-1.0535	10	0.14252	T	0.57	.	15.1471	0.72662	0.0:0.0:0.0:1.0	.	79	O43827	ANGL7_HUMAN	T	79	ENSP00000366015:M79T	ENSP00000366015:M79T	M	+	2	0	ANGPTL7	11172459	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.170000	0.58229	2.034000	0.60081	0.533000	0.62120	ATG	.	.		0.542	ANGPTL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005564.1	NM_021146	
RIMKLA	284716	hgsc.bcm.edu	37	1	42880608	42880608	+	Missense_Mutation	SNP	T	T	C			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr1:42880608T>C	ENST00000431473.3	+	5	1268	c.1139T>C	c.(1138-1140)aTt>aCt	p.I380T		NM_173642.3	NP_775913.2	Q8IXN7	RIMKA_HUMAN	ribosomal modification protein rimK-like family member A	380					cellular protein modification process (GO:0006464)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|N-acetyl-L-aspartate-L-glutamate ligase activity (GO:0072590)			NS(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	13						GGCTACAACATTAACAACAGG	0.468																																					p.I380T		Atlas-SNP	.											.	RIMKLA	32	.	0			c.T1139C						.						66.0	76.0	73.0					1																	42880608		2203	4300	6503	SO:0001583	missense	284716	exon5			ACAACATTAACAA	BC039737	CCDS466.2	1p34.2	2011-09-21	2008-10-13	2008-10-13	ENSG00000177181	ENSG00000177181	6.3.2.N6		28725	protein-coding gene	gene with protein product	"""N-acetylaspartylglutamate synthetase II"""		"""family with sequence similarity 80, member A"""	FAM80A		20657015, 21454531	Standard	NM_173642		Approved	MGC47816, RP11-157D18.1, NAAGS-II	uc001chi.2	Q8IXN7	OTTHUMG00000007335	ENST00000431473.3:c.1139T>C	chr1.hg19:g.42880608T>C	ENSP00000414330:p.Ile380Thr	56.0	0.0		53.0	7.0	NM_173642	Q5VUS5	Missense_Mutation	SNP	ENST00000431473.3	hg19	CCDS466.2	.	.	.	.	.	.	.	.	.	.	T	14.61	2.587225	0.46110	.	.	ENSG00000177181	ENST00000431473	.	.	.	5.38	5.38	0.77491	.	0.260843	0.37178	N	0.002217	T	0.39036	0.1063	L	0.34521	1.04	0.42964	D	0.994413	P	0.40144	0.704	B	0.30646	0.118	T	0.46925	-0.9156	9	0.87932	D	0	-11.314	13.3632	0.60667	0.0:0.0:0.0:1.0	.	380	Q8IXN7	RIMKA_HUMAN	T	380	.	ENSP00000414330:I380T	I	+	2	0	RIMKLA	42653195	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.033000	0.57282	2.043000	0.60533	0.459000	0.35465	ATT	.	.		0.468	RIMKLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019174.3	NM_173642	
MAST2	23139	hgsc.bcm.edu	37	1	46500510	46500510	+	Missense_Mutation	SNP	G	G	A			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr1:46500510G>A	ENST00000361297.2	+	29	4452	c.4169G>A	c.(4168-4170)cGg>cAg	p.R1390Q	MAST2_ENST00000372009.2_Missense_Mutation_p.R1200Q	NM_015112.2	NP_055927.2			microtubule associated serine/threonine kinase 2											breast(1)|lung(3)|ovary(5)|stomach(2)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					CAACTCTCACGGCCCAAGAGT	0.617																																					p.R1390Q		Atlas-SNP	.											.	MAST2	136	.	0			c.G4169A						.						88.0	95.0	93.0					1																	46500510		2055	4189	6244	SO:0001583	missense	23139	exon29			TCTCACGGCCCAA	AB047005	CCDS41326.1	1p34.1	2008-02-05			ENSG00000086015	ENSG00000086015			19035	protein-coding gene	gene with protein product		612257					Standard	NM_015112		Approved	MAST205, KIAA0807	uc001cov.3	Q6P0Q8	OTTHUMG00000008007	ENST00000361297.2:c.4169G>A	chr1.hg19:g.46500510G>A	ENSP00000354671:p.Arg1390Gln	115.0	0.0		119.0	27.0	NM_015112		Missense_Mutation	SNP	ENST00000361297.2	hg19	CCDS41326.1	.	.	.	.	.	.	.	.	.	.	g	28.1	4.887568	0.91814	.	.	ENSG00000086015	ENST00000361297;ENST00000372009	T;T	0.51325	0.71;0.71	4.4	4.4	0.53042	.	0.227913	0.32624	N	0.005859	T	0.69287	0.3094	M	0.76574	2.34	0.38821	D	0.955632	D;D	0.89917	1.0;1.0	P;D	0.85130	0.86;0.997	T	0.75986	-0.3124	10	0.87932	D	0	-4.7446	17.5359	0.87830	0.0:0.0:1.0:0.0	.	1200;1390	E7ERL6;Q6P0Q8	.;MAST2_HUMAN	Q	1390;1200	ENSP00000354671:R1390Q;ENSP00000361079:R1200Q	ENSP00000354671:R1390Q	R	+	2	0	MAST2	46273097	1.000000	0.71417	0.821000	0.32701	0.919000	0.55068	9.602000	0.98312	2.431000	0.82371	0.558000	0.71614	CGG	.	.		0.617	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112	
MIER1	57708	hgsc.bcm.edu	37	1	67423897	67423897	+	Missense_Mutation	SNP	A	A	C			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr1:67423897A>C	ENST00000355356.3	+	4	485	c.336A>C	c.(334-336)gaA>gaC	p.E112D	MIER1_ENST00000371014.1_Missense_Mutation_p.E165D|MIER1_ENST00000479067.1_3'UTR|MIER1_ENST00000371018.3_Missense_Mutation_p.E129D|MIER1_ENST00000357692.2_Missense_Mutation_p.E129D|MIER1_ENST00000371016.1_Missense_Mutation_p.E129D|MIER1_ENST00000355977.6_Missense_Mutation_p.E49D|MIER1_ENST00000401042.3_Missense_Mutation_p.E112D|MIER1_ENST00000401041.1_Missense_Mutation_p.E165D	NM_001077701.2|NM_001077704.2	NP_001071169.1|NP_001071172.1	Q8N108	MIER1_HUMAN	mesoderm induction early response 1, transcriptional regulator	112	Glu-rich.				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						GTAGTGGGGAAAATAAAGTAA	0.313																																					p.E165D		Atlas-SNP	.											.	MIER1	86	.	0			c.A495C						.						94.0	95.0	95.0					1																	67423897		1936	4141	6077	SO:0001583	missense	57708	exon5			TGGGGAAAATAAA		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.336A>C	chr1.hg19:g.67423897A>C	ENSP00000347514:p.Glu112Asp	98.0	0.0		97.0	21.0	NM_001077700	C9JFD4|Q08AE0|Q32NC4|Q5T104|Q5TAD1|Q5TAD2|Q5TAD4|Q5TAD5|Q6AHY8|Q86TB4|Q8N156|Q8N161|Q8NC37|Q8NES4|Q8NES5|Q8NES6|Q8WWG2|Q9HCG2	Missense_Mutation	SNP	ENST00000355356.3	hg19	CCDS41348.1	.	.	.	.	.	.	.	.	.	.	A	13.57	2.277692	0.40294	.	.	ENSG00000198160	ENST00000371017;ENST00000371018;ENST00000355977;ENST00000357692;ENST00000401041;ENST00000371016;ENST00000371014;ENST00000401042;ENST00000355356	T;T;T;T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96;0.96;0.96;0.96	5.25	4.13	0.48395	.	0.000000	0.64402	D	0.000008	T	0.26593	0.0650	L	0.42245	1.32	0.43275	D	0.995235	B;B;B;P;P;B;B;B;P	0.45044	0.013;0.034;0.046;0.849;0.765;0.067;0.046;0.114;0.788	B;B;B;P;B;B;B;B;B	0.47705	0.006;0.01;0.028;0.555;0.352;0.018;0.028;0.034;0.225	T	0.02610	-1.1134	10	0.30078	T	0.28	-41.7233	10.9968	0.47580	0.9266:0.0:0.0734:0.0	.	129;129;112;112;49;136;129;165;165	Q5TAD2;Q32NC4;Q8N108-3;Q8N108-6;Q08AE0;Q8N108;Q8N108-10;Q5TAD5;Q5TAD4	.;.;.;.;.;MIER1_HUMAN;.;.;.	D	133;129;49;129;165;129;165;112;112	ENSP00000360057:E129D;ENSP00000348253:E49D;ENSP00000350321:E129D;ENSP00000383820:E165D;ENSP00000360055:E129D;ENSP00000360053:E165D;ENSP00000383821:E112D;ENSP00000347514:E112D	ENSP00000347514:E112D	E	+	3	2	MIER1	67196485	1.000000	0.71417	1.000000	0.80357	0.864000	0.49448	6.212000	0.72188	0.954000	0.37851	0.383000	0.25322	GAA	.	.		0.313	MIER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025491.2	NM_020948	
COL11A1	1301	hgsc.bcm.edu	37	1	103387110	103387110	+	Silent	SNP	T	T	A			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr1:103387110T>A	ENST00000370096.3	-	48	3984	c.3672A>T	c.(3670-3672)ccA>ccT	p.P1224P	COL11A1_ENST00000358392.2_Silent_p.P1236P|COL11A1_ENST00000512756.1_Silent_p.P1108P|COL11A1_ENST00000353414.4_Silent_p.P1185P	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	1224	Triple-helical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		CTCTTGGGCCTGGAGGACCAG	0.358																																					p.P1236P		Atlas-SNP	.											.	COL11A1	972	.	0			c.A3708T						.						71.0	84.0	80.0					1																	103387110		2203	4300	6503	SO:0001819	synonymous_variant	1301	exon48			TGGGCCTGGAGGA	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"""Collagens"""	2186	protein-coding gene	gene with protein product	"""collagen XI, alpha-1 polypeptide"""	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.3672A>T	chr1.hg19:g.103387110T>A		917.0	0.0		1076.0	94.0	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Silent	SNP	ENST00000370096.3	hg19	CCDS778.1																																																																																			.	.		0.358	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630	
FBXO28	23219	hgsc.bcm.edu	37	1	224345064	224345064	+	Silent	SNP	G	G	A	rs201209850	byFrequency	TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr1:224345064G>A	ENST00000366862.5	+	5	766	c.723G>A	c.(721-723)ccG>ccA	p.P241P	FBXO28_ENST00000424254.2_Missense_Mutation_p.R176H	NM_015176.3	NP_055991.1	Q9NVF7	FBX28_HUMAN	F-box protein 28	241										endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|ovary(2)|skin(1)	10	Breast(184;0.206)			GBM - Glioblastoma multiforme(131;0.0363)		TTCCAGGACCGTCTGCAGCCC	0.418													G|||	3	0.000599042	0.0	0.0	5008	,	,		18746	0.0		0.0	False		,,,				2504	0.0031				p.R176H		Atlas-SNP	.											.	FBXO28	34	.	0			c.G527A						.	G	HIS/ARG,	0,4406		0,0,2203	107.0	107.0	107.0		527,723	-6.0	0.8	1		107	1,8599	1.2+/-3.3	0,1,4299	no	missense,coding-synonymous	FBXO28	NM_001136115.1,NM_015176.2	29,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	176/180,241/369	224345064	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	23219	exon4			AGGACCGTCTGCA	AK001628	CCDS1539.1, CCDS44320.1	1q42.12	2011-08-12			ENSG00000143756	ENSG00000143756		"""F-boxes /  ""other"""""	29046	protein-coding gene	gene with protein product	"""centromere protein 30"""	609100				9455484	Standard	NM_015176		Approved	FLJ10766, KIAA0483, Fbx28, CENP-30	uc001hoh.3	Q9NVF7	OTTHUMG00000037495	ENST00000366862.5:c.723G>A	chr1.hg19:g.224345064G>A		131.0	0.0		169.0	12.0	NM_001136115	E9PEM8|O75070	Missense_Mutation	SNP	ENST00000366862.5	hg19	CCDS1539.1	.	.	.	.	.	.	.	.	.	.	G	11.39	1.624414	0.28889	0.0	1.16E-4	ENSG00000143756	ENST00000424254	.	.	.	6.17	-6.01	0.02199	.	.	.	.	.	T	0.24547	0.0595	.	.	.	0.09310	N	0.999997	B	0.02656	0.0	B	0.01281	0.0	T	0.28106	-1.0054	7	0.87932	D	0	-9.0138	3.0686	0.06222	0.1404:0.2011:0.4336:0.2249	.	176	E9PEM8	.	H	176	.	ENSP00000416888:R176H	R	+	2	0	FBXO28	222411687	0.017000	0.18338	0.786000	0.31890	0.973000	0.67179	-1.043000	0.03535	-1.467000	0.01895	-1.140000	0.01884	CGT	.	G|0.999;A|0.001		0.418	FBXO28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091283.2	NM_015176	
FSHR	2492	hgsc.bcm.edu	37	2	49210076	49210076	+	Missense_Mutation	SNP	G	G	A			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr2:49210076G>A	ENST00000406846.2	-	8	762	c.643C>T	c.(643-645)Cac>Tac	p.H215Y	FSHR_ENST00000541117.1_5'UTR|FSHR_ENST00000346173.3_Missense_Mutation_p.H215Y|FSHR_ENST00000469138.1_5'UTR|FSHR_ENST00000304421.4_Missense_Mutation_p.H189Y	NM_000145.3	NP_000136.2	P23945	FSHR_HUMAN	follicle stimulating hormone receptor	215					female gamete generation (GO:0007292)|female gonad development (GO:0008585)|follicle-stimulating hormone signaling pathway (GO:0042699)|G-protein coupled receptor signaling pathway (GO:0007186)|gonad development (GO:0008406)|male gonad development (GO:0008584)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	follicle-stimulating hormone receptor activity (GO:0004963)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|liver(1)|lung(45)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	73		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Suramin(DB04786)|Urofollitropin(DB00094)	GAGGCTCCGTGGAAAACATCA	0.418									Gonadal Dysgenesis, 46 XX																												p.H215Y		Atlas-SNP	.											.	FSHR	164	.	0			c.C643T						.						98.0	95.0	96.0					2																	49210076		2203	4300	6503	SO:0001583	missense	2492	exon8	Familial Cancer Database		CTCCGTGGAAAAC		CCDS1843.1, CCDS1844.1, CCDS1844.2	2p21-p16	2014-09-17			ENSG00000170820	ENSG00000170820		"""GPCR / Class A : Gonadotropin and TSH receptors"""	3969	protein-coding gene	gene with protein product		136435		ODG1		8230163, 8855829	Standard	NM_000145		Approved	FSHRO, LGR1	uc002rww.3	P23945	OTTHUMG00000129259	ENST00000406846.2:c.643C>T	chr2.hg19:g.49210076G>A	ENSP00000384708:p.His215Tyr	272.0	0.0		268.0	57.0	NM_000145	A8K947|G5CBS7|G5E967|J3KQ00|Q05AH0|Q16225|Q4QRJ3|Q4ZFZ2|Q53RW2	Missense_Mutation	SNP	ENST00000406846.2	hg19	CCDS1843.1	.	.	.	.	.	.	.	.	.	.	G	3.548	-0.092336	0.07053	.	.	ENSG00000170820	ENST00000406846;ENST00000346173;ENST00000304421;ENST00000454032	T;D;T;D	0.90788	0.39;-2.73;0.39;-2.73	5.38	4.49	0.54785	.	0.669321	0.15520	N	0.258061	D	0.85057	0.5610	N	0.22421	0.69	0.80722	D	1	B;B;P	0.35401	0.355;0.103;0.499	B;B;B	0.38985	0.287;0.05;0.183	T	0.81077	-0.1096	9	.	.	.	.	13.127	0.59360	0.0:0.0:0.8404:0.1596	.	189;215;215	Q05AH0;G5E967;P23945	.;.;FSHR_HUMAN	Y	215;215;189;215	ENSP00000384708:H215Y;ENSP00000333908:H215Y;ENSP00000306780:H189Y;ENSP00000415504:H215Y	.	H	-	1	0	FSHR	49063580	1.000000	0.71417	0.987000	0.45799	0.920000	0.55202	3.606000	0.54095	1.490000	0.48466	0.655000	0.94253	CAC	.	.		0.418	FSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251367.2		
EIF2AK3	9451	hgsc.bcm.edu	37	2	88857341	88857341	+	Silent	SNP	G	G	A			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr2:88857341G>A	ENST00000303236.3	-	17	3565	c.3264C>T	c.(3262-3264)ctC>ctT	p.L1088L	AC104134.2_ENST00000413234.1_RNA|EIF2AK3_ENST00000419748.1_Silent_p.L937L	NM_004836.5	NP_004827.4	Q9NZJ5	E2AK3_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 3	1088					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|bone mineralization (GO:0030282)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|chondrocyte development (GO:0002063)|endocrine pancreas development (GO:0031018)|endoplasmic reticulum organization (GO:0007029)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|fat cell differentiation (GO:0045444)|insulin secretion (GO:0030073)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|lactation (GO:0007595)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|negative regulation of myelination (GO:0031642)|negative regulation of translation (GO:0017148)|negative regulation of translational initiation in response to stress (GO:0032057)|ossification (GO:0001503)|positive regulation of protein binding (GO:0032092)|positive regulation of signal transduction (GO:0009967)|protein autophosphorylation (GO:0046777)|protein homooligomerization (GO:0051260)|protein phosphorylation (GO:0006468)|regulation of fatty acid metabolic process (GO:0019217)|response to endoplasmic reticulum stress (GO:0034976)|skeletal system development (GO:0001501)|SREBP signaling pathway (GO:0032933)|translation (GO:0006412)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)			ovary(3)	3						ACCTCTGTCTGAGCACTGTTT	0.453																																					p.L1088L	GBM(138;671 1851 16235 39058 45249)	Atlas-SNP	.											EIF2AK3_ENST00000303236,NS,carcinoma,0,2	EIF2AK3	160	.	0			c.C3264T						.						257.0	243.0	248.0					2																	88857341		2203	4300	6503	SO:0001819	synonymous_variant	9451	exon17			CTGTCTGAGCACT	AF110146	CCDS33241.1	2p12	2008-05-21			ENSG00000172071	ENSG00000172071			3255	protein-coding gene	gene with protein product		604032				10026192, 10575235	Standard	NM_004836		Approved	PEK, PERK	uc002stc.4	Q9NZJ5	OTTHUMG00000155046	ENST00000303236.3:c.3264C>T	chr2.hg19:g.88857341G>A		182.0	0.0		158.0	35.0	NM_004836	A0AVH1|A0AVH2|B2RCU9|O95846|Q53QY0|Q53SB1	Silent	SNP	ENST00000303236.3	hg19	CCDS33241.1																																																																																			.	.		0.453	EIF2AK3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000338233.2	NM_004836	
LRP1B	53353	hgsc.bcm.edu	37	2	141526828	141526828	+	Missense_Mutation	SNP	C	C	A			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr2:141526828C>A	ENST00000389484.3	-	35	6683	c.5712G>T	c.(5710-5712)atG>atT	p.M1904I		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1904					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CTGATATAGGCATCAAAGCAT	0.353										TSP Lung(27;0.18)																											p.M1904I	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.G5712T						.						87.0	87.0	87.0					2																	141526828		2203	4300	6503	SO:0001583	missense	53353	exon35			TATAGGCATCAAA	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.5712G>T	chr2.hg19:g.141526828C>A	ENSP00000374135:p.Met1904Ile	107.0	0.0		105.0	27.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	19.82	3.897607	0.72639	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.90676	-2.71	5.59	5.59	0.84812	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	T	0.81494	0.4834	N	0.11023	0.085	0.80722	D	1	P	0.39831	0.69	B	0.36666	0.23	T	0.80448	-0.1378	10	0.11485	T	0.65	.	19.5947	0.95530	0.0:1.0:0.0:0.0	.	1904	Q9NZR2	LRP1B_HUMAN	I	1904;1842	ENSP00000374135:M1904I	ENSP00000374135:M1904I	M	-	3	0	LRP1B	141243298	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.640000	0.83355	2.636000	0.89361	0.655000	0.94253	ATG	.	.		0.353	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
MYO3B	140469	hgsc.bcm.edu	37	2	171355106	171355106	+	Missense_Mutation	SNP	T	T	C			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr2:171355106T>C	ENST00000408978.4	+	26	3162	c.3019T>C	c.(3019-3021)Tat>Cat	p.Y1007H	MYO3B_ENST00000602629.1_Intron|MYO3B_ENST00000334231.6_Missense_Mutation_p.Y1016H|MYO3B_ENST00000409044.3_Missense_Mutation_p.Y1007H	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	1007	Myosin motor.				peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						TTGCAGGTATTATTACTTGGC	0.393																																					p.Y1007H		Atlas-SNP	.											.	MYO3B	320	.	0			c.T3019C						.						110.0	102.0	105.0					2																	171355106		1839	4088	5927	SO:0001583	missense	140469	exon26			AGGTATTATTACT		CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909		"""Myosins / Myosin superfamily : Class III"""	15576	protein-coding gene	gene with protein product		610040					Standard	NM_001083615		Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.3019T>C	chr2.hg19:g.171355106T>C	ENSP00000386213:p.Tyr1007His	81.0	0.0		64.0	4.0	NM_001083615	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Missense_Mutation	SNP	ENST00000408978.4	hg19	CCDS42773.1	.	.	.	.	.	.	.	.	.	.	T	12.28	1.889567	0.33348	.	.	ENSG00000071909	ENST00000409044;ENST00000408978;ENST00000317915;ENST00000484338;ENST00000334231	D;D;D;D	0.87179	-2.22;-2.22;-2.22;-2.22	5.66	5.66	0.87406	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.85182	0.5638	L	0.35249	1.045	0.52501	D	0.999952	B;B;B	0.27932	0.02;0.194;0.107	B;B;B	0.39531	0.033;0.159;0.302	T	0.82267	-0.0542	10	0.35671	T	0.21	.	16.1831	0.81925	0.0:0.0:0.0:1.0	.	1007;1007;1007	Q8WXR4-5;Q8WXR4-4;Q8WXR4	.;.;MYO3B_HUMAN	H	1007;1007;1006;1016;1016	ENSP00000386497:Y1007H;ENSP00000386213:Y1007H;ENSP00000446237:Y1016H;ENSP00000335100:Y1016H	ENSP00000314213:Y1006H	Y	+	1	0	MYO3B	171063352	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	5.579000	0.67457	2.285000	0.76669	0.482000	0.46254	TAT	.	.		0.393	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1		
FGD5	152273	hgsc.bcm.edu	37	3	14939057	14939057	+	Missense_Mutation	SNP	C	C	A			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr3:14939057C>A	ENST00000285046.5	+	5	2900	c.2790C>A	c.(2788-2790)gaC>gaA	p.D930E	FGD5_ENST00000543601.1_Missense_Mutation_p.D689E|FGD5_ENST00000476851.1_3'UTR	NM_152536.3	NP_689749.3	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	930	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			NS(2)|breast(2)|endometrium(3)|kidney(5)|large_intestine(10)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(1)	54						ATGACATGGACCATGAAGGCA	0.552																																					p.D930E		Atlas-SNP	.											.	FGD5	248	.	0			c.C2790A						.						67.0	64.0	65.0					3																	14939057		1987	4176	6163	SO:0001583	missense	152273	exon5			CATGGACCATGAA	AK097276	CCDS46767.1	3p25.1	2013-01-10			ENSG00000154783	ENSG00000154783		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	19117	protein-coding gene	gene with protein product		614788					Standard	NM_152536		Approved	ZFYVE23, FLJ39957, FLJ00274	uc003bzc.3	Q6ZNL6	OTTHUMG00000155556	ENST00000285046.5:c.2790C>A	chr3.hg19:g.14939057C>A	ENSP00000285046:p.Asp930Glu	182.0	0.0		156.0	43.0	NM_152536	B3KVQ3|Q6MZY1|Q7Z303|Q8IYP3|Q8N861|Q8N8G4	Missense_Mutation	SNP	ENST00000285046.5	hg19	CCDS46767.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.177|0.177	-1.066289|-1.066289	0.01934|0.01934	.|.	.|.	ENSG00000154783|ENSG00000154783	ENST00000285046;ENST00000543601|ENST00000457774	T;T|.	0.73363|.	-0.74;-0.58|.	4.96|4.96	0.67|0.67	0.17923|0.17923	Dbl homology (DH) domain (5);|.	0.584200|.	0.15967|.	N|.	0.235992|.	T|T	0.14141|0.14141	0.0342|0.0342	N|N	0.04880|0.04880	-0.145|-0.145	0.09310|0.09310	N|N	1|1	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.06405|.	0.0;0.002|.	T|T	0.25363|0.25363	-1.0134|-1.0134	10|5	0.06099|.	T|.	0.92|.	-21.2749|-21.2749	3.9498|3.9498	0.09364|0.09364	0.1448:0.4823:0.279:0.0938|0.1448:0.4823:0.279:0.0938	.|.	689;930|.	B7ZM68;Q6ZNL6|.	.;FGD5_HUMAN|.	E|T	930;689|114	ENSP00000285046:D930E;ENSP00000445949:D689E|.	ENSP00000285046:D930E|.	D|P	+|+	3|1	2|0	FGD5|FGD5	14914061|14914061	0.989000|0.989000	0.36119|0.36119	0.200000|0.200000	0.23457|0.23457	0.651000|0.651000	0.38670|0.38670	0.285000|0.285000	0.18883|0.18883	0.444000|0.444000	0.26612|0.26612	0.591000|0.591000	0.81541|0.81541	GAC|CCA	.	.		0.552	FGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340628.1	NM_152536	
