#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Confidence	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_NTotCov	i_NVarCov	i_NVarRat	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_TVarRat	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	i_dbSNP_AF	i_dbSNP_PopFreq	i_dbSNP_Strength	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
MASP2	10747	hgsc.bcm.edu	37	1	11090277	11090277	+	Missense_Mutation	SNP	C	C	G			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr1:11090277C>G	ENST00000400897.3	-	10	1268	c.1253G>C	c.(1252-1254)tGg>tCg	p.W418S	RP4-635E18.8_ENST00000607145.1_RNA	NM_006610.3	NP_006601.2	O00187	MASP2_HUMAN	mannan-binding lectin serine peptidase 2	418	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|complement component C4b binding (GO:0001855)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			biliary_tract(1)|endometrium(2)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	Ovarian(185;0.249)	Lung NSC(185;1.04e-05)|all_lung(284;1.31e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.071)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.12e-07)|COAD - Colon adenocarcinoma(227;7.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|READ - Rectum adenocarcinoma(331;0.0487)|STAD - Stomach adenocarcinoma(313;0.192)		GGAGCTCGTCCAGAATCCATC	0.408																																					p.W418S	GBM(35;611 746 20780 22741 36496)	Atlas-SNP	.											.	MASP2	71	.	0			c.G1253C						PASS	.						131.0	126.0	128.0					1																	11090277		2203	4300	6503	SO:0001583	missense	10747	exon10			CTCGTCCAGAATC	X98400	CCDS123.1, CCDS124.1	1p36.3-p36.2	2014-09-17	2005-08-17		ENSG00000009724	ENSG00000009724			6902	protein-coding gene	gene with protein product		605102	"""mannan-binding lectin serine protease 2"", ""mannan-binding lectin serine peptidase 1 pseudogene 1"", ""mannan-binding lectin serine protease 1 pseudogene 1"""	MASP1P1		9087411, 9777418	Standard	NM_006610		Approved		uc001aru.3	O00187	OTTHUMG00000002121	ENST00000400897.3:c.1253G>C	chr1.hg19:g.11090277C>G	ENSP00000383690:p.Trp418Ser	87.0	0.0	.		69.0	27.0	.	NM_006610	A8K458|A8MWJ2|O75754|Q5TEQ5|Q5TER0|Q96QG4|Q9BZH0|Q9H498|Q9H499|Q9UBP3|Q9UC48|Q9ULC7|Q9UMV3|Q9Y270	Missense_Mutation	SNP	ENST00000400897.3	hg19	CCDS123.1	.	.	.	.	.	.	.	.	.	.	C	19.15	3.771585	0.69992	.	.	ENSG00000009724	ENST00000400897	D	0.91068	-2.78	5.63	5.63	0.86233	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.64402	D	0.000001	D	0.97111	0.9056	H	0.96048	3.76	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	D	0.97998	1.0358	10	0.87932	D	0	.	19.2809	0.94052	0.0:1.0:0.0:0.0	.	418	O00187	MASP2_HUMAN	S	418	ENSP00000383690:W418S	ENSP00000383690:W418S	W	-	2	0	MASP2	11012864	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.095000	0.64529	2.660000	0.90430	0.655000	0.94253	TGG	.	.	.	none		0.408	MASP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006072.1	NM_006610	
KCNT2	343450	hgsc.bcm.edu	37	1	196288615	196288615	+	Splice_Site	SNP	T	T	G			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr1:196288615T>G	ENST00000294725.9	-	20	3262	c.2347A>C	c.(2347-2349)Aac>Cac	p.N783H	KCNT2_ENST00000451324.2_Intron|KCNT2_ENST00000498426.1_Intron|KCNT2_ENST00000367431.4_Intron|KCNT2_ENST00000609185.1_Intron|KCNT2_ENST00000367433.5_Intron			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	783					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(16)|lung(43)|ovary(5)|pancreas(1)|prostate(1)|skin(11)|stomach(2)|upper_aerodigestive_tract(1)	97						GTCACCTACTTGTCAATAGAG	0.418																																					p.N783H		Atlas-SNP	.											.	KCNT2	243	.	0			c.A2347C						PASS	.						136.0	120.0	125.0					1																	196288615		2203	4300	6503	SO:0001630	splice_region_variant	343450	exon20			CCTACTTGTCAAT	BX647852, AY359444, AK127807	CCDS1384.1, CCDS72994.1, CCDS72995.1	1q31.3	2012-07-05			ENSG00000162687	ENSG00000162687		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	18866	protein-coding gene	gene with protein product	"""sodium and chloride activated ATP sensitive potassium channel"""	610044				16382103	Standard	NM_198503		Approved	KCa4.2, SLICK, SLO2.1	uc001gtd.1	Q6UVM3	OTTHUMG00000035611	ENST00000294725.9:c.2348+1A>C	chr1.hg19:g.196288615T>G		108.0	0.0	.		77.0	34.0	.	NM_198503	Q3SY59|Q5VTN1|Q6ZMT3	Missense_Mutation	SNP	ENST00000294725.9	hg19	CCDS1384.1	.	.	.	.	.	.	.	.	.	.	T	18.02	3.530130	0.64860	.	.	ENSG00000162687	ENST00000294725	T	0.75704	-0.96	5.83	5.83	0.93111	.	0.000000	0.64402	D	0.000002	D	0.83589	0.5287	M	0.72118	2.19	0.80722	D	1	D	0.65815	0.995	P	0.61800	0.894	T	0.83023	-0.0166	10	0.37606	T	0.19	-21.4942	16.1894	0.81975	0.0:0.0:0.0:1.0	.	783	Q6UVM3	KCNT2_HUMAN	H	783	ENSP00000294725:N783H	ENSP00000294725:N783H	N	-	1	0	KCNT2	194555238	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.826000	0.86716	2.222000	0.72286	0.477000	0.44152	AAC	.	.	.	none		0.418	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086418.2	NM_198503	Missense_Mutation
DENND1B	163486	hgsc.bcm.edu	37	1	197479793	197479793	+	IGR	SNP	G	G	A			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr1:197479793G>A								CRB1 (32208 upstream) : DENND1B (41591 downstream)																							TCTGAAATCTGGCTTAGTGTT	0.448																																					p.Q709X		Atlas-SNP	.											.	DENND1B	108	.	0			c.C2125T						PASS	.						142.0	127.0	132.0					1																	197479793		2203	4300	6503	SO:0001628	intergenic_variant	163486	exon23			AAATCTGGCTTAG																													chr1.hg19:g.197479793G>A		139.0	0.0	.		137.0	56.0	.	NM_001195215		Nonsense_Mutation	SNP		hg19		.	.	.	.	.	.	.	.	.	.	G	11.20	1.569014	0.28003	.	.	ENSG00000213047	ENST00000391979;ENST00000542760;ENST00000450419	.	.	.	5.43	4.49	0.54785	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.09590	T	0.72	.	9.2796	0.37720	0.0:0.1314:0.6622:0.2063	.	.	.	.	X	349;709;689	.	ENSP00000375839:Q349X	Q	-	1	0	DENND1B	195746416	1.000000	0.71417	0.378000	0.26068	0.024000	0.10985	2.407000	0.44565	1.377000	0.46286	0.563000	0.77884	CAG	.	.	.	none	0	0.448								
NRXN1	9378	hgsc.bcm.edu	37	2	50280612	50280612	+	Missense_Mutation	SNP	T	T	G	rs201877761		TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr2:50280612T>G	ENST00000406316.2	-	20	5311	c.3835A>C	c.(3835-3837)Aat>Cat	p.N1279H	NRXN1_ENST00000406859.3_Missense_Mutation_p.N1279H|NRXN1_ENST00000401710.1_Missense_Mutation_p.N297H|NRXN1_ENST00000405472.3_Missense_Mutation_p.N1301H|NRXN1_ENST00000404971.1_Missense_Mutation_p.N1349H|NRXN1_ENST00000401669.2_Missense_Mutation_p.N1309H|NRXN1_ENST00000342183.5_Missense_Mutation_p.N244H|NRXN1_ENST00000402717.3_Missense_Mutation_p.N1301H	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	1279	Laminin G-like 6. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			GCTGCCATATTCAGAACTTTC	0.507																																					p.N1349H		Atlas-SNP	.											.	NRXN1	1118	.	0			c.A4045C						PASS	.						97.0	89.0	92.0					2																	50280612		2203	4300	6503	SO:0001583	missense	9378	exon22			CCATATTCAGAAC	AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.3835A>C	chr2.hg19:g.50280612T>G	ENSP00000384311:p.Asn1279His	104.0	0.0	.		57.0	26.0	.	NM_001135659	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Missense_Mutation	SNP	ENST00000406316.2	hg19	CCDS54360.1	.	.	.	.	.	.	.	.	.	.	T	14.56	2.572415	0.45798	.	.	ENSG00000179915	ENST00000342183;ENST00000536347;ENST00000401710;ENST00000404971;ENST00000406316;ENST00000405472;ENST00000401669;ENST00000536085;ENST00000402717;ENST00000406859	T;T;T;T;T;T;T;T	0.71579	0.89;2.14;0.13;0.11;-0.58;-0.46;-0.17;-0.03	5.65	5.65	0.86999	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	0.093114	0.39687	U	0.001295	T	0.79822	0.4512	M	0.73962	2.25	0.39056	D	0.960425	B;D;P;P	0.59357	0.367;0.985;0.566;0.502	B;P;P;B	0.53518	0.246;0.712;0.728;0.261	D	0.84151	0.0423	10	0.87932	D	0	.	15.8691	0.79098	0.0:0.0:0.0:1.0	.	1349;244;1279;1301	Q9ULB1-3;P58400;F8WB18;A7E294	.;NRX1B_HUMAN;.;.	H	244;198;297;1349;1279;1301;1309;1350;1301;1279	ENSP00000341184:N244H;ENSP00000385580:N297H;ENSP00000385142:N1349H;ENSP00000384311:N1279H;ENSP00000434015:N1301H;ENSP00000385017:N1309H;ENSP00000385434:N1301H;ENSP00000385681:N1279H	ENSP00000341184:N244H	N	-	1	0	NRXN1	50134116	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.186000	0.72026	2.151000	0.67156	0.533000	0.62120	AAT	.	T|0.999;C|0.001	.	alt		0.507	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2		
KCNH8	131096	hgsc.bcm.edu	37	3	19479828	19479828	+	Silent	SNP	C	C	T			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr3:19479828C>T	ENST00000328405.2	+	8	1616	c.1350C>T	c.(1348-1350)ttC>ttT	p.F450F	KCNH8_ENST00000537696.1_Silent_p.F91F	NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8	450					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(3)|lung(37)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	77						AAAAGATCTTCTCCATCTGCA	0.473																																					p.F450F	NSCLC(124;1625 1765 8018 24930 42026)	Atlas-SNP	.											.	KCNH8	189	.	0			c.C1350T						PASS	.						74.0	66.0	69.0					3																	19479828		2203	4300	6503	SO:0001819	synonymous_variant	131096	exon8			GATCTTCTCCATC	AY053503	CCDS2632.1	3p24.3	2012-07-05			ENSG00000183960	ENSG00000183960		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18864	protein-coding gene	gene with protein product		608260				16382104	Standard	NM_144633		Approved	Kv12.1, elk3	uc003cbk.1	Q96L42	OTTHUMG00000129891	ENST00000328405.2:c.1350C>T	chr3.hg19:g.19479828C>T		129.0	0.0	.		110.0	52.0	.	NM_144633	B7Z2I7|Q59GQ6	Silent	SNP	ENST00000328405.2	hg19	CCDS2632.1																																																																																			.	.	.	none		0.473	KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2	NM_144633	
