#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_NTotCov	i_NVarCov	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	i_dbSNP_AF	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
MAP7D1	55700	hgsc.bcm.edu	37	1	36643703	36643703	+	Missense_Mutation	SNP	A	A	G	rs3045695|rs141305015|rs200892098	byFrequency	TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr1:36643703A>G	ENST00000373151.2	+	9	1825	c.1609A>G	c.(1609-1611)Aag>Gag	p.K537E	MAP7D1_ENST00000316156.4_Missense_Mutation_p.K500E|MAP7D1_ENST00000373150.4_Missense_Mutation_p.K505E|MAP7D1_ENST00000373148.4_Missense_Mutation_p.K83E	NM_018067.3	NP_060537.3	Q3KQU3	MA7D1_HUMAN	MAP7 domain containing 1	537	Pro-rich.				microtubule cytoskeleton organization (GO:0000226)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)				breast(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	19		Myeloproliferative disorder(586;0.0393)				CAGTAACGAGAAGGAGTCAGC	0.721																																					p.K537E		Atlas-SNP	.											.,2	MAP7D1	62	.	0			c.A1609G						.						29.0	29.0	29.0					1																	36643703		2192	4270	6462	SO:0001583	missense	55700	exon9			AACGAGAAGGAGT	AK096341	CCDS30673.1, CCDS65492.1, CCDS65493.1	1p34.3	2008-02-05	2007-02-08	2007-02-08	ENSG00000116871	ENSG00000116871			25514	protein-coding gene	gene with protein product			"""proline arginine rich coiled coil 1"", ""arginine/proline rich coiled-coil 1"""	PARCC1, RPRC1		10574461	Standard	XM_005271024		Approved	FLJ10350, FLJ39022	uc001bzz.3	Q3KQU3	OTTHUMG00000007714	ENST00000373151.2:c.1609A>G	chr1.hg19:g.36643703A>G	ENSP00000362244:p.Lys537Glu	1.0	1.0		7.0	7.0	NM_018067	D3DPS4|Q7L8J5|Q8N905|Q8TAK0|Q9HBQ2|Q9NW29|Q9ULN3	Missense_Mutation	SNP	ENST00000373151.2	hg19	CCDS30673.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	6.555|6.555	0.470598|0.470598	0.12461|0.12461	.|.	.|.	ENSG00000116871|ENSG00000116871	ENST00000530975|ENST00000316156;ENST00000373150;ENST00000373151;ENST00000373148	T|T;T;T;T	0.57752|0.49720	0.38|0.77;0.77;0.77;0.77	5.03|5.03	2.66|2.66	0.31614|0.31614	.|.	.|0.493263	.|0.17209	.|N	.|0.182837	T|T	0.36358|0.36358	0.0964|0.0964	L|L	0.50333|0.50333	1.59|1.59	0.31867|0.31867	N|N	0.620209|0.620209	.|B;B;B;B;B	.|0.12013	.|0.001;0.001;0.005;0.002;0.001	.|B;B;B;B;B	.|0.08055	.|0.003;0.001;0.003;0.003;0.001	T|T	0.34875|0.34875	-0.9811|-0.9811	7|10	0.62326|0.19147	D|T	0.03|0.46	-11.1212|-11.1212	7.538|7.538	0.27721|0.27721	0.8218:0.0:0.1782:0.0|0.8218:0.0:0.1782:0.0	.|.	.|83;537;500;505;537	.|Q3KQU3-3;D3DPS3;Q3KQU3-2;Q3KQU3-4;Q3KQU3	.|.;.;.;.;MA7D1_HUMAN	G|E	119|500;505;537;83	ENSP00000437046:E119G|ENSP00000320228:K500E;ENSP00000362243:K505E;ENSP00000362244:K537E;ENSP00000362241:K83E	ENSP00000437046:E119G|ENSP00000320228:K500E	E|K	+|+	2|1	0|0	MAP7D1|MAP7D1	36416290|36416290	0.997000|0.997000	0.39634|0.39634	0.990000|0.990000	0.47175|0.47175	0.119000|0.119000	0.20118|0.20118	1.102000|1.102000	0.31050|0.31050	0.951000|0.951000	0.37770|0.37770	0.528000|0.528000	0.53228|0.53228	GAA|AAG	.	.		0.721	MAP7D1-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382095.1	NM_018067	
ITGA10	8515	hgsc.bcm.edu	37	1	145537466	145537466	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr1:145537466G>C	ENST00000369304.3	+	20	2651	c.2476G>C	c.(2476-2478)Gta>Cta	p.V826L	ITGA10_ENST00000539363.1_Missense_Mutation_p.V683L|ITGA10_ENST00000538811.1_Missense_Mutation_p.V695L	NM_003637.3	NP_003628.2	O75578	ITA10_HUMAN	integrin, alpha 10	826					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	integrin alpha10-beta1 complex (GO:0034680)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GAAAGTGCTGGTATCTACAAC	0.517																																					p.V826L		Atlas-SNP	.											.	ITGA10	131	.	0			c.G2476C						.						193.0	205.0	201.0					1																	145537466		2203	4300	6503	SO:0001583	missense	8515	exon20			GTGCTGGTATCTA	AF074015	CCDS72869.1	1q21.1	2010-03-23			ENSG00000143127	ENSG00000143127		"""Integrins"""	6135	protein-coding gene	gene with protein product		604042				9685391, 10702680	Standard	NM_003637		Approved		uc001eoa.3	O75578	OTTHUMG00000013751	ENST00000369304.3:c.2476G>C	chr1.hg19:g.145537466G>C	ENSP00000358310:p.Val826Leu	110.0	0.0		68.0	6.0	NM_003637	B2RAM4|B2RTV5|Q6UXJ6|Q9UHZ8	Missense_Mutation	SNP	ENST00000369304.3	hg19	CCDS918.1	.	.	.	.	.	.	.	.	.	.	G	15.26	2.780770	0.49891	.	.	ENSG00000143127	ENST00000369304;ENST00000543043;ENST00000539363;ENST00000538811	T;T;T	0.41758	0.99;0.99;0.99	5.07	5.07	0.68467	Integrin alpha-2 (1);	0.000000	0.64402	D	0.000001	T	0.31949	0.0813	L	0.34521	1.04	0.58432	D	0.999999	B;B;P;B	0.36354	0.155;0.073;0.549;0.388	B;B;P;B	0.45753	0.17;0.076;0.492;0.189	T	0.12477	-1.0546	10	0.45353	T	0.12	.	15.9866	0.80157	0.0:0.0:1.0:0.0	.	792;695;683;826	F5H3T9;F5GY13;B2RTV5;O75578	.;.;.;ITA10_HUMAN	L	826;792;683;695	ENSP00000358310:V826L;ENSP00000439894:V683L;ENSP00000440011:V695L	ENSP00000358310:V826L	V	+	1	0	ITGA10	144248823	1.000000	0.71417	0.977000	0.42913	0.610000	0.37248	7.282000	0.78630	2.645000	0.89757	0.655000	0.94253	GTA	.	.		0.517	ITGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038537.2	NM_003637	
SLAMF9	89886	hgsc.bcm.edu	37	1	159923926	159923926	+	Start_Codon_SNP	SNP	A	A	G	rs147539315		TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr1:159923926A>G	ENST00000368093.3	-	1	118	c.2T>C	c.(1-3)aTg>aCg	p.M1T	SLAMF9_ENST00000368092.3_Start_Codon_SNP_p.M1T|SLAMF9_ENST00000466773.1_5'Flank	NM_033438.3	NP_254273.2	Q96A28	SLAF9_HUMAN	SLAM family member 9	1						integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(1)|endometrium(2)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	13	all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			AAAGGCACACATGTCAGCAGC	0.577																																					p.M1T		Atlas-SNP	.											.	SLAMF9	41	.	0			c.T2C						.	A	THR/MET,THR/MET,THR/MET	0,4406		0,0,2203	95.0	91.0	92.0		2,2,2	1.4	0.0	1	dbSNP_134	92	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	SLAMF9	NM_033438.3,NM_001146173.1,NM_001146172.1	81,81,81	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign,benign,benign	1/290,1/112,1/199	159923926	1,13005	2203	4300	6503	SO:0001582	initiator_codon_variant	89886	exon1			GCACACATGTCAG	AY034613	CCDS1191.1, CCDS53392.1	1q23.1	2013-01-11			ENSG00000162723	ENSG00000162723		"""Immunoglobulin superfamily / V-set domain containing"""	18430	protein-coding gene	gene with protein product		608589				11685473	Standard	NM_033438		Approved	CD2F-10, CD84-H1, SF2001	uc001fus.3	Q96A28	OTTHUMG00000024074	ENST00000368093.3:c.2T>C	chr1.hg19:g.159923926A>G	ENSP00000357072:p.Met1Thr	45.0	0.0		36.0	8.0	NM_033438	Q5JRQ9|Q5JRR0|Q6UWG1	Missense_Mutation	SNP	ENST00000368093.3	hg19	CCDS1191.1	.	.	.	.	.	.	.	.	.	.	A	13.07	2.128373	0.37533	0.0	1.16E-4	ENSG00000162723	ENST00000368093;ENST00000368092	T;T	0.32753	3.28;1.44	5.2	1.4	0.22301	.	0.556105	0.17292	N	0.179616	T	0.06005	0.0156	.	.	.	0.80722	D	1	B;B	0.19583	0.037;0.022	B;B	0.21917	0.037;0.017	T	0.25572	-1.0128	8	.	.	.	-15.19	1.9765	0.03417	0.5793:0.1689:0.0898:0.1621	.	1;1	Q96A28-2;Q96A28	.;SLAF9_HUMAN	T	1	ENSP00000357072:M1T;ENSP00000357071:M1T	.	M	-	2	0	SLAMF9	158190550	0.941000	0.31946	0.032000	0.17829	0.036000	0.12997	1.661000	0.37408	0.032000	0.15435	0.533000	0.62120	ATG	.	A|1.000;G|0.000		0.577	SLAMF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060630.1	NM_033438	Missense_Mutation
ATL2	64225	hgsc.bcm.edu	37	2	38604337	38604337	+	Silent	SNP	C	C	T			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr2:38604337C>T	ENST00000378954.4	-	1	67	c.66G>A	c.(64-66)cgG>cgA	p.R22R	ATL2_ENST00000539122.1_5'UTR|ATL2_ENST00000419554.2_Silent_p.R22R|ATL2_ENST00000452935.2_5'Flank|ATL2_ENST00000332337.4_5'Flank|ATL2_ENST00000406122.1_5'UTR|ATL2_ENST00000402054.1_5'Flank|ATL2_ENST00000546051.1_5'Flank	NM_001135673.1|NM_022374.2	NP_001129145.1|NP_071769.2	Q8NHH9	ATLA2_HUMAN	atlastin GTPase 2	22					endoplasmic reticulum organization (GO:0007029)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	22						GGTCGCTGGTCCGTCGCCGGC	0.672																																					p.R22R		Atlas-SNP	.											.	ATL2	49	.	0			c.G66A						.						20.0	26.0	24.0					2																	38604337		2202	4291	6493	SO:0001819	synonymous_variant	64225	exon1			GCTGGTCCGTCGC		CCDS1795.1, CCDS46260.1	2p22.3	2008-09-17	2008-09-17	2008-09-17	ENSG00000119787	ENSG00000119787			24047	protein-coding gene	gene with protein product		609368	"""ADP-ribosylation factor-like 6 interacting protein 2"""	ARL6IP2		10508919, 18270207	Standard	NM_022374		Approved		uc002rqq.3	Q8NHH9	OTTHUMG00000102074	ENST00000378954.4:c.66G>A	chr2.hg19:g.38604337C>T		151.0	0.0		162.0	15.0	NM_001135673	B7Z1X2|B7Z7X8|Q4ZG30|Q7Z630|Q8NHH8|Q9H5M7	Silent	SNP	ENST00000378954.4	hg19	CCDS46260.1	.	.	.	.	.	.	.	.	.	.	C	4.189	0.033727	0.08101	.	.	ENSG00000119787	ENST00000443098	.	.	.	3.68	2.78	0.32641	.	.	.	.	.	T	0.56381	0.1981	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50701	-0.8797	4	.	.	.	-2.2579	8.0452	0.30545	0.0:0.8784:0.0:0.1216	.	.	.	.	E	21	.	.	G	-	2	0	ATL2	38457841	1.000000	0.71417	0.966000	0.40874	0.040000	0.13550	0.826000	0.27407	0.812000	0.34326	0.650000	0.86243	GGA	.	.		0.672	ATL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219886.2	NM_022374	
ALMS1	7840	hgsc.bcm.edu	37	2	73613036	73613036	+	Missense_Mutation	SNP	G	G	C	rs61156725|rs72319667|rs3074417	byFrequency	TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr2:73613036G>C	ENST00000264448.6	+	1	151	c.40G>C	c.(40-42)Gag>Cag	p.E14Q	ALMS1_ENST00000409009.1_Missense_Mutation_p.E14Q|ALMS1_ENST00000377715.1_Missense_Mutation_p.E14Q	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	14	Glu-rich.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.E27_E28delEE(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CGAGCTggaggaggaggagga	0.692																																					p.E14Q		Atlas-SNP	.											.	ALMS1	384	.	1	Deletion - In frame(1)	ovary(1)	c.G40C						.						3.0	4.0	4.0					2																	73613036		1509	3234	4743	SO:0001583	missense	7840	exon1			CTGGAGGAGGAGG	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.40G>C	chr2.hg19:g.73613036G>C	ENSP00000264448:p.Glu14Gln	191.0	0.0		331.0	31.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	G	15.09	2.731519	0.48939	.	.	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.26373	2.4;2.61;1.74	3.19	3.19	0.36642	.	0.259523	0.20097	U	0.099311	T	0.32436	0.0829	N	0.19112	0.55	0.22317	N	0.999202	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.03493	-1.1031	10	0.87932	D	0	.	10.1262	0.42652	0.0:0.0:1.0:0.0	.	14;14	B8ZZJ3;Q8TCU4	.;ALMS1_HUMAN	Q	14	ENSP00000386627:E14Q;ENSP00000264448:E14Q;ENSP00000366944:E14Q	ENSP00000264448:E14Q	E	+	1	0	ALMS1	73466544	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	2.034000	0.41145	2.070000	0.61991	0.484000	0.47621	GAG	.	.		0.692	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