SCN5A	6331	hgsc.bcm.edu	37	3	38640520	38640520	+	Missense_Mutation	SNP	C	C	T			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr3:38640520C>T	ENST00000333535.4	-	13	2061	c.1912G>A	c.(1912-1914)Ggc>Agc	p.G638S	SCN5A_ENST00000443581.1_Missense_Mutation_p.G638S|SCN5A_ENST00000450102.2_Missense_Mutation_p.G638S|SCN5A_ENST00000449557.2_Missense_Mutation_p.G638S|SCN5A_ENST00000451551.2_Missense_Mutation_p.G638S|SCN5A_ENST00000413689.1_Missense_Mutation_p.G638S|SCN5A_ENST00000423572.2_Missense_Mutation_p.G638S|SCN5A_ENST00000455624.2_Missense_Mutation_p.G638S|SCN5A_ENST00000425664.1_Missense_Mutation_p.G638S|SCN5A_ENST00000414099.2_Missense_Mutation_p.G638S			Q14524	SCN5A_HUMAN	sodium channel, voltage-gated, type V, alpha subunit	638					AV node cell to bundle of His cell communication (GO:0086067)|brainstem development (GO:0003360)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|cardiac ventricle development (GO:0003231)|cellular response to calcium ion (GO:0071277)|cerebellum development (GO:0021549)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane depolarization during SA node cell action potential (GO:0086046)|neuronal action potential (GO:0019228)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of action potential (GO:0045760)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of sodium ion transport (GO:0010765)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|telencephalon development (GO:0021537)|ventricular cardiac muscle cell action potential (GO:0086005)	caveola (GO:0005901)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	ankyrin binding (GO:0030506)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|fibroblast growth factor binding (GO:0017134)|ion channel binding (GO:0044325)|nitric-oxide synthase binding (GO:0050998)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)			NS(3)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|lung(27)|ovary(6)|pancreas(3)|prostate(10)|skin(9)|upper_aerodigestive_tract(4)	107	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Ajmaline(DB01426)|Aprindine(DB01429)|Benzonatate(DB00868)|Carbamazepine(DB00564)|Cinchocaine(DB00527)|Cocaine(DB00907)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lidocaine(DB00281)|Mexiletine(DB00379)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine barbiturate(DB01346)|Quinidine(DB00908)|Ranolazine(DB00243)|Riluzole(DB00740)|Tocainide(DB01056)|Valproic Acid(DB00313)|Verapamil(DB00661)|Zonisamide(DB00909)	TGGGGCCCGCCTGGCTCCTCC	0.662																																					p.G638S		Atlas-SNP	.											.	SCN5A	634	.	0			c.G1912A						.						23.0	28.0	26.0					3																	38640520		2141	4247	6388	SO:0001583	missense	6331	exon13			GCCCGCCTGGCTC	AJ310893	CCDS46796.1, CCDS46797.1, CCDS46798.1, CCDS46799.1, CCDS54569.1, CCDS54570.1	3p21	2014-09-17	2007-01-23		ENSG00000183873	ENSG00000183873		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10593	protein-coding gene	gene with protein product	"""long QT syndrome 3"""	600163	"""sodium channel, voltage-gated, type V, alpha (long QT syndrome 3)"""	CMD1E		7842012, 15466643, 16382098	Standard	NM_198056		Approved	Nav1.5, LQT3, HB1, HBBD, PFHB1, IVF, HB2, HH1, SSS1, CDCD2, CMPD2, ICCD	uc021wvl.1	Q14524	OTTHUMG00000156166	ENST00000333535.4:c.1912G>A	chr3.hg19:g.38640520C>T	ENSP00000328968:p.Gly638Ser	89.0	0.0		97.0	20.0	NM_001160160	A5H1P8|A6N922|A6N923|B2RTU0|E7ET19|E9PEF3|E9PEK2|E9PFW7|Q59H93|Q75RX9|Q75RY0|Q86UR3|Q8IZC9|Q96J69	Missense_Mutation	SNP	ENST00000333535.4	hg19	CCDS46796.1	.	.	.	.	.	.	.	.	.	.	C	14.23	2.472782	0.43942	.	.	ENSG00000183873	ENST00000414099;ENST00000423572;ENST00000413689;ENST00000451551;ENST00000443581;ENST00000425664;ENST00000333535;ENST00000455624;ENST00000450102;ENST00000449557	D;D;D;D;D;D;D;D;D;D	0.90444	-2.67;-2.67;-2.67;-2.67;-2.67;-2.67;-2.67;-2.67;-2.67;-2.67	3.55	2.65	0.31530	Domain of unknown function DUF3451 (1);	0.520160	0.18714	N	0.133205	T	0.77565	0.4149	N	0.16307	0.4	0.31810	N	0.627219	B;B;B;B;B;B;B	0.18013	0.001;0.025;0.019;0.024;0.011;0.006;0.009	B;B;B;B;B;B;B	0.19666	0.006;0.026;0.013;0.022;0.013;0.007;0.007	T	0.67515	-0.5651	10	0.14252	T	0.57	.	3.4381	0.07453	0.0:0.593:0.0:0.407	.	638;638;638;638;638;638;638	E9PEF3;E9PHB6;Q14524-6;E9PG18;Q14524;Q14524-2;E9PEK2	.;.;.;.;SCN5A_HUMAN;.;.	S	638	ENSP00000398962:G638S;ENSP00000398266:G638S;ENSP00000410257:G638S;ENSP00000388797:G638S;ENSP00000397915:G638S;ENSP00000416634:G638S;ENSP00000328968:G638S;ENSP00000399524:G638S;ENSP00000403355:G638S;ENSP00000413996:G638S	ENSP00000328968:G638S	G	-	1	0	SCN5A	38615524	0.983000	0.35010	1.000000	0.80357	0.884000	0.51177	1.951000	0.40333	1.989000	0.58080	0.561000	0.74099	GGC	.	.		0.662	SCN5A-014	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377958.1	NM_198056	
CCK	885	hgsc.bcm.edu	37	3	42299622	42299622	+	Missense_Mutation	SNP	G	G	A	rs533678433		TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr3:42299622G>A	ENST00000396169.2	-	5	1221	c.316C>T	c.(316-318)Cgc>Tgc	p.R106C	CCK_ENST00000434608.1_Missense_Mutation_p.R106C|CCK_ENST00000334681.5_Missense_Mutation_p.R106C	NM_000729.4	NP_000720.1	P06307	CCKN_HUMAN	cholecystokinin	106					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axonogenesis (GO:0007409)|behavioral fear response (GO:0001662)|eating behavior (GO:0042755)|negative regulation of appetite (GO:0032099)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein oligomerization (GO:0032461)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|release of cytochrome c from mitochondria (GO:0001836)|signal transduction (GO:0007165)	axon (GO:0030424)|axon hillock (GO:0043203)|axon initial segment (GO:0043194)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|perikaryon (GO:0043204)|terminal bouton (GO:0043195)	hormone activity (GO:0005179)|neuropeptide hormone activity (GO:0005184)			central_nervous_system(1)|large_intestine(1)|lung(3)|skin(1)	6		Ovarian(412;0.0728)		KIRC - Kidney renal clear cell carcinoma(284;0.219)		TCGGCACTGCGACGGCCAAAA	0.562													G|||	1	0.000199681	0.0	0.0	5008	,	,		17782	0.0		0.001	False		,,,				2504	0.0				p.R106C		Atlas-SNP	.											CCK,colon,carcinoma,0,1	CCK	15	.	0			c.C316T						.						116.0	102.0	107.0					3																	42299622		2203	4300	6503	SO:0001583	missense	885	exon5			CACTGCGACGGCC		CCDS2696.1	3p22.1	2013-02-25			ENSG00000187094	ENSG00000187094		"""Endogenous ligands"""	1569	protein-coding gene	gene with protein product	"""prepro-cholecystokinin"", ""cholecystokinin triacontatriapeptide"""	118440				3856870	Standard	NM_001174138		Approved		uc021wwk.1	P06307	OTTHUMG00000131796	ENST00000396169.2:c.316C>T	chr3.hg19:g.42299622G>A	ENSP00000379472:p.Arg106Cys	138.0	0.0		139.0	18.0	NM_000729		Missense_Mutation	SNP	ENST00000396169.2	hg19	CCDS2696.1	.	.	.	.	.	.	.	.	.	.	G	33	5.260448	0.95368	.	.	ENSG00000187094	ENST00000396169;ENST00000334681;ENST00000434608	T;T;T	0.68765	-0.35;-0.35;-0.35	5.7	5.7	0.88788	Gastrin/cholecystokinin peptide hormone (2);	0.099413	0.64402	D	0.000001	D	0.85396	0.5687	M	0.88450	2.955	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87529	0.2451	10	0.87932	D	0	-23.505	18.8882	0.92388	0.0:0.0:1.0:0.0	.	106	P06307	CCKN_HUMAN	C	106	ENSP00000379472:R106C;ENSP00000335657:R106C;ENSP00000409124:R106C	ENSP00000335657:R106C	R	-	1	0	CCK	42274626	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.471000	0.97696	2.698000	0.92095	0.650000	0.86243	CGC	.	.		0.562	CCK-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343380.1	NM_000729	
DAG1	1605	hgsc.bcm.edu	37	3	49568955	49568955	+	Missense_Mutation	SNP	G	G	T			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr3:49568955G>T	ENST00000539901.1	+	3	1569	c.1011G>T	c.(1009-1011)agG>agT	p.R337S	DAG1_ENST00000538711.1_Missense_Mutation_p.R337S|DAG1_ENST00000541308.1_Missense_Mutation_p.R337S|DAG1_ENST00000515359.2_Missense_Mutation_p.R337S|DAG1_ENST00000545947.1_Missense_Mutation_p.R337S|DAG1_ENST00000308775.2_Missense_Mutation_p.R337S	NM_001177644.2	NP_001171115	Q14118	DAG1_HUMAN	dystroglycan 1 (dystrophin-associated glycoprotein 1)	337	Mucin-like domain.|Required for laminin recognition.|Thr-rich.				basement membrane organization (GO:0071711)|branching involved in salivary gland morphogenesis (GO:0060445)|calcium-dependent cell-matrix adhesion (GO:0016340)|commissural neuron axon guidance (GO:0071679)|cytoskeletal anchoring at plasma membrane (GO:0007016)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|extracellular matrix organization (GO:0030198)|membrane protein ectodomain proteolysis (GO:0006509)|microtubule anchoring (GO:0034453)|modulation by virus of host morphology or physiology (GO:0019048)|morphogenesis of an epithelial sheet (GO:0002011)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell migration (GO:0030336)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase B signaling (GO:0051898)|nerve maturation (GO:0021682)|NLS-bearing protein import into nucleus (GO:0006607)|response to peptide hormone (GO:0043434)	basement membrane (GO:0005604)|basolateral plasma membrane (GO:0016323)|cell outer membrane (GO:0009279)|cell-cell adherens junction (GO:0005913)|contractile ring (GO:0070938)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystroglycan complex (GO:0016011)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|node of Ranvier (GO:0033268)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|alpha-actinin binding (GO:0051393)|calcium ion binding (GO:0005509)|laminin-1 binding (GO:0043237)|SH2 domain binding (GO:0042169)|structural constituent of muscle (GO:0008307)|tubulin binding (GO:0015631)|vinculin binding (GO:0017166)|virus receptor activity (GO:0001618)			NS(1)|autonomic_ganglia(2)|breast(2)|endometrium(1)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)|skin(1)	23				BRCA - Breast invasive adenocarcinoma(193;5.13e-05)|Kidney(197;0.00241)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		CCCCATCCAGGATCGTGCCAA	0.617																																					p.R337S		Atlas-SNP	.											.	DAG1	60	.	0			c.G1011T						.						76.0	76.0	76.0					3																	49568955		2203	4300	6503	SO:0001583	missense	1605	exon4			ATCCAGGATCGTG	L19711	CCDS2799.1	3p21	2014-09-17			ENSG00000173402	ENSG00000173402			2666	protein-coding gene	gene with protein product	"""alpha-dystroglycan"", ""dystrophin-associated glycoprotein-1"", ""beta-dystroglycan"""	128239				7774920, 1741056	Standard	NM_001177643		Approved	A3a, 156DAG, AGRNR, DAG	uc021wyd.1	Q14118	OTTHUMG00000156869	ENST00000539901.1:c.1011G>T	chr3.hg19:g.49568955G>T	ENSP00000439334:p.Arg337Ser	79.0	0.0		61.0	10.0	NM_001177642	A8K6M7|Q969J9	Missense_Mutation	SNP	ENST00000539901.1	hg19	CCDS2799.1	.	.	.	.	.	.	.	.	.	.	G	15.18	2.758102	0.49468	.	.	ENSG00000173402	ENST00000515359;ENST00000308775;ENST00000545947;ENST00000541308;ENST00000539901;ENST00000538711	T;T;T;T;T;T	0.49720	0.77;0.77;0.77;0.77;0.77;0.77	5.74	1.42	0.22433	.	0.000000	0.85682	D	0.000000	T	0.60064	0.2240	M	0.67953	2.075	0.50313	D	0.999867	D	0.64830	0.994	D	0.75020	0.985	T	0.57423	-0.7814	9	.	.	.	-25.1431	8.5001	0.33152	0.4539:0.0:0.5461:0.0	.	337	Q14118	DAG1_HUMAN	S	337	ENSP00000440705:R337S;ENSP00000312435:R337S;ENSP00000442600:R337S;ENSP00000440590:R337S;ENSP00000439334:R337S;ENSP00000438421:R337S	.	R	+	3	2	DAG1	49543959	0.948000	0.32251	0.997000	0.53966	0.974000	0.67602	0.070000	0.14573	0.555000	0.29079	0.655000	0.94253	AGG	.	.		0.617	DAG1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346326.1		
ITIH1	3697	hgsc.bcm.edu	37	3	52824803	52824803	+	Missense_Mutation	SNP	T	T	C			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr3:52824803T>C	ENST00000273283.2	+	20	2384	c.2360T>C	c.(2359-2361)gTg>gCg	p.V787A	ITIH1_ENST00000540715.1_Missense_Mutation_p.V645A|ITIH1_ENST00000537050.1_Missense_Mutation_p.V499A|ITIH1_ENST00000405128.3_Missense_Mutation_p.V153A|ITIH1_ENST00000542827.1_3'UTR	NM_002215.3	NP_002206.2	P19827	ITIH1_HUMAN	inter-alpha-trypsin inhibitor heavy chain 1	787	Hyaluronan-binding.				hyaluronan metabolic process (GO:0030212)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(16)|lung(18)|ovary(4)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	52				BRCA - Breast invasive adenocarcinoma(193;7.04e-05)|Kidney(197;0.000659)|KIRC - Kidney renal clear cell carcinoma(197;0.000795)|OV - Ovarian serous cystadenocarcinoma(275;0.0498)		AACCTGGTGGTGTCTGTGGAC	0.597																																					p.V787A		Atlas-SNP	.											.	ITIH1	108	.	0			c.T2360C						.						187.0	154.0	165.0					3																	52824803		2203	4300	6503	SO:0001583	missense	3697	exon20			TGGTGGTGTCTGT		CCDS2864.1, CCDS54595.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055957	ENSG00000055957			6166	protein-coding gene	gene with protein product		147270	"""inter-alpha (globulin) inhibitor, H1 polypeptide"""			1385302, 10100603	Standard	NM_002215		Approved	H1P, IATIH, ITIH	uc003dfs.3	P19827	OTTHUMG00000150312	ENST00000273283.2:c.2360T>C	chr3.hg19:g.52824803T>C	ENSP00000273283:p.Val787Ala	108.0	0.0		108.0	14.0	NM_002215	A8K9N5|B2RAH9|B7Z558|B7Z8C0|F5H165|F5H7Y8|P78455|Q01746|Q562G1	Missense_Mutation	SNP	ENST00000273283.2	hg19	CCDS2864.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.106103	0.77096	.	.	ENSG00000055957	ENST00000273283;ENST00000540715;ENST00000537050;ENST00000428133;ENST00000405128	T;T;T;T;T	0.20200	2.09;2.09;2.09;2.09;2.09	5.75	5.75	0.90469	Inter-alpha-trypsin inhibitor heavy chain, C-terminal (1);	0.204155	0.41294	D	0.000906	T	0.47488	0.1448	M	0.86502	2.82	0.26781	N	0.9696	B;P;P;P	0.47484	0.402;0.881;0.896;0.881	B;P;P;P	0.56343	0.292;0.723;0.471;0.796	T	0.51849	-0.8653	10	0.59425	D	0.04	-15.6007	14.8895	0.70597	0.0:0.0:0.0:1.0	.	645;153;388;787	F5H165;B5MCP1;Q9P1C5;P19827	.;.;.;ITIH1_HUMAN	A	787;645;499;340;153	ENSP00000273283:V787A;ENSP00000443973:V645A;ENSP00000443847:V499A;ENSP00000395836:V340A;ENSP00000384589:V153A	ENSP00000273283:V787A	V	+	2	0	ITIH1	52799843	1.000000	0.71417	1.000000	0.80357	0.615000	0.37417	2.204000	0.42761	2.195000	0.70347	0.533000	0.62120	GTG	.	.		0.597	ITIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317522.1	NM_002215	
PDZRN3	23024	hgsc.bcm.edu	37	3	73673733	73673733	+	Missense_Mutation	SNP	A	A	G			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr3:73673733A>G	ENST00000263666.4	-	1	358	c.244T>C	c.(244-246)Tgc>Cgc	p.C82R	PDZRN3-AS1_ENST00000608743.1_RNA|PDZRN3-AS1_ENST00000608304.1_RNA|PDZRN3_ENST00000308537.4_Missense_Mutation_p.C82R|PDZRN3-AS1_ENST00000478988.1_RNA	NM_015009.1	NP_055824.1	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	82					neuromuscular junction development (GO:0007528)|protein ubiquitination (GO:0016567)	neuromuscular junction (GO:0031594)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(31)|ovary(4)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		GCGTACGCGCACTTGATGTCC	0.716																																					p.C82R		Atlas-SNP	.											.	PDZRN3	196	.	0			c.T244C						.						9.0	8.0	8.0					3																	73673733		2160	4218	6378	SO:0001583	missense	23024	exon1			ACGCGCACTTGAT	AB029018	CCDS33789.1	3p14.1	2013-01-09	2008-08-14		ENSG00000121440	ENSG00000121440		"""RING-type (C3HC4) zinc fingers"""	17704	protein-coding gene	gene with protein product	"""likely ortholog of mouse semaF cytoplasmic domain associated protein 3"""	609729				10470851	Standard	XM_005264718		Approved	KIAA1095, SEMACAP3, LNX3	uc003dpl.1	Q9UPQ7	OTTHUMG00000158865	ENST00000263666.4:c.244T>C	chr3.hg19:g.73673733A>G	ENSP00000263666:p.Cys82Arg	61.0	0.0		74.0	26.0	NM_015009	A7MCZ6|Q8N2N7|Q96CC2|Q9NSQ2	Missense_Mutation	SNP	ENST00000263666.4	hg19	CCDS33789.1	.	.	.	.	.	.	.	.	.	.	A	18.74	3.688731	0.68271	.	.	ENSG00000121440	ENST00000263666;ENST00000416926;ENST00000308537	D;D	0.94576	-3.46;-3.46	4.49	4.49	0.54785	TRAF-like (1);Seven In Absentia Homolog-type (1);	0.108090	0.64402	N	0.000014	D	0.96503	0.8859	M	0.71581	2.175	0.80722	D	1	D	0.71674	0.998	D	0.80764	0.994	D	0.96865	0.9635	10	0.87932	D	0	.	12.9606	0.58455	1.0:0.0:0.0:0.0	.	82	Q9UPQ7	PZRN3_HUMAN	R	82	ENSP00000263666:C82R;ENSP00000308831:C82R	ENSP00000263666:C82R	C	-	1	0	PDZRN3	73756423	1.000000	0.71417	1.000000	0.80357	0.591000	0.36615	6.538000	0.73852	1.638000	0.50547	0.260000	0.18958	TGC	.	.		0.716	PDZRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352460.1	XM_041363	
CCDC54	84692	hgsc.bcm.edu	37	3	107097051	107097051	+	Missense_Mutation	SNP	A	A	C			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr3:107097051A>C	ENST00000261058.1	+	1	864	c.617A>C	c.(616-618)gAc>gCc	p.D206A		NM_032600.2	NP_115989.1	Q8NEL0	CCD54_HUMAN	coiled-coil domain containing 54	206										NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	19						AAGTCCACTGACCATCTTGAG	0.398																																					p.D206A		Atlas-SNP	.											.	CCDC54	56	.	0			c.A617C						.						73.0	72.0	72.0					3																	107097051		2203	4300	6503	SO:0001583	missense	84692	exon1			CCACTGACCATCT	AF367469	CCDS2949.1	3q13.12	2013-10-11			ENSG00000138483	ENSG00000138483			30703	protein-coding gene	gene with protein product	"""sperm protein 17"""					15257753	Standard	NM_032600		Approved	NYD-SP17, FLJ25362, SP17	uc003dwi.1	Q8NEL0	OTTHUMG00000159169	ENST00000261058.1:c.617A>C	chr3.hg19:g.107097051A>C	ENSP00000261058:p.Asp206Ala	383.0	0.0		442.0	44.0	NM_032600	Q96A43	Missense_Mutation	SNP	ENST00000261058.1	hg19	CCDS2949.1	.	.	.	.	.	.	.	.	.	.	A	0.038	-1.296348	0.01364	.	.	ENSG00000138483	ENST00000261058	T	0.42900	0.96	5.19	-5.25	0.02781	.	1.285700	0.05794	N	0.610844	T	0.31295	0.0792	L	0.60455	1.87	0.09310	N	1	B	0.13145	0.007	B	0.12156	0.007	T	0.33471	-0.9867	10	0.08837	T	0.75	3.0096	7.0425	0.25029	0.2386:0.3308:0.4306:0.0	.	206	Q8NEL0	CCD54_HUMAN	A	206	ENSP00000261058:D206A	ENSP00000261058:D206A	D	+	2	0	CCDC54	108579741	0.000000	0.05858	0.000000	0.03702	0.431000	0.31685	-0.604000	0.05667	-0.690000	0.05142	0.377000	0.23210	GAC	.	.		0.398	CCDC54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353651.1	NM_032600	
POLQ	10721	hgsc.bcm.edu	37	3	121200637	121200637	+	Missense_Mutation	SNP	G	G	A			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr3:121200637G>A	ENST00000264233.5	-	19	6121	c.5993C>T	c.(5992-5994)cCa>cTa	p.P1998L		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	1998					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		CTGAGAATCTGGATCTAGTAA	0.418								DNA polymerases (catalytic subunits)																													p.P1998L	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.C5993T						.						77.0	78.0	77.0					3																	121200637		2203	4300	6503	SO:0001583	missense	10721	exon19			GAATCTGGATCTA	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"""DNA polymerases"""	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.5993C>T	chr3.hg19:g.121200637G>A	ENSP00000264233:p.Pro1998Leu	146.0	0.0		155.0	39.0	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	hg19	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.785376	0.90282	.	.	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.27104	1.69	5.17	5.17	0.71159	Ribonuclease H-like (1);	0.121109	0.64402	D	0.000020	T	0.51601	0.1684	M	0.68952	2.095	0.58432	D	0.999995	D;D	0.89917	1.0;1.0	D;D	0.79108	0.963;0.992	T	0.52909	-0.8512	10	0.87932	D	0	.	18.8557	0.92251	0.0:0.0:1.0:0.0	.	1998;1170	O75417;O75417-2	DPOLQ_HUMAN;.	L	1621;1998;2134	ENSP00000264233:P1998L	ENSP00000264233:P1998L	P	-	2	0	POLQ	122683327	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	8.348000	0.90064	2.688000	0.91661	0.650000	0.86243	CCA	.	.		0.418	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	