SLC4A7	9497	hgsc.bcm.edu	37	3	27477880	27477880	+	Splice_Site	SNP	T	T	C			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr3:27477880T>C	ENST00000295736.5	-	5	631	c.561A>G	c.(559-561)gcA>gcG	p.A187A	SLC4A7_ENST00000435667.2_Splice_Site_p.A196A|SLC4A7_ENST00000437179.1_Splice_Site_p.A192A|SLC4A7_ENST00000446700.1_Splice_Site_p.A192A|SLC4A7_ENST00000440156.1_Splice_Site_p.A196A|SLC4A7_ENST00000445684.1_Splice_Site_p.A196A|SLC4A7_ENST00000425128.2_Splice_Site_p.A192A|SLC4A7_ENST00000454389.1_Splice_Site_p.A196A|SLC4A7_ENST00000428386.1_Splice_Site_p.A187A|SLC4A7_ENST00000455077.1_Splice_Site_p.A192A|SLC4A7_ENST00000388777.4_5'UTR	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	187					auditory receptor cell development (GO:0060117)|bicarbonate transport (GO:0015701)|cochlear nucleus development (GO:0021747)|ion transport (GO:0006811)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal cell programmed cell death (GO:0046666)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(9)|ovary(4)|skin(1)	38					Sodium bicarbonate(DB01390)	TACTATAACCTGCTATTTCAT	0.373																																					p.A192A		Atlas-SNP	.											.	SLC4A7	119	.	0			c.A576G						PASS	.						76.0	74.0	74.0					3																	27477880		2203	4300	6503	SO:0001630	splice_region_variant	9497	exon5			ATAACCTGCTATT	AB012130	CCDS33721.1, CCDS58819.1, CCDS58820.1	3p24.1	2013-05-22			ENSG00000033867	ENSG00000033867		"""Solute carriers"""	11033	protein-coding gene	gene with protein product		603353		SLC4A6		10198178, 9610397	Standard	NM_003615		Approved	NBC3, SBC2	uc003cdv.4	Q9Y6M7	OTTHUMG00000155679	ENST00000295736.5:c.562+1A>G	chr3.hg19:g.27477880T>C		98.0	0.0	.		80.0	40.0	.	NM_001258379	A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Silent	SNP	ENST00000295736.5	hg19	CCDS33721.1																																																																																			.	.	.	none		0.373	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615	Silent
VEPH1	79674	hgsc.bcm.edu	37	3	157081265	157081265	+	Missense_Mutation	SNP	T	T	C			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr3:157081265T>C	ENST00000362010.2	-	9	1930	c.1623A>G	c.(1621-1623)atA>atG	p.I541M	VEPH1_ENST00000392833.2_Missense_Mutation_p.I541M|VEPH1_ENST00000543418.1_Missense_Mutation_p.I541M|RP11-550I24.2_ENST00000487238.1_RNA|VEPH1_ENST00000392832.2_Missense_Mutation_p.I541M	NM_001167912.1	NP_001161384.1	Q14D04	MELT_HUMAN	ventricular zone expressed PH domain-containing 1	541						plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(5)|cervix(1)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|pancreas(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)			CTTGGTATTCTATAGGACTTG	0.363																																					p.I541M		Atlas-SNP	.											.	VEPH1	129	.	0			c.A1623G						PASS	.						152.0	159.0	157.0					3																	157081265		2203	4300	6503	SO:0001583	missense	79674	exon9			GTATTCTATAGGA	AL713656	CCDS3179.1, CCDS54661.1, CCDS54662.1, CCDS54663.1	3q24-q25	2013-01-10	2012-12-10		ENSG00000197415	ENSG00000197415		"""Pleckstrin homology (PH) domain containing"""	25735	protein-coding gene	gene with protein product		609594	"""ventricular zone expressed PH domain homolog 1 (zebrafish)"""			11214970, 15388229	Standard	NM_024621		Approved	FLJ12604, KIAA1692	uc003fbk.2	Q14D04	OTTHUMG00000158711	ENST00000362010.2:c.1623A>G	chr3.hg19:g.157081265T>C	ENSP00000354919:p.Ile541Met	185.0	0.0	.		189.0	73.0	.	NM_001167911	D3DNL0|F5GZ91|Q2TAA9|Q3MIX2|Q6PEL3|Q86TL5|Q8TCR3|Q96SP7|Q9C0H1|Q9H9Q7	Missense_Mutation	SNP	ENST00000362010.2	hg19	CCDS3179.1	.	.	.	.	.	.	.	.	.	.	T	10.23	1.291609	0.23564	.	.	ENSG00000197415	ENST00000392833;ENST00000362010;ENST00000543418;ENST00000392832	T;T;T;T	0.08458	3.09;3.09;3.09;3.09	5.5	-4.25	0.03766	.	1.486880	0.03948	N	0.287996	T	0.05456	0.0144	N	0.14661	0.345	0.43708	D	0.996171	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.003	T	0.23511	-1.0186	10	0.44086	T	0.13	-14.1107	8.4805	0.33040	0.1087:0.5:0.0:0.3913	.	541;541	Q14D04-2;Q14D04	.;MELT_HUMAN	M	541	ENSP00000376578:I541M;ENSP00000354919:I541M;ENSP00000446258:I541M;ENSP00000376577:I541M	ENSP00000354919:I541M	I	-	3	3	VEPH1	158563959	0.000000	0.05858	0.016000	0.15963	0.611000	0.37282	-0.300000	0.08243	-0.666000	0.05310	0.533000	0.62120	ATA	.	.	.	none		0.363	VEPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351845.3	NM_024621	
HNRNPD	3184	hgsc.bcm.edu	37	4	83279841	83279841	+	Missense_Mutation	SNP	T	T	C			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr4:83279841T>C	ENST00000313899.7	-	4	869	c.592A>G	c.(592-594)Ata>Gta	p.I198V	HNRNPD_ENST00000541060.1_Missense_Mutation_p.I44V|HNRNPD_ENST00000543098.1_Missense_Mutation_p.I146V|HNRNPD_ENST00000353341.4_Missense_Mutation_p.I198V|HNRNPD_ENST00000508119.1_5'Flank|HNRNPD_ENST00000352301.4_Missense_Mutation_p.I179V	NM_031370.2	NP_112738.1	Q14103	HNRPD_HUMAN	heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA binding protein 1, 37kDa)	198	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				circadian regulation of translation (GO:0097167)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|regulation of circadian rhythm (GO:0042752)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|RNA catabolic process (GO:0006401)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|telomeric DNA binding (GO:0042162)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(1)	7						TACTCCCTTATTTTCTCTTCA	0.378																																					p.I198V		Atlas-SNP	.											.	HNRNPD	23	.	0			c.A592G						PASS	.						89.0	94.0	92.0					4																	83279841		2203	4300	6503	SO:0001583	missense	3184	exon4			CCCTTATTTTCTC	AF026126	CCDS3590.1, CCDS3591.1, CCDS3592.1	4q21	2013-02-12	2002-08-29	2008-04-18	ENSG00000138668	ENSG00000138668		"""RNA binding motif (RRM) containing"""	5036	protein-coding gene	gene with protein product		601324	"""heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA-binding protein 1, 37kD)"""	AUF1, HNRPD		9615222	Standard	NM_001003810		Approved		uc003hmm.1	Q14103	OTTHUMG00000130290	ENST00000313899.7:c.592A>G	chr4.hg19:g.83279841T>C	ENSP00000313199:p.Ile198Val	139.0	0.0	.		113.0	55.0	.	NM_031370	A8K9J2|P07029|Q01858|Q14100|Q14101|Q14102|Q4W5A1|Q9UCE8|Q9UCE9	Missense_Mutation	SNP	ENST00000313899.7	hg19	CCDS3592.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	8.992|8.992	0.977861|0.977861	0.18812|0.18812	.|.	.|.	ENSG00000138668|ENSG00000138668	ENST00000313899;ENST00000353341;ENST00000352301;ENST00000543098;ENST00000307213;ENST00000541060;ENST00000509263;ENST00000507010;ENST00000515432|ENST00000514671	T;T;T;T;T;T;T;T|.	0.18502|.	2.21;2.21;2.21;2.21;2.21;2.21;2.21;2.21|.	6.07|6.07	6.07|6.07	0.98685|0.98685	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);|.	0.042341|.	0.85682|.	D|.	0.000000|.	T|T	0.59838|0.59838	0.2223|0.2223	L|L	0.37630|0.37630	1.12|1.12	0.50467|0.50467	D|D	0.99987|0.99987	P;P;B;B|.	0.39964|.	0.697;0.697;0.112;0.136|.	B;B;B;B|.	0.44085|.	0.44;0.44;0.108;0.173|.	T|T	0.55425|0.55425	-0.8143|-0.8143	10|5	0.26408|.	T|.	0.33|.	.|.	16.6407|16.6407	0.85098|0.85098	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	179;198;179;198|.	Q14103-4;Q14103-3;Q14103-2;Q14103|.	.;.;.;HNRPD_HUMAN|.	V|S	198;198;179;146;173;44;131;198;100|101	ENSP00000313199:I198V;ENSP00000313327:I198V;ENSP00000305860:I179V;ENSP00000439380:I146V;ENSP00000437416:I44V;ENSP00000420926:I131V;ENSP00000421952:I198V;ENSP00000426666:I100V|.	ENSP00000307544:I173V|.	I|N	-|-	1|2	0|0	HNRNPD|HNRNPD	83498865|83498865	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.309000|0.309000	0.27889|0.27889	4.737000|4.737000	0.62066|0.62066	2.326000|2.326000	0.78906|0.78906	0.533000|0.533000	0.62120|0.62120	ATA|AAT	.	.	.	none		0.378	HNRNPD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252630.2	NM_031370	
HERC6	55008	hgsc.bcm.edu	37	4	89361148	89361148	+	Missense_Mutation	SNP	C	C	A			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr4:89361148C>A	ENST00000264346.7	+	21	2737	c.2678C>A	c.(2677-2679)cCt>cAt	p.P893H	HERC6_ENST00000380265.5_Missense_Mutation_p.P857H	NM_017912.3	NP_060382.3	Q8IVU3	HERC6_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 6	893	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				hematopoietic progenitor cell differentiation (GO:0002244)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)	11		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000222)		CATTTCTACCCTGAAGAACTA	0.363																																					p.P893H		Atlas-SNP	.											.	HERC6	104	.	0			c.C2678A						PASS	.						70.0	64.0	66.0					4																	89361148		1828	4104	5932	SO:0001583	missense	55008	exon21			TCTACCCTGAAGA	AF336798	CCDS47098.1, CCDS54777.1	4q22	2012-02-23	2012-02-23		ENSG00000138642	ENSG00000138642			26072	protein-coding gene	gene with protein product		609249	"""hect domain and RLD 6"""				Standard	NM_001165136		Approved	FLJ20637	uc011cdi.2	Q8IVU3	OTTHUMG00000160983	ENST00000264346.7:c.2678C>A	chr4.hg19:g.89361148C>A	ENSP00000264346:p.Pro893His	169.0	0.0	.		131.0	58.0	.	NM_017912	B4DIY5|Q5GC90|Q5GRH3|Q5HYM6|Q5JPB6|Q6PIF4|Q8NAN3|Q9NWS4	Missense_Mutation	SNP	ENST00000264346.7	hg19	CCDS47098.1	.	.	.	.	.	.	.	.	.	.	C	15.20	2.763291	0.49574	.	.	ENSG00000138642	ENST00000380265;ENST00000264346	T;T	0.50548	0.74;0.74	4.66	4.66	0.58398	HECT (4);	0.000000	0.64402	D	0.000012	T	0.72252	0.3437	M	0.86097	2.795	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.77734	-0.2477	10	0.87932	D	0	.	16.8302	0.85942	0.0:1.0:0.0:0.0	.	857;893	Q8IVU3-2;Q8IVU3	.;HERC6_HUMAN	H	857;893	ENSP00000369617:P857H;ENSP00000264346:P893H	ENSP00000264346:P893H	P	+	2	0	HERC6	89580171	1.000000	0.71417	0.891000	0.34965	0.024000	0.10985	6.932000	0.75869	2.581000	0.87130	0.585000	0.79938	CCT	.	.	.	none		0.363	HERC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363259.2		
DNAJC18	202052	hgsc.bcm.edu	37	5	138758461	138758461	+	Missense_Mutation	SNP	C	C	A			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr5:138758461C>A	ENST00000302060.5	-	6	795	c.715G>T	c.(715-717)Gtg>Ttg	p.V239L		NM_152686.3	NP_689899.1	Q9H819	DJC18_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 18	239						integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			GATATAATCACAATCACAAGA	0.318																																					p.V239L		Atlas-SNP	.											.	DNAJC18	30	.	0			c.G715T						PASS	.						85.0	87.0	86.0					5																	138758461		2203	4300	6503	SO:0001583	missense	202052	exon6			TAATCACAATCAC	AK024054	CCDS4214.1	5q31.2	2011-09-02		2005-08-09	ENSG00000170464	ENSG00000170464		"""Heat shock proteins / DNAJ (HSP40)"""	28429	protein-coding gene	gene with protein product							Standard	NM_152686		Approved	MGC29463	uc003len.3	Q9H819	OTTHUMG00000129225	ENST00000302060.5:c.715G>T	chr5.hg19:g.138758461C>A	ENSP00000302843:p.Val239Leu	250.0	0.0	.		230.0	89.0	.	NM_152686		Missense_Mutation	SNP	ENST00000302060.5	hg19	CCDS4214.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.10|18.10	3.547400|3.547400	0.65311|0.65311	.|.	.|.	ENSG00000170464|ENSG00000170464	ENST00000514052|ENST00000302060;ENST00000508445	.|T;T	.|0.55760	.|0.5;1.07	5.87|5.87	5.87|5.87	0.94306|0.94306	.|.	.|0.064922	.|0.64402	.|D	.|0.000004	T|T	0.30039|0.30039	0.0752|0.0752	N|N	0.25332|0.25332	0.735|0.735	0.52099|0.52099	D|D	0.999946|0.999946	.|P	.|0.43431	.|0.807	.|B	.|0.31495	.|0.131	T|T	0.12167|0.12167	-1.0558|-1.0558	5|10	.|0.12766	.|T	.|0.61	-13.8827|-13.8827	9.4781|9.4781	0.38884|0.38884	0.0:0.8512:0.0:0.1488|0.0:0.8512:0.0:0.1488	.|.	.|239	.|Q9H819	.|DJC18_HUMAN	F|L	30|239;72	.|ENSP00000302843:V239L;ENSP00000426338:V72L	.|ENSP00000302843:V239L	L|V	-|-	3|1	2|0	DNAJC18|DNAJC18	138786360|138786360	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	3.740000|3.740000	0.55082|0.55082	2.941000|2.941000	0.99782|0.99782	0.655000|0.655000	0.94253|0.94253	TTG|GTG	.	.	.	none		0.318	DNAJC18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374191.1	NM_152686	