C2orf66	401027	hgsc.bcm.edu	37	2	197672293	197672293	+	Silent	SNP	T	T	A			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr2:197672293T>A	ENST00000342506.2	-	2	1116	c.228A>T	c.(226-228)acA>acT	p.T76T		NM_213608.2	NP_998773.1	Q6UXQ4	CB066_HUMAN	chromosome 2 open reading frame 66	76						extracellular region (GO:0005576)				endometrium(2)|large_intestine(2)|lung(4)|ovary(1)	9						GATTTGGAAATGTTCCAAGAT	0.393																																					p.T76T		Atlas-SNP	.											.	C2orf66	15	.	0			c.A228T						.						134.0	141.0	139.0					2																	197672293		2203	4300	6503	SO:0001819	synonymous_variant	401027	exon2			TGGAAATGTTCCA		CCDS2317.1	2q33.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000187944	ENSG00000187944			33809	protein-coding gene	gene with protein product							Standard	NM_213608		Approved	UNQ6411	uc002utv.3	Q6UXQ4	OTTHUMG00000132742	ENST00000342506.2:c.228A>T	chr2.hg19:g.197672293T>A		150.0	0.0		36.0	6.0	NM_213608	B2RNW3	Silent	SNP	ENST00000342506.2	hg19	CCDS2317.1																																																																																			.	.		0.393	C2orf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256102.1	NM_213608	
PRRT3	285368	hgsc.bcm.edu	37	3	9989661	9989661	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr3:9989661C>T	ENST00000412055.1	-	4	1325	c.1196G>A	c.(1195-1197)cGc>cAc	p.R399H	PRRT3-AS1_ENST00000431558.1_RNA	NM_207351.3	NP_997234.3	Q5FWE3	PRRT3_HUMAN	proline-rich transmembrane protein 3	399	Pro-rich.					integral component of membrane (GO:0016021)				NS(2)|breast(1)|endometrium(3)|large_intestine(3)|lung(1)|skin(1)|stomach(2)	13						GCTTTGGGGGCGCCCCGGCCA	0.577																																					p.R399H		Atlas-SNP	.											.	PRRT3	35	.	0			c.G1196A						.						4.0	5.0	5.0					3																	9989661		1759	3881	5640	SO:0001583	missense	285368	exon4			TGGGGGCGCCCCG	AK090993	CCDS43049.1	3p25.3	2011-10-10			ENSG00000163704	ENSG00000163704		"""Proline-rich transmembrane proteins"""	26591	protein-coding gene	gene with protein product							Standard	NM_207351		Approved	FLJ33674	uc003bul.2	Q5FWE3	OTTHUMG00000155285	ENST00000412055.1:c.1196G>A	chr3.hg19:g.9989661C>T	ENSP00000392511:p.Arg399His	60.0	0.0		50.0	12.0	NM_207351	Q49AD0|Q6UXY6|Q8NBC9	Missense_Mutation	SNP	ENST00000412055.1	hg19	CCDS43049.1	.	.	.	.	.	.	.	.	.	.	C	18.66	3.671840	0.67928	.	.	ENSG00000163704	ENST00000412055	T	0.17370	2.28	4.89	3.98	0.46160	.	0.241759	0.28241	N	0.016072	T	0.20373	0.0490	L	0.27053	0.805	0.80722	D	1	D	0.64830	0.994	P	0.56916	0.809	T	0.00628	-1.1637	9	.	.	.	-9.6073	10.9219	0.47169	0.0:0.7032:0.2968:0.0	.	399	Q5FWE3	PRRT3_HUMAN	H	399	ENSP00000392511:R399H	.	R	-	2	0	PRRT3	9964661	0.998000	0.40836	1.000000	0.80357	0.992000	0.81027	2.125000	0.42016	2.527000	0.85204	0.655000	0.94253	CGC	.	.		0.577	PRRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339322.1	NM_207351	
ZNF35	7584	hgsc.bcm.edu	37	3	44692628	44692628	+	Silent	SNP	G	G	A			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr3:44692628G>A	ENST00000396056.2	+	2	304	c.69G>A	c.(67-69)gaG>gaA	p.E23E	ZNF35_ENST00000296092.3_Silent_p.E23E|ZNF35_ENST00000542250.1_5'UTR|ZNF35_ENST00000453164.1_Silent_p.E23E|RP11-944L7.4_ENST00000457331.1_RNA|ZNF35_ENST00000399560.2_Silent_p.E23E	NM_003420.3	NP_003411.3	P13682	ZNF35_HUMAN	zinc finger protein 35	23	Globular domain.|Poly-Glu.				cellular response to retinoic acid (GO:0071300)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cell (GO:0005623)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(3)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(1)	12		Ovarian(412;0.0228)		OV - Ovarian serous cystadenocarcinoma(275;2.49e-27)|KIRC - Kidney renal clear cell carcinoma(197;0.0475)|Kidney(197;0.0595)		AAAAGGAGGAGGAAGAAGAAG	0.542																																					p.E23E		Atlas-SNP	.											.	ZNF35	34	.	0			c.G69A						.						57.0	57.0	57.0					3																	44692628		2203	4300	6503	SO:0001819	synonymous_variant	7584	exon2			GGAGGAGGAAGAA	X07289	CCDS2718.2	3p21.32	2013-01-08	2006-05-11		ENSG00000169981	ENSG00000169981		"""Zinc fingers, C2H2-type"""	13099	protein-coding gene	gene with protein product		194533	"""zinc finger protein 35 (clone HF.10)"""			2108922, 1572646	Standard	NM_003420		Approved	HF.10, HF10, Zfp105	uc003cnq.3	P13682	OTTHUMG00000133091	ENST00000396056.2:c.69G>A	chr3.hg19:g.44692628G>A		295.0	0.0		158.0	16.0	NM_003420	B2RBU6|Q53Y54|Q96D01	Silent	SNP	ENST00000396056.2	hg19	CCDS2718.2																																																																																			.	.		0.542	ZNF35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256749.4	NM_003420	
SLC9C1	285335	hgsc.bcm.edu	37	3	111940054	111940054	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr3:111940054A>G	ENST00000305815.5	-	14	1843	c.1591T>C	c.(1591-1593)Tac>Cac	p.Y531H	SLC9C1_ENST00000487372.1_Missense_Mutation_p.Y483H	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	531					cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										TCATTCCTGTATTGTCTCTGG	0.368																																					p.Y531H		Atlas-SNP	.											.	.	.	.	0			c.T1591C						.						105.0	103.0	104.0					3																	111940054		2203	4300	6503	SO:0001583	missense	285335	exon14			TCCTGTATTGTCT	AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"""Solute carriers"""	31401	protein-coding gene	gene with protein product	"""sperm-NHE"""	612738	"""solute carrier family 9, isoform 10"", ""solute carrier family 9, member 10"""	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.1591T>C	chr3.hg19:g.111940054A>G	ENSP00000306627:p.Tyr531His	60.0	0.0		30.0	5.0	NM_183061	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	hg19	CCDS33817.1	.	.	.	.	.	.	.	.	.	.	A	14.56	2.572014	0.45798	.	.	ENSG00000172139	ENST00000305815;ENST00000487372	T;T	0.81330	-1.41;-1.48	5.7	5.7	0.88788	.	0.246358	0.29260	N	0.012677	D	0.83312	0.5227	L	0.32530	0.975	0.34533	D	0.709464	D;D	0.89917	0.999;1.0	D;D	0.77557	0.99;0.983	D	0.86396	0.1739	10	0.37606	T	0.19	.	12.3536	0.55163	1.0:0.0:0.0:0.0	.	483;531	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	H	531;483	ENSP00000306627:Y531H;ENSP00000420688:Y483H	ENSP00000306627:Y531H	Y	-	1	0	SLC9A10	113422744	1.000000	0.71417	0.996000	0.52242	0.728000	0.41692	4.551000	0.60740	2.170000	0.68504	0.482000	0.46254	TAC	.	.		0.368	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061	
COPG1	22820	hgsc.bcm.edu	37	3	128986867	128986867	+	Silent	SNP	A	A	G			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr3:128986867A>G	ENST00000314797.6	+	16	1736	c.1632A>G	c.(1630-1632)gcA>gcG	p.A544A		NM_016128.3	NP_057212.1	Q9Y678	COPG1_HUMAN	coatomer protein complex, subunit gamma 1	544					COPI coating of Golgi vesicle (GO:0048205)|establishment of Golgi localization (GO:0051683)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|organelle transport along microtubule (GO:0072384)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)	structural molecule activity (GO:0005198)										CCCTTAATGCAGGCTATATCC	0.517																																					p.A544A		Atlas-SNP	.											.	.	.	.	0			c.A1632G						.						153.0	127.0	136.0					3																	128986867		2203	4300	6503	SO:0001819	synonymous_variant	22820	exon16			TAATGCAGGCTAT	AB047846	CCDS33851.1	3q21.3	2012-02-23	2012-02-23	2012-02-23	ENSG00000181789	ENSG00000181789			2236	protein-coding gene	gene with protein product	"""coat protein gamma-cop"""	615525	"""coatomer protein complex, subunit gamma"""	COPG		11056392	Standard	NM_016128		Approved		uc003els.3	Q9Y678	OTTHUMG00000159451	ENST00000314797.6:c.1632A>G	chr3.hg19:g.128986867A>G		94.0	0.0		52.0	20.0	NM_016128	A8K6M8|B3KMF6|Q54AC4	Silent	SNP	ENST00000314797.6	hg19	CCDS33851.1																																																																																			.	.		0.517	COPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355456.1	NM_016128	
MAN2B2	23324	hgsc.bcm.edu	37	4	6611736	6611736	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr4:6611736C>T	ENST00000285599.3	+	13	2254	c.2218C>T	c.(2218-2220)Cgg>Tgg	p.R740W	MAN2B2_ENST00000504960.1_3'UTR|MAN2B2_ENST00000504248.1_Missense_Mutation_p.R689W	NM_015274.1	NP_056089.1	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	740					mannose metabolic process (GO:0006013)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(9)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	30						CCAGATGCAGCGGAGGCCCTA	0.582																																					p.R740W		Atlas-SNP	.											MAN2B2,colon,carcinoma,0,1	MAN2B2	80	.	0			c.C2218T						.						94.0	86.0	89.0					4																	6611736		2203	4300	6503	SO:0001583	missense	23324	exon13			ATGCAGCGGAGGC	BC033307	CCDS33951.1	4p16.2	2005-11-09			ENSG00000013288	ENSG00000013288			29623	protein-coding gene	gene with protein product	"""core-specific lysosomal alpha-1,6-Mannosidase"""					10231032, 16115860	Standard	XR_241647		Approved	KIAA0935	uc003gjf.1	Q9Y2E5	OTTHUMG00000160073	ENST00000285599.3:c.2218C>T	chr4.hg19:g.6611736C>T	ENSP00000285599:p.Arg740Trp	132.0	0.0		82.0	21.0	NM_015274	Q66MP2|Q86T67	Missense_Mutation	SNP	ENST00000285599.3	hg19	CCDS33951.1	.	.	.	.	.	.	.	.	.	.	c	18.48	3.632545	0.67015	.	.	ENSG00000013288	ENST00000285599;ENST00000504248	D;D	0.85013	-1.93;-1.93	3.98	2.94	0.34122	Glycosyl hydrolases 38, C-terminal (1);Glycoside hydrolase-type carbohydrate-binding (1);	0.217789	0.40818	N	0.001011	D	0.90345	0.6979	M	0.79475	2.455	0.36909	D	0.890791	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.75484	0.986;0.981;0.963	D	0.91764	0.5422	10	0.87932	D	0	-41.6707	8.7335	0.34514	0.4731:0.5269:0.0:0.0	.	689;740;740	E9PCD7;Q9Y2E5;Q9Y2E5-2	.;MA2B2_HUMAN;.	W	740;689	ENSP00000285599:R740W;ENSP00000423129:R689W	ENSP00000285599:R740W	R	+	1	2	MAN2B2	6662637	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	3.635000	0.54309	1.930000	0.55929	0.558000	0.71614	CGG	.	.		0.582	MAN2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359106.2	NM_015274	
PCDHGB2	56103	hgsc.bcm.edu	37	5	140741078	140741078	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr5:140741078T>C	ENST00000522605.1	+	1	1376	c.1376T>C	c.(1375-1377)gTt>gCt	p.V459A	PCDHGB1_ENST00000523390.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_5'Flank|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018923.2|NM_032096.1	NP_061746.1|NP_115267.1	Q9Y5G2	PCDGE_HUMAN	protocadherin gamma subfamily B, 2	459	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCTACATGGTTCACGTGGCA	0.557																																					p.V459A		Atlas-SNP	.											.	PCDHGB2	196	.	0			c.T1376C						.						93.0	95.0	94.0					5																	140741078		2044	4195	6239	SO:0001583	missense	56103	exon1			ACATGGTTCACGT	AF152331	CCDS54924.1, CCDS75332.1	5q31	2010-01-26				ENSG00000253910		"""Cadherins / Protocadherins : Clustered"""	8709	other	protocadherin		606300				10380929	Standard	NM_018923		Approved	PCDH-GAMMA-B2		Q9Y5G2		ENST00000522605.1:c.1376T>C	chr5.hg19:g.140741078T>C	ENSP00000429018:p.Val459Ala	118.0	0.0		81.0	19.0	NM_018923	Q3MIJ3|Q9UN65	Missense_Mutation	SNP	ENST00000522605.1	hg19	CCDS54924.1	.	.	.	.	.	.	.	.	.	.	.	0.006	-2.091274	0.00367	.	.	ENSG00000253910	ENST00000522605	T	0.01804	4.63	5.41	2.76	0.32466	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.02571	0.0078	N	0.17082	0.46	0.09310	N	0.999999	P;D	0.69078	0.675;0.997	B;D	0.72075	0.254;0.976	T	0.37502	-0.9703	9	0.06757	T	0.87	.	4.8317	0.13443	0.0:0.4297:0.0:0.5703	.	459;459	Q9Y5G2-2;Q9Y5G2	.;PCDGE_HUMAN	A	459	ENSP00000429018:V459A	ENSP00000429018:V459A	V	+	2	0	PCDHGB2	140721262	0.023000	0.18921	0.997000	0.53966	0.211000	0.24417	0.343000	0.19944	0.995000	0.38917	0.460000	0.39030	GTT	.	.		0.557	PCDHGB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374741.1	NM_018923	