KCNMB3	27094	hgsc.bcm.edu	37	3	178960728	178960728	+	Silent	SNP	A	A	G			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr3:178960728A>G	ENST00000314235.5	-	4	1315	c.804T>C	c.(802-804)atT>atC	p.I268I	KCNMB3_ENST00000349697.2_Silent_p.I266I|KCNMB3_ENST00000485523.1_Silent_p.I246I|KCNMB3_ENST00000497599.1_Intron|KCNMB3_ENST00000486944.1_Intron|KCNMB3_ENST00000392685.2_Silent_p.I264I	NM_014407.3	NP_055222.3	Q9NPA1	KCMB3_HUMAN	potassium large conductance calcium-activated channel, subfamily M beta member 3	268					action potential (GO:0001508)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|neuronal action potential (GO:0019228)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|potassium channel regulator activity (GO:0015459)			NS(1)|large_intestine(1)|lung(2)|stomach(1)	5	all_cancers(143;5.6e-17)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;2.41e-27)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.03)		Miconazole(DB01110)|Procaine(DB00721)	TCCTCCTCATAATGCACAGTT	0.418																																					p.I268I		Atlas-SNP	.											.	KCNMB3	46	.	0			c.T804C						.						120.0	115.0	117.0					3																	178960728		2203	4300	6503	SO:0001819	synonymous_variant	27094	exon4			CCTCATAATGCAC	AF139471	CCDS3225.1, CCDS3226.1, CCDS43172.1, CCDS43173.1, CCDS54683.1	3q26.3-q27	2010-09-30			ENSG00000171121	ENSG00000171121		"""Potassium channels"""	6287	protein-coding gene	gene with protein product		605222		KCNMB2, KCNMBL		10585773	Standard	NM_001163677		Approved		uc003fjm.3	Q9NPA1	OTTHUMG00000157337	ENST00000314235.5:c.804T>C	chr3.hg19:g.178960728A>G		242.0	0.0		242.0	46.0	NM_014407	B7Z9C9|D3DNR2|E9PER5|Q9NPG7|Q9NRM9|Q9UHN3	Silent	SNP	ENST00000314235.5	hg19	CCDS3226.1																																																																																			.	.		0.418	KCNMB3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000348484.1		
SENP5	205564	hgsc.bcm.edu	37	3	196613318	196613318	+	Silent	SNP	G	G	T			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr3:196613318G>T	ENST00000323460.5	+	2	1515	c.1266G>T	c.(1264-1266)gtG>gtT	p.V422V	SENP5_ENST00000445299.2_Silent_p.V422V|SENP5_ENST00000419026.1_Intron	NM_152699.4	NP_689912.2	Q96HI0	SENP5_HUMAN	SUMO1/sentrin specific peptidase 5	422					cell cycle (GO:0007049)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein sumoylation (GO:0016925)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)			NS(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(9)|lung(14)|skin(1)	32	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.14e-24)|all cancers(36;2.1e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.004)		ATACATCTGTGAGTAGCGTAG	0.438																																					p.V422V	Ovarian(47;891 1095 11174 13858 51271)	Atlas-SNP	.											.	SENP5	68	.	0			c.G1266T						.						96.0	96.0	96.0					3																	196613318		2203	4300	6503	SO:0001819	synonymous_variant	205564	exon2			ATCTGTGAGTAGC	BC030705	CCDS3322.1	3q29	2005-08-17	2005-08-17		ENSG00000119231	ENSG00000119231			28407	protein-coding gene	gene with protein product		612845	"""SUMO1/sentrin specific protease 5"""			12477932	Standard	NM_152699		Approved	MGC27076	uc003fwz.4	Q96HI0	OTTHUMG00000155527	ENST00000323460.5:c.1266G>T	chr3.hg19:g.196613318G>T		93.0	0.0		81.0	12.0	NM_152699	B4DY82|Q96SA5	Silent	SNP	ENST00000323460.5	hg19	CCDS3322.1																																																																																			.	.		0.438	SENP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340524.1	NM_152699	
WDFY3	23001	hgsc.bcm.edu	37	4	85626603	85626603	+	Missense_Mutation	SNP	G	G	A			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr4:85626603G>A	ENST00000295888.4	-	54	8686	c.8279C>T	c.(8278-8280)aCa>aTa	p.T2760I	WDFY3_ENST00000322366.6_Missense_Mutation_p.T2743I	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	2760	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.|Interaction with SQSTM1.|Sufficient for translocalization to p62 bodies/ALIS.				aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		TCGTTCATCTGTTTGTGCTCC	0.388																																					p.T2760I		Atlas-SNP	.											.	WDFY3	314	.	0			c.C8279T						.						233.0	203.0	213.0					4																	85626603		2203	4300	6503	SO:0001583	missense	23001	exon54			TCATCTGTTTGTG	AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"""Zinc fingers, FYVE domain containing"", ""WD repeat domain containing"""	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.8279C>T	chr4.hg19:g.85626603G>A	ENSP00000295888:p.Thr2760Ile	140.0	0.0		168.0	34.0	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	hg19	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	G	34	5.342568	0.95783	.	.	ENSG00000163625	ENST00000322366;ENST00000295888;ENST00000514711	T;T;T	0.64991	-0.13;-0.13;-0.13	5.64	5.64	0.86602	BEACH domain (4);	0.000000	0.85682	D	0.000000	D	0.83101	0.5181	M	0.91354	3.2	0.80722	D	1	D	0.62365	0.991	D	0.63192	0.912	D	0.85282	0.1062	10	0.59425	D	0.04	.	19.8946	0.96949	0.0:0.0:1.0:0.0	.	2760	Q8IZQ1	WDFY3_HUMAN	I	2743;2760;363	ENSP00000318466:T2743I;ENSP00000295888:T2760I;ENSP00000424987:T363I	ENSP00000295888:T2760I	T	-	2	0	WDFY3	85845627	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.544000	0.98092	2.937000	0.99478	0.650000	0.86243	ACA	.	.		0.388	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991	
KIAA1109	84162	hgsc.bcm.edu	37	4	123236737	123236737	+	Missense_Mutation	SNP	T	T	A			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr4:123236737T>A	ENST00000264501.4	+	61	10806	c.10433T>A	c.(10432-10434)cTg>cAg	p.L3478Q	KIAA1109_ENST00000455637.1_Missense_Mutation_p.L3478Q|KIAA1109_ENST00000388738.3_Missense_Mutation_p.L3478Q			Q2LD37	K1109_HUMAN	KIAA1109	3478					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						CTTACAACACTGACAGGAGAG	0.418																																					p.L3478Q		Atlas-SNP	.											.	KIAA1109	424	.	0			c.T10433A						.						197.0	184.0	188.0					4																	123236737		2012	4175	6187	SO:0001583	missense	84162	exon59			CAACACTGACAGG	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"""fragile site-associated"""	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.10433T>A	chr4.hg19:g.123236737T>A	ENSP00000264501:p.Leu3478Gln	153.0	0.0		152.0	27.0	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.786466	0.90367	.	.	ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000455637;ENST00000438707	T;T;T;T	0.46451	1.44;1.44;0.87;1.01	5.63	5.63	0.86233	.	0.000000	0.56097	D	0.000024	T	0.54255	0.1847	L	0.49126	1.545	0.54753	D	0.999985	D;P	0.54397	0.966;0.943	P;P	0.56700	0.804;0.642	T	0.57447	-0.7810	10	0.87932	D	0	.	15.8347	0.78789	0.0:0.0:0.0:1.0	.	3478;3478	Q2LD37-6;Q2LD37	.;K1109_HUMAN	Q	3478;3478;3478;94	ENSP00000264501:L3478Q;ENSP00000373390:L3478Q;ENSP00000389925:L3478Q;ENSP00000410874:L94Q	ENSP00000264501:L3478Q	L	+	2	0	KIAA1109	123456187	1.000000	0.71417	0.999000	0.59377	0.953000	0.61014	7.975000	0.88055	2.143000	0.66587	0.528000	0.53228	CTG	.	.		0.418	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797	
RXFP1	59350	hgsc.bcm.edu	37	4	159568324	159568324	+	Missense_Mutation	SNP	C	C	T			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr4:159568324C>T	ENST00000307765.5	+	16	1978	c.1727C>T	c.(1726-1728)gCc>gTc	p.A576V	RXFP1_ENST00000448688.2_Missense_Mutation_p.A471V|RXFP1_ENST00000470033.1_Missense_Mutation_p.A543V|RXFP1_ENST00000460056.2_Missense_Mutation_p.A495V|RXFP1_ENST00000343542.5_Missense_Mutation_p.A528V	NM_001253727.1|NM_001253728.1|NM_001253730.1|NM_001253732.1|NM_001253733.1|NM_021634.3	NP_001240656.1|NP_001240657.1|NP_001240659.1|NP_001240661.1|NP_001240662.1|NP_067647.2	Q9HBX9	RXFP1_HUMAN	relaxin/insulin-like family peptide receptor 1	576					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|lung connective tissue development (GO:0060427)|nipple morphogenesis (GO:0060658)|parturition (GO:0007567)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|hormone binding (GO:0042562)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|liver(2)|lung(22)|prostate(1)|skin(10)	49	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0219)		AGTATTGGAGCCCAGATTTAT	0.328																																					p.A603V		Atlas-SNP	.											.	RXFP1	98	.	0			c.C1808T						.						51.0	48.0	49.0					4																	159568324		1806	4079	5885	SO:0001583	missense	59350	exon16			TTGGAGCCCAGAT	AF190500	CCDS43276.1, CCDS58929.1, CCDS58930.1, CCDS75204.1, CCDS75205.1, CCDS75206.1	4q31.3	2012-08-08	2006-05-09	2006-05-09	ENSG00000171509	ENSG00000171509		"""GPCR / Class A : Relaxin family peptide receptors"""	19718	protein-coding gene	gene with protein product		606654	"""leucine-rich repeat-containing G protein-coupled receptor 7"""	LGR7		15956688, 16507880	Standard	NM_021634		Approved	RXFPR1	uc003ipz.3	Q9HBX9	OTTHUMG00000149973	ENST00000307765.5:c.1727C>T	chr4.hg19:g.159568324C>T	ENSP00000303248:p.Ala576Val	71.0	0.0		95.0	21.0	NM_001253727	B4DHD1|B4DTV2|Q2M215|Q3KU24|Q3KU25|Q3KU26	Missense_Mutation	SNP	ENST00000307765.5	hg19	CCDS43276.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.957387	0.73902	.	.	ENSG00000171509	ENST00000460056;ENST00000307765;ENST00000448688;ENST00000343542;ENST00000470033;ENST00000440678	T;T;T;T;T	0.36699	1.24;1.24;1.24;1.24;1.24	5.64	4.8	0.61643	GPCR, rhodopsin-like superfamily (1);	0.101317	0.64402	D	0.000003	T	0.52677	0.1749	M	0.68317	2.08	0.44547	D	0.997509	P;P;P;B;P;B;P;P	0.49253	0.872;0.851;0.872;0.221;0.921;0.025;0.872;0.612	P;P;P;B;P;B;P;P	0.56474	0.742;0.799;0.678;0.224;0.628;0.043;0.678;0.685	T	0.51220	-0.8733	10	0.34782	T	0.22	.	15.8211	0.78644	0.0:0.6816:0.3184:0.0	.	587;603;471;528;543;495;446;576	B3KV27;B4DGP2;B4DHD1;Q9HBX9-4;Q9HBX9-2;E9PCA3;Q59H16;Q9HBX9	.;.;.;.;.;.;.;RXFP1_HUMAN	V	495;576;471;528;543;446	ENSP00000423306:A495V;ENSP00000303248:A576V;ENSP00000414885:A471V;ENSP00000345889:A528V;ENSP00000420712:A543V	ENSP00000303248:A576V	A	+	2	0	RXFP1	159787774	1.000000	0.71417	1.000000	0.80357	0.795000	0.44927	5.120000	0.64685	1.387000	0.46486	-0.156000	0.13503	GCC	.	.		0.328	RXFP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314865.1	NM_021634	
TLL1	7092	hgsc.bcm.edu	37	4	167020507	167020507	+	Missense_Mutation	SNP	C	C	A			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr4:167020507C>A	ENST00000061240.2	+	20	3382	c.2735C>A	c.(2734-2736)cCa>cAa	p.P912Q	TLL1_ENST00000507499.1_Missense_Mutation_p.P935Q	NM_012464.4	NP_036596.3	O43897	TLL1_HUMAN	tolloid-like 1	912	CUB 5. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(21)|lung(26)|ovary(2)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		AACAACTACCCAGGACAGGTT	0.453																																					p.P912Q		Atlas-SNP	.											.	TLL1	194	.	0			c.C2735A						.						173.0	159.0	164.0					4																	167020507		2203	4300	6503	SO:0001583	missense	7092	exon20			ACTACCCAGGACA	AF282732	CCDS3811.1, CCDS56342.1	4q32-q33	2008-07-29			ENSG00000038295	ENSG00000038295			11843	protein-coding gene	gene with protein product		606742				10516436	Standard	NM_012464		Approved		uc003irh.2	O43897	OTTHUMG00000161112	ENST00000061240.2:c.2735C>A	chr4.hg19:g.167020507C>A	ENSP00000061240:p.Pro912Gln	289.0	0.0		274.0	78.0	NM_012464	B2RMU2|Q96AN3|Q9NQS4	Missense_Mutation	SNP	ENST00000061240.2	hg19	CCDS3811.1	.	.	.	.	.	.	.	.	.	.	C	18.70	3.679164	0.68042	.	.	ENSG00000038295	ENST00000061240;ENST00000507499	T;T	0.40476	1.03;1.03	5.76	5.76	0.90799	CUB (5);	0.000000	0.85682	U	0.000000	T	0.71500	0.3347	M	0.87547	2.89	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.74609	-0.3608	10	0.59425	D	0.04	.	19.9813	0.97326	0.0:1.0:0.0:0.0	.	935;912	E9PD25;O43897	.;TLL1_HUMAN	Q	912;935	ENSP00000061240:P912Q;ENSP00000426082:P935Q	ENSP00000061240:P912Q	P	+	2	0	TLL1	167239957	1.000000	0.71417	0.966000	0.40874	0.073000	0.16967	7.776000	0.85560	2.726000	0.93360	0.655000	0.94253	CCA	.	.		0.453	TLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363821.1		
TNPO1	3842	hgsc.bcm.edu	37	5	72179050	72179050	+	Missense_Mutation	SNP	T	T	A			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr5:72179050T>A	ENST00000337273.5	+	11	1567	c.1141T>A	c.(1141-1143)Tgg>Agg	p.W381R	TNPO1_ENST00000506351.2_Missense_Mutation_p.W373R|TNPO1_ENST00000454282.1_Missense_Mutation_p.W331R|TNPO1_ENST00000523768.1_Missense_Mutation_p.W331R	NM_002270.3	NP_002261.3	Q92973	TNPO1_HUMAN	transportin 1	381					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|protein import into nucleus, translocation (GO:0000060)|RNA metabolic process (GO:0016070)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	nuclear localization sequence binding (GO:0008139)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(6)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	36		Lung NSC(167;0.0053)|Ovarian(174;0.0175)		OV - Ovarian serous cystadenocarcinoma(47;6.14e-54)		AATTTCTGACTGGAATCTAAG	0.383																																					p.W381R		Atlas-SNP	.											.	TNPO1	90	.	0			c.T1141A						.						37.0	32.0	34.0					5																	72179050		2203	4300	6503	SO:0001583	missense	3842	exon11			TCTGACTGGAATC	U70322	CCDS4016.1, CCDS43329.1	5q13.1	2009-01-12	2004-01-29	2004-01-30	ENSG00000083312	ENSG00000083312		"""Importins"""	6401	protein-coding gene	gene with protein product	"""importin 2"""	602901	"""karyopherin (importin) beta 2"""	KPNB2		8808633, 9144189	Standard	NM_153188		Approved	MIP, TRN, IPO2, MIP1	uc003kci.4	Q92973	OTTHUMG00000100967	ENST00000337273.5:c.1141T>A	chr5.hg19:g.72179050T>A	ENSP00000336712:p.Trp381Arg	332.0	0.0		336.0	91.0	NM_002270	B4DVC6|Q92957|Q92975	Missense_Mutation	SNP	ENST00000337273.5	hg19	CCDS43329.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.317790	0.81469	.	.	ENSG00000083312	ENST00000337273;ENST00000454282;ENST00000523768;ENST00000506351	T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3	5.07	5.07	0.68467	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.87943	0.6305	H	0.97465	4.01	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.75484	0.986;0.976	D	0.92253	0.5810	10	0.87932	D	0	-2.574	15.1295	0.72511	0.0:0.0:0.0:1.0	.	331;381	Q92973-3;Q92973	.;TNPO1_HUMAN	R	381;331;331;373	ENSP00000336712:W381R;ENSP00000398524:W331R;ENSP00000428899:W331R;ENSP00000425118:W373R	ENSP00000336712:W381R	W	+	1	0	TNPO1	72214806	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.668000	0.83897	2.037000	0.60232	0.397000	0.26171	TGG	.	.		0.383	TNPO1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000218577.3	NM_002270	
PSD2	84249	hgsc.bcm.edu	37	5	139219625	139219625	+	Missense_Mutation	SNP	G	G	A	rs200345805		TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr5:139219625G>A	ENST00000274710.3	+	14	2187	c.1982G>A	c.(1981-1983)cGg>cAg	p.R661Q		NM_032289.2	NP_115665.1	Q9BQI7	PSD2_HUMAN	pleckstrin and Sec7 domain containing 2	661					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(10)|liver(2)|lung(15)|ovary(1)|prostate(2)	38			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAGCAACTGCGGTCTCATGAG	0.562																																					p.R661Q		Atlas-SNP	.											PSD2,NS,adenocarcinoma,0,1	PSD2	88	.	0			c.G1982A						.	G	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	91.0	84.0	86.0		1982	4.9	1.0	5		86	2,8598	2.2+/-6.3	0,2,4298	no	missense	PSD2	NM_032289.2	43	0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231	possibly-damaging	661/772	139219625	3,13003	2203	4300	6503	SO:0001583	missense	84249	exon14			AACTGCGGTCTCA	AL136559	CCDS4216.1	5q31.3	2013-01-10			ENSG00000146005	ENSG00000146005		"""Pleckstrin homology (PH) domain containing"""	19092	protein-coding gene	gene with protein product							Standard	NM_032289		Approved	DKFZp761B0514	uc003leu.1	Q9BQI7	OTTHUMG00000129240	ENST00000274710.3:c.1982G>A	chr5.hg19:g.139219625G>A	ENSP00000274710:p.Arg661Gln	68.0	0.0		60.0	9.0	NM_032289	D3DQD3|Q8N3J8	Missense_Mutation	SNP	ENST00000274710.3	hg19	CCDS4216.1	.	.	.	.	.	.	.	.	.	.	G	14.84	2.654046	0.47362	2.27E-4	2.33E-4	ENSG00000146005	ENST00000274710	T	0.12672	2.66	4.95	4.95	0.65309	.	0.222920	0.35291	N	0.003306	T	0.08537	0.0212	L	0.28556	0.865	0.36681	D	0.87907	P	0.34462	0.454	B	0.23150	0.044	T	0.22695	-1.0209	10	0.37606	T	0.19	.	9.3902	0.38367	0.16:0.0:0.84:0.0	.	661	Q9BQI7	PSD2_HUMAN	Q	661	ENSP00000274710:R661Q	ENSP00000274710:R661Q	R	+	2	0	PSD2	139199809	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	1.618000	0.36954	2.460000	0.83146	0.561000	0.74099	CGG	.	G|0.999;A|0.001		0.562	PSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251339.1	NM_032289	
PCDHGA10	56106	hgsc.bcm.edu	37	5	140793290	140793290	+	Missense_Mutation	SNP	C	C	A			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr5:140793290C>A	ENST00000398610.2	+	1	548	c.548C>A	c.(547-549)tCc>tAc	p.S183Y	PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron	NM_018913.2|NM_032090.1	NP_061736.1|NP_114479.1	Q9Y5H3	PCDGA_HUMAN	protocadherin gamma subfamily A, 10	183	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAGCACTTCTCCCTAAGAGTT	0.577																																					p.S183Y		Atlas-SNP	.											.	PCDHGA10	114	.	0			c.C548A						.						34.0	36.0	36.0					5																	140793290		1971	4153	6124	SO:0001583	missense	56106	exon1			ACTTCTCCCTAAG		CCDS47292.1, CCDS75343.1	5q31	2010-01-26			ENSG00000253846	ENSG00000253846		"""Cadherins / Protocadherins : Clustered"""	8697	other	protocadherin		606297				10380929	Standard	NM_018913		Approved	PCDH-GAMMA-A10		Q9Y5H3	OTTHUMG00000163688	ENST00000398610.2:c.548C>A	chr5.hg19:g.140793290C>A	ENSP00000381611:p.Ser183Tyr	79.0	0.0		81.0	24.0	NM_032090	Q9Y5E0	Missense_Mutation	SNP	ENST00000398610.2	hg19	CCDS47292.1	.	.	.	.	.	.	.	.	.	.	c	10.97	1.502992	0.26949	.	.	ENSG00000253846	ENST00000398610	T	0.52983	0.64	5.49	5.49	0.81192	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.71247	0.3317	M	0.90425	3.115	0.09310	N	1	D;D	0.64830	0.975;0.994	P;D	0.67231	0.819;0.95	T	0.66783	-0.5836	9	0.66056	D	0.02	.	9.9105	0.41403	0.0:0.7868:0.1397:0.0735	.	183;183	Q9Y5H3-2;Q9Y5H3	.;PCDGA_HUMAN	Y	183	ENSP00000381611:S183Y	ENSP00000381611:S183Y	S	+	2	0	PCDHGA10	140773474	0.000000	0.05858	0.947000	0.38551	0.350000	0.29205	0.287000	0.18920	2.590000	0.87494	0.557000	0.71058	TCC	.	.		0.577	PCDHGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374747.1	NM_018913	
PCDHGB7	56099	hgsc.bcm.edu	37	5	140799322	140799322	+	Missense_Mutation	SNP	G	G	C			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr5:140799322G>C	ENST00000398594.2	+	1	1896	c.1896G>C	c.(1894-1896)ttG>ttC	p.L632F	PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA11_ENST00000518882.1_5'Flank|PCDHGA10_ENST00000398610.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA11_ENST00000398587.2_5'Flank|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron	NM_018927.3	NP_061750.1	Q9Y5F8	PCDGJ_HUMAN	protocadherin gamma subfamily B, 7	632	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(13)|lung(15)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(3)	56			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGCGTGCTTTGGGTGACAAGG	0.647																																					p.L632F		Atlas-SNP	.											.	PCDHGB7	117	.	0			c.G1896C						.						60.0	66.0	64.0					5																	140799322		2182	4289	6471	SO:0001583	missense	56099	exon1			TGCTTTGGGTGAC	AF152523	CCDS47293.1, CCDS75344.1	5q31	2010-01-26			ENSG00000254122	ENSG00000254122		"""Cadherins / Protocadherins : Clustered"""	8714	other	protocadherin	"""cadherin ME6"""	606304				10380929	Standard	NM_032101		Approved	ME6, PCDH-GAMMA-B7		Q9Y5F8	OTTHUMG00000164054	ENST00000398594.2:c.1896G>C	chr5.hg19:g.140799322G>C	ENSP00000381594:p.Leu632Phe	91.0	0.0		102.0	17.0	NM_018927	Q9UN63	Missense_Mutation	SNP	ENST00000398594.2	hg19	CCDS47293.1	.	.	.	.	.	.	.	.	.	.	g	11.66	1.703845	0.30232	.	.	ENSG00000254122	ENST00000398594	T	0.74737	-0.87	5.57	4.71	0.59529	Cadherin (4);Cadherin-like (1);	0.000000	0.27700	U	0.018202	T	0.70954	0.3283	L	0.35249	1.045	0.21604	N	0.999624	P;P	0.50943	0.94;0.862	P;P	0.56434	0.798;0.551	T	0.60490	-0.7253	10	0.31617	T	0.26	.	5.6108	0.17404	0.0756:0.139:0.6419:0.1435	.	632;632	Q9Y5F8;Q9Y5F8-2	PCDGJ_HUMAN;.	F	632	ENSP00000381594:L632F	ENSP00000381594:L632F	L	+	3	2	PCDHGB7	140779506	0.997000	0.39634	0.988000	0.46212	0.665000	0.39181	3.193000	0.50997	1.356000	0.45884	0.491000	0.48974	TTG	.	.		0.647	PCDHGB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376973.1	NM_018927	