PCDHGA4	56111	hgsc.bcm.edu	37	5	140736033	140736033	+	Silent	SNP	A	A	T			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr5:140736033A>T	ENST00000571252.1	+	1	1266	c.1266A>T	c.(1264-1266)gtA>gtT	p.V422V	PCDHGA3_ENST00000253812.6_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018917.2	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4	422	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACATCACTGTAACTGCCACTG	0.433																																					p.V422V		Atlas-SNP	.											.	PCDHGA4	150	.	0			c.A1266T						PASS	.						55.0	57.0	57.0					5																	140736033		2042	4208	6250	SO:0001819	synonymous_variant	56111	exon1			CACTGTAACTGCC	AF152511	CCDS58979.1, CCDS58979.2, CCDS75331.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8702	other	protocadherin		606291				10380929	Standard	NM_018917		Approved	PCDH-GAMMA-A4		Q9Y5G9		ENST00000571252.1:c.1266A>T	chr5.hg19:g.140736033A>T		95.0	0.0	.		70.0	32.0	.	NM_018917	Q9Y5D3	Silent	SNP	ENST00000571252.1	hg19	CCDS58979.1																																																																																			.	.	.	none		0.433	PCDHGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437959.1	NM_018917	
SKIV2L	6499	hgsc.bcm.edu	37	6	31932058	31932058	+	Missense_Mutation	SNP	G	G	A			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr6:31932058G>A	ENST00000375394.2	+	17	2023	c.1910G>A	c.(1909-1911)aGc>aAc	p.S637N	SKIV2L_ENST00000544581.1_Missense_Mutation_p.S444N	NM_006929.4	NP_008860.4	Q15477	SKIV2_HUMAN	superkiller viralicidic activity 2-like (S. cerevisiae)	637	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)	nucleus (GO:0005634)|Ski complex (GO:0055087)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|large_intestine(1)|ovary(1)	4						GTGCACCATAGCGGCATCCTG	0.597																																					p.S637N		Atlas-SNP	.											.	SKIV2L	97	.	0			c.G1910A						PASS	.						115.0	87.0	97.0					6																	31932058		1511	2708	4219	SO:0001583	missense	6499	exon17			ACCATAGCGGCAT		CCDS4731.1	6p21	2010-02-17	2001-11-28		ENSG00000204351	ENSG00000204351			10898	protein-coding gene	gene with protein product		600478	"""superkiller viralicidic activity 2 (S. cerevisiae homolog)-like"""	SKIV2		7759100, 9799600	Standard	XM_006715168		Approved	HLP, DDX13, SKI2W, 170A	uc003nyn.1	Q15477	OTTHUMG00000031146	ENST00000375394.2:c.1910G>A	chr6.hg19:g.31932058G>A	ENSP00000364543:p.Ser637Asn	81.0	0.0	.		62.0	26.0	.	NM_006929	O15005|Q12902|Q15476|Q5ST66	Missense_Mutation	SNP	ENST00000375394.2	hg19	CCDS4731.1	.	.	.	.	.	.	.	.	.	.	G	33	5.219357	0.95139	.	.	ENSG00000204351	ENST00000375394;ENST00000433155;ENST00000544581	T;T	0.43294	0.95;0.95	5.95	5.95	0.96441	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.66665	0.2812	M	0.86805	2.84	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.70662	-0.4810	10	0.72032	D	0.01	-16.4781	19.1568	0.93514	0.0:0.0:1.0:0.0	.	637	Q15477	SKIV2_HUMAN	N	637;479;444	ENSP00000364543:S637N;ENSP00000442645:S444N	ENSP00000364543:S637N	S	+	2	0	SKIV2L	32040037	1.000000	0.71417	0.979000	0.43373	0.967000	0.64934	8.574000	0.90763	2.825000	0.97269	0.655000	0.94253	AGC	.	.	.	none		0.597	SKIV2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076264.3		
GSTA1	2938	hgsc.bcm.edu	37	6	52656735	52656735	+	Missense_Mutation	SNP	A	A	C			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr6:52656735A>C	ENST00000334575.5	-	7	745	c.590T>G	c.(589-591)tTt>tGt	p.F197C	GSTA1_ENST00000493331.1_5'UTR	NM_145740.3	NP_665683.1	P08263	GSTA1_HUMAN	glutathione S-transferase alpha 1	197	GST C-terminal.				epithelial cell differentiation (GO:0030855)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|metabolic process (GO:0008152)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glutathione transferase activity (GO:0004364)			large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	12	Lung NSC(77;0.118)				Azathioprine(DB00993)|Busulfan(DB01008)|Glutathione(DB00143)	AGGCTGTAGAAACTTCTTCAC	0.473																																					p.F197C		Atlas-SNP	.											.	GSTA1	40	.	0			c.T590G						PASS	.						128.0	127.0	127.0					6																	52656735		2203	4300	6503	SO:0001583	missense	2938	exon7			TGTAGAAACTTCT		CCDS4945.1	6p12.2	2012-06-21	2008-11-26		ENSG00000243955	ENSG00000243955	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4626	protein-coding gene	gene with protein product		138359	"""glutathione S-transferase A1"""			9503014	Standard	NM_145740		Approved		uc003paz.3	P08263	OTTHUMG00000014861	ENST00000334575.5:c.590T>G	chr6.hg19:g.52656735A>C	ENSP00000335620:p.Phe197Cys	93.0	0.0	.		75.0	41.0	.	NM_145740	Q14750|Q5GHF8|Q5SZC1	Missense_Mutation	SNP	ENST00000334575.5	hg19	CCDS4945.1	.	.	.	.	.	.	.	.	.	.	.	11.55	1.671100	0.29693	.	.	ENSG00000243955	ENST00000334575	T	0.11712	2.75	2.44	2.44	0.29823	Glutathione S-transferase, C-terminal-like (1);Glutathione S-transferase/chloride channel, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.30198	0.0757	H	0.94503	3.545	0.49582	D	0.999806	D	0.89917	1.0	D	0.97110	1.0	T	0.36359	-0.9751	10	0.87932	D	0	.	10.0672	0.42311	1.0:0.0:0.0:0.0	.	197	P08263	GSTA1_HUMAN	C	197	ENSP00000335620:F197C	ENSP00000335620:F197C	F	-	2	0	GSTA1	52764694	1.000000	0.71417	0.986000	0.45419	0.165000	0.22458	5.795000	0.69074	0.868000	0.35678	0.172000	0.16884	TTT	.	.	.	none		0.473	GSTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040922.1		
HBS1L	10767	hgsc.bcm.edu	37	6	135358073	135358073	+	Intron	SNP	C	C	T			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr6:135358073C>T	ENST00000367837.5	-	4	637				HBS1L_ENST00000367826.2_Intron|HBS1L_ENST00000314674.3_Intron|HBS1L_ENST00000415177.2_Intron|HBS1L_ENST00000367824.4_Intron|HBS1L_ENST00000367822.5_Missense_Mutation_p.D508N|HBS1L_ENST00000445176.2_Intron|HBS1L_ENST00000367820.2_Intron	NM_001145158.1|NM_006620.3	NP_001138630.1|NP_006611.1	Q9Y450	HBS1L_HUMAN	HBS1-like translational GTPase						signal transduction (GO:0007165)|translation (GO:0006412)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation elongation factor activity (GO:0003746)			NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	20	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0046)|GBM - Glioblastoma multiforme(68;0.00702)		ATGGATGGGTCTACTACAGGC	0.368																																					p.D508N		Atlas-SNP	.											.	HBS1L	75	.	0			c.G1522A						PASS	.						52.0	48.0	49.0					6																	135358073		692	1591	2283	SO:0001627	intron_variant	10767	exon5			ATGGGTCTACTAC	U87791	CCDS5173.1, CCDS47479.1, CCDS47480.1	6q23.3	2014-04-30	2014-04-30		ENSG00000112339	ENSG00000112339			4834	protein-coding gene	gene with protein product	"""eRF3 family member"""	612450	"""HBS1 (S. cerevisiae)-like"", ""HBS1-like (S. cerevisiae)"""			9872408, 23667253	Standard	NM_006620		Approved	ERFS, HBS1, HSPC276, KIAA1038, DKFZp434g247, EF-1a, eRF3c	uc003qez.2	Q9Y450	OTTHUMG00000015626	ENST00000367837.5:c.430+2637G>A	chr6.hg19:g.135358073C>T		159.0	0.0	.		128.0	55.0	.	NM_001145207	B7Z365|Q4VX89|Q4VX90|Q5T7G3|Q8NDW9|Q9UPW3	Missense_Mutation	SNP	ENST00000367837.5	hg19	CCDS5173.1	.	.	.	.	.	.	.	.	.	.	C	3.012	-0.203760	0.06180	.	.	ENSG00000112339	ENST00000367822	.	.	.	5.32	3.5	0.40072	.	.	.	.	.	T	0.21674	0.0522	.	.	.	0.24288	N	0.995175	B	0.12013	0.005	B	0.09377	0.004	T	0.32693	-0.9897	7	0.66056	D	0.02	.	12.4456	0.55649	0.0:0.8558:0.0:0.1442	.	508	Q9Y450-2	.	N	508	.	ENSP00000356796:D508N	D	-	1	0	HBS1L	135399766	0.002000	0.14202	0.020000	0.16555	0.158000	0.22134	0.745000	0.26259	1.373000	0.46208	0.655000	0.94253	GAC	.	.	.	none		0.368	HBS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042339.2		
MRPL32	64983	hgsc.bcm.edu	37	7	42974719	42974719	+	Missense_Mutation	SNP	A	A	G			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr7:42974719A>G	ENST00000223324.2	+	2	483	c.296A>G	c.(295-297)aAg>aGg	p.K99R	MRPL32_ENST00000496564.1_3'UTR|PSMA2_ENST00000538645.1_5'Flank|PSMA2_ENST00000442788.1_5'Flank|PSMA2_ENST00000445517.1_5'Flank|PSMA2_ENST00000223321.4_5'Flank	NM_031903.2	NP_114109.1	Q9BYC8	RM32_HUMAN	mitochondrial ribosomal protein L32	99					translation (GO:0006412)	large ribosomal subunit (GO:0015934)|mitochondrial ribosome (GO:0005761)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(1)|large_intestine(2)|lung(6)	10						AATCCGCAGAAGCTTATTAAA	0.403																																					p.K99R		Atlas-SNP	.											.	MRPL32	25	.	0			c.A296G						PASS	.						75.0	72.0	73.0					7																	42974719		2203	4300	6503	SO:0001583	missense	64983	exon2			CGCAGAAGCTTAT	AB051343	CCDS5468.1	7p14	2012-09-13			ENSG00000106591	ENSG00000106591		"""Mitochondrial ribosomal proteins / large subunits"""	14035	protein-coding gene	gene with protein product		611839				11543634	Standard	NM_031903		Approved	HSPC283, L32mt, MRP-L32, bMRP-59b	uc003tia.3	Q9BYC8	OTTHUMG00000155180	ENST00000223324.2:c.296A>G	chr7.hg19:g.42974719A>G	ENSP00000223324:p.Lys99Arg	129.0	0.0	.		210.0	56.0	.	NM_031903	Q96Q68|Q9P098	Missense_Mutation	SNP	ENST00000223324.2	hg19	CCDS5468.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.249005	0.80024	.	.	ENSG00000106591	ENST00000223324	.	.	.	5.33	5.33	0.75918	.	0.181632	0.64402	D	0.000020	T	0.79233	0.4411	M	0.77712	2.385	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	T	0.81870	-0.0734	9	0.62326	D	0.03	-29.9723	15.3359	0.74255	1.0:0.0:0.0:0.0	.	99	Q9BYC8	RM32_HUMAN	R	99	.	ENSP00000223324:K99R	K	+	2	0	MRPL32	42941244	1.000000	0.71417	0.793000	0.32043	0.740000	0.42216	9.300000	0.96151	2.000000	0.58554	0.528000	0.53228	AAG	.	.	.	none		0.403	MRPL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338669.1	NM_031903	