PCDHGA6	56109	hgsc.bcm.edu	37	5	140755848	140755848	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr5:140755848C>T	ENST00000517434.1	+	1	2198	c.2198C>T	c.(2197-2199)gCg>gTg	p.A733V	PCDHGB1_ENST00000523390.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB3_ENST00000576222.1_Intron	NM_018919.2|NM_032086.1	NP_061742.1|NP_114475.1	Q9Y5G7	PCDG6_HUMAN	protocadherin gamma subfamily A, 6	733					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|large_intestine(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTGGCTTAGCGAGCATGCCC	0.622																																					p.A733V		Atlas-SNP	.											.	PCDHGA6	219	.	0			c.C2198T						.						74.0	80.0	78.0					5																	140755848		2203	4300	6503	SO:0001583	missense	56109	exon1			GCTTAGCGAGCAT	AF152513	CCDS54926.1, CCDS75335.1	5q31	2010-01-26				ENSG00000253731		"""Cadherins / Protocadherins : Clustered"""	8704	other	protocadherin		606293				10380929	Standard	NM_018919		Approved	PCDH-GAMMA-A6		Q9Y5G7		ENST00000517434.1:c.2198C>T	chr5.hg19:g.140755848C>T	ENSP00000429601:p.Ala733Val	149.0	0.0		141.0	36.0	NM_018919	A6H8K7|B2RN55|Q9Y5D1	Missense_Mutation	SNP	ENST00000517434.1	hg19	CCDS54926.1	.	.	.	.	.	.	.	.	.	.	.	6.378	0.437859	0.12104	.	.	ENSG00000253731	ENST00000517434	T	0.44482	0.92	5.15	0.115	0.14643	.	0.925107	0.08507	U	0.935524	T	0.25791	0.0628	L	0.37630	1.12	0.09310	N	1	B;B	0.12013	0.005;0.003	B;B	0.09377	0.003;0.004	T	0.29119	-1.0022	10	0.06891	T	0.86	.	5.305	0.15799	0.0:0.4676:0.2001:0.3324	.	733;733	Q9Y5G7-2;Q9Y5G7	.;PCDG6_HUMAN	V	733	ENSP00000429601:A733V	ENSP00000429601:A733V	A	+	2	0	PCDHGA6	140736032	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.582000	0.05814	0.150000	0.19136	-0.136000	0.14681	GCG	.	.		0.622	PCDHGA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374743.1	NM_018919	
OR2J3	442186	hgsc.bcm.edu	37	6	29080267	29080267	+	Silent	SNP	G	G	T			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr6:29080267G>T	ENST00000377169.1	+	1	600	c.600G>T	c.(598-600)ctG>ctT	p.L200L		NM_001005216.2	NP_001005216.2	O76001	OR2J3_HUMAN	olfactory receptor, family 2, subfamily J, member 3	200						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(5)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	24						TCAATGAGCTGACCCTCATGA	0.463																																					p.L200L		Atlas-SNP	.											.	OR2J3	53	.	0			c.G600T						.						100.0	112.0	108.0					6																	29080267		1339	2597	3936	SO:0001819	synonymous_variant	442186	exon1			TGAGCTGACCCTC		CCDS43433.1	6p22.2-p21.31	2012-08-09			ENSG00000204701	ENSG00000204701		"""GPCR / Class A : Olfactory receptors"""	8261	protein-coding gene	gene with protein product		615016					Standard	NM_001005216		Approved	OR6-6	uc011dll.2	O76001	OTTHUMG00000031092	ENST00000377169.1:c.600G>T	chr6.hg19:g.29080267G>T		129.0	0.0		50.0	14.0	NM_001005216	B0UY52|B9EH11|Q5SUJ7|Q6IF25|Q96R15|Q9GZK5|Q9GZL4|Q9GZL5	Silent	SNP	ENST00000377169.1	hg19	CCDS43433.1																																																																																			.	.		0.463	OR2J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076132.2		
TRIM10	10107	hgsc.bcm.edu	37	6	30121906	30121906	+	Missense_Mutation	SNP	C	C	T	rs137941157	byFrequency	TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr6:30121906C>T	ENST00000449742.2	-	7	1361	c.1286G>A	c.(1285-1287)cGg>cAg	p.R429Q	TRIM10_ENST00000376704.3_Intron	NM_006778.3	NP_006769.2	Q9UDY6	TRI10_HUMAN	tripartite motif containing 10	429	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				erythrocyte differentiation (GO:0030218)|innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)	p.R429L(1)		ovary(1)	1						CCTCACCTGCCGGGGCTGCTC	0.642																																					p.R429Q		Atlas-SNP	.											.	TRIM10	65	.	1	Substitution - Missense(1)	lung(1)	c.G1286A						.						43.0	39.0	41.0					6																	30121906		1509	2708	4217	SO:0001583	missense	10107	exon7			ACCTGCCGGGGCT	Y07829	CCDS4676.1, CCDS34375.1	6p21.3	2013-01-09	2011-01-25	2001-11-23	ENSG00000204613	ENSG00000204613		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10072	protein-coding gene	gene with protein product		605701	"""tripartite motif-containing 10"""	RNF9		9271628, 10207104	Standard	NM_052828		Approved	RFB30, HERF1	uc003npo.3	Q9UDY6	OTTHUMG00000031295	ENST00000449742.2:c.1286G>A	chr6.hg19:g.30121906C>T	ENSP00000397073:p.Arg429Gln	132.0	0.0		93.0	16.0	NM_006778	A6NF84|Q5SRJ5|Q5SRK8|Q86Z08|Q96QB6|Q9C023|Q9C024	Missense_Mutation	SNP	ENST00000449742.2	hg19	CCDS34375.1	.	.	.	.	.	.	.	.	.	.	C	7.712	0.695347	0.15106	.	.	ENSG00000204613	ENST00000449742;ENST00000376706	T	0.70516	-0.49	6.01	-3.21	0.05140	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	1.261850	0.05437	N	0.547066	T	0.30070	0.0753	N	0.16166	0.38	0.09310	N	1	B	0.19583	0.037	B	0.09377	0.004	T	0.14420	-1.0473	10	0.23302	T	0.38	.	13.6023	0.62026	0.0:0.3426:0.0:0.6574	.	429	Q9UDY6	TRI10_HUMAN	Q	429	ENSP00000397073:R429Q	ENSP00000365896:R429Q	R	-	2	0	TRIM10	30229885	0.000000	0.05858	0.260000	0.24451	0.100000	0.18952	-0.606000	0.05654	-0.710000	0.05001	-1.157000	0.01802	CGG	.	C|1.000;A|0.000		0.642	TRIM10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076634.1		
EYS	346007	hgsc.bcm.edu	37	6	66042220	66042220	+	Intron	SNP	T	T	A			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr6:66042220T>A	ENST00000370621.3	-	11	2293				EYS_ENST00000503581.1_Intron|EYS_ENST00000393380.2_Silent_p.I619I|EYS_ENST00000370616.2_Intron			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)						detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						atcaaacttatattcttacga	0.294																																					p.I619I		Atlas-SNP	.											.	EYS	527	.	0			c.A1857T						.						173.0	152.0	159.0					6																	66042220		692	1590	2282	SO:0001627	intron_variant	346007	exon12			AACTTATATTCTT		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"""chromosome 6 open reading frame 180"", ""EGF-like-domain, multiple 11"", ""retinitis pigmentosa 25 (autosomal recessive)"", ""EGF-like-domain, multiple 10"", ""chromosome 6 open reading frame 178"", ""chromosome 6 open reading frame 179"""	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.1766+2652A>T	chr6.hg19:g.66042220T>A		70.0	0.0		29.0	6.0	NM_001142801	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Silent	SNP	ENST00000370621.3	hg19																																																																																				.	.		0.294	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
TBP	6908	hgsc.bcm.edu	37	6	170871004	170871004	+	Silent	SNP	G	G	A			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr6:170871004G>A	ENST00000392092.2	+	3	459	c.180G>A	c.(178-180)caG>caA	p.Q60Q	TBP_ENST00000540980.1_Silent_p.Q40Q|TBP_ENST00000230354.6_Silent_p.Q60Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	60	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		Ggcagcagcagcaacaacaac	0.542																																					p.Q60Q		Atlas-SNP	.											.	TBP	58	.	0			c.G180A						.						43.0	45.0	44.0					6																	170871004		2203	4300	6503	SO:0001819	synonymous_variant	6908	exon3			GCAGCAGCAACAA	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"""General transcription factors"""	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.180G>A	chr6.hg19:g.170871004G>A		61.0	0.0		36.0	8.0	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	hg19	CCDS5315.1																																																																																			.	.		0.542	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194	
RSBN1L	222194	hgsc.bcm.edu	37	7	77326048	77326048	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr7:77326048T>G	ENST00000334955.8	+	1	289	c.262T>G	c.(262-264)Ttt>Gtt	p.F88V	RSBN1L_ENST00000445288.1_5'Flank|RSBN1L-AS1_ENST00000440088.1_lincRNA	NM_198467.2	NP_940869.2	Q6PCB5	RSBNL_HUMAN	round spermatid basic protein 1-like	88	Ser-rich.					nucleus (GO:0005634)				central_nervous_system(1)|endometrium(12)|large_intestine(2)|lung(8)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GTCTTGGAGCTTTGCCCCTCT	0.657																																					p.F88V		Atlas-SNP	.											.	RSBN1L	74	.	0			c.T262G						.						23.0	32.0	29.0					7																	77326048		2021	4178	6199	SO:0001583	missense	222194	exon1			TGGAGCTTTGCCC	AK124517	CCDS43607.1	7q21.11	2004-08-11			ENSG00000187257	ENSG00000187257			24765	protein-coding gene	gene with protein product						12477932	Standard	NM_198467		Approved	FLJ42526, FLJ45813, MGC71764	uc010ldt.1	Q6PCB5	OTTHUMG00000155517	ENST00000334955.8:c.262T>G	chr7.hg19:g.77326048T>G	ENSP00000334040:p.Phe88Val	75.0	0.0		81.0	27.0	NM_198467	C9K0P1|Q6ZS58|Q6ZVI9|Q86X48	Missense_Mutation	SNP	ENST00000334955.8	hg19	CCDS43607.1	.	.	.	.	.	.	.	.	.	.	T	14.33	2.503703	0.44558	.	.	ENSG00000187257	ENST00000334955	.	.	.	3.84	0.104	0.14531	.	0.553074	0.16943	N	0.193215	T	0.33000	0.0848	L	0.27053	0.805	0.80722	D	1	B	0.28291	0.206	B	0.22601	0.04	T	0.06023	-1.0850	9	0.54805	T	0.06	-2.5694	6.4576	0.21938	0.0:0.3033:0.0:0.6967	.	88	Q6PCB5	RSBNL_HUMAN	V	88	.	ENSP00000334040:F88V	F	+	1	0	RSBN1L	77163984	1.000000	0.71417	0.950000	0.38849	0.664000	0.39144	1.572000	0.36461	-0.075000	0.12798	0.260000	0.18958	TTT	.	.		0.657	RSBN1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340455.3	NM_198467	