SLC34A1	6569	hgsc.bcm.edu	37	5	176825095	176825095	+	Nonsense_Mutation	SNP	G	G	A			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr5:176825095G>A	ENST00000324417.5	+	13	1819	c.1728G>A	c.(1726-1728)tgG>tgA	p.W576*	SLC34A1_ENST00000513614.1_3'UTR	NM_003052.4	NP_003043.3	Q06495	NPT2A_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 1	576					arsenate ion transmembrane transport (GO:1901684)|bone remodeling (GO:0046849)|cellular response to metal ion (GO:0071248)|cellular response to parathyroid hormone stimulus (GO:0071374)|cellular response to staurosporine (GO:0072734)|dentinogenesis (GO:0097187)|gentamycin metabolic process (GO:1901128)|glycoprotein metabolic process (GO:0009100)|indole metabolic process (GO:0042431)|ion transport (GO:0006811)|kidney development (GO:0001822)|ossification (GO:0001503)|phosphate ion homeostasis (GO:0055062)|phosphate ion transport (GO:0006817)|positive regulation of membrane potential (GO:0045838)|positive regulation of phosphate transmembrane transport (GO:2000187)|positive regulation of sodium-dependent phosphate transport (GO:2000120)|protein homooligomerization (GO:0051260)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to growth hormone (GO:0060416)|response to lead ion (GO:0010288)|response to magnesium ion (GO:0032026)|response to mercury ion (GO:0046689)|response to potassium ion (GO:0035864)|response to thyroid hormone (GO:0097066)|response to vitamin A (GO:0033189)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|tricarboxylic acid metabolic process (GO:0072350)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|membrane-bounded vesicle (GO:0031988)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|symporter activity (GO:0015293)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TACAGACATGGGACTTCCTGC	0.667																																					p.W576X		Atlas-SNP	.											.	SLC34A1	73	.	0			c.G1728A						.						74.0	78.0	77.0					5																	176825095		2203	4300	6503	SO:0001587	stop_gained	6569	exon13			GACATGGGACTTC	L13258	CCDS4418.1, CCDS54953.1	5q35.3	2013-07-17	2013-07-17		ENSG00000131183	ENSG00000131183		"""Solute carriers"""	11019	protein-coding gene	gene with protein product	"""sodium/phosphate co-transporter"", ""solute carrier family 17 (sodium phosphate), member 2"", ""Na+-phosphate cotransporter type II"""	182309	"""solute carrier family 34 (sodium phosphate), member 1"""	NPT2, SLC17A2		8327470, 8693007	Standard	NM_003052		Approved	NAPI-3, NPTIIa, SLC11	uc003mgk.4	Q06495	OTTHUMG00000130857	ENST00000324417.5:c.1728G>A	chr5.hg19:g.176825095G>A	ENSP00000321424:p.Trp576*	479.0	1.0		521.0	157.0	NM_003052	B4DPE3	Nonsense_Mutation	SNP	ENST00000324417.5	hg19	CCDS4418.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.647222	0.87958	.	.	ENSG00000131183	ENST00000324417	.	.	.	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.3697	19.057	0.93069	0.0:0.0:1.0:0.0	.	.	.	.	X	576	.	ENSP00000321424:W576X	W	+	3	0	SLC34A1	176757701	1.000000	0.71417	1.000000	0.80357	0.086000	0.17979	9.706000	0.98722	2.491000	0.84063	0.455000	0.32223	TGG	.	.		0.667	SLC34A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253431.1	NM_003052	
TBC1D22B	55633	hgsc.bcm.edu	37	6	37281660	37281660	+	Silent	SNP	G	G	T			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr6:37281660G>T	ENST00000373491.3	+	10	1304	c.1158G>T	c.(1156-1158)cgG>cgT	p.R386R		NM_017772.2	NP_060242.2	Q9NU19	TB22B_HUMAN	TBC1 domain family, member 22B	386	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|prostate(1)	15			OV - Ovarian serous cystadenocarcinoma(102;0.241)			TTGTCAGCCGGATTGATGGTA	0.493																																					p.R386R		Atlas-SNP	.											TBC1D22B,colon,carcinoma,0,1	TBC1D22B	37	.	0			c.G1158T						.						185.0	165.0	172.0					6																	37281660		2203	4300	6503	SO:0001819	synonymous_variant	55633	exon10			CAGCCGGATTGAT	AK096340	CCDS4832.1	6p21.2	2005-01-05	2005-01-05	2005-01-05	ENSG00000065491	ENSG00000065491			21602	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 197"""	C6orf197			Standard	NM_017772		Approved	FLJ20337, dJ744I24.2	uc003onn.3	Q9NU19	OTTHUMG00000014619	ENST00000373491.3:c.1158G>T	chr6.hg19:g.37281660G>T		170.0	0.0		191.0	35.0	NM_017772	A8KA28|Q32MQ8|Q5VUK9|Q6P4C3|Q7Z6P7|Q9BPV6|Q9BUT5|Q9NXB6	Silent	SNP	ENST00000373491.3	hg19	CCDS4832.1																																																																																			.	.		0.493	TBC1D22B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040402.1	NM_017772	
NCOA7	135112	hgsc.bcm.edu	37	6	126176369	126176369	+	Missense_Mutation	SNP	A	A	G			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr6:126176369A>G	ENST00000368357.3	+	4	606	c.254A>G	c.(253-255)aAg>aGg	p.K85R	NCOA7_ENST00000487635.1_3'UTR|NCOA7_ENST00000229634.9_Intron|NCOA7_ENST00000392477.2_Missense_Mutation_p.K85R	NM_001199619.1|NM_001199620.1	NP_001186548.1|NP_001186549.1	Q8NI08	NCOA7_HUMAN	nuclear receptor coactivator 7	85					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(2)	39				UCEC - Uterine corpus endometrioid carcinoma (4;0.0803)|GBM - Glioblastoma multiforme(226;0.0193)|all cancers(137;0.237)		ACAGAACTAAAGAGATATTAT	0.313																																					p.K85R		Atlas-SNP	.											.	NCOA7	92	.	0			c.A254G						.						84.0	94.0	90.0					6																	126176369		2203	4300	6503	SO:0001583	missense	135112	exon4			AACTAAAGAGATA	AJ420542	CCDS5132.1, CCDS56448.1	6q22.33	2013-03-14			ENSG00000111912	ENSG00000111912			21081	protein-coding gene	gene with protein product	"""TBC/LysM-associated domain containing 4"""	609752				11971969	Standard	NM_001199619		Approved	ERAP140, dJ187J11.3, TLDC4	uc003qai.3	Q8NI08	OTTHUMG00000015513	ENST00000368357.3:c.254A>G	chr6.hg19:g.126176369A>G	ENSP00000357341:p.Lys85Arg	92.0	0.0		99.0	23.0	NM_001199619	B2RNS2|B7Z2C4|B9EH71|G8JL91|Q3LID6|Q4G0V1|Q5TF95|Q6IPQ4|Q6NE83|Q86T89|Q8N1W4	Missense_Mutation	SNP	ENST00000368357.3	hg19	CCDS5132.1	.	.	.	.	.	.	.	.	.	.	A	16.89	3.248350	0.59103	.	.	ENSG00000111912	ENST00000368357;ENST00000431092;ENST00000392477;ENST00000453302;ENST00000417494;ENST00000428318;ENST00000419660	T;T;T;T	0.60548	2.56;2.56;0.67;0.18	5.39	5.39	0.77823	.	0.111289	0.64402	D	0.000013	T	0.57489	0.2057	L	0.29908	0.895	0.80722	D	1	D;P;D;P	0.76494	0.999;0.868;0.972;0.682	D;B;P;B	0.83275	0.996;0.359;0.737;0.141	T	0.63821	-0.6550	10	0.62326	D	0.03	-25.048	14.1421	0.65327	1.0:0.0:0.0:0.0	.	85;85;85;85	Q8NI08-6;Q8NI08-2;Q8NI08-4;Q8NI08	.;.;.;NCOA7_HUMAN	R	85	ENSP00000357341:K85R;ENSP00000376269:K85R;ENSP00000406363:K85R;ENSP00000408211:K85R	ENSP00000357341:K85R	K	+	2	0	NCOA7	126218062	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.487000	0.66863	2.267000	0.75376	0.528000	0.53228	AAG	.	.		0.313	NCOA7-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042083.4	XM_059748	
OSBPL3	26031	hgsc.bcm.edu	37	7	24870414	24870414	+	Missense_Mutation	SNP	G	G	T			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr7:24870414G>T	ENST00000313367.2	-	16	2308	c.1857C>A	c.(1855-1857)gaC>gaA	p.D619E	OSBPL3_ENST00000431825.2_Missense_Mutation_p.D552E|OSBPL3_ENST00000409069.1_Missense_Mutation_p.D552E|OSBPL3_ENST00000353930.1_Missense_Mutation_p.D583E|OSBPL3_ENST00000396431.1_Missense_Mutation_p.D588E|OSBPL3_ENST00000352860.1_Missense_Mutation_p.D588E|OSBPL3_ENST00000396429.1_Missense_Mutation_p.D583E	NM_015550.2	NP_056365.1	Q9H4L5	OSBL3_HUMAN	oxysterol binding protein-like 3	619					lipid transport (GO:0006869)	cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(19)|prostate(1)|skin(3)|urinary_tract(1)	43						GGAAGCCCTTGTCCTCCCGAA	0.428																																					p.D619E		Atlas-SNP	.											.	OSBPL3	100	.	0			c.C1857A						.						183.0	198.0	193.0					7																	24870414		2203	4300	6503	SO:0001583	missense	26031	exon16			GCCCTTGTCCTCC	AB014604	CCDS5390.1, CCDS5391.1, CCDS5392.1, CCDS47564.1	7p15.3	2013-01-10			ENSG00000070882	ENSG00000070882		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16370	protein-coding gene	gene with protein product		606732		OSBP3		9734811	Standard	XM_005249698		Approved	ORP-3, ORP3, KIAA0704	uc003sxf.3	Q9H4L5	OTTHUMG00000023277	ENST00000313367.2:c.1857C>A	chr7.hg19:g.24870414G>T	ENSP00000315410:p.Asp619Glu	120.0	0.0		140.0	34.0	NM_015550	A4D167|A4D168|A4D169|A4D170|A4D171|A4D172|B8ZZ79|B8ZZP0|O14591|O43357|O43358|Q8N702|Q8N703|Q8N704|Q8NFH0|Q8NFH1|Q8NI12|Q8NI13|Q9BZF4|Q9UED6	Missense_Mutation	SNP	ENST00000313367.2	hg19	CCDS5390.1	.	.	.	.	.	.	.	.	.	.	G	16.68	3.189334	0.57909	.	.	ENSG00000070882	ENST00000313367;ENST00000352860;ENST00000353930;ENST00000431825;ENST00000396431;ENST00000396429;ENST00000409069	T;T;T;T;T;T;T	0.35048	1.33;1.33;1.33;1.33;1.33;1.33;1.33	5.74	3.86	0.44501	.	0.045811	0.85682	D	0.000000	T	0.34106	0.0886	L	0.48986	1.54	0.51482	D	0.999923	B;B;B;B	0.25563	0.022;0.041;0.041;0.129	B;B;B;B	0.37387	0.073;0.073;0.073;0.248	T	0.29579	-1.0007	10	0.48119	T	0.1	-17.1482	5.568	0.17180	0.0975:0.1389:0.6216:0.142	.	552;588;583;619	Q9H4L5-4;Q9H4L5-2;Q9H4L5-3;Q9H4L5	.;.;.;OSBL3_HUMAN	E	619;588;583;552;588;583;552	ENSP00000315410:D619E;ENSP00000315331:D588E;ENSP00000315277:D583E;ENSP00000389779:D552E;ENSP00000379708:D588E;ENSP00000379706:D583E;ENSP00000386953:D552E	ENSP00000315410:D619E	D	-	3	2	OSBPL3	24836939	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.538000	0.36094	2.732000	0.93576	0.591000	0.81541	GAC	.	.		0.428	OSBPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214085.2		
POR	5447	hgsc.bcm.edu	37	7	75583458	75583458	+	Missense_Mutation	SNP	A	A	G			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr7:75583458A>G	ENST00000461988.1	+	2	253	c.148A>G	c.(148-150)Aaa>Gaa	p.K50E	POR_ENST00000394893.1_Missense_Mutation_p.K50E|POR_ENST00000419840.1_5'UTR	NM_000941.2	NP_000932.3	P16435	NCPR_HUMAN	P450 (cytochrome) oxidoreductase	47					carnitine metabolic process (GO:0009437)|cellular organofluorine metabolic process (GO:0090346)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to peptide hormone stimulus (GO:0071375)|demethylation (GO:0070988)|fatty acid oxidation (GO:0019395)|flavonoid metabolic process (GO:0009812)|internal peptidyl-lysine acetylation (GO:0018393)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of lipase activity (GO:0060192)|nitrate catabolic process (GO:0043602)|nitric oxide catabolic process (GO:0046210)|oxidation-reduction process (GO:0055114)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of monooxygenase activity (GO:0032770)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|regulation of growth plate cartilage chondrocyte proliferation (GO:0003420)|response to drug (GO:0042493)|response to nutrient (GO:0007584)	endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|hydrolase activity (GO:0016787)|iron ion binding (GO:0005506)|iron-cytochrome-c reductase activity (GO:0047726)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric oxide dioxygenase activity (GO:0008941)			central_nervous_system(1)|endometrium(2)|kidney(2)|lung(3)|ovary(1)	9					Benzphetamine(DB00865)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Ethylmorphine(DB01466)|Flavin adenine dinucleotide(DB03147)|Lipoic Acid(DB00166)|Mitomycin(DB00305)|Nilutamide(DB00665)|Nitrofurantoin(DB00698)	CTTCAGAAAGAAAAAAGAAGA	0.498																																					p.K50E		Atlas-SNP	.											.	POR	46	.	0			c.A148G						.						75.0	71.0	72.0					7																	75583458		1884	4113	5997	SO:0001583	missense	5447	exon2			AGAAAGAAAAAAG	AF258341	CCDS5579.1	7q11.2	2006-12-05			ENSG00000127948	ENSG00000127948			9208	protein-coding gene	gene with protein product		124015				2516426	Standard	NM_000941		Approved	CYPOR, FLJ26468	uc003udy.3	P16435	OTTHUMG00000130413	ENST00000461988.1:c.148A>G	chr7.hg19:g.75583458A>G	ENSP00000419970:p.Lys50Glu	123.0	0.0		173.0	12.0	NM_000941	Q16455|Q197M5|Q8N181|Q9H3M8|Q9UDT3	Missense_Mutation	SNP	ENST00000461988.1	hg19	CCDS5579.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.70|17.70	3.454134|3.454134	0.63290|0.63290	.|.	.|.	ENSG00000127948|ENSG00000127948	ENST00000447222|ENST00000453773;ENST00000439963;ENST00000461988;ENST00000394893;ENST00000412521;ENST00000414186;ENST00000432753;ENST00000449920;ENST00000418341	.|T;T;T	.|0.46819	.|0.86;4.28;4.28	4.86|4.86	4.86|4.86	0.63082|0.63082	.|.	.|0.102540	.|0.64402	.|D	.|0.000004	T|T	0.51024|0.51024	0.1650|0.1650	M|M	0.76328|0.76328	2.33|2.33	0.80722|0.80722	D|D	1|1	.|B	.|0.31968	.|0.349	.|B	.|0.36885	.|0.235	T|T	0.52990|0.52990	-0.8501|-0.8501	5|10	.|0.40728	.|T	.|0.16	-2.0478|-2.0478	12.4164|12.4164	0.55496|0.55496	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|56	.|Q59ED7	.|.	G|E	22|50	.|ENSP00000390540:K50E;ENSP00000419970:K50E;ENSP00000378355:K50E	.|ENSP00000378355:K50E	E|K	+|+	2|1	0|0	POR|POR	75421394|75421394	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.977000|0.977000	0.68977|0.68977	6.192000|6.192000	0.72069|0.72069	1.823000|1.823000	0.53134|0.53134	0.533000|0.533000	0.62120|0.62120	GAA|AAA	.	.		0.498	POR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252796.7	NM_000941	
GIGYF1	64599	hgsc.bcm.edu	37	7	100285497	100285497	+	Missense_Mutation	SNP	C	C	G			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr7:100285497C>G	ENST00000275732.5	-	3	1384	c.175G>C	c.(175-177)Gag>Cag	p.E59Q	GIGYF1_ENST00000471340.2_5'UTR	NM_022574.4	NP_072096.2	O75420	PERQ1_HUMAN	GRB10 interacting GYF protein 1	59					insulin-like growth factor receptor signaling pathway (GO:0048009)					central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)					TCCTGCAGCTCTTCCGGGACC	0.682																																					p.E59Q		Atlas-SNP	.											.	GIGYF1	113	.	0			c.G175C						.						58.0	62.0	61.0					7																	100285497		2203	4299	6502	SO:0001583	missense	64599	exon3			GCAGCTCTTCCGG	AF053356	CCDS34708.1	7q22	2008-02-11	2008-02-11	2008-02-11	ENSG00000146830	ENSG00000146830			9126	protein-coding gene	gene with protein product	"""GYF domain containing 1"""	612064	"""PERQ amino acid rich, with GYF domain 1"""	PERQ1		9799793, 12771153	Standard	NM_022574		Approved	GYF1	uc003uwg.1	O75420	OTTHUMG00000157036	ENST00000275732.5:c.175G>C	chr7.hg19:g.100285497C>G	ENSP00000275732:p.Glu59Gln	95.0	0.0		121.0	38.0	NM_022574	Q6Y7W7|Q8WZ38	Missense_Mutation	SNP	ENST00000275732.5	hg19	CCDS34708.1	.	.	.	.	.	.	.	.	.	.	.	22.6	4.316445	0.81469	.	.	ENSG00000146830	ENST00000275732	D	0.83914	-1.78	5.01	5.01	0.66863	.	0.063489	0.64402	D	0.000008	D	0.84379	0.5459	L	0.52573	1.65	0.58432	D	0.999998	D	0.56521	0.976	P	0.52598	0.703	T	0.83303	-0.0027	10	0.35671	T	0.21	-23.1894	15.8586	0.79005	0.0:1.0:0.0:0.0	.	59	O75420	PERQ1_HUMAN	Q	59	ENSP00000275732:E59Q	ENSP00000275732:E59Q	E	-	1	0	GIGYF1	100123433	1.000000	0.71417	0.958000	0.39756	0.517000	0.34286	7.320000	0.79064	2.597000	0.87782	0.563000	0.77884	GAG	.	.		0.682	GIGYF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347205.2	NM_022574	
DOCK4	9732	hgsc.bcm.edu	37	7	111398823	111398823	+	Missense_Mutation	SNP	G	G	T			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr7:111398823G>T	ENST00000437633.1	-	40	4415	c.4159C>A	c.(4159-4161)Ccc>Acc	p.P1387T	DOCK4_ENST00000428084.1_Missense_Mutation_p.P1396T|DOCK4_ENST00000494651.2_Missense_Mutation_p.P270T	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	1387	DHR-2.				cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				TCTGGAATGGGAGTCACAGCA	0.483																																					p.P1387T		Atlas-SNP	.											.	DOCK4	365	.	0			c.C4159A						.						77.0	72.0	74.0					7																	111398823		1925	4117	6042	SO:0001583	missense	9732	exon40			GAATGGGAGTCAC		CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512			19192	protein-coding gene	gene with protein product		607679				12432077, 12628187	Standard	XM_006716188		Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.4159C>A	chr7.hg19:g.111398823G>T	ENSP00000404179:p.Pro1387Thr	99.0	0.0		143.0	28.0	NM_014705	O14584|O94824|Q8NB45	Missense_Mutation	SNP	ENST00000437633.1	hg19	CCDS47688.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.660933	0.88154	.	.	ENSG00000128512	ENST00000352877;ENST00000428084;ENST00000494651;ENST00000437633;ENST00000342288	T;T;T	0.21932	2.57;1.98;2.55	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.57257	0.2041	M	0.91249	3.19	0.80722	D	1	D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;1.0	D;D;D;D;D	0.78314	0.96;0.982;0.988;0.988;0.991	T	0.66763	-0.5841	10	0.87932	D	0	.	19.1084	0.93307	0.0:0.0:1.0:0.0	.	294;270;1432;1387;1396	B7Z2K9;F5GXW1;Q149N5;Q8N1I0;Q8N1I0-2	.;.;.;DOCK4_HUMAN;.	T	1375;1396;270;1387;1384	ENSP00000410746:P1396T;ENSP00000440944:P270T;ENSP00000404179:P1387T	ENSP00000345432:P1384T	P	-	1	0	DOCK4	111186059	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	9.585000	0.98223	2.820000	0.97059	0.650000	0.86243	CCC	.	.		0.483	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705	
CPED1	79974	hgsc.bcm.edu	37	7	120906375	120906375	+	Missense_Mutation	SNP	G	G	T			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr7:120906375G>T	ENST00000310396.5	+	19	2872	c.2405G>T	c.(2404-2406)gGc>gTc	p.G802V		NM_024913.4	NP_079189.4	A4D0V7	CPED1_HUMAN	cadherin-like and PC-esterase domain containing 1	802						endoplasmic reticulum (GO:0005783)											AAAGTACATGGCACTAAATTC	0.393																																					p.G802V		Atlas-SNP	.											.	.	.	.	0			c.G2405T						.						218.0	195.0	203.0					7																	120906375		2203	4300	6503	SO:0001583	missense	79974	exon19			TACATGGCACTAA		CCDS34739.1, CCDS47690.1	7q31.31	2012-06-12	2012-06-12	2012-06-12	ENSG00000106034	ENSG00000106034			26159	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 58"""	C7orf58		20056006	Standard	NM_024913		Approved	FLJ21986	uc003vjq.4	A4D0V7	OTTHUMG00000156982	ENST00000310396.5:c.2405G>T	chr7.hg19:g.120906375G>T	ENSP00000309772:p.Gly802Val	116.0	0.0		160.0	19.0	NM_024913	A8K1R3|Q6UXT1|Q86T76|Q86T84|Q8N2T5|Q96NC9	Missense_Mutation	SNP	ENST00000310396.5	hg19	CCDS34739.1	.	.	.	.	.	.	.	.	.	.	G	18.63	3.665015	0.67700	.	.	ENSG00000106034	ENST00000310396	T	0.17528	2.27	5.94	5.94	0.96194	.	0.247982	0.41001	D	0.000967	T	0.32346	0.0826	L	0.56769	1.78	0.80722	D	1	D	0.63880	0.993	D	0.65874	0.939	T	0.05194	-1.0900	10	0.72032	D	0.01	-15.2066	6.9921	0.24761	0.1083:0.1734:0.7183:0.0	.	802	A4D0V7	CG058_HUMAN	V	802	ENSP00000309772:G802V	ENSP00000309772:G802V	G	+	2	0	C7orf58	120693611	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	4.588000	0.60999	2.816000	0.96949	0.561000	0.74099	GGC	.	.		0.393	CPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346959.1	NM_024913	
AASS	10157	hgsc.bcm.edu	37	7	121758381	121758381	+	Missense_Mutation	SNP	C	C	T			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr7:121758381C>T	ENST00000393376.1	-	5	762	c.667G>A	c.(667-669)Gga>Aga	p.G223R	AASS_ENST00000473553.1_Intron|AASS_ENST00000417368.2_Missense_Mutation_p.G223R			Q9UDR5	AASS_HUMAN	aminoadipate-semialdehyde synthase	223	Lysine-ketoglutarate reductase.				cellular nitrogen compound metabolic process (GO:0034641)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity (GO:0047131)|saccharopine dehydrogenase (NADP+, L-lysine-forming) activity (GO:0047130)			autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(6)|large_intestine(12)|lung(27)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	54						TTACCAGTTCCTGTGAACACA	0.403																																					p.G223R		Atlas-SNP	.											.	AASS	123	.	0			c.G667A						.						92.0	86.0	88.0					7																	121758381		2203	4300	6503	SO:0001583	missense	10157	exon6			CAGTTCCTGTGAA	AF229180	CCDS5783.1	7q31.3	2010-12-14			ENSG00000008311	ENSG00000008311			17366	protein-coding gene	gene with protein product		605113				10775527	Standard	NM_005763		Approved	LORSDH, LKRSDH	uc003vkb.3	Q9UDR5	OTTHUMG00000157058	ENST00000393376.1:c.667G>A	chr7.hg19:g.121758381C>T	ENSP00000377040:p.Gly223Arg	49.0	0.0		91.0	18.0	NM_005763	O95462	Missense_Mutation	SNP	ENST00000393376.1	hg19	CCDS5783.1	.	.	.	.	.	.	.	.	.	.	.	27.9	4.868839	0.91587	.	.	ENSG00000008311	ENST00000393376;ENST00000417368	D;D	0.94280	-3.39;-3.39	5.02	5.02	0.67125	Alanine dehydrogenase/PNT, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.97334	0.9128	M	0.89904	3.07	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98055	1.0390	10	0.87932	D	0	-16.5808	18.1242	0.89581	0.0:1.0:0.0:0.0	.	223	Q9UDR5	AASS_HUMAN	R	223	ENSP00000377040:G223R;ENSP00000403768:G223R	ENSP00000351834:G223R	G	-	1	0	AASS	121545617	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.627000	0.83176	2.610000	0.88304	0.655000	0.94253	GGA	.	.		0.403	AASS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347300.1	NM_005763	