EPHB6	2051	hgsc.bcm.edu	37	7	142562102	142562102	+	Missense_Mutation	SNP	G	G	A			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr7:142562102G>A	ENST00000392957.2	+	7	1331	c.544G>A	c.(544-546)Gga>Aga	p.G182R	EPHB6_ENST00000411471.2_Intron|EPHB6_ENST00000442129.1_Missense_Mutation_p.G182R	NM_004445.3	NP_004436.3	O15197	EPHB6_HUMAN	EPH receptor B6	182	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(46)|ovary(2)|pancreas(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	87	Melanoma(164;0.059)					GTGGGCTGTGGGACCCCACGG	0.622																																					p.G182R		Atlas-SNP	.											.	EPHB6	168	.	0			c.G544A						PASS	.						106.0	126.0	119.0					7																	142562102		2201	4293	6494	SO:0001583	missense	2051	exon7			GCTGTGGGACCCC	D83492	CCDS5873.2, CCDS75672.1	7q33-q35	2013-02-11	2004-10-28		ENSG00000106123	ENSG00000106123		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3396	protein-coding gene	gene with protein product		602757	"""EphB6"""				Standard	XM_006715881		Approved	HEP	uc011kst.2	O15197	OTTHUMG00000155707	ENST00000392957.2:c.544G>A	chr7.hg19:g.142562102G>A	ENSP00000376684:p.Gly182Arg	98.0	0.0	.		115.0	82.0	.	NM_004445	A4D2I7|A8CDT5|D3DXD3|Q2TB23|Q2TB24	Missense_Mutation	SNP	ENST00000392957.2	hg19	CCDS5873.2	.	.	.	.	.	.	.	.	.	.	G	16.30	3.084918	0.55861	.	.	ENSG00000106123	ENST00000392957;ENST00000442129	T;T	0.70045	-0.45;-0.45	5.24	5.24	0.73138	Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.000000	0.40302	N	0.001135	T	0.58807	0.2148	N	0.08118	0	0.80722	D	1	P	0.45672	0.864	P	0.52554	0.702	T	0.61535	-0.7043	10	0.39692	T	0.17	.	15.0592	0.71939	0.0:0.0:1.0:0.0	.	182	O15197	EPHB6_HUMAN	R	182	ENSP00000376684:G182R;ENSP00000410789:G182R	ENSP00000376684:G182R	G	+	1	0	EPHB6	142272224	0.903000	0.30736	0.871000	0.34182	0.427000	0.31564	0.820000	0.27323	2.837000	0.97791	0.655000	0.94253	GGA	.	.	.	none		0.622	EPHB6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341329.1		
HAUS6	54801	hgsc.bcm.edu	37	9	19050301	19050301	+	IGR	SNP	C	C	T			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr9:19050301C>T	ENST00000380502.3	-	0	6536				RRAGA_ENST00000380527.1_Missense_Mutation_p.S215F	NM_001270890.1|NM_017645.4	NP_001257819.1|NP_060115.3	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6						centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)				autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						TTGGTTATTTCCCACTACCAG	0.488																																					p.S215F		Atlas-SNP	.											.	RRAGA	17	.	0			c.C644T						PASS	.						130.0	122.0	125.0					9																	19050301		2203	4300	6503	SO:0001628	intergenic_variant	10670	exon1			TTATTTCCCACTA	AL832495	CCDS6489.1	9p22.1	2011-10-24	2009-04-20	2009-04-20	ENSG00000147874	ENSG00000147874		"""HAUS augmin-like complex subunits"""	25948	protein-coding gene	gene with protein product		613433	"""family with sequence similarity 29, member A"""	FAM29A		10997877, 19427217	Standard	NM_001270890		Approved	FLJ20060, KIAA1574, dgt6	uc003znk.4	Q7Z4H7	OTTHUMG00000019622		chr9.hg19:g.19050301C>T		100.0	0.0	.		95.0	40.0	.	NM_006570	B3KPK4|B4DX82|Q05CG1|Q14CB6|Q14CD9|Q2TA91|Q6IQ10|Q6NZX5|Q8IZQ4|Q96FN0|Q9H950|Q9H998|Q9HCJ8|Q9NXT8	Missense_Mutation	SNP	ENST00000380502.3	hg19	CCDS6489.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.970361	0.74246	.	.	ENSG00000155876	ENST00000380527	T	0.67171	-0.25	4.92	4.92	0.64577	.	0.000000	0.85682	D	0.000000	D	0.83894	0.5353	M	0.89095	3.005	0.80722	D	1	D	0.61080	0.989	D	0.71870	0.975	D	0.86791	0.1985	10	0.87932	D	0	-11.9386	16.0156	0.80439	0.0:1.0:0.0:0.0	.	215	Q7L523	RRAGA_HUMAN	F	215	ENSP00000369899:S215F	ENSP00000369899:S215F	S	+	2	0	RRAGA	19040301	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	7.104000	0.77024	2.735000	0.93741	0.655000	0.94253	TCC	.	.	.	none		0.488	HAUS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051825.1	NM_017645	
FBP2	8789	hgsc.bcm.edu	37	9	97329630	97329630	+	Silent	SNP	A	A	T			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr9:97329630A>T	ENST00000375337.3	-	5	693	c.627T>A	c.(625-627)atT>atA	p.I209I	PCAT7_ENST00000452148.2_RNA	NM_003837.2	NP_003828.2	O00757	F16P2_HUMAN	fructose-1,6-bisphosphatase 2	209					carbohydrate metabolic process (GO:0005975)|fructose metabolic process (GO:0006000)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|small molecule metabolic process (GO:0044281)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	fructose 1,6-bisphosphate 1-phosphatase activity (GO:0042132)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(3)|lung(5)	9		Acute lymphoblastic leukemia(62;0.136)				TCAGGCTGTAAATCTTTCCTT	0.443																																					p.I209I		Atlas-SNP	.											.	FBP2	26	.	0			c.T627A						PASS	.						164.0	164.0	164.0					9																	97329630		2203	4300	6503	SO:0001819	synonymous_variant	8789	exon5			GCTGTAAATCTTT	Y10812	CCDS6711.1	9q22.3	2012-08-13			ENSG00000130957	ENSG00000130957	3.1.3.11		3607	protein-coding gene	gene with protein product		603027				9678974	Standard	NM_003837		Approved		uc004auv.3	O00757	OTTHUMG00000020269	ENST00000375337.3:c.627T>A	chr9.hg19:g.97329630A>T		74.0	0.0	.		65.0	26.0	.	NM_003837	Q17R39|Q6FI53	Silent	SNP	ENST00000375337.3	hg19	CCDS6711.1																																																																																			.	.	.	none		0.443	FBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053189.1	NM_003837	
SWAP70	23075	hgsc.bcm.edu	37	11	9746244	9746244	+	Missense_Mutation	SNP	G	G	A			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr11:9746244G>A	ENST00000318950.6	+	4	557	c.454G>A	c.(454-456)Gga>Aga	p.G152R	SWAP70_ENST00000447399.2_Missense_Mutation_p.G94R	NM_015055.2	NP_055870.2	Q9UH65	SWP70_HUMAN	SWAP switching B-cell complex 70kDa subunit	152					isotype switching (GO:0045190)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|DNA binding (GO:0003677)			NS(1)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(2)|pancreas(1)	11				all cancers(16;1.21e-10)|Epithelial(150;2.81e-09)|BRCA - Breast invasive adenocarcinoma(625;0.00649)		AGCTATGGGAGGAGGTTGGCA	0.318																																					p.G152R		Atlas-SNP	.											.	SWAP70	40	.	0			c.G454A						PASS	.						71.0	69.0	70.0					11																	9746244		2201	4294	6495	SO:0001583	missense	23075	exon4			ATGGGAGGAGGTT	AB014540	CCDS31426.1, CCDS73257.1	11p15	2013-01-10			ENSG00000133789	ENSG00000133789		"""Pleckstrin homology (PH) domain containing"", ""EF-hand domain containing"""	17070	protein-coding gene	gene with protein product		604762				9734811, 10681448	Standard	XM_005252829		Approved	KIAA0640, SWAP-70	uc001mhw.3	Q9UH65	OTTHUMG00000165865	ENST00000318950.6:c.454G>A	chr11.hg19:g.9746244G>A	ENSP00000315630:p.Gly152Arg	121.0	0.0	.		108.0	56.0	.	NM_015055	D3DQV1|O75135|Q7LCY6|Q9P061|Q9P0Z8	Missense_Mutation	SNP	ENST00000318950.6	hg19	CCDS31426.1	.	.	.	.	.	.	.	.	.	.	G	12.38	1.920223	0.33908	.	.	ENSG00000133789	ENST00000447399;ENST00000318950;ENST00000534662	T;T;T	0.11930	2.73;2.73;3.18	5.51	4.59	0.56863	.	0.108656	0.64402	D	0.000007	T	0.12390	0.0301	L	0.43152	1.355	0.40606	D	0.981623	P;P;P	0.39964	0.697;0.664;0.612	B;B;B	0.38655	0.276;0.278;0.091	T	0.10200	-1.0640	10	0.32370	T	0.25	-6.8811	9.8943	0.41309	0.0725:0.0:0.7885:0.139	.	94;152;94	E7EMB1;Q9UH65;B3KUB9	.;SWP70_HUMAN;.	R	94;152;3	ENSP00000399056:G94R;ENSP00000315630:G152R;ENSP00000435587:G3R	ENSP00000315630:G152R	G	+	1	0	SWAP70	9702820	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.623000	0.54224	1.313000	0.45069	0.467000	0.42956	GGA	.	.	.	none		0.318	SWAP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386766.2	NM_015055	
ARHGEF17	9828	hgsc.bcm.edu	37	11	73021391	73021391	+	Missense_Mutation	SNP	G	G	A			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr11:73021391G>A	ENST00000263674.3	+	1	2058	c.1708G>A	c.(1708-1710)Gag>Aag	p.E570K	RP11-800A3.7_ENST00000546324.1_RNA	NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	570					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						CAGCTCCTCCGAGCTCCTGCT	0.622																																					p.E570K		Atlas-SNP	.											.	ARHGEF17	117	.	0			c.G1708A						PASS	.						37.0	40.0	39.0					11																	73021391		2200	4293	6493	SO:0001583	missense	9828	exon1			TCCTCCGAGCTCC	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.1708G>A	chr11.hg19:g.73021391G>A	ENSP00000263674:p.Glu570Lys	84.0	0.0	.		54.0	25.0	.	NM_014786	B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	Missense_Mutation	SNP	ENST00000263674.3	hg19	CCDS8221.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.419170	0.83559	.	.	ENSG00000110237	ENST00000263674	T	0.62364	0.03	4.62	4.62	0.57501	.	0.082023	0.49305	D	0.000152	T	0.68412	0.2998	L	0.29908	0.895	0.41778	D	0.989808	D	0.89917	1.0	D	0.66351	0.943	T	0.73404	-0.3993	10	0.87932	D	0	-17.8299	16.1961	0.82025	0.0:0.0:1.0:0.0	.	570	Q96PE2	ARHGH_HUMAN	K	570	ENSP00000263674:E570K	ENSP00000263674:E570K	E	+	1	0	ARHGEF17	72699039	1.000000	0.71417	0.997000	0.53966	0.641000	0.38312	9.074000	0.93998	2.384000	0.81235	0.561000	0.74099	GAG	.	.	.	none		0.622	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397365.1	NM_014786	