RUNX1T1	862	hgsc.bcm.edu	37	8	93003968	93003968	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr8:93003968G>A	ENST00000523629.1	-	7	1344	c.890C>T	c.(889-891)cCt>cTt	p.P297L	RUNX1T1_ENST00000265814.3_Missense_Mutation_p.P297L|RUNX1T1_ENST00000436581.2_Missense_Mutation_p.P308L|RUNX1T1_ENST00000520724.1_Missense_Mutation_p.P260L|RUNX1T1_ENST00000360348.2_Missense_Mutation_p.P260L|RUNX1T1_ENST00000396218.1_Missense_Mutation_p.P270L|RUNX1T1_ENST00000518844.1_Missense_Mutation_p.P270L|RUNX1T1_ENST00000422361.2_Missense_Mutation_p.P260L	NM_001198626.1|NM_001198630.1|NM_001198633.1|NM_175634.2	NP_001185555.1|NP_001185559.1|NP_001185562.1|NP_783552.1	Q06455	MTG8_HUMAN	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	297	Poly-Pro.				fat cell differentiation (GO:0045444)|generation of precursor metabolites and energy (GO:0006091)|regulation of DNA binding (GO:0051101)|transcription, DNA-templated (GO:0006351)	nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(54)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	86			BRCA - Breast invasive adenocarcinoma(11;0.0141)			GTAATGCTGAGGTGGAGGTGG	0.562																																					p.P356L		Atlas-SNP	.											.	RUNX1T1	516	.	0			c.C1067T						.						218.0	176.0	190.0					8																	93003968		2203	4300	6503	SO:0001583	missense	862	exon7			TGCTGAGGTGGAG	D43638	CCDS6256.1, CCDS6257.1, CCDS47891.1, CCDS56544.1, CCDS75766.1, CCDS75767.1	8q22	2007-01-29	2005-01-20	2005-01-22	ENSG00000079102	ENSG00000079102		"""Zinc fingers, MYND-type"""	1535	protein-coding gene	gene with protein product		133435	"""core-binding factor, runt domain, alpha subunit 2; translocated to, 1; cyclin D-related"""	AML1T1, CBFA2T1		1391946, 9790752	Standard	NM_004349		Approved	CDR, ETO, MTG8, ZMYND2	uc011lgi.2	Q06455	OTTHUMG00000164066	ENST00000523629.1:c.890C>T	chr8.hg19:g.93003968G>A	ENSP00000428543:p.Pro297Leu	119.0	0.0		101.0	35.0	NM_001198679	B7Z4P4|E7EPN4|O14784|Q06456|Q14873|Q16239|Q16346|Q16347|Q6IBL1|Q6NXH1|Q7Z4J5|Q92479|Q9BRZ0	Missense_Mutation	SNP	ENST00000523629.1	hg19	CCDS6256.1	.	.	.	.	.	.	.	.	.	.	G	12.14	1.847410	0.32606	.	.	ENSG00000079102	ENST00000523629;ENST00000396218;ENST00000265814;ENST00000360348;ENST00000422361;ENST00000520724;ENST00000436581;ENST00000518844	T;T;T;T;T;T;T;T	0.29655	1.56;1.57;1.56;1.57;1.57;1.57;1.56;1.57	6.17	6.17	0.99709	.	0.094035	0.85682	D	0.000000	T	0.28234	0.0697	L	0.36672	1.1	0.80722	D	1	B;B;B	0.16802	0.001;0.0;0.019	B;B;B	0.25405	0.002;0.002;0.06	T	0.12604	-1.0541	10	0.07813	T	0.8	-12.043	20.4745	0.99168	0.0:0.0:1.0:0.0	.	308;297;270	E7EPN4;Q06455;Q06455-2	.;MTG8_HUMAN;.	L	297;270;297;260;260;260;308;270	ENSP00000428543:P297L;ENSP00000379520:P270L;ENSP00000265814:P297L;ENSP00000353504:P260L;ENSP00000390137:P260L;ENSP00000428742:P260L;ENSP00000402257:P308L;ENSP00000430728:P270L	ENSP00000265814:P297L	P	-	2	0	RUNX1T1	93073144	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.375000	0.73137	2.941000	0.99782	0.655000	0.94253	CCT	.	.		0.562	RUNX1T1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377045.3	NM_004349, NM_175635	
TSPYL5	85453	hgsc.bcm.edu	37	8	98289975	98289975	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr8:98289975G>A	ENST00000322128.3	-	1	201	c.98C>T	c.(97-99)cCg>cTg	p.P33L		NM_033512.2	NP_277047.2	Q86VY4	TSYL5_HUMAN	TSPY-like 5	33					cellular response to gamma radiation (GO:0071480)|nucleosome assembly (GO:0006334)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein ubiquitination (GO:0031398)|regulation of growth (GO:0040008)	nucleus (GO:0005634)				cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|lung(3)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	20	Breast(36;2.56e-06)					CGGGTCGCGCGGGGCGTCGTC	0.711																																					p.P33L		Atlas-SNP	.											.	TSPYL5	48	.	0			c.C98T						.						8.0	10.0	9.0					8																	98289975		2131	4131	6262	SO:0001583	missense	85453	exon1			TCGCGCGGGGCGT	AB051537	CCDS34927.1	8q22.1	2011-05-24			ENSG00000180543	ENSG00000180543			29367	protein-coding gene	gene with protein product		614721				11214970	Standard	NM_033512		Approved	KIAA1750	uc003yhy.3	Q86VY4	OTTHUMG00000164857	ENST00000322128.3:c.98C>T	chr8.hg19:g.98289975G>A	ENSP00000322802:p.Pro33Leu	61.0	0.0		144.0	22.0	NM_033512	B3KRF0|Q9C0B3	Missense_Mutation	SNP	ENST00000322128.3	hg19	CCDS34927.1	.	.	.	.	.	.	.	.	.	.	G	10.42	1.344730	0.24426	.	.	ENSG00000180543	ENST00000322128	T	0.48836	0.8	3.82	0.903	0.19296	.	0.813650	0.10113	N	0.714458	T	0.37839	0.1018	L	0.52011	1.625	0.09310	N	1	B	0.19583	0.037	B	0.06405	0.002	T	0.28459	-1.0043	10	0.40728	T	0.16	-0.2151	5.9128	0.19037	0.1124:0.3597:0.5279:0.0	.	33	Q86VY4	TSYL5_HUMAN	L	33	ENSP00000322802:P33L	ENSP00000322802:P33L	P	-	2	0	TSPYL5	98359151	0.052000	0.20516	0.001000	0.08648	0.272000	0.26649	0.680000	0.25306	0.172000	0.19760	0.561000	0.74099	CCG	.	.		0.711	TSPYL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380611.1	NM_033512	
COL15A1	1306	hgsc.bcm.edu	37	9	101816900	101816900	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr9:101816900A>G	ENST00000375001.3	+	32	3416	c.2993A>G	c.(2992-2994)aAg>aGg	p.K998R		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	998	Triple-helical region 6 (COL6).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				CCTGGCTCAAAGGGAGAAAAA	0.438																																					p.K998R		Atlas-SNP	.											.	COL15A1	211	.	0			c.A2993G						.						83.0	89.0	87.0					9																	101816900		2203	4300	6503	SO:0001583	missense	1306	exon32			GCTCAAAGGGAGA	L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2192	protein-coding gene	gene with protein product	"""collagen type XV proteoglycan"""	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	ENST00000375001.3:c.2993A>G	chr9.hg19:g.101816900A>G	ENSP00000364140:p.Lys998Arg	218.0	0.0		83.0	4.0	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Missense_Mutation	SNP	ENST00000375001.3	hg19	CCDS35081.1	.	.	.	.	.	.	.	.	.	.	A	17.49	3.401480	0.62288	.	.	ENSG00000204291	ENST00000375001	T	0.30981	1.51	5.67	5.67	0.87782	C-type lectin fold (1);	0.188258	0.46758	D	0.000274	T	0.47820	0.1466	L	0.54863	1.705	0.45747	D	0.998644	D	0.63880	0.993	D	0.72625	0.978	T	0.31308	-0.9948	10	0.28530	T	0.3	-17.9351	12.5857	0.56416	1.0:0.0:0.0:0.0	.	998	P39059	COFA1_HUMAN	R	998	ENSP00000364140:K998R	ENSP00000364140:K998R	K	+	2	0	COL15A1	100856721	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.419000	0.66435	2.288000	0.76882	0.533000	0.62120	AAG	.	.		0.438	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855	
MSANTD3	91283	hgsc.bcm.edu	37	9	103204372	103204372	+	Missense_Mutation	SNP	C	C	T	rs139409577	byFrequency	TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr9:103204372C>T	ENST00000395067.2	+	2	423	c.152C>T	c.(151-153)gCg>gTg	p.A51V	MSANTD3-TMEFF1_ENST00000502978.1_5'Flank|MSANTD3_ENST00000374885.1_Missense_Mutation_p.A51V|TMEFF1_ENST00000334943.6_5'Flank	NM_001198805.1|NM_001198806.1|NM_080655.2	NP_001185734.1|NP_001185735.1|NP_542386.1	Q96H12	MSD3_HUMAN	Myb/SANT-like DNA-binding domain containing 3	51	Myb-like.									endometrium(2)|lung(2)	4						ACCTGGCAGGCGCTGGCCCAC	0.483																																					p.A51V		Atlas-SNP	.											.	MSANTD3	10	.	0			c.C152T						.						42.0	43.0	43.0					9																	103204372		2203	4300	6503	SO:0001583	missense	91283	exon2			GGCAGGCGCTGGC	BC008993	CCDS6749.1, CCDS56579.1	9q31.1	2012-03-13	2012-03-13	2012-03-13	ENSG00000066697	ENSG00000066697			23370	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 30"""	C9orf30			Standard	NM_080655		Approved	MGC17337		Q96H12	OTTHUMG00000020365	ENST00000395067.2:c.152C>T	chr9.hg19:g.103204372C>T	ENSP00000378506:p.Ala51Val	90.0	0.0		33.0	13.0	NM_001198805	B2RC35|Q5T726|Q5T727|Q5T728	Missense_Mutation	SNP	ENST00000395067.2	hg19	CCDS6749.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.743003	0.89663	.	.	ENSG00000066697	ENST00000395067;ENST00000398977;ENST00000374885;ENST00000374886	.	.	.	5.84	5.84	0.93424	.	.	.	.	.	T	0.45875	0.1364	N	0.08118	0	0.48830	D	0.99971	D	0.56746	0.977	P	0.51806	0.68	T	0.44682	-0.9312	8	0.30078	T	0.28	-4.2443	19.1261	0.93384	0.0:1.0:0.0:0.0	.	51	Q96H12	CI030_HUMAN	V	51	.	ENSP00000364020:A51V	A	+	2	0	C9orf30	102244193	0.997000	0.39634	0.983000	0.44433	0.977000	0.68977	3.765000	0.55272	2.779000	0.95612	0.655000	0.94253	GCG	.	C|1.000;T|0.000		0.483	MSANTD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053410.1	NM_080655	
GPR158	57512	hgsc.bcm.edu	37	10	25887911	25887911	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr10:25887911A>C	ENST00000376351.3	+	11	3715	c.3356A>C	c.(3355-3357)gAa>gCa	p.E1119A	GPR158_ENST00000490549.1_3'UTR	NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158	1119					protein localization to plasma membrane (GO:0072659)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|cervix(1)|endometrium(9)|kidney(10)|large_intestine(20)|lung(56)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	119						CAGAGCGAAGAACTGCCCCCC	0.478																																					p.E1119A		Atlas-SNP	.											.	GPR158	255	.	0			c.A3356C						.						87.0	90.0	89.0					10																	25887911		2203	4300	6503	SO:0001583	missense	57512	exon11			GCGAAGAACTGCC	AB032962	CCDS31166.1	10p12.31	2012-08-21			ENSG00000151025	ENSG00000151025		"""GPCR / Class C : Orphans"""	23689	protein-coding gene	gene with protein product		614573					Standard	NM_020752		Approved	KIAA1136	uc001isj.3	Q5T848	OTTHUMG00000017832	ENST00000376351.3:c.3356A>C	chr10.hg19:g.25887911A>C	ENSP00000365529:p.Glu1119Ala	108.0	0.0		46.0	19.0	NM_020752	Q6QR81|Q9ULT3	Missense_Mutation	SNP	ENST00000376351.3	hg19	CCDS31166.1	.	.	.	.	.	.	.	.	.	.	A	9.726	1.161006	0.21538	.	.	ENSG00000151025	ENST00000376351	T	0.67698	-0.28	5.69	5.69	0.88448	.	0.240296	0.35555	N	0.003129	T	0.62792	0.2457	L	0.29908	0.895	0.50632	D	0.999889	P	0.52316	0.952	P	0.49477	0.612	T	0.62134	-0.6918	10	0.33940	T	0.23	.	14.5105	0.67784	1.0:0.0:0.0:0.0	.	1119	Q5T848	GP158_HUMAN	A	1119	ENSP00000365529:E1119A	ENSP00000365529:E1119A	E	+	2	0	GPR158	25927917	1.000000	0.71417	0.208000	0.23602	0.083000	0.17756	7.984000	0.88150	2.162000	0.67917	0.533000	0.62120	GAA	.	.		0.478	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047248.2	XM_166110	
WDFY4	57705	hgsc.bcm.edu	37	10	49982595	49982595	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr10:49982595G>T	ENST00000325239.5	+	13	2673	c.2646G>T	c.(2644-2646)ttG>ttT	p.L882F	WDFY4_ENST00000413659.2_Missense_Mutation_p.L882F	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	882						integral component of membrane (GO:0016021)				NS(2)|breast(5)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(3)|pancreas(2)|prostate(5)|skin(6)|stomach(1)	48						AAGCAGGCTTGCTTGGGACCC	0.602																																					p.L882F		Atlas-SNP	.											.	WDFY4	205	.	0			c.G2646T						.						47.0	59.0	55.0					10																	49982595		692	1591	2283	SO:0001583	missense	57705	exon14			AGGCTTGCTTGGG	AK074085	CCDS44385.1	10q11.23	2013-01-10			ENSG00000128815	ENSG00000128815		"""WD repeat domain containing"""	29323	protein-coding gene	gene with protein product		613316	"""chromosome 10 open reading frame 64"""	C10orf64		10997877	Standard	NM_020945		Approved	KIAA1607, Em:AC060234.3, FLJ45748	uc001jha.4	Q6ZS81	OTTHUMG00000018180	ENST00000325239.5:c.2646G>T	chr10.hg19:g.49982595G>T	ENSP00000320563:p.Leu882Phe	77.0	0.0		58.0	22.0	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Missense_Mutation	SNP	ENST00000325239.5	hg19	CCDS44385.1	.	.	.	.	.	.	.	.	.	.	G	14.66	2.601465	0.46423	.	.	ENSG00000128815	ENST00000454161;ENST00000426033;ENST00000325239;ENST00000413659	T;T	0.58940	0.3;0.3	5.42	5.42	0.78866	Armadillo-like helical (1);Armadillo-type fold (1);	.	.	.	.	T	0.49966	0.1588	L	0.28400	0.85	0.36734	D	0.88184	P	0.39883	0.693	B	0.40506	0.331	T	0.54241	-0.8323	8	.	.	.	.	18.2153	0.89884	0.0:0.0:1.0:0.0	.	882	Q6ZS81	WDFY4_HUMAN	F	891;882;882;882	ENSP00000320563:L882F;ENSP00000403789:L882F	.	L	+	3	2	WDFY4	49652601	1.000000	0.71417	0.976000	0.42696	0.012000	0.07955	5.959000	0.70339	2.521000	0.84997	0.655000	0.94253	TTG	.	.		0.602	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