KCNB2	9312	hgsc.bcm.edu	37	8	73848214	73848214	+	Silent	SNP	T	T	C			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr8:73848214T>C	ENST00000523207.1	+	3	1212	c.624T>C	c.(622-624)atT>atC	p.I208I		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	208					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	TTTCCACCATTGCTTTGTCTC	0.483																																					p.I208I		Atlas-SNP	.											.	KCNB2	228	.	0			c.T624C						.						233.0	223.0	226.0					8																	73848214		2203	4300	6503	SO:0001819	synonymous_variant	9312	exon3			CACCATTGCTTTG	U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.624T>C	chr8.hg19:g.73848214T>C		159.0	0.0		449.0	167.0	NM_004770	Q7Z7D0|Q9BXD3	Silent	SNP	ENST00000523207.1	hg19	CCDS6209.1																																																																																			.	.		0.483	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770	
KCNB2	9312	hgsc.bcm.edu	37	8	73848327	73848327	+	Missense_Mutation	SNP	T	T	C			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr8:73848327T>C	ENST00000523207.1	+	3	1325	c.737T>C	c.(736-738)aTg>aCg	p.M246T		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	246					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	TGGTTTACCATGGAGTACCTT	0.463																																					p.M246T		Atlas-SNP	.											.	KCNB2	228	.	0			c.T737C						.						202.0	173.0	183.0					8																	73848327		2203	4300	6503	SO:0001583	missense	9312	exon3			TTACCATGGAGTA	U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.737T>C	chr8.hg19:g.73848327T>C	ENSP00000430846:p.Met246Thr	203.0	0.0		585.0	41.0	NM_004770	Q7Z7D0|Q9BXD3	Missense_Mutation	SNP	ENST00000523207.1	hg19	CCDS6209.1	.	.	.	.	.	.	.	.	.	.	T	19.26	3.792524	0.70452	.	.	ENSG00000182674	ENST00000523207	D	0.98400	-4.91	5.93	5.93	0.95920	Ion transport (1);	0.000000	0.56097	D	0.000035	D	0.97657	0.9232	N	0.21097	0.63	0.58432	D	0.999994	D	0.67145	0.996	D	0.64877	0.93	D	0.99470	1.0945	10	0.66056	D	0.02	.	16.3871	0.83514	0.0:0.0:0.0:1.0	.	246	Q92953	KCNB2_HUMAN	T	246	ENSP00000430846:M246T	ENSP00000430846:M246T	M	+	2	0	KCNB2	74010881	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	6.289000	0.72696	2.265000	0.75225	0.533000	0.62120	ATG	.	.		0.463	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770	
FBXO43	286151	hgsc.bcm.edu	37	8	101146559	101146559	+	Silent	SNP	G	G	T			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr8:101146559G>T	ENST00000428847.2	-	4	2024	c.1708C>A	c.(1708-1710)Cgg>Agg	p.R570R		NM_001029860.3	NP_001025031.2	Q4G163	FBX43_HUMAN	F-box protein 43	570					meiotic nuclear division (GO:0007126)|negative regulation of meiosis (GO:0045835)|negative regulation of protein catabolic process (GO:0042177)|protein ubiquitination (GO:0016567)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(4)|large_intestine(5)|lung(14)|prostate(1)|skin(5)|urinary_tract(1)	31	all_cancers(14;0.000139)|all_epithelial(15;2.84e-07)|Lung NSC(17;0.000274)|all_lung(17;0.000798)		Epithelial(11;1.17e-09)|all cancers(13;1.34e-07)|OV - Ovarian serous cystadenocarcinoma(57;3.82e-05)|STAD - Stomach adenocarcinoma(118;0.0957)			AGCTGGAGCCGAGTGGCAGCA	0.493																																					p.R570R		Atlas-SNP	.											.	FBXO43	155	.	0			c.C1708A						.						90.0	90.0	90.0					8																	101146559		1910	4137	6047	SO:0001819	synonymous_variant	286151	exon4			GGAGCCGAGTGGC	BC028709	CCDS47904.1	8q22.3	2004-08-24			ENSG00000156509	ENSG00000156509		"""F-boxes /  ""other"""""	28521	protein-coding gene	gene with protein product		609110					Standard	NR_036491		Approved	Fbx43	uc003yjd.3	Q4G163	OTTHUMG00000164803	ENST00000428847.2:c.1708C>A	chr8.hg19:g.101146559G>T		120.0	0.0		384.0	42.0	NM_001029860		Silent	SNP	ENST00000428847.2	hg19	CCDS47904.1																																																																																			.	.		0.493	FBXO43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380380.1	XM_209918	
SLC30A8	169026	hgsc.bcm.edu	37	8	118159313	118159313	+	Silent	SNP	G	G	A			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr8:118159313G>A	ENST00000456015.2	+	2	192	c.192G>A	c.(190-192)gcG>gcA	p.A64A	SLC30A8_ENST00000519688.1_Silent_p.A15A|SLC30A8_ENST00000427715.2_Silent_p.A15A|SLC30A8_ENST00000521243.1_Silent_p.A15A	NM_173851.2	NP_776250.2	Q8IWU4	ZNT8_HUMAN	solute carrier family 30 (zinc transporter), member 8	64					cellular zinc ion homeostasis (GO:0006882)|insulin secretion (GO:0030073)|positive regulation of insulin secretion (GO:0032024)|regulation of sequestering of zinc ion (GO:0061088)|regulation of vesicle-mediated transport (GO:0060627)|response to glucose (GO:0009749)|response to interferon-gamma (GO:0034341)|response to interleukin-1 (GO:0070555)|sequestering of zinc ion (GO:0032119)|transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)|zinc ion transport (GO:0006829)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|secretory granule membrane (GO:0030667)	protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)			breast(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(18)|ovary(2)|pancreas(2)|skin(5)	41	all_cancers(13;2.11e-22)|Lung NSC(37;6.08e-05)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.203)			AAAAGGGGGCGAATGAGTACG	0.507																																					p.A64A	Ovarian(162;1202 1922 6011 16223 52092)	Atlas-SNP	.											.	SLC30A8	102	.	0			c.G192A						.						174.0	147.0	156.0					8																	118159313		2203	4300	6503	SO:0001819	synonymous_variant	169026	exon2			GGGGGCGAATGAG		CCDS6322.1, CCDS55272.1	8q24.11	2014-08-12			ENSG00000164756			"""Solute carriers"""	20303	protein-coding gene	gene with protein product		611145					Standard	NM_001172811		Approved		uc003yoh.3	Q8IWU4	OTTHUMG00000164962	ENST00000456015.2:c.192G>A	chr8.hg19:g.118159313G>A		172.0	0.0		488.0	97.0	NM_173851	A0AVP9|A5YM39|B4DPE0|Q8TCL3	Silent	SNP	ENST00000456015.2	hg19	CCDS6322.1																																																																																			.	.		0.507	SLC30A8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381205.1	NM_173851	
AP2A2	161	hgsc.bcm.edu	37	11	1000560	1000560	+	Silent	SNP	C	C	T	rs376836623		TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr11:1000560C>T	ENST00000448903.2	+	15	2226	c.2085C>T	c.(2083-2085)gtC>gtT	p.V695V	AP2A2_ENST00000534328.1_Intron|AP2A2_ENST00000332231.5_Silent_p.V696V|AP2A2_ENST00000525891.1_3'UTR	NM_001242837.1|NM_012305.3	NP_001229766.1|NP_036437.1	O94973	AP2A2_HUMAN	adaptor-related protein complex 2, alpha 2 subunit	695					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(2)	21		all_cancers(49;9.46e-06)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.75e-24)|BRCA - Breast invasive adenocarcinoma(625;5.73e-05)|Lung(200;0.0696)|LUSC - Lung squamous cell carcinoma(625;0.082)		CCTCTGTGGTCGCGCCTCTCG	0.697																																					p.V696V		Atlas-SNP	.											.	AP2A2	50	.	0			c.C2088T						.	C	,	1,3965		0,1,1982	11.0	11.0	11.0		2088,2085	-6.6	0.0	11		11	1,8253		0,1,4126	no	coding-synonymous,coding-synonymous	AP2A2	NM_001242837.1,NM_012305.3	,	0,2,6108	TT,TC,CC		0.0121,0.0252,0.0164	,	696/941,695/940	1000560	2,12218	1983	4127	6110	SO:0001819	synonymous_variant	161	exon15			TGTGGTCGCGCCT	AB020706	CCDS44512.1, CCDS73234.1	11p15.5	2008-07-18			ENSG00000183020	ENSG00000183020			562	protein-coding gene	gene with protein product	"""alpha-adaptin C; Huntingtin interacting protein J"", ""adaptin, alpha B"", ""clathrin-associated/assembly/adaptor protein, large, alpha 2"""	607242		CLAPA2, ADTAB		9700202, 2564002	Standard	NM_012305		Approved	DKFZP564D1864, HYPJ, KIAA0899, HIP9	uc001lst.2	O94973	OTTHUMG00000165627	ENST00000448903.2:c.2085C>T	chr11.hg19:g.1000560C>T		38.0	0.0		26.0	8.0	NM_001242837	O75403|Q53ET1|Q96SI8	Silent	SNP	ENST00000448903.2	hg19	CCDS44512.1																																																																																			.	.		0.697	AP2A2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000385431.2	NM_012305	
TUB	7275	hgsc.bcm.edu	37	11	8118839	8118839	+	Missense_Mutation	SNP	T	T	G			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr11:8118839T>G	ENST00000299506.2	+	7	901	c.752T>G	c.(751-753)cTt>cGt	p.L251R	TUB_ENST00000305253.4_Missense_Mutation_p.L306R|TUB_ENST00000534099.1_Missense_Mutation_p.L257R	NM_177972.2	NP_813977.1	P50607	TUB_HUMAN	tubby bipartite transcription factor	251					multicellular organismal macromolecule metabolic process (GO:0044259)|phagocytosis (GO:0006909)|phototransduction (GO:0007602)|positive regulation of phagocytosis (GO:0050766)|response to hormone (GO:0009725)|retina development in camera-type eye (GO:0060041)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled photoreceptor activity (GO:0008020)|protein complex binding (GO:0032403)			breast(1)|cervix(1)|endometrium(9)|large_intestine(7)|lung(5)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	26		all_lung(207;6.91e-20)|Lung NSC(207;3.36e-17)		Epithelial(150;1.69e-62)|BRCA - Breast invasive adenocarcinoma(625;8.54e-06)|LUSC - Lung squamous cell carcinoma(625;0.000184)		GTCCAGGATCTTGAGGAGTTT	0.602																																					p.L306R		Atlas-SNP	.											.	TUB	71	.	0			c.T917G						.						88.0	82.0	84.0					11																	8118839		2201	4296	6497	SO:0001583	missense	7275	exon8			AGGATCTTGAGGA	U54644	CCDS7786.1, CCDS7787.1	11p15.5	2013-08-06	2013-08-06		ENSG00000166402	ENSG00000166402			12406	protein-coding gene	gene with protein product		601197	"""tubby (mouse) homolog"", ""tubby homolog (mouse)"""			8612280	Standard	NM_003320		Approved	rd5	uc001mfy.3	P50607	OTTHUMG00000165690	ENST00000299506.2:c.752T>G	chr11.hg19:g.8118839T>G	ENSP00000299506:p.Leu251Arg	179.0	0.0		203.0	21.0	NM_003320	D3DQU4|O00293|Q6B007	Missense_Mutation	SNP	ENST00000299506.2	hg19	CCDS7787.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.439687	0.83885	.	.	ENSG00000166402	ENST00000534099;ENST00000305253;ENST00000299506	D;D;D	0.85773	-2.03;-2.03;-2.03	4.71	4.71	0.59529	Tubby, C-terminal (1);	0.061993	0.64402	D	0.000003	D	0.92645	0.7663	M	0.86651	2.83	0.80722	D	1	P;D;D	0.76494	0.901;0.999;0.999	B;D;D	0.71656	0.226;0.97;0.974	D	0.93879	0.7169	10	0.72032	D	0.01	-12.0625	14.6238	0.68605	0.0:0.0:0.0:1.0	.	257;251;306	E9PQR4;P50607;P50607-2	.;TUB_HUMAN;.	R	257;306;251	ENSP00000434400:L257R;ENSP00000305426:L306R;ENSP00000299506:L251R	ENSP00000299506:L251R	L	+	2	0	TUB	8075415	1.000000	0.71417	0.910000	0.35882	0.992000	0.81027	7.776000	0.85560	2.115000	0.64714	0.477000	0.44152	CTT	.	.		0.602	TUB-003	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385823.1	NM_003320	
ARHGEF17	9828	hgsc.bcm.edu	37	11	73076531	73076531	+	Missense_Mutation	SNP	G	G	T	rs141322412	byFrequency	TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr11:73076531G>T	ENST00000263674.3	+	19	5997	c.5647G>T	c.(5647-5649)Gtg>Ttg	p.V1883L		NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	1883					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|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)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(2)	32						TAGTGCCCACGTGTGTCTCTA	0.557																																					p.V1883L		Atlas-SNP	.											.	ARHGEF17	117	.	0			c.G5647T						.						160.0	116.0	131.0					11																	73076531		2200	4293	6493	SO:0001583	missense	9828	exon19			GCCCACGTGTGTC	AF378754	CCDS8221.1	11q13.3	2011-11-16			ENSG00000110237	ENSG00000110237		"""Rho guanine nucleotide exchange factors"""	21726	protein-coding gene	gene with protein product	"""Rho-specific guanine-nucleotide exchange factor 164 kDa"", ""tumor endothelial marker 4"""					11559528, 12071859	Standard	NM_014786		Approved	TEM4, KIAA0337, p164-RhoGEF	uc001otu.3	Q96PE2	OTTHUMG00000167971	ENST00000263674.3:c.5647G>T	chr11.hg19:g.73076531G>T	ENSP00000263674:p.Val1883Leu	100.0	0.0		93.0	22.0	NM_014786	B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	Missense_Mutation	SNP	ENST00000263674.3	hg19	CCDS8221.1	.	.	.	.	.	.	.	.	.	.	G	17.35	3.367681	0.61513	.	.	ENSG00000110237	ENST00000263674	T	0.37058	1.22	5.8	4.9	0.64082	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.37404	0.1002	N	0.11000	0.08	0.58432	D	0.999995	D	0.89917	1.0	D	0.81914	0.995	T	0.19647	-1.0299	10	0.13853	T	0.58	-21.1515	14.2313	0.65895	0.0713:0.0:0.9287:0.0	.	1883	Q96PE2	ARHGH_HUMAN	L	1883	ENSP00000263674:V1883L	ENSP00000263674:V1883L	V	+	1	0	ARHGEF17	72754179	1.000000	0.71417	0.997000	0.53966	0.982000	0.71751	7.914000	0.87478	1.484000	0.48361	-0.119000	0.15052	GTG	.	G|0.999;A|0.001		0.557	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397365.1	NM_014786	
BACE1	23621	hgsc.bcm.edu	37	11	117162462	117162462	+	Missense_Mutation	SNP	T	T	G			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr11:117162462T>G	ENST00000313005.6	-	6	1368	c.908A>C	c.(907-909)gAa>gCa	p.E303A	BACE1_ENST00000513780.1_Missense_Mutation_p.E278A|BACE1_ENST00000445823.2_Missense_Mutation_p.E259A|BACE1_ENST00000392937.6_Missense_Mutation_p.E203A|BACE1_ENST00000428381.2_Missense_Mutation_p.E234A|BACE1_ENST00000528053.1_Intron|BACE1_ENST00000514464.1_5'Flank|BACE1_ENST00000510630.1_Missense_Mutation_p.E178A	NM_012104.4|NM_138971.3|NM_138972.3|NM_138973.3	NP_036236|NP_620427.1|NP_620428.1|NP_620429.1	P56817	BACE1_HUMAN	beta-site APP-cleaving enzyme 1	303					beta-amyloid metabolic process (GO:0050435)|membrane protein ectodomain proteolysis (GO:0006509)|proteolysis (GO:0006508)	axon (GO:0030424)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	aspartic-type endopeptidase activity (GO:0004190)|beta-amyloid binding (GO:0001540)|beta-aspartyl-peptidase activity (GO:0008798)|enzyme binding (GO:0019899)			breast(2)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)	19	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.69e-05)|Epithelial(105;0.000563)|all cancers(92;0.0032)		GACTGCAGCTTCAAACACTTT	0.483																																					p.E303A		Atlas-SNP	.											.	BACE1	33	.	0			c.A908C						.						169.0	140.0	150.0					11																	117162462		2201	4296	6497	SO:0001583	missense	23621	exon6			GCAGCTTCAAACA	AF190725	CCDS8383.1, CCDS44739.1, CCDS44740.1, CCDS44741.1, CCDS55787.1, CCDS55786.1	11q23-q24	2011-07-27	2004-04-02	2004-04-02	ENSG00000186318	ENSG00000186318			933	protein-coding gene	gene with protein product		604252	"""beta-site APP-cleaving enzyme"""	BACE		10531052	Standard	NM_012104		Approved		uc001pqz.3	P56817	OTTHUMG00000160636	ENST00000313005.6:c.908A>C	chr11.hg19:g.117162462T>G	ENSP00000318585:p.Glu303Ala	128.0	0.0		127.0	12.0	NM_012104	A0M8W7|B0YIU9|E9PE65|H7BXJ9|Q9BYB9|Q9BYC0|Q9BYC1|Q9UJT5|Q9ULS1	Missense_Mutation	SNP	ENST00000313005.6	hg19	CCDS8383.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.37|14.37	2.514037|2.514037	0.44763|0.44763	.|.	.|.	ENSG00000186318|ENSG00000186318	ENST00000313005;ENST00000392937;ENST00000510630;ENST00000428381;ENST00000513780;ENST00000445823;ENST00000292095|ENST00000530844	T;T;T;T;T|.	0.58060|.	0.36;0.36;0.36;0.36;0.36|.	5.88|5.88	4.7|4.7	0.59300|0.59300	Peptidase aspartic (1);Peptidase aspartic, catalytic (1);|.	0.162995|.	0.53938|.	D|.	0.000042|.	T|.	0.39226|.	0.1070|.	N|N	0.12471|0.12471	0.22|0.22	0.51012|0.51012	D|D	0.9999|0.9999	B;B;B;B;B;B|.	0.10296|.	0.003;0.0;0.001;0.0;0.0;0.0|.	B;B;B;B;B;B|.	0.18871|.	0.022;0.002;0.023;0.005;0.001;0.002|.	T|.	0.23547|.	-1.0185|.	10|.	0.33141|.	T|.	0.24|.	.|.	12.1005|12.1005	0.53780|0.53780	0.0:0.0:0.1432:0.8568|0.0:0.0:0.1432:0.8568	.|.	203;178;303;259;234;278|.	F8W807;E9PE65;P56817;P56817-3;P56817-4;P56817-2|.	.;.;BACE1_HUMAN;.;.;.|.	A|C	303;203;178;234;278;259;69|172	ENSP00000318585:E303A;ENSP00000422461:E178A;ENSP00000402228:E234A;ENSP00000424536:E278A;ENSP00000403685:E259A|.	ENSP00000292095:E69A|.	E|X	-|-	2|3	0|0	BACE1|BACE1	116667672|116667672	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.502000|5.502000	0.66956|0.66956	2.239000|2.239000	0.73571|0.73571	0.533000|0.533000	0.62120|0.62120	GAA|TGA	.	.		0.483	BACE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361505.1		
DNAH10	196385	hgsc.bcm.edu	37	12	124268707	124268707	+	Missense_Mutation	SNP	G	G	C			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr12:124268707G>C	ENST00000409039.3	+	8	1055	c.1030G>C	c.(1030-1032)Gtg>Ctg	p.V344L		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	344	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		TCTCTCCACCGTGGAGCGTTA	0.463																																					p.V344L		Atlas-SNP	.											.	DNAH10	888	.	0			c.G1030C						.						119.0	103.0	108.0					12																	124268707		2203	4300	6503	SO:0001583	missense	196385	exon8			TCCACCGTGGAGC	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"""Axonemal dyneins"""	2941	protein-coding gene	gene with protein product		605884	"""dynein, axonemal, heavy polypeptide 10"""				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.1030G>C	chr12.hg19:g.124268707G>C	ENSP00000386770:p.Val344Leu	91.0	0.0		131.0	38.0	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	hg19	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	G	2.529	-0.308906	0.05458	.	.	ENSG00000197653	ENST00000409039	T	0.31510	1.49	5.87	5.87	0.94306	Dynein heavy chain, domain-1 (1);	0.181280	0.35970	N	0.002870	T	0.09818	0.0241	N	0.00823	-1.155	0.37538	D	0.918198	B	0.10296	0.003	B	0.12837	0.008	T	0.24693	-1.0153	10	0.02654	T	1	.	14.5995	0.68429	0.0:0.2572:0.7428:0.0	.	344	Q8IVF4	DYH10_HUMAN	L	344	ENSP00000386770:V344L	ENSP00000386770:V344L	V	+	1	0	DNAH10	122834660	1.000000	0.71417	0.986000	0.45419	0.624000	0.37722	5.347000	0.65998	2.785000	0.95823	0.655000	0.94253	GTG	.	.		0.463	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
DIS3	22894	hgsc.bcm.edu	37	13	73346861	73346861	+	Silent	SNP	C	C	A			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr13:73346861C>A	ENST00000377767.4	-	9	1456	c.1356G>T	c.(1354-1356)ctG>ctT	p.L452L	DIS3_ENST00000377780.4_Silent_p.L422L|DIS3_ENST00000545453.1_Silent_p.L290L	NM_014953.3	NP_055768.3	Q9Y2L1	RRP44_HUMAN	DIS3 exosome endoribonuclease and 3'-5' exoribonuclease	452					CUT catabolic process (GO:0071034)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of GTPase activity (GO:0043547)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA catabolic process (GO:0016075)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|membrane (GO:0016020)|nuclear exosome (RNase complex) (GO:0000176)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|endonuclease activity (GO:0004519)|guanyl-nucleotide exchange factor activity (GO:0005085)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(7)|kidney(5)|large_intestine(10)|lung(6)|prostate(2)|skin(1)	35		Breast(118;0.0074)|Acute lymphoblastic leukemia(28;0.0195)		GBM - Glioblastoma multiforme(99;0.000181)		GCATCTTTGGCAGAAAACTAA	0.348										Multiple Myeloma(4;0.011)																											p.L452L		Atlas-SNP	.											.	DIS3	103	.	0			c.G1356T						.						103.0	106.0	105.0					13																	73346861		2203	4300	6503	SO:0001819	synonymous_variant	22894	exon9			CTTTGGCAGAAAA	AB023225	CCDS9447.1, CCDS45057.1	13q21.32	2014-03-05	2014-03-05	2007-01-12	ENSG00000083520	ENSG00000083520			20604	protein-coding gene	gene with protein product	"""exosome component 11"""	607533	"""KIAA1008"", ""DIS3 mitotic control homolog (S. cerevisiae)"""	KIAA1008		11935316, 9562621	Standard	XM_005266294		Approved	dis3p, RRP44, EXOSC11	uc001vix.4	Q9Y2L1	OTTHUMG00000017070	ENST00000377767.4:c.1356G>T	chr13.hg19:g.73346861C>A		395.0	1.0		490.0	172.0	NM_014953	A6NI21|B2RBL2|Q5W0P7|Q5W0P8|Q658Z7|Q7Z481|Q8WWI2|Q9UG36	Silent	SNP	ENST00000377767.4	hg19	CCDS9447.1																																																																																			.	.		0.348	DIS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045250.2	NM_014953	
INSM2	84684	hgsc.bcm.edu	37	14	36005072	36005072	+	Silent	SNP	A	A	G			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr14:36005072A>G	ENST00000307169.3	+	1	1825	c.1614A>G	c.(1612-1614)ccA>ccG	p.P538P		NM_032594.3	NP_115983.3	Q96T92	INSM2_HUMAN	insulinoma-associated 2	538					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(1)|large_intestine(1)|lung(3)|skin(1)|urinary_tract(1)	10	Breast(36;0.122)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(9;2.16e-07)|Lung(238;2.63e-07)|Epithelial(34;0.00145)|all cancers(34;0.00452)	GBM - Glioblastoma multiforme(112;0.0223)		TTAGCTCTCCAGGGCTGACCC	0.617																																					p.P538P		Atlas-SNP	.											.	INSM2	39	.	0			c.A1614G						.						33.0	36.0	35.0					14																	36005072		2197	4289	6486	SO:0001819	synonymous_variant	84684	exon1			CTCTCCAGGGCTG	AF260323	CCDS9657.1	14q13.1	2013-01-08			ENSG00000168348	ENSG00000168348		"""Zinc fingers, C2H2-type"""	17539	protein-coding gene	gene with protein product	"""mlt 1"""	614027					Standard	NM_032594		Approved	IA-6	uc001wth.1	Q96T92	OTTHUMG00000140223	ENST00000307169.3:c.1614A>G	chr14.hg19:g.36005072A>G		102.0	0.0		130.0	38.0	NM_032594	A1L432|J9Y024|Q8N8K7|Q96Q84	Silent	SNP	ENST00000307169.3	hg19	CCDS9657.1																																																																																			.	.		0.617	INSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276686.1		