XRRA1	143570	hgsc.bcm.edu	37	11	74563097	74563097	+	Missense_Mutation	SNP	C	C	T			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr11:74563097C>T	ENST00000340360.6	-	13	1508	c.1177G>A	c.(1177-1179)Gct>Act	p.A393T	XRRA1_ENST00000321448.8_Missense_Mutation_p.A118T|XRRA1_ENST00000527087.1_Intron	NM_182969.2	NP_892014.1			X-ray radiation resistance associated 1											breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(3)	20						GGGAAGAGAGCTACTGGTAGG	0.537																																					p.A393T		Atlas-SNP	.											.	XRRA1	46	.	0			c.G1177A						PASS	.						137.0	140.0	139.0					11																	74563097		2057	4183	6240	SO:0001583	missense	143570	exon13			AGAGAGCTACTGG	AK074152	CCDS44680.1, CCDS58159.1, CCDS58160.1	11q13.4	2010-03-19			ENSG00000166435	ENSG00000166435			18868	protein-coding gene	gene with protein product		609788				12908878, 17295261	Standard	NM_182969		Approved	FLJ00225	uc009yub.3	Q6P2D8		ENST00000340360.6:c.1177G>A	chr11.hg19:g.74563097C>T	ENSP00000339918:p.Ala393Thr	117.0	0.0	.		73.0	26.0	.	NM_182969		Missense_Mutation	SNP	ENST00000340360.6	hg19	CCDS44680.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.908003	0.92107	.	.	ENSG00000166435	ENST00000340360;ENST00000321448;ENST00000344880;ENST00000398418	T;T	0.51817	1.83;0.69	6.07	6.07	0.98685	.	.	.	.	.	T	0.63558	0.2521	L	0.46614	1.455	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;0.999	D;D;D;D	0.87578	0.996;0.986;0.998;0.986	T	0.63363	-0.6654	9	0.87932	D	0	-7.6097	16.1526	0.81632	0.0:1.0:0.0:0.0	.	393;337;18;379	Q6P2D8;Q6P2D8-4;Q8TEH2;Q6P2D8-3	XRRA1_HUMAN;.;.;.	T	393;118;379;337	ENSP00000339918:A393T;ENSP00000319303:A118T	ENSP00000319303:A118T	A	-	1	0	XRRA1	74240745	1.000000	0.71417	0.988000	0.46212	0.716000	0.41182	4.186000	0.58337	2.890000	0.99128	0.585000	0.79938	GCT	.	.	.	none		0.537	XRRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384715.1	NM_182969	
PCSK7	9159	hgsc.bcm.edu	37	11	117097999	117097999	+	Missense_Mutation	SNP	C	C	T			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr11:117097999C>T	ENST00000320934.3	-	5	1273	c.643G>A	c.(643-645)Gac>Aac	p.D215N		NM_004716.2	NP_004707.2	Q16549	PCSK7_HUMAN	proprotein convertase subtilisin/kexin type 7	215	Peptidase S8.				peptide hormone processing (GO:0016486)|protein processing (GO:0016485)	integral component of Golgi membrane (GO:0030173)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|skin(1)	16	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;1.72e-06)|Epithelial(105;6.71e-05)|all cancers(92;0.000537)		GGCATGGGGTCAGGGTCATTA	0.567			T	IGH@	MLCLS																																p.D215N		Atlas-SNP	.		Dom	yes		11	11q23.3	9159	proprotein convertase subtilisin/kexin type 7		L	.	PCSK7	59	.	0			c.G643A						PASS	.						111.0	109.0	110.0					11																	117097999		2201	4296	6497	SO:0001583	missense	9159	exon5			TGGGGTCAGGGTC	U40623	CCDS8382.1	11q23-q24	2008-02-01			ENSG00000160613	ENSG00000160613			8748	protein-coding gene	gene with protein product		604872				8615762, 9820811	Standard	XM_006718938		Approved	PC7, PC8, LPC, SPC7	uc001pqr.3	Q16549	OTTHUMG00000165640	ENST00000320934.3:c.643G>A	chr11.hg19:g.117097999C>T	ENSP00000325917:p.Asp215Asn	99.0	0.0	.		58.0	27.0	.	NM_004716	B0YJ60|Q3C1X1|Q53GM4|Q96FK8|Q9UL57	Missense_Mutation	SNP	ENST00000320934.3	hg19	CCDS8382.1	.	.	.	.	.	.	.	.	.	.	C	36	5.694404	0.96793	.	.	ENSG00000160613	ENST00000320934;ENST00000543900;ENST00000525027	D;D	0.87103	-2.21;-2.21	5.61	5.61	0.85477	Peptidase S8/S53, subtilisin/kexin/sedolisin (3);	0.000000	0.85682	D	0.000000	D	0.87621	0.6223	L	0.52126	1.63	0.80722	D	1	P	0.44139	0.827	P	0.45856	0.495	D	0.88316	0.2959	10	0.59425	D	0.04	-34.5595	18.6171	0.91306	0.0:1.0:0.0:0.0	.	215	Q16549	PCSK7_HUMAN	N	215	ENSP00000325917:D215N;ENSP00000431181:D215N	ENSP00000325917:D215N	D	-	1	0	PCSK7	116603209	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.818000	0.86416	2.633000	0.89246	0.655000	0.94253	GAC	.	.	.	none		0.567	PCSK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385529.2	NM_004716	
BCDIN3D	144233	hgsc.bcm.edu	37	12	50232321	50232321	+	Silent	SNP	A	A	G			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr12:50232321A>G	ENST00000333924.4	-	2	753	c.712T>C	c.(712-714)Ttg>Ctg	p.L238L	BCDIN3D-AS1_ENST00000548872.1_RNA|BCDIN3D-AS1_ENST00000549124.1_RNA	NM_181708.2	NP_859059.1	Q7Z5W3	BN3D2_HUMAN	BCDIN3 domain containing	238	Bin3-type SAM. {ECO:0000255|PROSITE- ProRule:PRU00848}.				miRNA metabolic process (GO:0010586)|negative regulation of pre-miRNA processing (GO:2000632)|RNA methylation (GO:0001510)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	O-methyltransferase activity (GO:0008171)|RNA methyltransferase activity (GO:0008173)			endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|skin(1)|stomach(1)	9						TCCTGGGTCAAGATCTGCACA	0.502																																					p.L238L		Atlas-SNP	.											.	BCDIN3D	20	.	0			c.T712C						PASS	.						130.0	121.0	124.0					12																	50232321		2203	4300	6503	SO:0001819	synonymous_variant	144233	exon2			GGGTCAAGATCTG		CCDS8790.1	12q13.13	2008-03-12				ENSG00000186666			27050	protein-coding gene	gene with protein product							Standard	NM_181708		Approved		uc001rvh.3	Q7Z5W3	OTTHUMG00000169807	ENST00000333924.4:c.712T>C	chr12.hg19:g.50232321A>G		84.0	0.0	.		64.0	36.0	.	NM_181708	A8K829	Silent	SNP	ENST00000333924.4	hg19	CCDS8790.1																																																																																			.	.	.	none		0.502	BCDIN3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405982.1	NM_181708	
CCDC59	29080	hgsc.bcm.edu	37	12	82752072	82752072	+	Silent	SNP	C	C	T			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr12:82752072C>T	ENST00000256151.7	-	1	495	c.84G>A	c.(82-84)agG>agA	p.R28R	METTL25_ENST00000248306.3_5'Flank|CCDC59_ENST00000548126.1_Intron	NM_014167.4	NP_054886.2	Q9P031	TAP26_HUMAN	coiled-coil domain containing 59	28					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)	5						CATTCTTATTCCTGTACCCGA	0.587											OREG0022008	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R28R		Atlas-SNP	.											.	CCDC59	17	.	0			c.G84A						PASS	.						69.0	63.0	65.0					12																	82752072		2203	4300	6503	SO:0001819	synonymous_variant	29080	exon1			CTTATTCCTGTAC	AF213377	CCDS9023.1	12q21.31	2007-10-17				ENSG00000133773			25005	protein-coding gene	gene with protein product						16630564, 12882447	Standard	NM_014167		Approved	HSPC128, TAP26, BR22	uc001szp.4	Q9P031		ENST00000256151.7:c.84G>A	chr12.hg19:g.82752072C>T		76.0	0.0	.	1216	81.0	29.0	.	NM_014167	Q9H2V5|Q9NW62	Silent	SNP	ENST00000256151.7	hg19	CCDS9023.1																																																																																			.	.	.	none		0.587	CCDC59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408186.1	NM_014167	
RAN	5901	hgsc.bcm.edu	37	12	131360202	131360202	+	Missense_Mutation	SNP	T	T	G			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr12:131360202T>G	ENST00000543796.1	+	6	739	c.481T>G	c.(481-483)Ttc>Gtc	p.F161V	RAN_ENST00000254675.3_Missense_Mutation_p.F73V|RAN_ENST00000392369.2_Missense_Mutation_p.F161V|RAN_ENST00000541630.1_Missense_Mutation_p.F73V|RAN_ENST00000392367.3_Missense_Mutation_p.F178V			P62826	RAN_HUMAN	RAN, member RAS oncogene family	161					actin cytoskeleton organization (GO:0030036)|androgen receptor signaling pathway (GO:0030521)|cellular protein complex localization (GO:0034629)|DNA metabolic process (GO:0006259)|gene expression (GO:0010467)|intracellular transport of virus (GO:0075733)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription, DNA-templated (GO:0045893)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|ribosomal large subunit export from nucleus (GO:0000055)|ribosomal small subunit export from nucleus (GO:0000056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(2)	9	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	Lung NSC(355;7.46e-07)|all_epithelial(31;7.36e-06)		OV - Ovarian serous cystadenocarcinoma(86;9.18e-49)|Epithelial(86;1.42e-45)|all cancers(50;6.28e-40)		TGAAAAGCCCTTCCTCTGGCT	0.408																																					p.F161V		Atlas-SNP	.											.	RAN	18	.	0			c.T481G						PASS	.						52.0	53.0	53.0					12																	131360202		2203	4300	6503	SO:0001583	missense	5901	exon6			AAGCCCTTCCTCT	M31469	CCDS9271.1, CCDS73546.1	12q24.33	2014-05-09			ENSG00000132341	ENSG00000132341			9846	protein-coding gene	gene with protein product		601179				8421051	Standard	XM_005253592		Approved	ARA24, TC4, Gsp1	uc001uir.3	P62826	OTTHUMG00000134328	ENST00000543796.1:c.481T>G	chr12.hg19:g.131360202T>G	ENSP00000446215:p.Phe161Val	126.0	0.0	.		117.0	58.0	.	NM_006325	A8K3Z8|P17080|P28746|P28747|Q6IPB2|Q86V08|Q8NI90|Q9CSP3|Q9CWI7|Q9CZA2|Q9UDJ5|Q9UEU9	Missense_Mutation	SNP	ENST00000543796.1	hg19	CCDS9271.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.415702	0.83449	.	.	ENSG00000132341	ENST00000543796;ENST00000448750;ENST00000541630;ENST00000392369;ENST00000254675;ENST00000535090;ENST00000392367	D;D;D;D;D;D;D	0.83419	-1.72;-1.72;-1.72;-1.72;-1.72;-1.72;-1.72	3.94	3.94	0.45596	.	0.000000	0.85682	D	0.000000	D	0.92136	0.7507	M	0.93594	3.435	0.80722	D	1	D;D	0.59767	0.986;0.986	D;D	0.66497	0.944;0.944	D	0.93640	0.6964	10	0.87932	D	0	-8.6508	12.2939	0.54833	0.0:0.0:0.0:1.0	.	161;161	A8K3Z8;P62826	.;RAN_HUMAN	V	161;179;73;161;73;157;178	ENSP00000446215:F161V;ENSP00000396127:F179V;ENSP00000441210:F73V;ENSP00000376176:F161V;ENSP00000254675:F73V;ENSP00000444042:F157V;ENSP00000376174:F178V	ENSP00000254675:F73V	F	+	1	0	RAN	129926155	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.590000	0.82653	1.554000	0.49487	0.460000	0.39030	TTC	.	.	.	none		0.408	RAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259441.2	NM_006325	
CENPJ	55835	hgsc.bcm.edu	37	13	25486722	25486722	+	Nonsense_Mutation	SNP	G	G	A			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr13:25486722G>A	ENST00000381884.4	-	2	627	c.442C>T	c.(442-444)Cag>Tag	p.Q148*	CENPJ_ENST00000545981.1_Nonsense_Mutation_p.Q148*	NM_018451.4	NP_060921.3	Q9HC77	CENPJ_HUMAN	centromere protein J	148					cell division (GO:0051301)|centriole replication (GO:0007099)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|microtubule polymerization (GO:0046785)|mitotic cell cycle (GO:0000278)|regulation of centriole replication (GO:0046599)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|gamma-tubulin small complex (GO:0008275)|microtubule (GO:0005874)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|tubulin binding (GO:0015631)			endometrium(5)|kidney(4)|large_intestine(14)|lung(13)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.00793)|Epithelial(112;0.0411)|OV - Ovarian serous cystadenocarcinoma(117;0.139)		TATTGTACCTGTTCAAGTTTT	0.368																																					p.Q148X		Atlas-SNP	.											.	CENPJ	116	.	0			c.C442T						PASS	.						68.0	70.0	69.0					13																	25486722		2203	4300	6503	SO:0001587	stop_gained	55835	exon2			GTACCTGTTCAAG	AF139625	CCDS9310.1	13q12.12	2013-11-05			ENSG00000151849	ENSG00000151849			17272	protein-coding gene	gene with protein product	"""centrosomal P4.1-associated protein"""	609279	"""microcephaly, primary autosomal recessive 6"""	MCPH6		11003675, 22699936	Standard	NM_018451		Approved	CPAP, BM032, LAP, LIP1, Sas-4, SASS4, SCKL4	uc001upt.5	Q9HC77	OTTHUMG00000016595	ENST00000381884.4:c.442C>T	chr13.hg19:g.25486722G>A	ENSP00000371308:p.Gln148*	91.0	0.0	.		57.0	30.0	.	NM_018451	Q2KHM6|Q5JPD5|Q5T6R5|Q96KS5|Q9C067	Nonsense_Mutation	SNP	ENST00000381884.4	hg19	CCDS9310.1	.	.	.	.	.	.	.	.	.	.	G	38	6.752924	0.97813	.	.	ENSG00000151849	ENST00000381884;ENST00000545981;ENST00000445729	.	.	.	5.9	5.9	0.94986	.	0.000000	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22109	T	0.4	.	17.1723	0.86833	0.0:0.0:1.0:0.0	.	.	.	.	X	148	.	ENSP00000371308:Q148X	Q	-	1	0	CENPJ	24384722	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	6.301000	0.72782	2.791000	0.96007	0.655000	0.94253	CAG	.	.	.	none		0.368	CENPJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044209.1	NM_018451	