LZTS2	84445	hgsc.bcm.edu	37	10	102770293	102770293	+	IGR	SNP	T	T	G	rs200896335|rs71013480	byFrequency	TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr10:102770293T>G	ENST00000370220.1	+	0	5741									leucine zipper, putative tumor suppressor 2											breast(1)|large_intestine(6)|lung(7)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22				Epithelial(162;7.3e-09)|all cancers(201;3.72e-07)		TGACCCCGgctgctgcggctg	0.697																																					p.S785R	Esophageal Squamous(8;38 437 13604 19902 37640)	Atlas-SNP	.											.	PDZD7	101	.	0			c.A2353C						.																																			SO:0001628	intergenic_variant	79955	exon15			CCCGGCTGCTGCG	AB058716	CCDS7507.1	10q24	2004-03-18			ENSG00000107816	ENSG00000107816			29381	protein-coding gene	gene with protein product		610454				11347906, 11709705	Standard	NM_032429		Approved	KIAA1813, LAPSER1	uc001ksj.3	Q9BRK4	OTTHUMG00000018914		chr10.hg19:g.102770293T>G		351.0	0.0		413.0	20.0	NM_001195263		Missense_Mutation	SNP	ENST00000370220.1	hg19	CCDS7507.1	.	.	.	.	.	.	.	.	.	.	T	2.648	-0.282573	0.05642	.	.	ENSG00000186862	ENST00000393462	.	.	.	3.99	2.83	0.33086	.	.	.	.	.	T	0.29716	0.0742	N	0.24115	0.695	0.28374	N	0.919888	.	.	.	.	.	.	T	0.21793	-1.0235	6	0.20046	T	0.44	.	9.5348	0.39216	0.0:0.0:0.1777:0.8222	.	.	.	.	R	785	.	ENSP00000377106:S785R	S	-	1	0	PDZD7	102760283	0.123000	0.22298	0.736000	0.30914	0.083000	0.17756	0.220000	0.17660	0.649000	0.30751	-0.680000	0.03767	AGC	.	.		0.697	LZTS2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049872.1	XM_046743	
PDCD11	22984	hgsc.bcm.edu	37	10	105203771	105203771	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr10:105203771G>T	ENST00000369797.3	+	34	5318	c.5224G>T	c.(5224-5226)Gca>Tca	p.A1742S		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	1742					mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	64		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		GAGCCAGGCTGCAGCCAGTCA	0.607																																					p.A1742S		Atlas-SNP	.											.	PDCD11	160	.	0			c.G5224T						.						43.0	45.0	44.0					10																	105203771		2203	4300	6503	SO:0001583	missense	22984	exon34			CAGGCTGCAGCCA	D80007	CCDS31276.1	10q24.32	2010-07-06			ENSG00000148843	ENSG00000148843			13408	protein-coding gene	gene with protein product		612333				10229231	Standard	XM_005269647		Approved	KIAA0185, ALG-4, RRP5	uc001kwy.1	Q14690	OTTHUMG00000018988	ENST00000369797.3:c.5224G>T	chr10.hg19:g.105203771G>T	ENSP00000358812:p.Ala1742Ser	79.0	0.0		42.0	12.0	NM_014976	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Missense_Mutation	SNP	ENST00000369797.3	hg19	CCDS31276.1	.	.	.	.	.	.	.	.	.	.	G	19.36	3.812101	0.70797	.	.	ENSG00000148843	ENST00000369797	T	0.41065	1.01	5.67	5.67	0.87782	Tetratricopeptide-like helical (1);Suppressor of forked (1);Tetratricopeptide repeat-containing (1);	0.258158	0.45361	D	0.000363	T	0.31857	0.0810	N	0.14661	0.345	0.28154	N	0.929268	B	0.06786	0.001	B	0.04013	0.001	T	0.21552	-1.0242	10	0.51188	T	0.08	-6.3898	19.7629	0.96329	0.0:0.0:1.0:0.0	.	1742	Q14690	RRP5_HUMAN	S	1742	ENSP00000358812:A1742S	ENSP00000358812:A1742S	A	+	1	0	PDCD11	105193761	1.000000	0.71417	0.403000	0.26384	0.834000	0.47266	5.643000	0.67895	2.666000	0.90696	0.561000	0.74099	GCA	.	.		0.607	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1		
MKI67	4288	hgsc.bcm.edu	37	10	129914055	129914055	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr10:129914055A>G	ENST00000368654.3	-	7	992	c.617T>C	c.(616-618)aTt>aCt	p.I206T	MKI67_ENST00000368653.3_Intron	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	206					cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				AACGCTGGAAATTTCTTTAAA	0.403																																					p.I206T		Atlas-SNP	.											.	MKI67	363	.	0			c.T617C						.						94.0	95.0	95.0					10																	129914055		2203	4300	6503	SO:0001583	missense	4288	exon7			CTGGAAATTTCTT	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.617T>C	chr10.hg19:g.129914055A>G	ENSP00000357643:p.Ile206Thr	44.0	0.0		24.0	4.0	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	hg19	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	A	6.685	0.495074	0.12762	.	.	ENSG00000148773	ENST00000368654;ENST00000537609	T	0.20881	2.04	3.69	-1.44	0.08856	.	1.520410	0.03934	N	0.285756	T	0.10165	0.0249	N	0.14661	0.345	0.09310	N	0.999999	B	0.23377	0.084	B	0.18561	0.022	T	0.19257	-1.0311	9	.	.	.	.	1.0409	0.01559	0.1777:0.3431:0.1655:0.3137	.	206	P46013	KI67_HUMAN	T	206	ENSP00000357643:I206T	.	I	-	2	0	MKI67	129804045	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	-0.148000	0.10219	-0.267000	0.09325	-0.339000	0.08088	ATT	.	.		0.403	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
PYGM	5837	hgsc.bcm.edu	37	11	64518935	64518935	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr11:64518935C>T	ENST00000164139.3	-	16	2229	c.1831G>A	c.(1831-1833)Gca>Aca	p.A611T	PYGM_ENST00000377432.3_Missense_Mutation_p.A523T|PYGM_ENST00000462303.1_5'UTR	NM_005609.2	NP_005600.1	P11217	PYGM_HUMAN	phosphorylase, glycogen, muscle	611					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glycogen phosphorylase activity (GO:0008184)|nucleotide binding (GO:0000166)|pyridoxal phosphate binding (GO:0030170)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						TACCCAGGTGCAGCCTGAGGG	0.592																																					p.A611T		Atlas-SNP	.											.	PYGM	77	.	0			c.G1831A						.						92.0	97.0	95.0					11																	64518935		2201	4297	6498	SO:0001583	missense	5837	exon16			CAGGTGCAGCCTG		CCDS8079.1, CCDS53659.1	11q12-q13.2	2013-03-01	2008-07-31		ENSG00000068976	ENSG00000068976	2.4.1.1	"""Glycogen phosphorylases"""	9726	protein-coding gene	gene with protein product	"""McArdle syndrome"", ""glycogen storage disease type V"", ""glycogen phosphorylase, muscle form"""	608455	"""phosphorylase, glycogen; muscle"""				Standard	NM_005609		Approved		uc001oax.4	P11217	OTTHUMG00000066835	ENST00000164139.3:c.1831G>A	chr11.hg19:g.64518935C>T	ENSP00000164139:p.Ala611Thr	90.0	0.0		70.0	21.0	NM_005609	A0AVK1|A6NDY6	Missense_Mutation	SNP	ENST00000164139.3	hg19	CCDS8079.1	.	.	.	.	.	.	.	.	.	.	C	38	6.677460	0.97755	.	.	ENSG00000068976	ENST00000377432;ENST00000164139;ENST00000540450	D;D	0.94184	-3.37;-3.37	5.25	5.25	0.73442	.	0.000000	0.64402	D	0.000019	D	0.98169	0.9395	H	0.98802	4.335	0.80722	D	1	P;D	0.56521	0.946;0.976	D;D	0.71870	0.975;0.922	D	0.99211	1.0876	10	0.87932	D	0	-16.4427	16.3883	0.83523	0.0:1.0:0.0:0.0	.	523;611	A6NDY6;P11217	.;PYGM_HUMAN	T	523;611;592	ENSP00000366650:A523T;ENSP00000164139:A611T	ENSP00000164139:A611T	A	-	1	0	PYGM	64275511	1.000000	0.71417	0.576000	0.28549	0.910000	0.53928	7.616000	0.83018	2.739000	0.93911	0.561000	0.74099	GCA	.	.		0.592	PYGM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143254.2	NM_005609	
CACNA1C	775	hgsc.bcm.edu	37	12	2800310	2800310	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr12:2800310G>T	ENST00000347598.4	+	49	6506	c.6506G>T	c.(6505-6507)gGt>gTt	p.G2169V	CACNA1C_ENST00000399644.1_Missense_Mutation_p.G2121V|CACNA1C_ENST00000399621.1_Missense_Mutation_p.G2140V|CACNA1C_ENST00000399638.1_Missense_Mutation_p.G2149V|CACNA1C_ENST00000399637.1_Missense_Mutation_p.G2140V|CACNA1C_ENST00000399601.1_Missense_Mutation_p.G2121V|CACNA1C-AS1_ENST00000544517.1_RNA|CACNA1C_ENST00000399606.1_Missense_Mutation_p.G2141V|CACNA1C_ENST00000399634.1_Missense_Mutation_p.G2192V|CACNA1C_ENST00000399641.1_Missense_Mutation_p.G2121V|CACNA1C_ENST00000406454.3_Missense_Mutation_p.G2192V|CACNA1C_ENST00000399649.1_Missense_Mutation_p.G2127V|CACNA1C-AS1_ENST00000501371.1_RNA|CACNA1C_ENST00000402845.3_Missense_Mutation_p.G2140V|CACNA1C_ENST00000335762.5_Missense_Mutation_p.G2146V|CACNA1C_ENST00000344100.3_Missense_Mutation_p.G2162V|CACNA1C_ENST00000327702.7_Missense_Mutation_p.G2156V|CACNA1C_ENST00000399591.1_Missense_Mutation_p.G2129V|CACNA1C_ENST00000399603.1_Missense_Mutation_p.G2121V|CACNA1C_ENST00000399655.1_Missense_Mutation_p.G2121V|CACNA1C-AS1_ENST00000541673.1_RNA|CACNA1C_ENST00000399617.1_Missense_Mutation_p.G2156V|CACNA1C_ENST00000399629.1_Missense_Mutation_p.G2138V|CACNA1C_ENST00000399597.1_Missense_Mutation_p.G2121V|CACNA1C_ENST00000399595.1_Missense_Mutation_p.G2129V	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	2204			A -> T.		adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CGCGCGCGGGGTCGACCGAGT	0.632																																					p.G2204V		Atlas-SNP	.											.	CACNA1C	1023	.	0			c.G6611T						.						21.0	28.0	26.0					12																	2800310		1962	4124	6086	SO:0001583	missense	775	exon50			CGCGGGGTCGACC	AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.6506G>T	chr12.hg19:g.2800310G>T	ENSP00000266376:p.Gly2169Val	175.0	0.0		114.0	34.0	NM_199460	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Missense_Mutation	SNP	ENST00000347598.4	hg19	CCDS44788.1	.	.	.	.	.	.	.	.	.	.	G	2.365	-0.345696	0.05208	.	.	ENSG00000151067	ENST00000335762;ENST00000399655;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000399641;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399603;ENST00000399634;ENST00000399617;ENST00000406454;ENST00000399595;ENST00000322367	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.56941	0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43	4.49	1.08	0.20341	.	0.941163	0.08901	N	0.877252	T	0.32346	0.0826	N	0.08118	0	0.20403	N	0.999908	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.31548	0.0;0.002;0.02;0.001;0.0;0.098;0.078;0.001;0.029;0.001;0.098;0.069;0.02;0.001;0.041;0.148;0.02;0.002;0.0;0.0;0.145;0.0;0.328;0.13;0.02	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.37239	0.001;0.004;0.023;0.001;0.004;0.107;0.053;0.004;0.03;0.001;0.107;0.055;0.034;0.004;0.01;0.046;0.034;0.004;0.002;0.0;0.099;0.001;0.244;0.101;0.023	T	0.32214	-0.9915	10	0.46703	T	0.11	.	4.4188	0.11470	0.4164:0.4475:0.1361:0.0	.	812;2162;2118;2204;2156;2140;2121;2138;2149;2121;2141;2121;2152;2169;2121;2156;2192;2129;2127;2129;2110;2140;2140;2121;2121	B7Z7Z5;Q13936-14;Q13936-35;Q13936;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-23;Q13936-28;Q13936-11;E9PDJ1;E9PDJ0;F5GY28;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;Q13936-12	.;.;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	V	2146;2121;2121;2149;2121;2140;2140;2129;2121;2169;2141;2121;2162;2138;2156;2127;2140;2121;2192;2156;2192;2129;2022	ENSP00000336982:G2146V;ENSP00000382563:G2121V;ENSP00000382552:G2121V;ENSP00000382547:G2149V;ENSP00000382506:G2121V;ENSP00000382530:G2140V;ENSP00000382546:G2140V;ENSP00000382500:G2129V;ENSP00000382549:G2121V;ENSP00000266376:G2169V;ENSP00000382515:G2141V;ENSP00000382510:G2121V;ENSP00000341092:G2162V;ENSP00000382537:G2138V;ENSP00000329877:G2156V;ENSP00000382557:G2127V;ENSP00000385724:G2140V;ENSP00000382512:G2121V;ENSP00000382542:G2192V;ENSP00000382526:G2156V;ENSP00000385896:G2192V;ENSP00000382504:G2129V	ENSP00000323129:G2022V	G	+	2	0	CACNA1C	2670571	1.000000	0.71417	0.004000	0.12327	0.024000	0.10985	1.395000	0.34520	0.108000	0.17862	0.591000	0.81541	GGT	.	.		0.632	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719	