SNAPC1	6617	hgsc.bcm.edu	37	14	62248976	62248976	+	Silent	SNP	A	A	G			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr14:62248976A>G	ENST00000216294.4	+	8	941	c.837A>G	c.(835-837)tcA>tcG	p.S279S		NM_003082.3	NP_003073.1	Q16533	SNPC1_HUMAN	small nuclear RNA activating complex, polypeptide 1, 43kDa	279					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)	13				OV - Ovarian serous cystadenocarcinoma(108;0.0639)|BRCA - Breast invasive adenocarcinoma(234;0.186)		CATCCAAATCAAGAAGGCATC	0.343																																					p.S279S	NSCLC(27;223 907 37180 39193 46568)	Atlas-SNP	.											.	SNAPC1	32	.	0			c.A837G						.						88.0	82.0	84.0					14																	62248976		2203	4300	6503	SO:0001819	synonymous_variant	6617	exon8			CAAATCAAGAAGG	Z47542	CCDS9755.1	14q22	2008-08-11	2002-08-29		ENSG00000023608	ENSG00000023608			11134	protein-coding gene	gene with protein product		600591	"""small nuclear RNA activating complex, polypeptide 1, 43kD"""			9644240	Standard	NM_003082		Approved	SNAP43, PTFgamma	uc001xft.3	Q16533	OTTHUMG00000140343	ENST00000216294.4:c.837A>G	chr14.hg19:g.62248976A>G		105.0	0.0		136.0	54.0	NM_003082		Silent	SNP	ENST00000216294.4	hg19	CCDS9755.1																																																																																			.	.		0.343	SNAPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276976.2	NM_003082	
TECPR2	9895	hgsc.bcm.edu	37	14	102916924	102916924	+	Missense_Mutation	SNP	G	G	A			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr14:102916924G>A	ENST00000359520.7	+	15	3570	c.3344G>A	c.(3343-3345)cGt>cAt	p.R1115H	TECPR2_ENST00000558678.1_Missense_Mutation_p.R1115H	NM_014844.3	NP_055659.2	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2	1115					autophagy (GO:0006914)|cell death (GO:0008219)					breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(21)|ovary(2)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	50						GTGGTTCCCCGTGGGACAGCT	0.463																																					p.R1115H		Atlas-SNP	.											.	TECPR2	114	.	0			c.G3344A						.						110.0	89.0	96.0					14																	102916924		2203	4300	6503	SO:0001583	missense	9895	exon15			TTCCCCGTGGGAC	AB019441	CCDS32162.1, CCDS58337.1	14q32.33	2009-02-27	2009-02-27	2009-02-27		ENSG00000196663			19957	protein-coding gene	gene with protein product		615000	"""KIAA0329"""	KIAA0329		9205841	Standard	NM_014844		Approved		uc001ylw.2	O15040		ENST00000359520.7:c.3344G>A	chr14.hg19:g.102916924G>A	ENSP00000352510:p.Arg1115His	97.0	0.0		107.0	10.0	NM_001172631	A5PKY3|A6NFY9|A7E2X3|H0YMM9|Q9UEG6	Missense_Mutation	SNP	ENST00000359520.7	hg19	CCDS32162.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.842649	0.91197	.	.	ENSG00000196663	ENST00000359520	T	0.16897	2.31	5.38	4.49	0.54785	.	0.057959	0.64402	D	0.000003	T	0.28830	0.0715	L	0.27053	0.805	0.54753	D	0.999986	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.997;0.996;0.998	T	0.03910	-1.0993	10	0.56958	D	0.05	.	14.0237	0.64573	0.073:0.0:0.927:0.0	.	298;1115;1115	B4DSD3;A5PKY3;O15040	.;.;TCPR2_HUMAN	H	1115	ENSP00000352510:R1115H	ENSP00000352510:R1115H	R	+	2	0	TECPR2	101986677	1.000000	0.71417	0.994000	0.49952	0.997000	0.91878	6.980000	0.76160	1.279000	0.44446	0.655000	0.94253	CGT	.	.		0.463	TECPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415056.2	NM_014844	
HERC2	8924	hgsc.bcm.edu	37	15	28437148	28437148	+	Missense_Mutation	SNP	C	C	A	rs571204932		TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr15:28437148C>A	ENST00000261609.7	-	53	8518	c.8410G>T	c.(8410-8412)Ggc>Tgc	p.G2804C		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		GGCTCGCTGCCGTCAATGAGA	0.592											OREG0022997	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G2804C		Atlas-SNP	.											.	HERC2	501	.	0			c.G8410T						.						108.0	96.0	100.0					15																	28437148		2203	4300	6503	SO:0001583	missense	8924	exon53			CGCTGCCGTCAAT	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"""hect domain and RLD 2"""			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.8410G>T	chr15.hg19:g.28437148C>A	ENSP00000261609:p.Gly2804Cys	76.0	0.0	801	70.0	12.0	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	hg19	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	C	15.86	2.957381	0.53400	.	.	ENSG00000128731	ENST00000261609	T	0.71934	-0.61	5.51	4.59	0.56863	Anaphase-promoting complex, subunit 10/DOC domain (2);Galactose-binding domain-like (1);	0.230238	0.45126	D	0.000382	T	0.67458	0.2895	L	0.52011	1.625	0.49798	D	0.999827	B;B	0.18968	0.02;0.032	B;B	0.20955	0.032;0.031	T	0.65553	-0.6140	10	0.54805	T	0.06	.	16.7446	0.85469	0.0:0.8707:0.1293:0.0	.	271;2804	A8KAQ8;O95714	.;HERC2_HUMAN	C	2804	ENSP00000261609:G2804C	ENSP00000261609:G2804C	G	-	1	0	HERC2	26110743	1.000000	0.71417	0.918000	0.36340	0.990000	0.78478	3.938000	0.56583	1.446000	0.47643	0.579000	0.79373	GGC	.	.		0.592	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
FAM98B	283742	hgsc.bcm.edu	37	15	38773609	38773609	+	Silent	SNP	T	T	A			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr15:38773609T>A	ENST00000491535.1	+	7	854	c.846T>A	c.(844-846)atT>atA	p.I282I	FAM98B_ENST00000397609.2_Silent_p.I282I	NM_001042429.1	NP_001035894.1	Q52LJ0	FA98B_HUMAN	family with sequence similarity 98, member B	282						cytoplasm (GO:0005737)|nucleus (GO:0005634)|tRNA-splicing ligase complex (GO:0072669)	poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|skin(1)	8		all_cancers(109;3.11e-17)|all_epithelial(112;2.64e-15)|Lung NSC(122;2.11e-11)|all_lung(180;5.61e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;9e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0209)		CCAAGATCATTAGGACAAGTA	0.418																																					p.I282I		Atlas-SNP	.											.	FAM98B	53	.	0			c.T846A						.						140.0	126.0	131.0					15																	38773609		2200	4297	6497	SO:0001819	synonymous_variant	283742	exon7			GATCATTAGGACA		CCDS10047.2	15q14	2006-11-29		2005-11-20	ENSG00000171262	ENSG00000171262			26773	protein-coding gene	gene with protein product						12477932	Standard	NM_173611		Approved	FLJ38426	uc001zkc.3	Q52LJ0	OTTHUMG00000129831	ENST00000491535.1:c.846T>A	chr15.hg19:g.38773609T>A		188.0	0.0		191.0	38.0	NM_001042429	A8MUW5|Q8N935	Silent	SNP	ENST00000491535.1	hg19	CCDS42015.1																																																																																			.	.		0.418	FAM98B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252071.2	NM_173611	
SEC14L5	9717	hgsc.bcm.edu	37	16	5050723	5050723	+	Silent	SNP	G	G	A	rs534122915		TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr16:5050723G>A	ENST00000251170.7	+	9	1218	c.1038G>A	c.(1036-1038)ggG>ggA	p.G346G		NM_014692.1	NP_055507.1	O43304	S14L5_HUMAN	SEC14-like 5 (S. cerevisiae)	346	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.					integral component of membrane (GO:0016021)|intracellular (GO:0005622)	transporter activity (GO:0005215)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|skin(1)	29						AGGCCGTGGGGGAGGAGGCGC	0.657																																					p.G346G		Atlas-SNP	.											.	SEC14L5	79	.	0			c.G1038A						.						13.0	15.0	15.0					16																	5050723		2010	4126	6136	SO:0001819	synonymous_variant	9717	exon9			CGTGGGGGAGGAG	AB007880	CCDS45403.1	16p13.3	2008-02-05				ENSG00000103184			29032	protein-coding gene	gene with protein product						9455477	Standard	NM_014692		Approved	KIAA0420, PRELID4B	uc002cye.2	O43304		ENST00000251170.7:c.1038G>A	chr16.hg19:g.5050723G>A		112.0	0.0		101.0	19.0	NM_014692		Silent	SNP	ENST00000251170.7	hg19	CCDS45403.1																																																																																			.	.		0.657	SEC14L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434379.1		
KIAA0430	9665	hgsc.bcm.edu	37	16	15706458	15706458	+	Missense_Mutation	SNP	A	A	G			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr16:15706458A>G	ENST00000396368.3	-	17	3636	c.3430T>C	c.(3430-3432)Tcc>Ccc	p.S1144P	CTB-193M12.1_ENST00000549756.1_RNA|KIAA0430_ENST00000548025.1_Missense_Mutation_p.S1141P|KIAA0430_ENST00000602337.1_Missense_Mutation_p.S1141P|KIAA0430_ENST00000344181.3_Missense_Mutation_p.S746P|KIAA0430_ENST00000551742.1_Missense_Mutation_p.S1144P|KIAA0430_ENST00000540441.2_Missense_Mutation_p.S979P	NM_001184998.1|NM_001184999.1|NM_014647.3	NP_001171927.1|NP_001171928.1|NP_055462.2	Q9Y4F3	MARF1_HUMAN	KIAA0430	1144	HTH OST-type 3. {ECO:0000255|PROSITE- ProRule:PRU00975}.				double-strand break repair (GO:0006302)|female meiotic division (GO:0007143)|negative regulation of phosphatase activity (GO:0010923)|oogenesis (GO:0048477)|regulation of gene expression (GO:0010468)	membrane (GO:0016020)|peroxisome (GO:0005777)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(4)|endometrium(8)|kidney(4)|large_intestine(2)|lung(13)|ovary(3)|prostate(5)|skin(1)	40						ATCAGCTTGGAGTATCCGTAG	0.463																																					p.S1144P		Atlas-SNP	.											.	KIAA0430	154	.	0			c.T3430C						.						156.0	158.0	158.0					16																	15706458		2051	4211	6262	SO:0001583	missense	9665	exon17			GCTTGGAGTATCC	AB007890	CCDS10562.2, CCDS53990.1, CCDS55991.1	16p13.11	2013-01-11			ENSG00000166783	ENSG00000166783		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29562	protein-coding gene	gene with protein product	"""limkain b1"", ""protein phosphatase 1, regulatory subunit 34"", ""meiosis arrest female 1"""	614593				9455477, 10493829, 15932519, 22442484, 23090997	Standard	NM_014647		Approved	LKAP, PPP1R34, Marf1	uc010uzw.2	Q9Y4F3	OTTHUMG00000129884	ENST00000396368.3:c.3430T>C	chr16.hg19:g.15706458A>G	ENSP00000379654:p.Ser1144Pro	102.0	0.0		116.0	29.0	NM_001184998	A8MSK2|B2RNX2|B4DYY9|B7ZMG1|B7ZMG2|F8VV09|Q6P1R6|Q8WYR2|Q9Y4J9	Missense_Mutation	SNP	ENST00000396368.3	hg19	CCDS10562.2	.	.	.	.	.	.	.	.	.	.	A	19.38	3.817101	0.70912	.	.	ENSG00000166783	ENST00000396368;ENST00000540441;ENST00000321370;ENST00000344181;ENST00000548025;ENST00000551742;ENST00000551298	T;T;T;T;T	0.50548	0.74;0.74;0.74;0.74;0.74	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.58264	0.2110	L	0.40543	1.245	0.58432	D	0.99999	D;D;D;D	0.89917	0.999;1.0;1.0;0.999	D;D;D;D	0.87578	0.996;0.982;0.982;0.998	T	0.58842	-0.7565	10	0.49607	T	0.09	.	11.5189	0.50539	0.8659:0.0:0.0:0.1341	.	1143;1141;1140;1143	Q9Y4F3-5;F8VV09;Q9Y4F3-4;Q9Y4F3	.;.;.;LKAP_HUMAN	P	1144;979;1084;746;1141;1144;924	ENSP00000379654:S1144P;ENSP00000439819:S979P;ENSP00000341939:S746P;ENSP00000449376:S1141P;ENSP00000450309:S1144P	ENSP00000315718:S1084P	S	-	1	0	KIAA0430	15613959	1.000000	0.71417	0.994000	0.49952	0.886000	0.51366	5.497000	0.66924	2.124000	0.65301	0.523000	0.50628	TCC	.	.		0.463	KIAA0430-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252131.2	NM_014647	
MTSS1L	92154	hgsc.bcm.edu	37	16	70710812	70710812	+	Missense_Mutation	SNP	A	A	C			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr16:70710812A>C	ENST00000338779.6	-	10	1076	c.802T>G	c.(802-804)Tcc>Gcc	p.S268A		NM_138383.2	NP_612392.1	Q765P7	MTSSL_HUMAN	metastasis suppressor 1-like	268	Ser-rich.				filopodium assembly (GO:0046847)|signal transduction (GO:0007165)					breast(1)|central_nervous_system(2)|endometrium(1)|liver(1)|lung(1)|skin(1)	7						CGGGAGCTGGAGCTGCTGGGT	0.607																																					p.S268A		Atlas-SNP	.											.	MTSS1L	22	.	0			c.T802G						.						64.0	59.0	61.0					16																	70710812		2198	4300	6498	SO:0001583	missense	92154	exon10			AGCTGGAGCTGCT		CCDS32476.1	16q22.1	2008-12-16				ENSG00000132613			25094	protein-coding gene	gene with protein product	"""actin-bundling protein with BAIAP2 homology"""					12477932	Standard	XM_006721335		Approved	ABBA-1, LOC92154	uc002ezj.3	Q765P7		ENST00000338779.6:c.802T>G	chr16.hg19:g.70710812A>C	ENSP00000341171:p.Ser268Ala	109.0	0.0		103.0	24.0	NM_138383	A6NJI7|Q9BUA8	Missense_Mutation	SNP	ENST00000338779.6	hg19	CCDS32476.1	.	.	.	.	.	.	.	.	.	.	A	15.88	2.962178	0.53400	.	.	ENSG00000132613	ENST00000338779	T	0.32753	1.44	4.57	4.57	0.56435	.	0.059652	0.64402	D	0.000002	T	0.29652	0.0740	L	0.56769	1.78	0.31391	N	0.677799	B	0.20459	0.045	B	0.17098	0.017	T	0.25433	-1.0132	10	0.19147	T	0.46	-28.5471	13.6248	0.62157	1.0:0.0:0.0:0.0	.	268	Q765P7	MTSSL_HUMAN	A	268	ENSP00000341171:S268A	ENSP00000341171:S268A	S	-	1	0	MTSS1L	69268313	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.057000	0.41365	1.696000	0.51158	0.460000	0.39030	TCC	.	.		0.607	MTSS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434927.3	NM_138383	
PRPF8	10594	hgsc.bcm.edu	37	17	1584925	1584925	+	Missense_Mutation	SNP	A	A	C			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr17:1584925A>C	ENST00000572621.1	-	5	978	c.713T>G	c.(712-714)cTc>cGc	p.L238R	PRPF8_ENST00000304992.6_Missense_Mutation_p.L238R			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	238					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)|U5 snRNA binding (GO:0030623)|U6 snRNA binding (GO:0017070)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		CAGGCGGTAGAGAGTCGACAT	0.468																																					p.L238R		Atlas-SNP	.											.	PRPF8	169	.	0			c.T713G						.						146.0	142.0	143.0					17																	1584925		2203	4300	6503	SO:0001583	missense	10594	exon6			CGGTAGAGAGTCG	AB007510	CCDS11010.1	17p13.3	2013-07-16	2013-06-10		ENSG00000174231	ENSG00000174231			17340	protein-coding gene	gene with protein product		607300	"""PRP8 pre-mRNA processing factor 8 homolog (yeast)"", ""PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)"""	RP13		11468273, 10411133	Standard	NM_006445		Approved	PRPC8, Prp8, hPrp8, SNRNP220	uc002fte.3	Q6P2Q9	OTTHUMG00000090553	ENST00000572621.1:c.713T>G	chr17.hg19:g.1584925A>C	ENSP00000460348:p.Leu238Arg	158.0	0.0		137.0	33.0	NM_006445	O14547|O75965	Missense_Mutation	SNP	ENST00000572621.1	hg19	CCDS11010.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.613477	0.87359	.	.	ENSG00000174231	ENST00000304992	D	0.88664	-2.41	5.84	5.84	0.93424	.	0.061562	0.64402	D	0.000003	D	0.95671	0.8592	M	0.91872	3.25	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96508	0.9376	10	0.87932	D	0	.	16.2141	0.82191	1.0:0.0:0.0:0.0	.	238	Q6P2Q9	PRP8_HUMAN	R	238	ENSP00000304350:L238R	ENSP00000304350:L238R	L	-	2	0	PRPF8	1531675	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.307000	0.96226	2.230000	0.72887	0.528000	0.53228	CTC	.	.		0.468	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438412.2		
TEKT3	64518	hgsc.bcm.edu	37	17	15234544	15234544	+	Missense_Mutation	SNP	A	A	T			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr17:15234544A>T	ENST00000395930.1	-	3	545	c.359T>A	c.(358-360)cTa>cAa	p.L120Q	TEKT3_ENST00000338696.2_Missense_Mutation_p.L120Q	NM_031898.2	NP_114104.1	Q9BXF9	TEKT3_HUMAN	tektin 3	120					cilium morphogenesis (GO:0060271)|regulation of fertilization (GO:0080154)|sperm motility (GO:0030317)	acrosomal membrane (GO:0002080)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				endometrium(1)|kidney(3)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	23				UCEC - Uterine corpus endometrioid carcinoma (92;0.0877)		ATCCACTCTTAGTTTCTCCGA	0.413																																					p.L120Q		Atlas-SNP	.											.	TEKT3	64	.	0			c.T359A						.						241.0	220.0	227.0					17																	15234544		2203	4300	6503	SO:0001583	missense	64518	exon3			ACTCTTAGTTTCT	AF334676	CCDS11169.1	17p12	2011-05-23			ENSG00000125409	ENSG00000125409			14293	protein-coding gene	gene with protein product		612683				11381029, 14735490	Standard	NM_031898		Approved	FLJ32828	uc002gon.3	Q9BXF9	OTTHUMG00000058965	ENST00000395930.1:c.359T>A	chr17.hg19:g.15234544A>T	ENSP00000379263:p.Leu120Gln	170.0	0.0		159.0	44.0	NM_031898	B2RAS7|D3DTT0|Q8N5R5|Q96M48	Missense_Mutation	SNP	ENST00000395930.1	hg19	CCDS11169.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.505815	0.85282	.	.	ENSG00000125409	ENST00000395930;ENST00000338696;ENST00000536146;ENST00000539316	T;T;T;T	0.54479	4.03;4.03;4.03;0.57	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.73674	0.3617	M	0.79011	2.435	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.77448	-0.2584	10	0.87932	D	0	1.5702	16.1054	0.81216	1.0:0.0:0.0:0.0	.	120	Q9BXF9	TEKT3_HUMAN	Q	120	ENSP00000379263:L120Q;ENSP00000343995:L120Q;ENSP00000446111:L120Q;ENSP00000439713:L120Q	ENSP00000343995:L120Q	L	-	2	0	TEKT3	15175269	1.000000	0.71417	0.974000	0.42286	0.932000	0.56968	8.910000	0.92685	2.266000	0.75297	0.533000	0.62120	CTA	.	.		0.413	TEKT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130385.2	NM_031898	
RNF112	7732	hgsc.bcm.edu	37	17	19319264	19319264	+	Missense_Mutation	SNP	C	C	T			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr17:19319264C>T	ENST00000461366.1	+	14	1887	c.1672C>T	c.(1672-1674)Ctc>Ttc	p.L558F	CTB-187M2.2_ENST00000579897.1_RNA	NM_007148.4	NP_009079.2	Q9ULX5	RN112_HUMAN	ring finger protein 112	558						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|zinc ion binding (GO:0008270)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)|urinary_tract(1)	12						GGGGGCCGGGCTCATGGGCCT	0.692																																					p.L558F		Atlas-SNP	.											.	RNF112	37	.	0			c.C1672T						.						10.0	11.0	11.0					17																	19319264		1932	4110	6042	SO:0001583	missense	7732	exon14			GCCGGGCTCATGG	AF054587	CCDS58529.1	17p11.2	2013-01-16	2008-06-13	2008-06-13	ENSG00000128482	ENSG00000128482		"""RING-type (C3HC4) zinc fingers"""	12968	protein-coding gene	gene with protein product		601237	"""zinc finger protein 179"""	ZNF179		8660987, 9806830	Standard	NM_007148		Approved	BFP	uc010vyw.2	Q9ULX5	OTTHUMG00000059601	ENST00000461366.1:c.1672C>T	chr17.hg19:g.19319264C>T	ENSP00000454919:p.Leu558Phe	39.0	0.0		38.0	10.0	NM_007148	O60633|Q7Z5V9	Missense_Mutation	SNP	ENST00000461366.1	hg19	CCDS58529.1																																																																																			.	.		0.692	RNF112-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132549.4	NM_007148	