CHD8	57680	hgsc.bcm.edu	37	14	21862288	21862288	+	Missense_Mutation	SNP	C	C	T			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr14:21862288C>T	ENST00000557364.1	-	32	5929	c.5666G>A	c.(5665-5667)cGt>cAt	p.R1889H	CHD8_ENST00000555962.1_5'Flank|CHD8_ENST00000430710.3_Missense_Mutation_p.R1610H|CHD8_ENST00000399982.2_Missense_Mutation_p.R1889H|SNORD9_ENST00000362566.1_RNA			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	1889					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|canonical Wnt signaling pathway (GO:0060070)|DNA duplex unwinding (GO:0032508)|in utero embryonic development (GO:0001701)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	MLL1 complex (GO:0071339)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(33)|ovary(6)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	85	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		CAATTCTATACGGTAGAGAGT	0.512																																					p.R1889H		Atlas-SNP	.											.	CHD8	339	.	0			c.G5666A						PASS	.						51.0	50.0	50.0					14																	21862288		1868	4106	5974	SO:0001583	missense	57680	exon31			TCTATACGGTAGA	AB046784	CCDS45081.1, CCDS53885.1	14q11.2	2008-02-05	2004-06-22	2004-06-23		ENSG00000100888			20153	protein-coding gene	gene with protein product		610528	"""helicase with SNF2 domain 1"""	HELSNF1		10997877	Standard	NM_020920		Approved	KIAA1564, DUPLIN	uc001war.2	Q9HCK8		ENST00000557364.1:c.5666G>A	chr14.hg19:g.21862288C>T	ENSP00000451601:p.Arg1889His	30.0	0.0	.		35.0	15.0	.	NM_001170629	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Missense_Mutation	SNP	ENST00000557364.1	hg19	CCDS53885.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.382302	0.82792	.	.	ENSG00000100888	ENST00000430710;ENST00000399982;ENST00000262707;ENST00000557364	D;D;D	0.83335	-1.71;-1.71;-1.71	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	D	0.91868	0.7426	M	0.83774	2.66	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.92496	0.6004	10	0.87932	D	0	-13.5033	18.1345	0.89614	0.0:1.0:0.0:0.0	.	1610	Q9HCK8-2	.	H	1610;1889;1609;1889	ENSP00000406288:R1610H;ENSP00000382863:R1889H;ENSP00000451601:R1889H	ENSP00000262707:R1609H	R	-	2	0	CHD8	20932128	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	7.651000	0.83577	2.816000	0.96949	0.563000	0.77884	CGT	.	.	.	none		0.512	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920	
STRN3	29966	hgsc.bcm.edu	37	14	31382758	31382758	+	Missense_Mutation	SNP	A	A	T			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr14:31382758A>T	ENST00000357479.5	-	10	1542	c.1346T>A	c.(1345-1347)gTa>gAa	p.V449E	STRN3_ENST00000366206.2_Intron|STRN3_ENST00000355683.5_Missense_Mutation_p.V365E	NM_001083893.1	NP_001077362.1	Q13033	STRN3_HUMAN	striatin, calmodulin binding protein 3	449					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to estradiol (GO:0032355)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	armadillo repeat domain binding (GO:0070016)|calmodulin binding (GO:0005516)|protein complex binding (GO:0032403)|protein phosphatase 2A binding (GO:0051721)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	20	Hepatocellular(127;0.0877)|Breast(36;0.148)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)|BRCA - Breast invasive adenocarcinoma(188;0.0805)	GBM - Glioblastoma multiforme(265;0.0124)		ATCATTTGTTACCGTCAAGTC	0.343																																					p.V449E		Atlas-SNP	.											.	STRN3	117	.	0			c.T1346A						PASS	.						96.0	89.0	91.0					14																	31382758		2203	4300	6503	SO:0001583	missense	29966	exon10			TTTGTTACCGTCA		CCDS9641.1, CCDS41938.1	14q13-q21	2013-01-10			ENSG00000196792	ENSG00000196792		"""WD repeat domain containing"""	15720	protein-coding gene	gene with protein product	"""cell cycle S/G2 nuclear autoantigen"""	614766				7864889, 10681496	Standard	NM_014574		Approved	SG2NA	uc001wqu.2	Q13033	OTTHUMG00000140201	ENST00000357479.5:c.1346T>A	chr14.hg19:g.31382758A>T	ENSP00000350071:p.Val449Glu	104.0	0.0	.		102.0	49.0	.	NM_001083893	A2RTX7|A6NHZ7|Q9NRA5	Missense_Mutation	SNP	ENST00000357479.5	hg19	CCDS41938.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.099076	0.76983	.	.	ENSG00000196792	ENST00000355683;ENST00000357479;ENST00000554991	T;T	0.64438	-0.1;2.37	5.97	4.84	0.62591	WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.78591	0.4307	M	0.81682	2.555	0.80722	D	1	D;P	0.89917	1.0;0.931	D;B	0.77004	0.989;0.444	T	0.80756	-0.1240	10	0.87932	D	0	-15.1617	11.8795	0.52566	0.9324:0.0:0.0676:0.0	.	365;449	Q13033-2;Q13033	.;STRN3_HUMAN	E	365;449;130	ENSP00000347909:V365E;ENSP00000350071:V449E	ENSP00000347909:V365E	V	-	2	0	STRN3	30452509	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.639000	0.91023	1.097000	0.41459	0.533000	0.62120	GTA	.	.	.	none		0.343	STRN3-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409713.1	NM_014574	
TRPM1	4308	hgsc.bcm.edu	37	15	31327765	31327765	+	Nonsense_Mutation	SNP	A	A	T			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr15:31327765A>T	ENST00000256552.6	-	21	2831	c.2684T>A	c.(2683-2685)tTa>tAa	p.L895*	RP11-348B17.1_ENST00000558755.1_RNA|RP11-348B17.1_ENST00000561299.1_RNA|TRPM1_ENST00000397795.2_Nonsense_Mutation_p.L873*|TRPM1_ENST00000542188.1_Nonsense_Mutation_p.L912*	NM_001252024.1	NP_001238953.1			transient receptor potential cation channel, subfamily M, member 1											NS(2)|breast(3)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(15)|lung(48)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(3)	99		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		TATCTTCTCTAACGCCAGGCT	0.542																																					p.L912X		Atlas-SNP	.											.	TRPM1	183	.	0			c.T2735A						PASS	.						80.0	81.0	80.0					15																	31327765		2047	4192	6239	SO:0001587	stop_gained	4308	exon20			TTCTCTAACGCCA	AF071787	CCDS10024.2, CCDS58345.1, CCDS58346.1, CCDS58347.1	15q13.3	2014-01-28		2002-01-18	ENSG00000134160	ENSG00000134160		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	7146	protein-coding gene	gene with protein product		603576	"""melastatin 1"""	MLSN1		9806836, 9537257, 16382100	Standard	NM_001252020		Approved	LTRPC1, CSNB1C	uc021sia.1	Q7Z4N2	OTTHUMG00000129267	ENST00000256552.6:c.2684T>A	chr15.hg19:g.31327765A>T	ENSP00000256552:p.Leu895*	79.0	0.0	.		72.0	39.0	.	NM_001252020		Nonsense_Mutation	SNP	ENST00000256552.6	hg19	CCDS58346.1	.	.	.	.	.	.	.	.	.	.	A	37	6.205158	0.97376	.	.	ENSG00000134160	ENST00000397795;ENST00000542188;ENST00000256552;ENST00000397793	.	.	.	5.57	5.57	0.84162	.	0.157867	0.42682	D	0.000679	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15952	T	0.53	-13.7367	15.7279	0.77777	1.0:0.0:0.0:0.0	.	.	.	.	X	873;912;895;873	.	ENSP00000256552:L895X	L	-	2	0	TRPM1	29115057	0.009000	0.17119	0.004000	0.12327	0.180000	0.23129	2.643000	0.46604	2.124000	0.65301	0.533000	0.62120	TTA	.	.	.	none		0.542	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420	
SLC7A5	8140	hgsc.bcm.edu	37	16	87902587	87902587	+	Missense_Mutation	SNP	C	C	A			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr16:87902587C>A	ENST00000261622.4	-	1	507	c.442G>T	c.(442-444)Gtg>Ttg	p.V148L		NM_003486.5	NP_003477.4	Q01650	LAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, L system), member 5	148					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|nervous system development (GO:0007399)|neutral amino acid transport (GO:0015804)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-amino acid transmembrane transporter activity (GO:0015179)|neutral amino acid transmembrane transporter activity (GO:0015175)|peptide antigen binding (GO:0042605)			endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(80;0.049)	Dextrothyroxine(DB00509)|L-DOPA(DB01235)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Melphalan(DB01042)	ACCAGGGCCACGATGTACTGC	0.652																																					p.V148L		Atlas-SNP	.											.	SLC7A5	28	.	0			c.G442T						PASS	.						15.0	13.0	13.0					16																	87902587		2119	4119	6238	SO:0001583	missense	8140	exon1			GGGCCACGATGTA	AF077866	CCDS10964.1	16q24.3	2013-05-22	2011-07-12		ENSG00000103257	ENSG00000103257		"""CD molecules"", ""Solute carriers"""	11063	protein-coding gene	gene with protein product		600182				9751058, 7829099	Standard	XM_006721286		Approved	LAT1, E16, D16S469E, MPE16, CD98	uc002fkm.3	Q01650	OTTHUMG00000137658	ENST00000261622.4:c.442G>T	chr16.hg19:g.87902587C>A	ENSP00000261622:p.Val148Leu	190.0	0.0	.		195.0	61.0	.	NM_003486	Q8IV97|Q9UBN8|Q9UP15|Q9UQC0	Missense_Mutation	SNP	ENST00000261622.4	hg19	CCDS10964.1	.	.	.	.	.	.	.	.	.	.	c	35	5.508315	0.96386	.	.	ENSG00000103257	ENST00000261622	D	0.89196	-2.48	4.34	4.34	0.51931	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	D	0.89904	0.6850	L	0.33137	0.985	0.80722	D	1	D	0.64830	0.994	P	0.59761	0.863	D	0.91451	0.5181	10	0.72032	D	0.01	.	15.8578	0.78994	0.0:1.0:0.0:0.0	.	148	Q01650	LAT1_HUMAN	L	148	ENSP00000261622:V148L	ENSP00000261622:V148L	V	-	1	0	SLC7A5	86460088	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	3.077000	0.50089	1.972000	0.57404	0.400000	0.26472	GTG	.	.	.	none		0.652	SLC7A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269110.2	NM_003486	