NACA	4666	hgsc.bcm.edu	37	12	57113526	57113526	+	Silent	SNP	C	C	T			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr12:57113526C>T	ENST00000454682.1	-	3	2069	c.1788G>A	c.(1786-1788)ggG>ggA	p.G596G	NACA_ENST00000356769.3_Intron|NACA_ENST00000551793.1_Intron|NACA_ENST00000393891.4_Intron|NACA_ENST00000546392.1_Intron|NACA_ENST00000550952.1_Silent_p.G596G|NACA_ENST00000552540.1_Intron|NACA_ENST00000548563.1_Intron	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	596	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						GGAGAGGCTCCCCAAGGCTTT	0.512			T	BCL6	NHL																																p.G596G		Atlas-SNP	.		Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	.	NACA	131	.	0			c.G1788A						.						45.0	46.0	46.0					12																	57113526		1568	3582	5150	SO:0001819	synonymous_variant	4666	exon3			AGGCTCCCCAAGG	X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"""nascent-polypeptide-associated complex alpha polypeptide"""			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.1788G>A	chr12.hg19:g.57113526C>T		159.0	0.0		77.0	16.0	NM_001113203		Silent	SNP	ENST00000454682.1	hg19																																																																																				.	.		0.512	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594	
CUX2	23316	hgsc.bcm.edu	37	12	111772269	111772269	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr12:111772269C>T	ENST00000261726.6	+	19	3105	c.2951C>T	c.(2950-2952)tCa>tTa	p.S984L		NM_015267.3	NP_056082.2	O14529	CUX2_HUMAN	cut-like homeobox 2	984					cellular response to organic substance (GO:0071310)|cognition (GO:0050890)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of synapse assembly (GO:0051965)|short-term memory (GO:0007614)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(24)|ovary(5)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	55						CCAAGGTCCTCACCATCCCCA	0.592																																					p.S984L		Atlas-SNP	.											.	CUX2	145	.	0			c.C2951T						.						29.0	37.0	34.0					12																	111772269		1946	4130	6076	SO:0001583	missense	23316	exon19			GGTCCTCACCATC	AB006631	CCDS41837.1	12q24.12	2011-06-20	2007-11-07	2007-11-07	ENSG00000111249	ENSG00000111249		"""Homeoboxes / CUT class"""	19347	protein-coding gene	gene with protein product		610648	"""cut-like 2 (Drosophila)"""	CUTL2			Standard	NM_015267		Approved	KIAA0293, CDP2	uc001tsa.2	O14529	OTTHUMG00000169546	ENST00000261726.6:c.2951C>T	chr12.hg19:g.111772269C>T	ENSP00000261726:p.Ser984Leu	126.0	0.0		76.0	11.0	NM_015267	A7E2Y4	Missense_Mutation	SNP	ENST00000261726.6	hg19	CCDS41837.1	.	.	.	.	.	.	.	.	.	.	C	18.91	3.723477	0.68959	.	.	ENSG00000111249	ENST00000261726	T	0.53206	0.63	5.09	5.09	0.68999	.	0.060756	0.64402	D	0.000002	T	0.41719	0.1171	L	0.32530	0.975	0.80722	D	1	P	0.39060	0.657	B	0.37650	0.255	T	0.41840	-0.9486	10	0.52906	T	0.07	-10.7296	18.4597	0.90734	0.0:1.0:0.0:0.0	.	984	O14529	CUX2_HUMAN	L	984	ENSP00000261726:S984L	ENSP00000261726:S984L	S	+	2	0	CUX2	110256652	1.000000	0.71417	0.956000	0.39512	0.642000	0.38348	5.903000	0.69877	2.530000	0.85305	0.655000	0.94253	TCA	.	.		0.592	CUX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404765.1	NM_015267	
SPERT	220082	hgsc.bcm.edu	37	13	46287798	46287798	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr13:46287798G>A	ENST00000310521.1	+	3	718	c.638G>A	c.(637-639)cGg>cAg	p.R213Q	SPERT_ENST00000378966.3_Missense_Mutation_p.R177Q	NM_152719.1	NP_689932.1	Q8NA61	SPERT_HUMAN	spermatid associated	213						cytoplasmic membrane-bounded vesicle (GO:0016023)				NS(1)|central_nervous_system(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	15		Breast(56;0.000819)|Lung NSC(96;0.00227)|Prostate(109;0.00703)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;7.26e-05)		GAGGAGAGCCGGGCCCCCTCG	0.652																																					p.R213Q		Atlas-SNP	.											.	SPERT	54	.	0			c.G638A						.						41.0	41.0	41.0					13																	46287798		2203	4300	6503	SO:0001583	missense	220082	exon3			AGAGCCGGGCCCC	AK093129	CCDS9399.1, CCDS66540.1	13q14.13	2010-03-23			ENSG00000174015	ENSG00000174015			30720	protein-coding gene	gene with protein product	"""spermatid flower-like structure protein"", ""testis specific leucine zipper protein nurit"", ""chibby homolog 2 (Drosophila)"""					12204287, 20096028	Standard	NM_001286341		Approved	NURIT, CBY2	uc001van.1	Q8NA61	OTTHUMG00000016861	ENST00000310521.1:c.638G>A	chr13.hg19:g.46287798G>A	ENSP00000309189:p.Arg213Gln	38.0	0.0		38.0	9.0	NM_152719	A8K8I5|Q8NHV2	Missense_Mutation	SNP	ENST00000310521.1	hg19	CCDS9399.1	.	.	.	.	.	.	.	.	.	.	G	0.735	-0.778610	0.02929	.	.	ENSG00000174015	ENST00000310521;ENST00000378966	T;T	0.41400	1.0;1.0	5.31	2.5	0.30297	.	0.533809	0.17062	N	0.188531	T	0.18509	0.0444	N	0.14661	0.345	0.09310	N	1	B;B	0.27971	0.196;0.043	B;B	0.14578	0.011;0.002	T	0.12142	-1.0559	10	0.17832	T	0.49	.	4.1666	0.10310	0.291:0.1885:0.5204:0.0	.	177;213	Q8NA61-2;Q8NA61	.;SPERT_HUMAN	Q	213;177	ENSP00000309189:R213Q;ENSP00000368249:R177Q	ENSP00000309189:R213Q	R	+	2	0	SPERT	45185799	0.005000	0.15991	0.022000	0.16811	0.109000	0.19521	1.176000	0.31957	0.800000	0.34041	0.609000	0.83330	CGG	.	.		0.652	SPERT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044786.2	NM_152719	
WDR90	197335	hgsc.bcm.edu	37	16	717526	717526	+	Silent	SNP	C	C	T	rs373944645		TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr16:717526C>T	ENST00000293879.4	+	41	5184	c.5184C>T	c.(5182-5184)tcC>tcT	p.S1728S	WDR90_ENST00000549091.1_Silent_p.S1730S|WDR90_ENST00000315764.4_Silent_p.S279S|RHOT2_ENST00000315082.4_5'Flank|WDR90_ENST00000547944.1_Silent_p.S327S			Q96KV7	WDR90_HUMAN	WD repeat domain 90	1728										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				TTACACCGTCCGCCAGGCTGC	0.637													C|||	1	0.000199681	0.0	0.0014	5008	,	,		19457	0.0		0.0	False		,,,				2504	0.0				p.S1728S		Atlas-SNP	.											.	WDR90	107	.	0			c.C5184T						.	C		0,4264		0,0,2132	50.0	57.0	55.0		5184	-9.8	0.0	16		55	1,8449		0,1,4224	no	coding-synonymous	WDR90	NM_145294.4		0,1,6356	TT,TC,CC		0.0118,0.0,0.0079		1728/1749	717526	1,12713	2132	4225	6357	SO:0001819	synonymous_variant	197335	exon41			ACCGTCCGCCAGG	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"""WD repeat domain containing"""	26960	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 17"", ""chromosome 16 open reading frame 15"", ""chromosome 16 open reading frame 16"", ""chromosome 16 open reading frame 19"", ""chromosome 16 open reading frame 18"""	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.5184C>T	chr16.hg19:g.717526C>T		33.0	0.0		23.0	10.0	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Silent	SNP	ENST00000293879.4	hg19	CCDS42092.1	.	.	.	.	.	.	.	.	.	.	C	3.305	-0.141970	0.06669	0.0	1.18E-4	ENSG00000161996	ENST00000546896	.	.	.	4.9	-9.79	0.00494	.	.	.	.	.	T	0.63908	0.2551	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.81716	-0.0806	5	0.87932	D	0	.	10.4405	0.44462	0.1527:0.5885:0.0772:0.1816	.	.	.	.	L	31	.	ENSP00000447915:P31L	P	+	2	0	WDR90	657527	0.000000	0.05858	0.000000	0.03702	0.125000	0.20455	-7.334000	0.00038	-4.518000	0.00044	-2.126000	0.00345	CCG	.	.		0.637	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294	
UNC45B	146862	hgsc.bcm.edu	37	17	33513464	33513464	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr17:33513464C>G	ENST00000268876.5	+	20	2779	c.2682C>G	c.(2680-2682)atC>atG	p.I894M	UNC45B_ENST00000591048.1_Missense_Mutation_p.I813M|UNC45B_ENST00000394570.2_Missense_Mutation_p.I892M|UNC45B_ENST00000433649.1_Missense_Mutation_p.I892M|UNC45B_ENST00000378449.1_Missense_Mutation_p.I813M|RP11-799D4.2_ENST00000590144.1_RNA	NM_173167.2	NP_775259.1	Q8IWX7	UN45B_HUMAN	unc-45 homolog B (C. elegans)	894					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(10)|lung(24)|ovary(3)|prostate(2)|skin(1)|stomach(1)|urinary_tract(3)	59		Ovarian(249;0.17)				TGCTGGAGATCCTGACTGTGG	0.537																																					p.I894M		Atlas-SNP	.											.	UNC45B	133	.	0			c.C2682G						.						121.0	100.0	107.0					17																	33513464		2203	4300	6503	SO:0001583	missense	146862	exon20			GGAGATCCTGACT	AW755253	CCDS11292.1, CCDS45648.1	17q12	2008-02-05	2005-11-17	2005-11-17	ENSG00000141161	ENSG00000141161			14304	protein-coding gene	gene with protein product		611220	"""cardiomyopathy associated 4"""	CMYA4		12356907	Standard	NM_001267052		Approved	UNC45	uc002hja.3	Q8IWX7	OTTHUMG00000132931	ENST00000268876.5:c.2682C>G	chr17.hg19:g.33513464C>G	ENSP00000268876:p.Ile894Met	127.0	0.0		66.0	15.0	NM_173167	Q495Q8|Q495Q9	Missense_Mutation	SNP	ENST00000268876.5	hg19	CCDS11292.1	.	.	.	.	.	.	.	.	.	.	C	14.92	2.678120	0.47886	.	.	ENSG00000141161	ENST00000394570;ENST00000268876;ENST00000433649;ENST00000378449	T;T;T	0.33216	3.52;1.42;2.9	6.02	2.68	0.31781	Armadillo-like helical (1);	0.000000	0.85682	D	0.000000	T	0.47857	0.1468	M	0.68952	2.095	0.43771	D	0.996295	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.91635	0.996;0.999;0.987	T	0.40384	-0.9566	10	0.56958	D	0.05	-26.3805	7.3734	0.26815	0.1302:0.716:0.0:0.1539	.	813;892;894	Q8IWX7-2;Q8IWX7-3;Q8IWX7	.;.;UN45B_HUMAN	M	894;894;892;813	ENSP00000268876:I894M;ENSP00000412840:I892M;ENSP00000367710:I813M	ENSP00000268876:I894M	I	+	3	3	UNC45B	30537577	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.548000	0.36201	0.737000	0.32582	0.655000	0.94253	ATC	.	.		0.537	UNC45B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256458.2	NM_173167	
KRT24	192666	hgsc.bcm.edu	37	17	38858134	38858135	+	Missense_Mutation	DNP	CA	CA	GC	rs201305125|rs11309872	byFrequency	TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	C|A	C|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr17:38858134_38858135CA>GC	ENST00000264651.2	-	2	722_723	c.666_667TG>GC	c.(664-669)aaTGcc>aaGCcc	p.222_223NA>KP		NM_019016.2	NP_061889.2	Q2M2I5	K1C24_HUMAN	keratin 24	222	Coil 1B.|Rod.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Breast(137;0.00526)				GCCAATCTGGCATTGTCAATGT	0.332																																					p.A223P|p.N222K	GBM(61;380 1051 14702 23642 31441)	Atlas-SNP	.											KRT24,NS,lymphoid_neoplasm,0,1|.,1	KRT24	60	.	0			c.G667C|c.T666G						.																																			SO:0001583	missense	192666	exon2			ATCTGGCATTGTC|TCTGGCATTGTCA		CCDS11372.1	17q21.2	2013-06-25			ENSG00000167916	ENSG00000167916		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	18527	protein-coding gene	gene with protein product		607742				16831889	Standard	NM_019016		Approved	FLJ20261, MGC138169, MGC138173	uc002hvd.3	Q2M2I5	OTTHUMG00000133372	ENST00000264651.2:c.666_667delinsGC	chr17.hg19:g.38858134_38858135delinsGC	ENSP00000264651:p.N222_A223delinsKP	500.0|496.0	0.0		188.0|190.0	12.0|15.0	NM_019016	Q9NXG7	Missense_Mutation	SNP	ENST00000264651.2	hg19	CCDS11372.1																																																																																			.	.		0.332	KRT24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257217.1	NM_019016	