IKZF3	22806	hgsc.bcm.edu	37	17	37922198	37922198	+	Missense_Mutation	SNP	C	C	T	rs149299224		TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr17:37922198C>T	ENST00000346872.3	-	8	1436	c.1375G>A	c.(1375-1377)Gtc>Atc	p.V459I	IKZF3_ENST00000377945.3_Missense_Mutation_p.V325I|IKZF3_ENST00000377944.3_Missense_Mutation_p.V316I|RP11-94L15.2_ENST00000488188.2_lincRNA|IKZF3_ENST00000467757.1_Missense_Mutation_p.V403I|IKZF3_ENST00000351680.3_Missense_Mutation_p.V420I|IKZF3_ENST00000350532.3_Missense_Mutation_p.V420I|IKZF3_ENST00000377958.2_Missense_Mutation_p.V372I|IKZF3_ENST00000535189.1_Missense_Mutation_p.V425I|IKZF3_ENST00000346243.3_Missense_Mutation_p.V381I|IKZF3_ENST00000583368.1_Missense_Mutation_p.V212I|IKZF3_ENST00000377952.2_Missense_Mutation_p.V238I|IKZF3_ENST00000439167.2_Missense_Mutation_p.V386I|IKZF3_ENST00000439016.2_Missense_Mutation_p.V364I|IKZF3_ENST00000394189.2_Missense_Mutation_p.V277I	NM_012481.4	NP_036613.2	Q9UKT9	IKZF3_HUMAN	IKAROS family zinc finger 3 (Aiolos)	459					B cell activation (GO:0042113)|mesoderm development (GO:0007498)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of B cell proliferation (GO:0030888)|regulation of lymphocyte differentiation (GO:0045619)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(6)|large_intestine(4)|liver(1)|lung(13)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	42	Breast(7;4.5e-103)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			AGGAAGAGGACGCGGCAGTGG	0.547													C|||	1	0.000199681	0.0	0.0	5008	,	,		20447	0.0		0.0	False		,,,				2504	0.001				p.V459I		Atlas-SNP	.											.	IKZF3	79	.	0			c.G1375A						.	C	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	0,4406		0,0,2203	161.0	145.0	150.0		1375,1207,1258,1258,1090,1141	3.5	1.0	17	dbSNP_134	150	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense,missense,missense,missense	IKZF3	NM_012481.3,NM_183228.1,NM_183229.1,NM_183230.1,NM_183231.1,NM_183232.1	29,29,29,29,29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	459/510,403/454,420/471,420/471,364/415,381/432	37922198	1,13005	2203	4300	6503	SO:0001583	missense	22806	exon8			AGAGGACGCGGCA	AF129512	CCDS11346.1, CCDS11347.1, CCDS11348.1, CCDS11349.1, CCDS11350.1, CCDS11351.1, CCDS58539.1, CCDS58540.1, CCDS58541.1, CCDS58542.1, CCDS58543.1, CCDS58544.1, CCDS58545.1, CCDS74055.1	17q11.2	2013-01-08	2006-08-25	2006-08-25	ENSG00000161405	ENSG00000161405		"""Zinc fingers, C2H2-type"", ""IKAROS zinc fingers"""	13178	protein-coding gene	gene with protein product		606221	"""zinc finger protein, subfamily 1A, 3 (Aiolos)"""	ZNFN1A3		9155026, 10552935	Standard	NM_012481		Approved	Aiolos	uc002hsu.4	Q9UKT9	OTTHUMG00000133250	ENST00000346872.3:c.1375G>A	chr17.hg19:g.37922198C>T	ENSP00000344544:p.Val459Ile	113.0	0.0		123.0	19.0	NM_012481	B4DVV5|Q69BL6|Q69BL7|Q69BL8|Q69BL9|Q69BM0|Q69BM1|Q69BM2|Q69BM3|Q69BM5|Q8N574|Q8WWQ9|Q8WWR0|Q8WWR1|Q8WWR2|Q8WWR3	Missense_Mutation	SNP	ENST00000346872.3	hg19	CCDS11346.1	.	.	.	.	.	.	.	.	.	.	C	14.41	2.527813	0.44969	0.0	1.16E-4	ENSG00000161405	ENST00000488188;ENST00000346872;ENST00000377945;ENST00000394189;ENST00000377944;ENST00000377958;ENST00000377952;ENST00000535189;ENST00000351680;ENST00000346243;ENST00000350532;ENST00000467757	T;T;T;T;T;T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99;0.99;0.99;0.99;0.99;0.99	5.51	3.54	0.40534	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	0.000000	0.50627	D	0.000109	T	0.27559	0.0677	N	0.25332	0.735	0.50467	D	0.99987	B;B;P;B;B;B;B;B;B;B;B;B;B	0.37061	0.039;0.295;0.58;0.141;0.22;0.112;0.006;0.427;0.417;0.205;0.039;0.039;0.075	B;B;B;B;B;B;B;B;B;B;B;B;B	0.30029	0.023;0.038;0.088;0.038;0.036;0.102;0.007;0.061;0.102;0.11;0.023;0.023;0.029	T	0.06552	-1.0820	10	0.54805	T	0.06	-15.4234	12.4038	0.55428	0.0:0.8628:0.0:0.1372	.	372;238;277;325;316;425;381;364;420;403;420;386;459	Q9UKT9-9;Q9UKT9-12;Q9UKT9-11;Q9UKT9-13;Q9UKT9-10;Q9UKT9-7;Q9UKT9-6;Q9UKT9-5;Q9UKT9-4;Q9UKT9-2;Q9UKT9-3;Q9UKT9-8;Q9UKT9	.;.;.;.;.;.;.;.;.;.;.;.;IKZF3_HUMAN	I	459;364;325;277;316;372;238;425;420;381;420;403	ENSP00000367180:V325I;ENSP00000377741:V277I;ENSP00000367179:V316I;ENSP00000367194:V372I;ENSP00000367188:V238I;ENSP00000438972:V425I;ENSP00000345622:V420I;ENSP00000341977:V381I;ENSP00000344471:V420I;ENSP00000420463:V403I	ENSP00000341977:V381I	V	-	1	0	IKZF3	35175724	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	4.980000	0.63812	0.718000	0.32166	-0.942000	0.02676	GTC	.	C|1.000;T|0.000		0.547	IKZF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257004.2	NM_012481	
SLC39A11	201266	hgsc.bcm.edu	37	17	70845832	70845832	+	Missense_Mutation	SNP	C	C	T	rs373163649		TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr17:70845832C>T	ENST00000542342.2	-	6	651	c.563G>A	c.(562-564)gGc>gAc	p.G188D	SLC39A11_ENST00000255559.3_Missense_Mutation_p.G181D|SLC39A11_ENST00000579732.1_Missense_Mutation_p.G181D	NM_001159770.1	NP_001153242.1	Q8N1S5	S39AB_HUMAN	solute carrier family 39, member 11	188					zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)			endometrium(1)|large_intestine(4)|liver(2)|lung(4)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	16						CCAGCTGCTGCCGCCGGGCTG	0.597																																					p.G188D	NSCLC(95;736 1527 12296 39625 41839)	Atlas-SNP	.											.	SLC39A11	32	.	0			c.G563A						.						96.0	84.0	88.0					17																	70845832		2203	4300	6503	SO:0001583	missense	201266	exon6			CTGCTGCCGCCGG	AF331643	CCDS11690.1, CCDS54160.1	17q24.3-q25.1	2014-08-12	2013-07-17	2003-10-24	ENSG00000133195	ENSG00000133195		"""Solute carriers"""	14463	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 26"""	C17orf26		11707075	Standard	NM_139177		Approved		uc002jjb.3	Q8N1S5	OTTHUMG00000178306	ENST00000542342.2:c.563G>A	chr17.hg19:g.70845832C>T	ENSP00000445829:p.Gly188Asp	74.0	0.0		62.0	14.0	NM_001159770	B2R8H7|Q8WZ81	Missense_Mutation	SNP	ENST00000542342.2	hg19	CCDS54160.1	.	.	.	.	.	.	.	.	.	.	C	10.15	1.272106	0.23221	.	.	ENSG00000133195	ENST00000542342;ENST00000255559	T;T	0.76448	-0.98;-1.02	5.79	2.56	0.30785	.	0.520844	0.20319	N	0.094663	T	0.52484	0.1737	N	0.02960	-0.455	0.09310	N	0.999999	B;B	0.23316	0.083;0.032	B;B	0.28784	0.094;0.038	T	0.39781	-0.9597	10	0.12430	T	0.62	.	11.1194	0.48279	0.1332:0.6095:0.2572:0.0	.	188;181	Q8N1S5;Q8N1S5-2	S39AB_HUMAN;.	D	188;181	ENSP00000445829:G188D;ENSP00000255559:G181D	ENSP00000255559:G181D	G	-	2	0	SLC39A11	68357427	0.089000	0.21612	0.011000	0.14972	0.044000	0.14063	1.079000	0.30766	0.757000	0.33036	-0.165000	0.13383	GGC	.	.		0.597	SLC39A11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441442.1		
COG1	9382	hgsc.bcm.edu	37	17	71202364	71202364	+	Missense_Mutation	SNP	T	T	G			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr17:71202364T>G	ENST00000299886.4	+	11	2662	c.2582T>G	c.(2581-2583)cTc>cGc	p.L861R		NM_018714.2	NP_061184.1	Q8WTW3	COG1_HUMAN	component of oligomeric golgi complex 1	861					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18			LUSC - Lung squamous cell carcinoma(166;0.197)			ACGCCACACCTCAACAGCAAC	0.443																																					p.L861R		Atlas-SNP	.											.	COG1	46	.	0			c.T2582G						.						132.0	114.0	120.0					17																	71202364		2203	4300	6503	SO:0001583	missense	9382	exon11			CACACCTCAACAG		CCDS11692.1	17q25.1	2008-05-14	2002-05-28	2002-05-31		ENSG00000166685		"""Components of oligomeric golgi complex"""	6545	protein-coding gene	gene with protein product		606973	"""low density lipoprotein receptor defect B complementing"""	LDLB		9927668	Standard	NM_018714		Approved	KIAA1381	uc002jjg.3	Q8WTW3		ENST00000299886.4:c.2582T>G	chr17.hg19:g.71202364T>G	ENSP00000299886:p.Leu861Arg	88.0	0.0		95.0	23.0	NM_018714	Q9NPV9|Q9P2G6	Missense_Mutation	SNP	ENST00000299886.4	hg19	CCDS11692.1	.	.	.	.	.	.	.	.	.	.	T	12.75	2.030189	0.35797	.	.	ENSG00000166685	ENST00000438720;ENST00000299886	T;T	0.47528	0.84;0.85	5.7	5.7	0.88788	.	0.063724	0.64402	D	0.000006	T	0.72581	0.3478	M	0.85859	2.78	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.99;0.999;0.99	T	0.77816	-0.2447	10	0.87932	D	0	-20.1055	15.9745	0.80049	0.0:0.0:0.0:1.0	.	861;861;861	E9PBL8;Q8WTW3;Q4G0L8	.;COG1_HUMAN;.	R	861	ENSP00000400111:L861R;ENSP00000299886:L861R	ENSP00000299886:L861R	L	+	2	0	COG1	68713959	1.000000	0.71417	0.999000	0.59377	0.333000	0.28666	5.748000	0.68697	2.168000	0.68352	0.533000	0.62120	CTC	.	.		0.443	COG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441638.1		
ME2	4200	hgsc.bcm.edu	37	18	48444552	48444552	+	Missense_Mutation	SNP	A	A	G	rs532005925		TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr18:48444552A>G	ENST00000321341.5	+	7	975	c.703A>G	c.(703-705)Att>Gtt	p.I235V	ME2_ENST00000382927.3_Missense_Mutation_p.I235V	NM_002396.4	NP_002387.1	P23368	MAOM_HUMAN	malic enzyme 2, NAD(+)-dependent, mitochondrial	235					malate metabolic process (GO:0006108)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|malate dehydrogenase (decarboxylating) (NAD+) activity (GO:0004471)|metal ion binding (GO:0046872)|NAD binding (GO:0051287)|oxaloacetate decarboxylase activity (GO:0008948)			breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(11)|upper_aerodigestive_tract(3)	23		Colorectal(6;0.0273)|all_epithelial(6;0.118)		Colorectal(21;0.0313)|READ - Rectum adenocarcinoma(32;0.105)|STAD - Stomach adenocarcinoma(97;0.184)		TGATGACCTGATTGATGAGTT	0.353													A|||	1	0.000199681	0.0	0.0	5008	,	,		14551	0.0		0.0	False		,,,				2504	0.001				p.I235V		Atlas-SNP	.											.	ME2	49	.	0			c.A703G						.						71.0	67.0	68.0					18																	48444552		2203	4300	6503	SO:0001583	missense	4200	exon7			GACCTGATTGATG	M55905	CCDS11948.1, CCDS54187.1	18q21	2012-10-02			ENSG00000082212	ENSG00000082212	1.1.1.40		6984	protein-coding gene	gene with protein product		154270				1993674	Standard	NM_002396		Approved		uc002ley.3	P23368	OTTHUMG00000132694	ENST00000321341.5:c.703A>G	chr18.hg19:g.48444552A>G	ENSP00000321070:p.Ile235Val	351.0	0.0		351.0	29.0	NM_001168335	B2R8J2|Q9BWL6|Q9BYG1|Q9H4B2	Missense_Mutation	SNP	ENST00000321341.5	hg19	CCDS11948.1	.	.	.	.	.	.	.	.	.	.	A	10.57	1.387601	0.25031	.	.	ENSG00000082212	ENST00000321341;ENST00000382927	T;T	0.39787	1.06;1.06	5.29	5.29	0.74685	Malic enzyme, N-terminal (2);	0.046188	0.85682	D	0.000000	T	0.25901	0.0631	N	0.16016	0.355	0.58432	D	0.999994	B;B	0.06786	0.0;0.001	B;B	0.20767	0.006;0.031	T	0.08889	-1.0700	10	0.08837	T	0.75	-14.2031	14.5043	0.67743	1.0:0.0:0.0:0.0	.	235;235	Q9BWL6;P23368	.;MAOM_HUMAN	V	235	ENSP00000321070:I235V;ENSP00000372384:I235V	ENSP00000321070:I235V	I	+	1	0	ME2	46698550	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	7.207000	0.77899	2.126000	0.65437	0.528000	0.53228	ATT	.	.		0.353	ME2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255991.1	NM_002396	
DCC	1630	hgsc.bcm.edu	37	18	50923690	50923690	+	Missense_Mutation	SNP	A	A	G			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr18:50923690A>G	ENST00000442544.2	+	18	3317	c.2701A>G	c.(2701-2703)Aca>Gca	p.T901A	DCC_ENST00000581580.1_Missense_Mutation_p.T536A|DCC_ENST00000412726.1_Missense_Mutation_p.T729A	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	901	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		AGAAGACACAACATCTCTAAG	0.343																																					p.T901A		Atlas-SNP	.											.	DCC	360	.	0			c.A2701G						.						108.0	97.0	101.0					18																	50923690		2203	4300	6503	SO:0001583	missense	1630	exon18			GACACAACATCTC	X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2701	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 1"""	120470	"""deleted in colorectal carcinoma"""			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.2701A>G	chr18.hg19:g.50923690A>G	ENSP00000389140:p.Thr901Ala	122.0	0.0		133.0	13.0	NM_005215		Missense_Mutation	SNP	ENST00000442544.2	hg19	CCDS11952.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.54|14.54	2.567038|2.567038	0.45694|0.45694	.|.	.|.	ENSG00000187323|ENSG00000187323	ENST00000304775|ENST00000442544;ENST00000412726	.|T;T	.|0.59224	.|0.28;0.28	5.8|5.8	5.8|5.8	0.92144|0.92144	.|Fibronectin, type III (4);Immunoglobulin-like fold (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.72003|0.72003	0.3407|0.3407	M|M	0.79475|0.79475	2.455|2.455	0.80722|0.80722	D|D	1|1	.|P;P;D	.|0.60160	.|0.947;0.947;0.987	.|D;D;D	.|0.65773	.|0.931;0.931;0.938	T|T	0.69924|0.69924	-0.5013|-0.5013	6|10	0.20046|0.08837	T|T	0.44|0.75	.|.	15.1301|15.1301	0.72517|0.72517	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|729;729;901	.|E7EQM8;B4DYX2;P43146	.|.;.;DCC_HUMAN	S|A	756|901;729	.|ENSP00000389140:T901A;ENSP00000397322:T729A	ENSP00000304146:N756S|ENSP00000397322:T729A	N|T	+|+	2|1	0|0	DCC|DCC	49177688|49177688	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.413000|7.413000	0.80104|0.80104	2.213000|2.213000	0.71641|0.71641	0.528000|0.528000	0.53228|0.53228	AAC|ACA	.	.		0.343	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215	
ZNF57	126295	hgsc.bcm.edu	37	19	2917323	2917323	+	Missense_Mutation	SNP	G	G	A			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr19:2917323G>A	ENST00000306908.5	+	4	852	c.704G>A	c.(703-705)gGg>gAg	p.G235E	ZNF57_ENST00000523428.1_Missense_Mutation_p.G203E|AC006277.2_ENST00000520090.2_RNA	NM_173480.2	NP_775751.1	Q68EA5	ZNF57_HUMAN	zinc finger protein 57	235					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|GBM - Glioblastoma multiforme(1328;0.00161)|STAD - Stomach adenocarcinoma(1328;0.18)		GCGTTTAATGGGTTCGCAAGC	0.463																																					p.G235E	NSCLC(150;910 1964 4303 10464 26498)	Atlas-SNP	.											.	ZNF57	57	.	0			c.G704A						.						97.0	91.0	93.0					19																	2917323		2203	4300	6503	SO:0001583	missense	126295	exon4			TTAATGGGTTCGC	M88368	CCDS12098.1	19p13.3	2013-01-08			ENSG00000171970	ENSG00000171970		"""Zinc fingers, C2H2-type"", ""-"""	13125	protein-coding gene	gene with protein product			"""zinc finger protein 424"""	ZNF424		1505991	Standard	NM_173480		Approved		uc002lwr.3	Q68EA5	OTTHUMG00000164485	ENST00000306908.5:c.704G>A	chr19.hg19:g.2917323G>A	ENSP00000303696:p.Gly235Glu	109.0	0.0		129.0	28.0	NM_173480	Q8N6R9	Missense_Mutation	SNP	ENST00000306908.5	hg19	CCDS12098.1	.	.	.	.	.	.	.	.	.	.	G	9.426	1.084342	0.20309	.	.	ENSG00000171970	ENST00000306908;ENST00000395204;ENST00000523428	T;T	0.14766	2.48;2.48	1.98	-3.96	0.04106	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04452	0.0122	N	0.04508	-0.205	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.35351	-0.9792	9	0.27785	T	0.31	.	2.5155	0.04667	0.3776:0.0:0.2684:0.3539	.	235	Q68EA5	ZNF57_HUMAN	E	235;237;203	ENSP00000303696:G235E;ENSP00000430223:G203E	ENSP00000303696:G235E	G	+	2	0	ZNF57	2868323	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.033000	0.00636	-1.772000	0.01292	-0.424000	0.05967	GGG	.	.		0.463	ZNF57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378969.1	NM_173480	
NRTN	4902	hgsc.bcm.edu	37	19	5827964	5827964	+	Missense_Mutation	SNP	T	T	C			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr19:5827964T>C	ENST00000303212.2	+	2	738	c.374T>C	c.(373-375)gTg>gCg	p.V125A		NM_004558.3	NP_004549.1	Q99748	NRTN_HUMAN	neurturin	125					axon guidance (GO:0007411)|MAPK cascade (GO:0000165)|nerve development (GO:0021675)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neuron projection development (GO:0031175)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	axon (GO:0030424)|extracellular region (GO:0005576)	receptor binding (GO:0005102)			large_intestine(1)	1						GACGAGACGGTGCTGTTCCGC	0.781																																					p.V125A		Atlas-SNP	.											.	NRTN	4	.	0			c.T374C						.																																			SO:0001583	missense	4902	exon2			AGACGGTGCTGTT	U78110	CCDS12151.1	19p13.3	2014-01-30				ENSG00000171119		"""Endogenous ligands"""	8007	protein-coding gene	gene with protein product	"""prepro-neurturin"""	602018				8945474	Standard	NM_004558		Approved	NTN	uc002mde.3	Q99748		ENST00000303212.2:c.374T>C	chr19.hg19:g.5827964T>C	ENSP00000302648:p.Val125Ala	24.0	0.0		35.0	8.0	NM_004558	B2RPE8	Missense_Mutation	SNP	ENST00000303212.2	hg19	CCDS12151.1	.	.	.	.	.	.	.	.	.	.	T	26.8	4.772326	0.90108	.	.	ENSG00000171119	ENST00000303212	D	0.84442	-1.85	4.47	2.26	0.28386	Transforming growth factor-beta, C-terminal (3);	0.155857	0.42420	D	0.000715	D	0.87410	0.6170	L	0.61218	1.895	0.37760	D	0.926282	D	0.53885	0.963	P	0.62491	0.903	D	0.85333	0.1091	10	0.72032	D	0.01	-13.1242	4.9046	0.13791	0.1634:0.0954:0.0:0.7412	.	125	Q99748	NRTN_HUMAN	A	125	ENSP00000302648:V125A	ENSP00000302648:V125A	V	+	2	0	NRTN	5778964	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	4.275000	0.58927	0.171000	0.19730	0.397000	0.26171	GTG	.	.		0.781	NRTN-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451882.2	NM_004558	
FARSA	2193	hgsc.bcm.edu	37	19	13039211	13039211	+	Silent	SNP	G	G	T			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr19:13039211G>T	ENST00000314606.4	-	7	804	c.786C>A	c.(784-786)ctC>ctA	p.L262L	FARSA_ENST00000588025.1_Silent_p.L302L|CTC-425F1.2_ENST00000592636.1_RNA|FARSA_ENST00000423140.2_Silent_p.L231L	NM_004461.2	NP_004452.1	Q9Y285	SYFA_HUMAN	phenylalanyl-tRNA synthetase, alpha subunit	262					gene expression (GO:0010467)|phenylalanyl-tRNA aminoacylation (GO:0006432)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|phenylalanine-tRNA ligase activity (GO:0004826)|poly(A) RNA binding (GO:0044822)|tRNA binding (GO:0000049)			NS(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(3)|upper_aerodigestive_tract(1)	20					L-Phenylalanine(DB00120)	GGGGCTGGAAGAGGGCGTCAA	0.602																																					p.L262L		Atlas-SNP	.											.	FARSA	46	.	0			c.C786A						.						103.0	99.0	100.0					19																	13039211		2203	4300	6503	SO:0001819	synonymous_variant	2193	exon7			CTGGAAGAGGGCG	U07424	CCDS12287.1	19p13.2	2014-05-06	2007-02-23	2007-02-23	ENSG00000179115	ENSG00000179115	6.1.1.20	"""Aminoacyl tRNA synthetases / Class II"""	3592	protein-coding gene	gene with protein product	"""phenylalanine tRNA ligase 1, alpha, cytoplasmic"""	602918	"""phenylalanine-tRNA synthetase-like"", ""phenylalanyl-tRNA synthetase-like, alpha subunit"""	FARSL, FARSLA		9177188	Standard	NM_004461		Approved	CML33	uc002mvs.2	Q9Y285	OTTHUMG00000180569	ENST00000314606.4:c.786C>A	chr19.hg19:g.13039211G>T		133.0	0.0		117.0	21.0	NM_004461	B4E363|Q9NSD8|Q9Y4W8	Silent	SNP	ENST00000314606.4	hg19	CCDS12287.1																																																																																			.	.		0.602	FARSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451935.1	NM_004461	
CEACAM7	1087	hgsc.bcm.edu	37	19	42192077	42192077	+	Silent	SNP	G	G	T			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr19:42192077G>T	ENST00000006724.3	-	1	219	c.18C>A	c.(16-18)gcC>gcA	p.A6A	CEACAM7_ENST00000599715.1_Intron|CEACAM7_ENST00000401731.1_Silent_p.A6A|CEACAM7_ENST00000602225.1_Silent_p.A6A|CEACAM7_ENST00000338196.4_Silent_p.A6A	NM_006890.3	NP_008821.1	Q14002	CEAM7_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 7	6						anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	18				OV - Ovarian serous cystadenocarcinoma(3;0.0027)|all cancers(3;0.00979)|Epithelial(262;0.0366)		TGTATGGACAGGCTGAAGGGG	0.612																																					p.A6A		Atlas-SNP	.											.	CEACAM7	33	.	0			c.C18A						.						82.0	69.0	74.0					19																	42192077		2203	4300	6503	SO:0001819	synonymous_variant	1087	exon1			TGGACAGGCTGAA	X98311	CCDS12583.1	19q13.2	2013-01-29			ENSG00000007306	ENSG00000007306		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1819	protein-coding gene	gene with protein product	"""carcinoembryonic antigen gene family member 2"""			CGM2		7806520, 9135022	Standard	XM_005278379		Approved	CEA	uc002ori.1	Q14002	OTTHUMG00000151063	ENST00000006724.3:c.18C>A	chr19.hg19:g.42192077G>T		73.0	0.0		73.0	19.0	NM_006890	A8K848|O15148|O15149|Q0VAC1|Q13983|Q9UPJ2	Silent	SNP	ENST00000006724.3	hg19	CCDS12583.1																																																																																			.	.		0.612	CEACAM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321145.1	NM_006890	
CD79A	973	hgsc.bcm.edu	37	19	42383663	42383663	+	Silent	SNP	A	A	G			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr19:42383663A>G	ENST00000221972.3	+	3	623	c.438A>G	c.(436-438)acA>acG	p.T146T	CD79A_ENST00000444740.2_Silent_p.T108T	NM_001783.3|NM_021601.3	NP_001774.1|NP_067612.1	P11912	CD79A_HUMAN	CD79a molecule, immunoglobulin-associated alpha	146					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)	B cell receptor complex (GO:0019815)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			large_intestine(3)|lung(3)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	11						GAATCATCACAGCCGAGGGGA	0.667			"""O, S"""		DLBCL																																p.T146T		Atlas-SNP	.		Dom	yes		19	19q13.2	973	"""CD79a molecule, immunoglobulin-associated alpha"""		L	.	CD79A	25	.	0			c.A438G						.						64.0	34.0	44.0					19																	42383663		2203	4297	6500	SO:0001819	synonymous_variant	973	exon3			CATCACAGCCGAG	M80462	CCDS12589.1, CCDS46088.1	19q13.2	2014-09-17	2006-03-28					"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1698	protein-coding gene	gene with protein product		112205	"""CD79A antigen (immunoglobulin-associated alpha)"""	IGA		1538135	Standard	NM_001783		Approved	MB-1	uc002orv.3	P11912		ENST00000221972.3:c.438A>G	chr19.hg19:g.42383663A>G		52.0	0.0		46.0	16.0	NM_001783	A0N775|Q53FB8	Silent	SNP	ENST00000221972.3	hg19	CCDS12589.1																																																																																			.	.		0.667	CD79A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463058.1		