ALKBH5	54890	hgsc.bcm.edu	37	17	18088007	18088007	+	Silent	SNP	C	C	T			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr17:18088007C>T	ENST00000399138.4	+	1	455	c.450C>T	c.(448-450)ccC>ccT	p.P150P	ALKBH5_ENST00000541285.1_Intron|RP11-258F1.1_ENST00000583062.1_RNA|RP11-258F1.1_ENST00000577847.1_RNA	NM_017758.3	NP_060228.3	Q6P6C2	ALKB5_HUMAN	AlkB family member 5, RNA demethylase	150					cell differentiation (GO:0030154)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|oxidative single-stranded RNA demethylation (GO:0035553)|response to hypoxia (GO:0001666)|spermatogenesis (GO:0007283)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|oxidative RNA demethylase activity (GO:0035515)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|ovary(1)|skin(1)	10	all_neural(463;0.228)					AGCGCGGGCCCGGCCAGGAGC	0.672																																					p.P150P	Ovarian(166;154 1953 40235 46283 46309)	Atlas-SNP	.											.	ALKBH5	24	.	0			c.C450T						PASS	.						26.0	31.0	30.0					17																	18088007		1901	4074	5975	SO:0001819	synonymous_variant	54890	exon1			CGGGCCCGGCCAG	AK000315	CCDS42272.1	17p11.2	2014-07-23	2014-07-23	2006-02-09	ENSG00000091542	ENSG00000091542	1.14.11.-	"""Alkylation repair homologs"""	25996	protein-coding gene	gene with protein product		613303	"""oxoglutarate and iron-dependent oxygenase domain containing"", ""alkB, alkylation repair homolog 5 (E. coli)"""	OFOXD1		11997338, 24778178	Standard	NM_017758		Approved	FLJ20308	uc010cpw.3	Q6P6C2	OTTHUMG00000059397	ENST00000399138.4:c.450C>T	chr17.hg19:g.18088007C>T		115.0	0.0	.		137.0	40.0	.	NM_017758	B4DVJ4|D3DXC6|Q9NXD6	Silent	SNP	ENST00000399138.4	hg19	CCDS42272.1																																																																																			.	.	.	none		0.672	ALKBH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132069.3	NM_017758	
EVPLL	645027	hgsc.bcm.edu	37	17	18284974	18284974	+	Nonsense_Mutation	SNP	C	C	G	rs567752730		TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr17:18284974C>G	ENST00000399134.4	+	4	634	c.276C>G	c.(274-276)taC>taG	p.Y92*	RP1-37N7.1_ENST00000579352.1_RNA	NM_001145127.1	NP_001138599.1	A8MZ36	EVPLL_HUMAN	envoplakin-like	92										NS(1)|endometrium(1)|large_intestine(1)|lung(2)	5						GTGCCCTGTACGAGAAGATGG	0.627																																					p.Y92X		Atlas-SNP	.											.	EVPLL	10	.	0			c.C276G						PASS	.						134.0	123.0	126.0					17																	18284974		692	1591	2283	SO:0001587	stop_gained	645027	exon4			CCTGTACGAGAAG		CCDS45626.1	17p11.2	2009-08-25			ENSG00000214860	ENSG00000214860			35236	protein-coding gene	gene with protein product							Standard	NM_001145127		Approved		uc002gte.3	A8MZ36	OTTHUMG00000059095	ENST00000399134.4:c.276C>G	chr17.hg19:g.18284974C>G	ENSP00000382086:p.Tyr92*	124.0	0.0	.		112.0	35.0	.	NM_001145127	B4DPD4	Nonsense_Mutation	SNP	ENST00000399134.4	hg19	CCDS45626.1	.	.	.	.	.	.	.	.	.	.	.	16.41	3.116101	0.56505	.	.	ENSG00000214860	ENST00000399134	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	2.8319	0.05503	0.0:0.5931:0.0:0.4069	.	.	.	.	X	92	.	ENSP00000382086:Y92X	Y	+	3	2	EVPLL	18225699	0.225000	0.23685	0.990000	0.47175	0.206000	0.24218	-1.410000	0.02480	0.432000	0.26286	0.074000	0.15403	TAC	.	.	.	none		0.627	EVPLL-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000130836.2	NM_001145127	
EVI2B	2124	hgsc.bcm.edu	37	17	29632360	29632360	+	Missense_Mutation	SNP	C	C	G			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr17:29632360C>G	ENST00000330927.4	-	2	422	c.268G>C	c.(268-270)Gaa>Caa	p.E90Q	EVI2B_ENST00000544462.1_Missense_Mutation_p.E105Q|EVI2B_ENST00000577894.1_Missense_Mutation_p.E90Q|NF1_ENST00000356175.3_Intron|NF1_ENST00000358273.4_Intron|CTD-2370N5.3_ENST00000578584.1_3'UTR	NM_006495.3	NP_006486.3	P34910	EVI2B_HUMAN	ecotropic viral integration site 2B	90						integral component of plasma membrane (GO:0005887)		p.0?(8)|p.?(3)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|urinary_tract(1)	12		all_cancers(10;6.97e-11)|all_epithelial(10;0.0051)|all_hematologic(16;0.0149)|Breast(31;0.0155)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|all_lung(9;0.0468)|Lung NSC(157;0.094)		UCEC - Uterine corpus endometrioid carcinoma (4;6.64e-05)|all cancers(4;6.88e-13)|Epithelial(4;8.95e-12)|OV - Ovarian serous cystadenocarcinoma(4;1.01e-11)|GBM - Glioblastoma multiforme(4;0.184)		TCTGGTTTTTCAGAAGAGGTA	0.478																																					p.E90Q		Atlas-SNP	.											.	EVI2B	33	.	11	Whole gene deletion(8)|Unknown(3)	soft_tissue(7)|autonomic_ganglia(2)|lung(1)|central_nervous_system(1)	c.G268C						PASS	.						379.0	306.0	331.0					17																	29632360		2203	4300	6503	SO:0001583	missense	2124	exon2			GTTTTTCAGAAGA		CCDS11266.1	17q11.2	2011-08-11			ENSG00000185862	ENSG00000185862		"""CD molecules"""	3500	protein-coding gene	gene with protein product		158381				1903357	Standard	NM_006495		Approved	D17S376, EVDB, CD361	uc002hgk.2	P34910	OTTHUMG00000132869	ENST00000330927.4:c.268G>C	chr17.hg19:g.29632360C>G	ENSP00000333779:p.Glu90Gln	268.0	0.0	.		275.0	98.0	.	NM_006495	B7Z4A7	Missense_Mutation	SNP	ENST00000330927.4	hg19	CCDS11266.1	.	.	.	.	.	.	.	.	.	.	C	13.43	2.233965	0.39498	.	.	ENSG00000185862	ENST00000330927;ENST00000544462	T;T	0.46819	0.87;0.86	5.04	4.06	0.47325	.	0.894418	0.09273	N	0.824825	T	0.39009	0.1062	L	0.44542	1.39	0.80722	D	1	P;P	0.42296	0.775;0.775	B;B	0.40825	0.341;0.341	T	0.09509	-1.0671	10	0.15499	T	0.54	-17.1445	8.413	0.32655	0.0:0.8949:0.0:0.1051	.	105;90	B7Z4A7;P34910	.;EVI2B_HUMAN	Q	90;105	ENSP00000333779:E90Q;ENSP00000439738:E105Q	ENSP00000333779:E90Q	E	-	1	0	EVI2B	26656486	0.456000	0.25744	0.876000	0.34364	0.015000	0.08874	0.763000	0.26517	2.348000	0.79779	0.561000	0.74099	GAA	.	.	.	none		0.478	EVI2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256349.2	NM_006495	
NAT9	26151	hgsc.bcm.edu	37	17	72768111	72768111	+	Silent	SNP	A	A	G			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr17:72768111A>G	ENST00000357814.3	-	6	550	c.477T>C	c.(475-477)ctT>ctC	p.L159L	NAT9_ENST00000580301.1_Silent_p.L158L|NAT9_ENST00000582524.1_Intron|NAT9_ENST00000578822.1_Silent_p.L164L|NAT9_ENST00000582870.1_Silent_p.L163L|NAT9_ENST00000580632.1_Silent_p.L159L|NAT9_ENST00000583476.1_Missense_Mutation_p.S134P|NAT9_ENST00000581136.1_Silent_p.L154L|NAT9_ENST00000583757.1_Intron|NAT9_ENST00000580216.1_5'Flank	NM_015654.3	NP_056469.2	Q9BTE0	NAT9_HUMAN	N-acetyltransferase 9 (GCN5-related, putative)	159	N-acetyltransferase.					protein complex (GO:0043234)	N-acetyltransferase activity (GO:0008080)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)	8						GCTCAAAGTGAAGTTTCTGGA	0.512																																					p.L159L		Atlas-SNP	.											.	NAT9	16	.	0			c.T477C						PASS	.						158.0	153.0	155.0					17																	72768111		2203	4300	6503	SO:0001819	synonymous_variant	26151	exon6			AAAGTGAAGTTTC	AK123115	CCDS11706.1	17q25.2	2011-11-25	2008-09-24		ENSG00000109065	ENSG00000109065			23133	protein-coding gene	gene with protein product			"""N-acetyltransferase 9"""			14608357	Standard	NM_015654		Approved	DKFZP564C103	uc002jlq.3	Q9BTE0		ENST00000357814.3:c.477T>C	chr17.hg19:g.72768111A>G		151.0	0.0	.		182.0	110.0	.	NM_015654	B2R7F0|Q9BTD0|Q9Y3T3	Silent	SNP	ENST00000357814.3	hg19	CCDS11706.1																																																																																			.	.	.	none		0.512	NAT9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000443700.1	NM_015654	
SMARCA4	6597	hgsc.bcm.edu	37	19	11144020	11144020	+	Missense_Mutation	SNP	G	G	C			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr19:11144020G>C	ENST00000429416.3	+	27	3882	c.3601G>C	c.(3601-3603)Gtg>Ctg	p.V1201L	SMARCA4_ENST00000444061.3_Missense_Mutation_p.V1201L|SMARCA4_ENST00000413806.3_Missense_Mutation_p.V1201L|SMARCA4_ENST00000344626.4_Missense_Mutation_p.V1201L|SMARCA4_ENST00000590574.1_Missense_Mutation_p.V1201L|SMARCA4_ENST00000358026.2_Missense_Mutation_p.V1201L|SMARCA4_ENST00000541122.2_Missense_Mutation_p.V1201L|SMARCA4_ENST00000450717.3_Missense_Mutation_p.V1201L|SMARCA4_ENST00000589677.1_Missense_Mutation_p.V1201L	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	1201	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				CGAGGTGCGTGTGCTCCGCCT	0.622			"""F, N, Mis"""		NSCLC																																p.V1201L		Atlas-SNP	.		Rec	yes		19	19p13.2	6597	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"""		E	.	SMARCA4	502	.	1	Unknown(1)	lung(1)	c.G3601C						PASS	.						86.0	82.0	83.0					19																	11144020		2203	4300	6503	SO:0001583	missense	6597	exon26			GTGCGTGTGCTCC	D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"""SNF2-like 4"", ""global transcription activator homologous sequence"", ""sucrose nonfermenting-like 4"", ""mitotic growth and transcription activator"", ""BRM/SWI2-related gene 1"", ""homeotic gene regulator"", ""nuclear protein GRB1"", ""brahma protein-like 1"", ""ATP-dependent helicase SMARCA4"""	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.3601G>C	chr19.hg19:g.11144020G>C	ENSP00000395654:p.Val1201Leu	216.0	0.0	.		164.0	83.0	.	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	hg19	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.549924	0.86127	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	T;T;T;T;T;T;T	0.79749	-1.3;-1.3;-1.3;-1.3;-1.3;-1.3;-1.3	4.74	4.74	0.60224	Helicase, C-terminal (1);	0.146662	0.44902	D	0.000416	D	0.90827	0.7119	H	0.95365	3.66	0.58432	D	0.999996	P;P;P;B;P;D;B	0.55605	0.887;0.887;0.887;0.139;0.589;0.972;0.139	P;P;P;B;B;P;B	0.54590	0.656;0.723;0.723;0.139;0.239;0.756;0.139	D	0.93705	0.7019	10	0.87932	D	0	-33.2279	16.7067	0.85374	0.0:0.0:1.0:0.0	.	1201;1201;1201;1201;1201;421;1201	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;P51532	.;.;.;.;.;.;SMCA4_HUMAN	L	1201;1201;1265;1201;1201;1201;1201;1201	ENSP00000395654:V1201L;ENSP00000350720:V1201L;ENSP00000343896:V1201L;ENSP00000445036:V1201L;ENSP00000392837:V1201L;ENSP00000397783:V1201L;ENSP00000414727:V1201L	ENSP00000343896:V1201L	V	+	1	0	SMARCA4	11005020	1.000000	0.71417	0.963000	0.40424	0.961000	0.63080	9.319000	0.96338	2.488000	0.83962	0.558000	0.71614	GTG	.	.	.	none		0.622	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072	