RPTOR	57521	hgsc.bcm.edu	37	17	78796082	78796082	+	Silent	SNP	G	G	A	rs375226529		TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr17:78796082G>A	ENST00000306801.3	+	8	1334	c.972G>A	c.(970-972)gcG>gcA	p.A324A	RPTOR_ENST00000575542.1_3'UTR|RPTOR_ENST00000570891.1_Silent_p.A324A|RPTOR_ENST00000537330.1_Silent_p.A139A|RPTOR_ENST00000544334.2_Silent_p.A324A	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	324					cell cycle arrest (GO:0007050)|cell growth (GO:0016049)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nutrient levels (GO:0031669)|insulin receptor signaling pathway (GO:0008286)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of TOR signaling (GO:0032008)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|regulation of cell size (GO:0008361)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|TORC1 complex (GO:0031931)	14-3-3 protein binding (GO:0071889)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	44						ACACCATCGCGTGGAACGTGC	0.647																																					p.A324A		Atlas-SNP	.											.	RPTOR	122	.	0			c.G972A						.	G	,	1,4405	2.1+/-5.4	0,1,2202	154.0	152.0	153.0		972,972	-9.8	0.3	17		153	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	RPTOR	NM_001163034.1,NM_020761.2	,	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	,	324/1178,324/1336	78796082	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	57521	exon8			CATCGCGTGGAAC		CCDS11773.1, CCDS54175.1	17q25.3	2013-01-10				ENSG00000141564		"""WD repeat domain containing"""	30287	protein-coding gene	gene with protein product	"""regulatory associated protein of mTOR"""	607130				10718198, 12150926	Standard	NM_001163034		Approved	KOG1, Mip1, KIAA1303, raptor	uc002jyt.1	Q8N122		ENST00000306801.3:c.972G>A	chr17.hg19:g.78796082G>A		95.0	0.0		94.0	29.0	NM_001163034	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Silent	SNP	ENST00000306801.3	hg19	CCDS11773.1																																																																																			.	.		0.647	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761	
C3	718	hgsc.bcm.edu	37	19	6713207	6713207	+	Silent	SNP	C	C	T			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr19:6713207C>T	ENST00000245907.6	-	9	1088	c.996G>A	c.(994-996)ttG>ttA	p.L332L		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	332					complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|fatty acid metabolic process (GO:0006631)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of activation of membrane attack complex (GO:0001970)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of glucose transport (GO:0010828)|positive regulation of lipid storage (GO:0010884)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|regulation of immune response (GO:0050776)|regulation of triglyceride biosynthetic process (GO:0010866)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	C5L2 anaphylatoxin chemotactic receptor binding (GO:0031715)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Intravenous Immunoglobulin(DB00028)	CACCTGAGTGCAAGATGACGG	0.597																																					p.L332L		Atlas-SNP	.											.	C3	192	.	0			c.G996A						.						58.0	52.0	54.0					19																	6713207		2203	4300	6503	SO:0001819	synonymous_variant	718	exon9			TGAGTGCAAGATG	J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	3.4.21.43	"""Complement system"", ""Endogenous ligands"""	1318	protein-coding gene	gene with protein product	"""C3a anaphylatoxin"", ""complement component C3a"", ""complement component C3b"", ""prepro-C3"""	120700					Standard	NM_000064		Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.996G>A	chr19.hg19:g.6713207C>T		95.0	0.0		72.0	19.0	NM_000064	A7E236	Silent	SNP	ENST00000245907.6	hg19	CCDS32883.1																																																																																			.	.		0.597	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064	
CACNA1A	773	hgsc.bcm.edu	37	19	13318671	13318671	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr19:13318671G>T	ENST00000360228.5	-	47	6976	c.6977C>A	c.(6976-6978)gCg>gAg	p.A2326E	CACNA1A_ENST00000573710.2_3'UTR	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	2325					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	CCTGGCCACCGCctgctgctg	0.766																																					p.A2326E		Atlas-SNP	.											.	CACNA1A	715	.	0			c.C6977A						.						1.0	1.0	1.0					19																	13318671		333	860	1193	SO:0001583	missense	773	exon47			GCCACCGCCTGCT	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.6977C>A	chr19.hg19:g.13318671G>T	ENSP00000353362:p.Ala2326Glu	425.0	0.0		482.0	23.0	NM_001127222	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	ENST00000360228.5	hg19	CCDS45998.1	.	.	.	.	.	.	.	.	.	.	g	5.356	0.250903	0.10130	.	.	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018	D	0.95690	-3.78	2.6	0.109	0.14578	.	0.390690	0.08080	U	1.000000	D	0.85915	0.5808	N	0.08118	0	0.09310	N	0.999993	B;B;B	0.13145	0.007;0.0;0.004	B;B;B	0.08055	0.003;0.001;0.001	T	0.73642	-0.3918	10	0.19590	T	0.45	.	3.0397	0.06134	0.275:0.0:0.5237:0.2013	.	2332;2326;2315	E9PD31;Q9NS88;E7EVF2	.;.;.	E	2326;2332;2315	ENSP00000353362:A2326E	ENSP00000349520:A2315E	A	-	2	0	CACNA1A	13179671	0.977000	0.34250	0.145000	0.22337	0.879000	0.50718	0.936000	0.28938	-0.367000	0.08052	0.281000	0.19383	GCG	.	.		0.766	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068	
RYR1	6261	hgsc.bcm.edu	37	19	38976748	38976748	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr19:38976748C>T	ENST00000359596.3	+	34	5453	c.5453C>T	c.(5452-5454)gCg>gTg	p.A1818V	RYR1_ENST00000360985.3_Missense_Mutation_p.A1818V|RYR1_ENST00000355481.4_Missense_Mutation_p.A1818V			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1818	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.A1818G(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CTGGGGGAGGCGGTGCGCGAC	0.706																																					p.A1818V		Atlas-SNP	.											RYR1,NS,carcinoma,0,1	RYR1	708	.	1	Substitution - Missense(1)	lung(1)	c.C5453T						.						52.0	52.0	52.0					19																	38976748		2201	4292	6493	SO:0001583	missense	6261	exon34			GGGAGGCGGTGCG	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.5453C>T	chr19.hg19:g.38976748C>T	ENSP00000352608:p.Ala1818Val	99.0	0.0		49.0	6.0	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	C	19.50	3.840101	0.71488	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	T;T;T	0.74737	-0.87;-0.87;-0.87	3.7	3.7	0.42460	.	0.000000	0.64402	U	0.000005	D	0.85617	0.5738	M	0.81341	2.54	0.52501	D	0.999957	D;P	0.89917	1.0;0.909	D;B	0.71656	0.974;0.432	D	0.88490	0.3075	10	0.87932	D	0	.	15.2171	0.73277	0.0:1.0:0.0:0.0	.	1818;1818	P21817-2;P21817	.;RYR1_HUMAN	V	1818	ENSP00000352608:A1818V;ENSP00000347667:A1818V;ENSP00000354254:A1818V	ENSP00000347667:A1818V	A	+	2	0	RYR1	43668588	1.000000	0.71417	0.992000	0.48379	0.898000	0.52572	5.840000	0.69402	1.886000	0.54624	0.585000	0.79938	GCG	.	.		0.706	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
APP	351	hgsc.bcm.edu	37	21	27369713	27369713	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr21:27369713T>C	ENST00000346798.3	-	8	1085	c.1052A>G	c.(1051-1053)aAg>aGg	p.K351R	APP_ENST00000440126.3_Intron|APP_ENST00000348990.5_Intron|APP_ENST00000448388.2_Intron|APP_ENST00000359726.3_Missense_Mutation_p.K295R|APP_ENST00000439274.2_Missense_Mutation_p.K295R|APP_ENST00000357903.3_Intron|APP_ENST00000358918.3_Missense_Mutation_p.K351R|APP_ENST00000354192.3_Intron	NM_000484.3	NP_000475.1	P05067	A4_HUMAN	amyloid beta (A4) precursor protein	351					adult locomotory behavior (GO:0008344)|axon cargo transport (GO:0008088)|axon midline choice point recognition (GO:0016199)|axonogenesis (GO:0007409)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|collateral sprouting in absence of injury (GO:0048669)|dendrite development (GO:0016358)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|ionotropic glutamate receptor signaling pathway (GO:0035235)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|mRNA polyadenylation (GO:0006378)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron differentiation (GO:0045665)|neuromuscular process controlling balance (GO:0050885)|neuron apoptotic process (GO:0051402)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of multicellular organism growth (GO:0040014)|regulation of protein binding (GO:0043393)|regulation of synapse structure and activity (GO:0050803)|regulation of translation (GO:0006417)|response to oxidative stress (GO:0006979)|smooth endoplasmic reticulum calcium ion homeostasis (GO:0051563)|suckling behavior (GO:0001967)|synaptic growth at neuromuscular junction (GO:0051124)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|ciliary rootlet (GO:0035253)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endosome (GO:0005768)|ER to Golgi transport vesicle (GO:0030134)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|receptor complex (GO:0043235)|spindle midzone (GO:0051233)|synapse (GO:0045202)	acetylcholine receptor binding (GO:0033130)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|peptidase activator activity (GO:0016504)|PTB domain binding (GO:0051425)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)			endometrium(5)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(209;0.00295)				CTGGGTAGTCTTGAGTAAACT	0.438																																					p.K351R		Atlas-SNP	.											.	APP	90	.	0			c.A1052G						.						107.0	100.0	103.0					21																	27369713		2203	4300	6503	SO:0001583	missense	351	exon8			GTAGTCTTGAGTA	M15533	CCDS13576.1, CCDS13577.1, CCDS33523.1, CCDS46638.1, CCDS46639.1, CCDS56211.1, CCDS56212.1, CCDS56213.1	21q21.2	2014-01-30	2008-07-31		ENSG00000142192	ENSG00000142192		"""Endogenous ligands"""	620	protein-coding gene	gene with protein product	"""peptidase nexin-II"""	104760	"""Alzheimer disease"""	AD1		1679289	Standard	NM_001136130		Approved		uc002ylz.3	P05067	OTTHUMG00000078438	ENST00000346798.3:c.1052A>G	chr21.hg19:g.27369713T>C	ENSP00000284981:p.Lys351Arg	137.0	0.0		60.0	11.0	NM_000484	B2R5V1|B4DII8|D3DSD1|D3DSD2|D3DSD3|P09000|P78438|Q13764|Q13778|Q13793|Q16011|Q16014|Q16019|Q16020|Q6GSC0|Q8WZ99|Q9BT38|Q9UC33|Q9UCA9|Q9UCB6|Q9UCC8|Q9UCD1|Q9UQ58	Missense_Mutation	SNP	ENST00000346798.3	hg19	CCDS13576.1	.	.	.	.	.	.	.	.	.	.	T	12.02	1.812066	0.32053	.	.	ENSG00000142192	ENST00000346798;ENST00000358918;ENST00000359726;ENST00000439274	D;D;D;D	0.96232	-2.02;-1.87;-3.95;-2.02	4.35	4.35	0.52113	.	0.342318	0.26023	N	0.026820	D	0.95277	0.8468	L	0.41710	1.295	0.80722	D	1	P;P	0.34587	0.458;0.458	P;P	0.51742	0.678;0.678	D	0.91420	0.5158	10	0.11794	T	0.64	-34.2354	10.2299	0.43250	0.0:0.0:0.0:1.0	.	295;351	E9PG40;P05067	.;A4_HUMAN	R	351;351;295;295	ENSP00000284981:K351R;ENSP00000351796:K351R;ENSP00000352760:K295R;ENSP00000398879:K295R	ENSP00000284981:K351R	K	-	2	0	APP	26291584	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	3.093000	0.50217	2.198000	0.70561	0.533000	0.62120	AAG	.	.		0.438	APP-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171340.1	NM_000484	