ZNF772	400720	hgsc.bcm.edu	37	19	57985762	57985762	+	Missense_Mutation	SNP	T	T	C			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr19:57985762T>C	ENST00000343280.4	-	5	610	c.350A>G	c.(349-351)gAg>gGg	p.E117G	AC004076.9_ENST00000415705.3_Intron|ZNF772_ENST00000600175.1_Intron|AC004076.9_ENST00000596831.1_Intron|ZNF772_ENST00000427512.2_Missense_Mutation_p.E5G|ZNF772_ENST00000601768.1_Intron|ZNF772_ENST00000425074.3_Missense_Mutation_p.R34G|ZNF772_ENST00000356584.3_Missense_Mutation_p.E76G	NM_001024596.2	NP_001019767.1	Q68DY9	ZN772_HUMAN	zinc finger protein 772	117					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|large_intestine(4)|lung(3)	9		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)|Lung(386;0.174)		AAAAGGTATCTCTTCATCCTC	0.468																																					p.E117G	Melanoma(5;289 436 14293 15924 30817)	Atlas-SNP	.											.	ZNF772	42	.	0			c.A350G						.						76.0	81.0	79.0					19																	57985762		2203	4300	6503	SO:0001583	missense	400720	exon5			GGTATCTCTTCAT	BX647068	CCDS33133.1, CCDS46210.1	19q13.43	2013-01-08				ENSG00000197128		"""Zinc fingers, C2H2-type"", ""-"""	33106	protein-coding gene	gene with protein product							Standard	NM_001024596		Approved	DKFZp686I1569	uc002qot.3	Q68DY9		ENST00000343280.4:c.350A>G	chr19.hg19:g.57985762T>C	ENSP00000341165:p.Glu117Gly	26.0	0.0		25.0	6.0	NM_001024596	A6NJK9|B4DH56|B4DYS0	Missense_Mutation	SNP	ENST00000343280.4	hg19	CCDS33133.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.597|9.597	1.127675|1.127675	0.20959|0.20959	.|.	.|.	ENSG00000197128|ENSG00000197128	ENST00000343280;ENST00000427512;ENST00000319969;ENST00000356584;ENST00000291809|ENST00000415705	T;T;T|.	0.08634|.	3.25;3.07;5.6|.	3.36|3.36	3.36|3.36	0.38483|0.38483	.|.	.|.	.|.	.|.	.|.	T|T	0.40670|0.40670	0.1126|0.1126	L|L	0.43923|0.43923	1.385|1.385	0.09310|0.09310	N|N	1|1	P;P;P|.	0.48016|.	0.904;0.734;0.734|.	B;B;B|.	0.42798|.	0.305;0.247;0.398|.	T|T	0.23048|0.23048	-1.0199|-1.0199	9|5	0.45353|.	T|.	0.12|.	.|.	10.0555|10.0555	0.42241|0.42241	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	5;76;117|.	Q68DY9-2;A6NJK9;Q68DY9|.	.;.;ZN772_HUMAN|.	G|G	117;5;63;76;96|34	ENSP00000341165:E117G;ENSP00000395967:E5G;ENSP00000348992:E76G|.	ENSP00000291809:E96G|.	E|R	-|-	2|1	0|2	ZNF772|ZNF772	62677574|62677574	0.173000|0.173000	0.23056|0.23056	0.010000|0.010000	0.14722|0.14722	0.201000|0.201000	0.24016|0.24016	3.454000|3.454000	0.52986|0.52986	1.553000|1.553000	0.49476|0.49476	0.402000|0.402000	0.26972|0.26972	GAG|AGA	.	.		0.468	ZNF772-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397447.1	NM_001024596	
CYYR1	116159	hgsc.bcm.edu	37	21	27840930	27840930	+	Missense_Mutation	SNP	C	C	A	rs371412046		TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr21:27840930C>A	ENST00000299340.4	-	4	698	c.355G>T	c.(355-357)Gac>Tac	p.D119Y	CYYR1_ENST00000435845.2_3'UTR|AP001596.6_ENST00000421771.1_RNA|AP001596.6_ENST00000429340.1_RNA|AP001596.6_ENST00000444306.1_RNA|AP001597.1_ENST00000414486.1_RNA|AP001597.1_ENST00000357401.3_RNA	NM_052954.2	NP_443186.1	Q96J86	CYYR1_HUMAN	cysteine/tyrosine-rich 1	119						integral component of membrane (GO:0016021)				large_intestine(2)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	15						ATCTCGTGGTCGTGACCGTAG	0.532																																					p.D119Y		Atlas-SNP	.											.	CYYR1	38	.	0			c.G355T						.						114.0	93.0	100.0					21																	27840930		2203	4300	6503	SO:0001583	missense	116159	exon4			CGTGGTCGTGACC	AY061853	CCDS13578.1	21q21.2	2014-07-04	2005-07-24		ENSG00000166265	ENSG00000166265			16274	protein-coding gene	gene with protein product			"""cysteine and tyrosine-rich 1"""	C21orf95		12036297, 12062809, 24981926	Standard	NM_052954		Approved		uc002ymd.3	Q96J86	OTTHUMG00000078689	ENST00000299340.4:c.355G>T	chr21.hg19:g.27840930C>A	ENSP00000299340:p.Asp119Tyr	79.0	0.0		53.0	11.0	NM_052954	A0A059TD09|A8MTU9|B2R845|Q53ER3|Q5JPD0|Q96NV7|R9QAJ4|W8CQB3	Missense_Mutation	SNP	ENST00000299340.4	hg19	CCDS13578.1	.	.	.	.	.	.	.	.	.	.	C	11.18	1.562065	0.27915	.	.	ENSG00000166265	ENST00000299340	T	0.37752	1.18	3.99	2.18	0.27775	.	0.240351	0.47852	D	0.000201	T	0.46151	0.1378	L	0.53249	1.67	0.51233	D	0.999916	D;D	0.63880	0.993;0.989	P;P	0.62649	0.884;0.905	T	0.39800	-0.9596	10	0.87932	D	0	-18.5615	6.5007	0.22168	0.0:0.7817:0.0:0.2183	.	120;119	Q96J86-2;Q96J86	.;CYYR1_HUMAN	Y	119	ENSP00000299340:D119Y	ENSP00000299340:D119Y	D	-	1	0	CYYR1	26762801	0.922000	0.31269	0.609000	0.28983	0.139000	0.21198	1.633000	0.37113	0.652000	0.30806	0.555000	0.69702	GAC	.	.		0.532	CYYR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171654.2	NM_052954	
FOXRED2	80020	hgsc.bcm.edu	37	22	36900813	36900813	+	Splice_Site	SNP	G	G	A			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr22:36900813G>A	ENST00000397224.4	-	3	621	c.528C>T	c.(526-528)agC>agT	p.S176S	FOXRED2_ENST00000216187.6_Splice_Site_p.S176S|FOXRED2_ENST00000397223.4_Splice_Site_p.S176S	NM_001102371.1	NP_001095841.1	Q8IWF2	FXRD2_HUMAN	FAD-dependent oxidoreductase domain containing 2	176					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	endoplasmic reticulum lumen (GO:0005788)	flavin adenine dinucleotide binding (GO:0050660)|glycoprotein binding (GO:0001948)|oxidoreductase activity (GO:0016491)			breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						CAAAGAGGACGCTGCAGGCGG	0.562																																					p.S176S		Atlas-SNP	.											.	FOXRED2	48	.	0			c.C528T						.						36.0	39.0	38.0					22																	36900813		2203	4300	6503	SO:0001630	splice_region_variant	80020	exon3			GAGGACGCTGCAG	BC027716	CCDS13929.1	22q12.3	2006-07-05			ENSG00000100350	ENSG00000100350			26264	protein-coding gene	gene with protein product		613777				12477932	Standard	NM_024955		Approved	FLJ23322	uc003app.4	Q8IWF2	OTTHUMG00000044614	ENST00000397224.4:c.528-1C>T	chr22.hg19:g.36900813G>A		105.0	0.0		116.0	29.0	NM_001102371	B2RDI4|Q8N378|Q96BD1|Q9H5L5|Q9H6M8	Silent	SNP	ENST00000397224.4	hg19	CCDS13929.1																																																																																			.	.		0.562	FOXRED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104098.2	NM_024955	Silent
SHANK3	85358	hgsc.bcm.edu	37	22	51117297	51117297	+	Silent	SNP	G	G	A			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr22:51117297G>A	ENST00000414786.2	+	5	776	c.549G>A	c.(547-549)ggG>ggA	p.G183G	SHANK3_ENST00000445220.2_Silent_p.G183G|SHANK3_ENST00000262795.3_Silent_p.G183G			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	183					adult behavior (GO:0030534)|alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|brain morphogenesis (GO:0048854)|dendritic spine morphogenesis (GO:0060997)|guanylate kinase-associated protein clustering (GO:0097117)|learning (GO:0007612)|MAPK cascade (GO:0000165)|memory (GO:0007613)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell volume (GO:0045794)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glutamate receptor signaling pathway (GO:1900451)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse structural plasticity (GO:0051835)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density assembly (GO:0097107)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of long term synaptic depression (GO:1900452)|regulation of long-term synaptic potentiation (GO:1900271)|social behavior (GO:0035176)|striatal medium spiny neuron differentiation (GO:0021773)|synapse assembly (GO:0007416)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(5)	8		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)		CTCGCGATGGGCTCACTGCCG	0.667																																					p.G183G		Atlas-SNP	.											.	SHANK3	96	.	0			c.G549A						.						32.0	35.0	34.0					22																	51117297		2118	4218	6336	SO:0001819	synonymous_variant	85358	exon5			CGATGGGCTCACT	AB051437		22q13.3	2013-11-14			ENSG00000251322	ENSG00000251322		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	14294	protein-coding gene	gene with protein product	"""proline rich synapse associated protein 2"", ""shank postsynaptic density protein"""	606230				11258795, 11431708, 10806096, 17173049	Standard	NM_033517		Approved	SPANK-2, prosap2, KIAA1650, PSAP2	uc031ryd.1	Q9BYB0	OTTHUMG00000150169	ENST00000414786.2:c.549G>A	chr22.hg19:g.51117297G>A		97.0	0.0		93.0	17.0	NM_033517	D7UT47|Q8TET3	Silent	SNP	ENST00000414786.2	hg19																																																																																				.	.		0.667	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420	
PRKX	5613	hgsc.bcm.edu	37	X	3573254	3573254	+	Silent	SNP	G	G	A			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chrX:3573254G>A	ENST00000262848.5	-	3	889	c.535C>T	c.(535-537)Ctg>Ttg	p.L179L	PRKX_ENST00000425240.1_5'UTR	NM_005044.4	NP_005035.1	P51817	PRKX_HUMAN	protein kinase, X-linked	179	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|endothelial cell migration (GO:0043542)|endothelial cell proliferation (GO:0001935)|epithelial tube morphogenesis (GO:0060562)|kidney morphogenesis (GO:0060993)|myeloid cell differentiation (GO:0030099)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of epithelial cell differentiation involved in kidney development (GO:2000696)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)			kidney(1)|large_intestine(2)|lung(6)|pancreas(1)|skin(2)	12		all_lung(23;0.000396)|Lung NSC(23;0.00123)				CTATCCAGCAGGATGTTCTCT	0.522																																					p.L179L		Atlas-SNP	.											.	PRKX	29	.	0			c.C535T						.						157.0	128.0	138.0					X																	3573254		2203	4300	6503	SO:0001819	synonymous_variant	5613	exon3			CCAGCAGGATGTT		CCDS14125.1	Xp22.3	2008-08-01			ENSG00000183943	ENSG00000183943	2.7.11.1		9441	protein-coding gene	gene with protein product		300083				7633447	Standard	NM_005044		Approved	PKX1	uc010nde.3	P51817	OTTHUMG00000021087	ENST00000262848.5:c.535C>T	chrX.hg19:g.3573254G>A		127.0	0.0		118.0	51.0	NM_005044		Silent	SNP	ENST00000262848.5	hg19	CCDS14125.1																																																																																			.	.		0.522	PRKX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055659.1	NM_005044	
MT-ND5	4540	hgsc.bcm.edu	37	M	12818	12818	+	Missense_Mutation	SNP	G	G	A			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chrM:12818G>A	ENST00000361567.2	+	1	482	c.482G>A	c.(481-483)cGa>cAa	p.R161Q	MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TH_ENST00000387441.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-CYB_ENST00000361789.2_5'Flank			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	161					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						ATGATACGCCCGAGCAGATGC	0.458																																					p.R161Q		Atlas-SNP	.											.	.	.	.	0			c.G482A						.																																			SO:0001583	missense	0	exon1			ACGCCCGAGCAGA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.482G>A	chrM.hg19:g.12818G>A	ENSP00000354813:p.Arg161Gln	25.0	0.0		71.0	15.0	ENST00000361567	Q34773|Q8WCY3	Missense_Mutation	SNP	ENST00000361567.2	hg19																																																																																				.	.		0.458	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
MT-ND6	4541	hgsc.bcm.edu	37	M	14384	14384	+	Missense_Mutation	SNP	G	G	A			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chrM:14384G>A	ENST00000361681.2	-	1	289	c.290C>T	c.(289-291)gCg>gTg	p.A97V	MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TE_ENST00000387459.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-TH_ENST00000387441.1_RNA|MT-CYB_ENST00000361789.2_5'Flank			P03923	NU6M_HUMAN	mitochondrially encoded NADH dehydrogenase 6	97					cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|respiratory chain (GO:0070469)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(10)|kidney(17)|urinary_tract(1)	29						CTACCTCCATCGCTAACCCCA	0.468																																					p.A97V		Atlas-SNP	.											.	.	.	.	0			c.C290T						.																																			SO:0001583	missense	0	exon1			TCCATCGCTAACC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198695	ENSG00000198695	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7462	protein-coding gene	gene with protein product	"""complex I ND6 subunit"", ""NADH-ubiquinone oxidoreductase chain 6"""	516006	"""NADH dehydrogenase 6"""	MTND6			Standard			Approved	NAD6, ND6		P03923		ENST00000361681.2:c.290C>T	chrM.hg19:g.14384G>A	ENSP00000354665:p.Ala97Val	44.0	0.0		109.0	6.0	ENST00000361681	Q34774|Q8HG30	Missense_Mutation	SNP	ENST00000361681.2	hg19																																																																																				.	.		0.468	MT-ND6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024037	
TAT	6898	hgsc.bcm.edu	37	16	71604656	71604657	+	Frame_Shift_Ins	INS	-	-	G			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr16:71604656_71604657insG	ENST00000355962.4	-	8	970_971	c.837_838insC	c.(835-840)gccaagfs	p.K280fs	RP11-432I5.1_ENST00000561529.1_RNA	NM_000353.2	NP_000344.1	P17735	ATTY_HUMAN	tyrosine aminotransferase	280					2-oxoglutarate metabolic process (GO:0006103)|biosynthetic process (GO:0009058)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate metabolic process (GO:0006536)|L-phenylalanine catabolic process (GO:0006559)|response to glucocorticoid (GO:0051384)|response to mercury ion (GO:0046689)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|L-phenylalanine:2-oxoglutarate aminotransferase activity (GO:0080130)|L-tyrosine:2-oxoglutarate aminotransferase activity (GO:0004838)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(3)	29		Ovarian(137;0.125)		Kidney(780;0.0157)	L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)	AGCCAGCGCTTGGCCAGCCCTC	0.52																																					p.K280fs	Melanoma(198;542 2142 10292 21661 50033)|Esophageal Squamous(48;487 1013 5572 44395 52594)	Atlas-Indel,Pindel	.											.	TAT	80	.	0			c.838_839insC						.																																			SO:0001589	frameshift_variant	6898	exon8			.		CCDS10903.1	16q22.1	2012-10-02			ENSG00000198650	ENSG00000198650	2.6.1.5		11573	protein-coding gene	gene with protein product		613018					Standard	NM_000353		Approved		uc002fap.2	P17735	OTTHUMG00000137590	ENST00000355962.4:c.838dupC	chr16.hg19:g.71604658_71604658dupG	ENSP00000348234:p.Lys280fs	159.0	0.0		124.0	25.0	NM_000353	B2R8I1|D3DWS2	Frame_Shift_Ins	INS	ENST00000355962.4	hg19	CCDS10903.1																																																																																			.	.		0.520	TAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268989.1		
PPAP2C	8612	hgsc.bcm.edu	37	19	287737	287737	+	Frame_Shift_Del	DEL	T	T	-			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr19:287737delT	ENST00000269812.3	-	3	268	c.219delA	c.(217-219)gaafs	p.E73fs	PPAP2C_ENST00000327790.3_Frame_Shift_Del_p.E94fs|PPAP2C_ENST00000434325.2_Frame_Shift_Del_p.E17fs	NM_003712.2|NM_177526.1	NP_003703.1|NP_803545.1	O43688	LPP2_HUMAN	phosphatidic acid phosphatase type 2C	73					dephosphorylation (GO:0016311)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidate phosphatase activity (GO:0008195)|phosphoprotein phosphatase activity (GO:0004721)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(1)|skin(1)	5		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCAGGTAGGCTTCCCCGGCCG	0.642																																					p.A95fs		Atlas-INDEL	.											.	PPAP2C	38	.	0			c.283delG						.						114.0	134.0	127.0					19																	287737		2203	4300	6503	SO:0001589	frameshift_variant	8612	exon3			.	AF035959	CCDS12023.1, CCDS12024.1, CCDS45889.1	19p13	2009-05-27				ENSG00000141934	3.1.3.4		9230	protein-coding gene	gene with protein product		607126				9570154, 9607309	Standard	NM_177543		Approved	PAP-2c, LPP2	uc002loh.3	O43688		ENST00000269812.3:c.219delA	chr19.hg19:g.287737delT	ENSP00000269812:p.Glu73fs	75.0	0.0		81.0	11.0	NM_177543	A6NLV0|E9PAY8	Frame_Shift_Del	DEL	ENST00000269812.3	hg19	CCDS12023.1																																																																																			.	.		0.642	PPAP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451777.2		
EHBP1L1	254102	hgsc.bcm.edu	37	11	65350076	65350076	+	Frame_Shift_Del	DEL	G	G	-			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr11:65350076delG	ENST00000309295.4	+	9	2198	c.1933delG	c.(1933-1935)gggfs	p.G645fs		NM_001099409.1	NP_001092879.1	Q8N3D4	EH1L1_HUMAN	EH domain binding protein 1-like 1	645	Glu-rich.					membrane (GO:0016020)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						AGAGACCCCAGGGACAGAGAC	0.547																																					p.P644fs		Atlas-Indel,Pindel	.											.	EHBP1L1	64	.	0			c.1932delA						.						51.0	56.0	54.0					11																	65350076		1914	4144	6058	SO:0001589	frameshift_variant	254102	exon9			.	AL834433	CCDS44649.1	11q13.1	2008-02-05			ENSG00000173442	ENSG00000173442			30682	protein-coding gene	gene with protein product							Standard	NM_001099409		Approved	DKFZp762C186, TANGERIN	uc001oeo.4	Q8N3D4	OTTHUMG00000166520	ENST00000309295.4:c.1933delG	chr11.hg19:g.65350076delG	ENSP00000312671:p.Gly645fs	140.0	0.0		118.0	29.0	NM_001099409	Q8TB89|Q9H7M7	Frame_Shift_Del	DEL	ENST00000309295.4	hg19	CCDS44649.1																																																																																			.	.		0.547	EHBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390145.1	XM_170658	
HRG	3273	hgsc.bcm.edu	37	3	186386775	186386776	+	Frame_Shift_Ins	INS	-	-	C	rs4516605	byFrequency	TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr3:186386775_186386776insC	ENST00000232003.4	+	2	315_316	c.235_236insC	c.(235-237)tcgfs	p.S79fs		NM_000412.2	NP_000403.1	P04196	HRG_HUMAN	histidine-rich glycoprotein	79	Cystatin 1.|Interaction with ATP5A1.		S -> L (in dbSNP:rs4516605).		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|chemotaxis (GO:0006935)|defense response to fungus (GO:0050832)|fibrinolysis (GO:0042730)|heme export (GO:0097037)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel remodeling (GO:2000504)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of immune response to tumor cell (GO:0002839)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet activation (GO:0010543)|regulation of protein complex assembly (GO:0043254)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|response to organic cyclic compound (GO:0014070)	blood microparticle (GO:0072562)|endolysosome (GO:0036019)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|phagolysosome membrane (GO:0061474)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heme binding (GO:0020037)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|immunoglobulin binding (GO:0019865)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(12)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0683)		ATCGGACTGTTCGGTCCTATCC	0.436																																					p.S79fs		Atlas-Indel,Pindel	.											.	HRG	81	.	0			c.235_236insC						.																																			SO:0001589	frameshift_variant	3273	exon2			.		CCDS3280.1	3q27	2008-07-18			ENSG00000113905	ENSG00000113905			5181	protein-coding gene	gene with protein product	"""histidine-proline rich glycoprotein"", ""thrombophilia due to elevated HRG"""	142640				1678514	Standard	NM_000412		Approved	HRGP, HPRG	uc003fqq.3	P04196	OTTHUMG00000156578	ENST00000232003.4:c.236dupC	chr3.hg19:g.186386776_186386776dupC	ENSP00000232003:p.Ser79fs	89.0	0.0		103.0	15.0	NM_000412	B9EK35|D3DNU7	Frame_Shift_Ins	INS	ENST00000232003.4	hg19	CCDS3280.1																																																																																			.	.		0.436	HRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344655.1	NM_000412	
MRPL22	29093	hgsc.bcm.edu	37	5	154320807	154320807	+	Frame_Shift_Del	DEL	G	G	-			TCGA-2Y-A9GW-01A-11D-A382-10	TCGA-2Y-A9GW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8a09bb43-1c6d-4d41-901b-0dac97a29aee	c1a9c723-e7ce-4a26-a984-08403614980f	g.chr5:154320807delG	ENST00000523037.1	+	2	100	c.59delG	c.(58-60)cggfs	p.R20fs	MRPL22_ENST00000522038.1_Frame_Shift_Del_p.R20fs|MRPL22_ENST00000439747.3_Frame_Shift_Del_p.R46fs|MRPL22_ENST00000265229.8_5'UTR	NM_014180.3	NP_054899.2	Q9NWU5	RM22_HUMAN	mitochondrial ribosomal protein L22	20					translation (GO:0006412)	large ribosomal subunit (GO:0015934)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|urinary_tract(2)	10	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			CTGAGGAGCCGGGGGAAGCTG	0.537																																					p.R20fs		Atlas-Indel,Pindel	.											.	MRPL22	18	.	0			c.58delC						.						107.0	110.0	109.0					5																	154320807		2203	4300	6503	SO:0001589	frameshift_variant	29093	exon2			.	AB051622	CCDS4331.1, CCDS43391.1	5q33.2	2012-09-13			ENSG00000082515	ENSG00000082515		"""Mitochondrial ribosomal proteins / large subunits"""	14480	protein-coding gene	gene with protein product		611835					Standard	NM_014180		Approved	MRP-L25, RPML25, HSPC158	uc003lvy.4	Q9NWU5	OTTHUMG00000130190	ENST00000523037.1:c.59delG	chr5.hg19:g.154320807delG	ENSP00000431040:p.Arg20fs	130.0	0.0		170.0	42.0	NM_014180	A6NGJ8|Q5H9Q1|Q96Q51|Q9P006	Frame_Shift_Del	DEL	ENST00000523037.1	hg19	CCDS4331.1																																																																																			.	.		0.537	MRPL22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252508.2		