CYP4F3	4051	hgsc.bcm.edu	37	19	15752326	15752326	+	Missense_Mutation	SNP	T	T	G			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr19:15752326T>G	ENST00000221307.8	+	2	148	c.101T>G	c.(100-102)aTc>aGc	p.I34S	CYP4F3_ENST00000591058.1_Missense_Mutation_p.I34S|CYP4F3_ENST00000586182.2_Missense_Mutation_p.I34S|CYP4F3_ENST00000585846.1_Missense_Mutation_p.I34S	NM_000896.2	NP_000887.2	Q08477	CP4F3_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 3	34					arachidonic acid metabolic process (GO:0019369)|icosanoid metabolic process (GO:0006690)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alpha-tocopherol omega-hydroxylase activity (GO:0052871)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|monooxygenase activity (GO:0004497)			endometrium(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|stomach(1)	34						CTGGCCCGCATCCTGGCCTGG	0.637																																					p.I34S		Atlas-SNP	.											.	CYP4F3	69	.	0			c.T101G						PASS	.						60.0	63.0	62.0					19																	15752326		2203	4300	6503	SO:0001583	missense	4051	exon2			CCCGCATCCTGGC	AB002454	CCDS12332.1, CCDS59362.1	19p13.12	2013-02-21	2003-01-14		ENSG00000186529	ENSG00000186529		"""Cytochrome P450s"""	2646	protein-coding gene	gene with protein product		601270	"""cytochrome P450, subfamily IVF, polypeptide 3 (leukotriene B4 omega hydroxylase)"""	LTB4H		8486631, 9539102	Standard	NM_000896		Approved	CYP4F	uc010xol.2	Q08477	OTTHUMG00000182374	ENST00000221307.8:c.101T>G	chr19.hg19:g.15752326T>G	ENSP00000221307:p.Ile34Ser	150.0	0.0	.		98.0	39.0	.	NM_001199209	B7Z8Z3|O60634|Q5U740	Missense_Mutation	SNP	ENST00000221307.8	hg19	CCDS12332.1	.	.	.	.	.	.	.	.	.	.	.	9.352	1.065809	0.20067	.	.	ENSG00000186529	ENST00000221307	D	0.90069	-2.61	3.9	0.0418	0.14214	.	1.091210	0.07176	U	0.853302	D	0.85877	0.5799	L	0.48642	1.525	0.09310	N	1	B;B	0.26363	0.147;0.147	B;B	0.31337	0.128;0.128	T	0.74711	-0.3573	10	0.62326	D	0.03	.	9.4966	0.38993	0.0:0.0:0.5539:0.4461	.	34;34	B7Z8Z3;Q08477	.;CP4F3_HUMAN	S	34	ENSP00000221307:I34S	ENSP00000221307:I34S	I	+	2	0	CYP4F3	15613326	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	0.096000	0.15147	-0.033000	0.13736	-0.811000	0.03165	ATC	.	.	.	none		0.637	CYP4F3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460819.3	NM_000896	
TTC3	7267	hgsc.bcm.edu	37	21	38494269	38494269	+	Missense_Mutation	SNP	A	A	T			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr21:38494269A>T	ENST00000399017.2	+	12	3800	c.1053A>T	c.(1051-1053)gaA>gaT	p.E351D	TTC3_ENST00000540756.1_Missense_Mutation_p.E41D|TTC3_ENST00000355666.1_Missense_Mutation_p.E351D|TTC3_ENST00000354749.2_Missense_Mutation_p.E351D|TTC3_ENST00000479930.1_3'UTR	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	351					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				AACAAATAGAAGACCTACAAG	0.373																																					p.E351D	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.A1053T						PASS	.						64.0	65.0	65.0					21																	38494269		2203	4300	6503	SO:0001583	missense	7267	exon12			AATAGAAGACCTA	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"""RING-type (C3HC4) zinc fingers"", ""Tetratricopeptide (TTC) repeat domain containing"""	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.1053A>T	chr21.hg19:g.38494269A>T	ENSP00000381981:p.Glu351Asp	267.0	0.0	.		205.0	92.0	.	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	hg19	CCDS13651.1	.	.	.	.	.	.	.	.	.	.	A	14.03	2.413394	0.42817	.	.	ENSG00000182670	ENST00000418766;ENST00000450533;ENST00000438055;ENST00000355666;ENST00000540756;ENST00000399017;ENST00000354749	T;T;T;T;T;T;T	0.48836	1.03;1.03;1.03;2.93;0.8;2.93;2.93	5.41	4.26	0.50523	Tetratricopeptide-like helical (1);	0.000000	0.56097	D	0.000032	T	0.34048	0.0884	L	0.27053	0.805	0.32047	N	0.597515	B;B	0.21753	0.009;0.06	B;B	0.17433	0.007;0.018	T	0.39035	-0.9633	10	0.56958	D	0.05	-16.3909	10.2565	0.43401	0.8212:0.1788:0.0:0.0	.	41;351	B4DSZ9;P53804	.;TTC3_HUMAN	D	351;351;333;351;41;351;351	ENSP00000403943:E351D;ENSP00000408456:E351D;ENSP00000391891:E333D;ENSP00000347889:E351D;ENSP00000442875:E41D;ENSP00000381981:E351D;ENSP00000346791:E351D	ENSP00000346791:E351D	E	+	3	2	TTC3	37416139	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.903000	0.28475	0.895000	0.36342	0.528000	0.53228	GAA	.	.	.	none		0.373	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1		
MTM1	4534	hgsc.bcm.edu	37	X	149767104	149767104	+	Missense_Mutation	SNP	G	G	T			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chrX:149767104G>T	ENST00000370396.2	+	4	239	c.185G>T	c.(184-186)aGa>aTa	p.R62I	MTM1_ENST00000542741.1_Intron|MTM1_ENST00000306167.7_3'UTR|MTM1_ENST00000543350.1_Intron|MTM1_ENST00000413012.2_Missense_Mutation_p.R62I	NM_000252.2	NP_000243.1	Q13496	MTM1_HUMAN	myotubularin 1	62	GRAM.				endosome to lysosome transport (GO:0008333)|intermediate filament organization (GO:0045109)|mitochondrion distribution (GO:0048311)|mitochondrion morphogenesis (GO:0070584)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|protein transport (GO:0015031)|regulation of vacuole organization (GO:0044088)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|late endosome (GO:0005770)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	intermediate filament binding (GO:0019215)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|liver(1)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Acute lymphoblastic leukemia(192;6.56e-05)					ATTAAGGGAAGAGTTTACATC	0.299																																					p.R62I		Atlas-SNP	.											.	MTM1	89	.	0			c.G185T						PASS	.						72.0	71.0	71.0					X																	149767104		2202	4295	6497	SO:0001583	missense	4534	exon4			AGGGAAGAGTTTA	U46024	CCDS14694.1	Xq27.3-q28	2014-09-17			ENSG00000171100	ENSG00000171100		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7448	protein-coding gene	gene with protein product		300415	"""myotubular myopathy 1"""				Standard	NM_000252		Approved		uc004fef.4	Q13496	OTTHUMG00000024158	ENST00000370396.2:c.185G>T	chrX.hg19:g.149767104G>T	ENSP00000359423:p.Arg62Ile	356.0	1.0	.		297.0	272.0	.	NM_000252	A6NDB1|B7Z491|F2Z330|Q8NEL1	Missense_Mutation	SNP	ENST00000370396.2	hg19	CCDS14694.1	.	.	.	.	.	.	.	.	.	.	G	14.82	2.650071	0.47362	.	.	ENSG00000171100	ENST00000370396;ENST00000424519;ENST00000413012	D;D;D	0.88818	-2.43;-2.43;-2.43	5.62	4.75	0.60458	GRAM (2);	0.096235	0.64402	D	0.000001	D	0.84115	0.5401	L	0.43923	1.385	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.19666	0.026;0.026	T	0.79200	-0.1901	10	0.30854	T	0.27	.	11.9192	0.52783	0.0872:0.0:0.9128:0.0	.	62;62	B7Z491;Q13496	.;MTM1_HUMAN	I	62	ENSP00000359423:R62I;ENSP00000400699:R62I;ENSP00000389157:R62I	ENSP00000359423:R62I	R	+	2	0	MTM1	149517762	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.671000	0.54576	2.363000	0.80096	0.600000	0.82982	AGA	.	.	.	none		0.299	MTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060847.3	NM_000252	
SPTBN1	6711	hgsc.bcm.edu	37	2	54884994	54884994	+	Frame_Shift_Del	DEL	G	G	-			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr2:54884994delG	ENST00000356805.4	+	30	6335	c.6054delG	c.(6052-6054)gagfs	p.E2018fs	SPTBN1_ENST00000333896.5_Frame_Shift_Del_p.E2005fs	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	2018	Interaction with ANK2.				actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			CAGTTCTGGAGGTCCATCAGT	0.592											OREG0014619	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E2018fs		Atlas-Indel,Pindel	.											.	SPTBN1	378	.	0			c.6053delA						PASS	.						67.0	61.0	63.0					2																	54884994		2203	4300	6503	SO:0001589	frameshift_variant	6711	exon30			.		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"""Pleckstrin homology (PH) domain containing"""	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.6054delG	chr2.hg19:g.54884994delG	ENSP00000349259:p.Glu2018fs	99.0	0.0	0	1003	67.0	31.0	0.462687	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Frame_Shift_Del	DEL	ENST00000356805.4	hg19	CCDS33198.1																																																																																			.	.	.	none		0.592	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3		
CACNA1E	777	hgsc.bcm.edu	37	1	181695257	181695258	+	Frame_Shift_Ins	INS	-	-	GAGGTCA			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr1:181695257_181695258insGAGGTCA	ENST00000367573.2	+	18	2199_2200	c.2199_2200insGAGGTCA	c.(2200-2202)gagfs	p.-734fs	CACNA1E_ENST00000526775.1_Frame_Shift_Ins_p.-734fs|CACNA1E_ENST00000357570.5_Frame_Shift_Ins_p.-685fs|CACNA1E_ENST00000367570.1_Frame_Shift_Ins_p.-734fs|CACNA1E_ENST00000367567.4_Frame_Shift_Ins_p.-341fs|CACNA1E_ENST00000360108.3_Frame_Shift_Ins_p.-734fs|CACNA1E_ENST00000358338.5_Frame_Shift_Ins_p.-685fs	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit						calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						AGAAGGCCAAGGAGGTCAGCCC	0.54																																					p.K733fs		Atlas-Indel,Pindel	.											.	CACNA1E	778	.	0			c.2199_2200insGAGGTCA						PASS	.																																			SO:0001589	frameshift_variant	777	exon18			.	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.2200_2206dupGAGGTCA	chr1.hg19:g.181695258_181695264dupGAGGTCA	ENSP00000356545:p.Glu734fs	101.0	0.0	0		78.0	23.0	0.294872	NM_000721	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Frame_Shift_Ins	INS	ENST00000367573.2	hg19	CCDS55664.1																																																																																			.	.	.	none		0.540	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721	
MAML2	84441	hgsc.bcm.edu	37	11	95826617	95826617	+	Frame_Shift_Del	DEL	T	T	-			TCGA-SX-A71R-01A-12D-A33Q-10	TCGA-SX-A71R-10A-01D-A33Q-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c23b8a50-fec8-4f6d-86be-42ae4bb3feee	25cf82fb-bcef-43f2-866b-078527b0881a	g.chr11:95826617delT	ENST00000524717.1	-	2	1862	c.578delA	c.(577-579)aatfs	p.N193fs		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	193					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				CACAAAGCCATTGGGTCGCTT	0.418			T	"""MECT1, CRTC3"""	salivary gland mucoepidermoid																																p.N193fs		Atlas-Indel,Pindel	.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2	94	.	0			c.579delT						PASS	.						106.0	100.0	102.0					11																	95826617		1855	4114	5969	SO:0001589	frameshift_variant	84441	exon2			.	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"""mastermind (Drosophila)-like 2"""			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.578delA	chr11.hg19:g.95826617delT	ENSP00000434552:p.Asn193fs	167.0	0.0	0		138.0	63.0	0.456522	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Frame_Shift_Del	DEL	ENST00000524717.1	hg19	CCDS44714.1																																																																																			.	.	.	none		0.418	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1		