CENPF	1063	hgsc.bcm.edu	37	1	214819555	214819558	+	Frame_Shift_Del	DEL	TCTG	TCTG	-	rs565584032		TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	TCTG	TCTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr1:214819555_214819558delTCTG	ENST00000366955.3	+	13	6810_6813	c.6642_6645delTCTG	c.(6640-6645)aatctgfs	p.NL2214fs		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	2310	2 X 177 AA tandem repeats.|Interaction with NDE1 and NDEL1.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		AAAAAGAAAATCTGACAAAACAAA	0.353																																					p.2214_2215del	Colon(80;575 1284 11000 14801 43496)	Atlas-INDEL	.											.	CENPF	321	.	0			c.6641_6644del						.																																			SO:0001589	frameshift_variant	1063	exon13			.	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"""mitosin"""	600236	"""centromere protein F, 350/400kDa (mitosin)"""			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.6642_6645delTCTG	chr1.hg19:g.214819555_214819558delTCTG	ENSP00000355922:p.Asn2214fs	332.0	0.0		223.0	14.0	NM_016343	Q13171|Q13246|Q5VVM7	Frame_Shift_Del	DEL	ENST00000366955.3	hg19	CCDS31023.1																																																																																			.	.		0.353	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
IQCA1	79781	hgsc.bcm.edu	37	2	237327837	237327839	+	In_Frame_Del	DEL	GGG	GGG	-			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	GGG	GGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr2:237327837_237327839delGGG	ENST00000409907.3	-	8	1361_1363	c.1087_1089delCCC	c.(1087-1089)cccdel	p.P363del	IQCA1_ENST00000465621.1_5'UTR|IQCA1_ENST00000309507.5_In_Frame_Del_p.P359del|IQCA1_ENST00000431676.2_Intron	NM_024726.4	NP_079002.3	Q86XH1	IQCA1_HUMAN	IQ motif containing with AAA domain 1	363	Lys-rich.						ATP binding (GO:0005524)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)	26						TGGCTTTCTTGGGTTGTttttcc	0.266																																					p.370_371del		Atlas-INDEL	.											.	IQCA1	170	.	0			c.1109_1111del						.																																			SO:0001651	inframe_deletion	79781	exon8			.	AK026180	CCDS46549.1, CCDS59441.1, CCDS74677.1	2q37.3	2014-07-18	2008-07-02	2008-07-02	ENSG00000132321	ENSG00000132321		"""ATPases / AAA-type"""	26195	protein-coding gene	gene with protein product	"""dynein regulatory complex subunit 11"""		"""IQ motif containing with AAA domain"""	IQCA		23427265	Standard	NM_024726		Approved	FLJ22527, DRC11	uc002vwb.3	Q86XH1	OTTHUMG00000153058	ENST00000409907.3:c.1087_1089delCCC	chr2.hg19:g.237327837_237327839delGGG	ENSP00000387347:p.Pro363del	501.0	0.0		260.0	17.0	NM_001270585	B4DFH9|E7EWQ0|Q4G164|Q53R37|Q53RV3|Q96NS7|Q9H680	In_Frame_Del	DEL	ENST00000409907.3	hg19	CCDS46549.1																																																																																			.	.		0.266	IQCA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000329266.1	NM_024726	
IQCA1	79781	hgsc.bcm.edu	37	2	237327828	237327830	+	In_Frame_Del	DEL	GGC	GGC	-	rs559244816		TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	GGC	GGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr2:237327828_237327830delGGC	ENST00000409907.3	-	8	1370_1372	c.1096_1098delGCC	c.(1096-1098)gccdel	p.A366del	IQCA1_ENST00000465621.1_5'UTR|IQCA1_ENST00000309507.5_In_Frame_Del_p.A362del|IQCA1_ENST00000431676.2_Intron	NM_024726.4	NP_079002.3	Q86XH1	IQCA1_HUMAN	IQ motif containing with AAA domain 1	366	Lys-rich.						ATP binding (GO:0005524)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)	26						TTTGTTTTTTGGCTTTCTTGGGT	0.271																																					p.373_374del		Atlas-INDEL	.											.	IQCA1	170	.	0			c.1118_1120del						.																																			SO:0001651	inframe_deletion	79781	exon8			.	AK026180	CCDS46549.1, CCDS59441.1, CCDS74677.1	2q37.3	2014-07-18	2008-07-02	2008-07-02	ENSG00000132321	ENSG00000132321		"""ATPases / AAA-type"""	26195	protein-coding gene	gene with protein product	"""dynein regulatory complex subunit 11"""		"""IQ motif containing with AAA domain"""	IQCA		23427265	Standard	NM_024726		Approved	FLJ22527, DRC11	uc002vwb.3	Q86XH1	OTTHUMG00000153058	ENST00000409907.3:c.1096_1098delGCC	chr2.hg19:g.237327828_237327830delGGC	ENSP00000387347:p.Ala366del	508.0	0.0		275.0	17.0	NM_001270585	B4DFH9|E7EWQ0|Q4G164|Q53R37|Q53RV3|Q96NS7|Q9H680	In_Frame_Del	DEL	ENST00000409907.3	hg19	CCDS46549.1																																																																																			.	.		0.271	IQCA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000329266.1	NM_024726	
XIRP2	129446	hgsc.bcm.edu	37	2	168105575	168105577	+	In_Frame_Del	DEL	TTG	TTG	-	rs533159553		TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	TTG	TTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr2:168105575_168105577delTTG	ENST00000409195.1	+	9	7762_7764	c.7673_7675delTTG	c.(7672-7677)attgaa>aaa	p.2558_2559IE>K	XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000295237.9_In_Frame_Del_p.2558_2559IE>K|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409273.1_In_Frame_Del_p.2336_2337IE>K|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409605.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2383					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AAAGAAGAAATTGAAAAACAGAA	0.315																																					p.2558_2558del		Atlas-INDEL	.											.	XIRP2	914	.	0			c.7672_7674del						.																																			SO:0001651	inframe_deletion	129446	exon9			.	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.7673_7675delTTG	chr2.hg19:g.168105575_168105577delTTG	ENSP00000386840:p.Ile2558_Glu2559delinsLys	299.0	0.0		140.0	12.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	In_Frame_Del	DEL	ENST00000409195.1	hg19	CCDS42769.1																																																																																			.	.		0.315	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
CCDC18	343099	hgsc.bcm.edu	37	1	93672688	93672690	+	In_Frame_Del	DEL	CGG	CGG	-	rs2783499	byFrequency	TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	CGG	CGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr1:93672688_93672690delCGG	ENST00000343253.7	+	9	1444_1446	c.942_944delCGG	c.(940-945)aacgga>aaa	p.314_315NG>K	CCDC18_ENST00000334652.5_5'UTR|CCDC18_ENST00000401026.3_In_Frame_Del_p.314_315NG>K|CCDC18_ENST00000557479.1_In_Frame_Del_p.432_433NG>K|CCDC18_ENST00000338949.4_In_Frame_Del_p.113_114NG>K			Q5T9S5	CCD18_HUMAN	coiled-coil domain containing 18	314										breast(5)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	42		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)		AAAATAACAACGGAAAAGAAAAA	0.276																																					p.314_315del		Atlas-INDEL	.											.	CCDC18	93	.	0			c.941_943del						.																																			SO:0001651	inframe_deletion	343099	exon9			.			1p22.1	2008-02-05			ENSG00000122483	ENSG00000122483			30370	protein-coding gene	gene with protein product						12601173	Standard	XM_006710609		Approved	NY-SAR-41	uc021opx.1	Q5T9S5	OTTHUMG00000010598	ENST00000343253.7:c.942_944delCGG	chr1.hg19:g.93672688_93672690delCGG	ENSP00000343377:p.Asn314_Gly315delinsLys	479.0	0.0		115.0	12.0	NM_206886	Q6ZU17	In_Frame_Del	DEL	ENST00000343253.7	hg19																																																																																				.	.		0.276	CCDC18-008	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000382327.1	NM_206886	
LSS	4047	hgsc.bcm.edu	37	21	47647474	47647475	+	Frame_Shift_Ins	INS	-	-	T			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr21:47647474_47647475insT	ENST00000397728.3	-	3	388_389	c.310_311insA	c.(310-312)ctcfs	p.L104fs	MCM3AP-AS1_ENST00000591223.1_RNA|LSS_ENST00000464357.1_5'UTR|MCM3AP-AS1_ENST00000444998.1_RNA|MCM3AP-AS1_ENST00000420074.1_RNA|LSS_ENST00000522411.1_Frame_Shift_Ins_p.L104fs|MCM3AP-AS1_ENST00000432735.1_RNA|MCM3AP-AS1_ENST00000588753.1_RNA|LSS_ENST00000457828.2_Frame_Shift_Ins_p.L24fs|LSS_ENST00000356396.4_Frame_Shift_Ins_p.L104fs|MCM3AP-AS1_ENST00000590829.1_RNA|MCM3AP-AS1_ENST00000414659.1_RNA|MCM3AP-AS1_ENST00000455567.1_RNA|MCM3AP-AS1_ENST00000421927.1_RNA	NM_001145436.1|NM_002340.5	NP_001138908.1|NP_002331.3	P48449	ERG7_HUMAN	lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)	104					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|lipid particle (GO:0005811)|membrane (GO:0016020)	lanosterol synthase activity (GO:0000250)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|skin(1)|urinary_tract(1)	21	Breast(49;0.214)					ACCTGGCAGGAGGAAAAGTGGG	0.594																																					p.L104fs	Pancreas(114;955 2313 34923 50507)	Atlas-INDEL	.											.	LSS	50	.	0			c.311_312insA						.																																			SO:0001589	frameshift_variant	4047	exon3			.	U22526	CCDS13733.1, CCDS46654.1, CCDS54489.1	21q22.3	1998-05-07			ENSG00000160285	ENSG00000160285	5.4.99.7		6708	protein-coding gene	gene with protein product		600909				7639730, 8655142	Standard	NM_001001438		Approved	OSC	uc002zij.3	P48449	OTTHUMG00000090633	ENST00000397728.3:c.310_311insA	chr21.hg19:g.47647474_47647475insT	ENSP00000380837:p.Leu104fs	119.0	0.0		56.0	13.0	NM_001145436	B4DJZ9|D3DSN0|E9PEI9|G5E9Q9|Q8IYL6|Q9UEZ1	Frame_Shift_Ins	INS	ENST00000397728.3	hg19	CCDS13733.1																																																																																			.	.		0.594	LSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207274.2		
HOOK2	29911	hgsc.bcm.edu	37	19	12880808	12880808	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-AAVW-01A-11D-A40R-10	TCGA-DD-AAVW-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	da6c81eb-ba15-434a-ad41-00e436b1f3da	ded7e2a3-f782-4a5f-88a5-ea073d078eb9	g.chr19:12880808delC	ENST00000397668.3	-	11	1064	c.991delG	c.(991-993)gtgfs	p.V331fs	HOOK2_ENST00000264827.5_Frame_Shift_Del_p.V331fs|HOOK2_ENST00000589965.1_Intron	NM_013312.2	NP_037444.2	Q96ED9	HOOK2_HUMAN	hook microtubule-tethering protein 2	331	Sufficient for interaction with microtubules.				early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|protein transport (GO:0015031)	centrosome (GO:0005813)|FHF complex (GO:0070695)|microtubule (GO:0005874)	identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(5)|skin(1)	20						AGCTGCCGCACCTGCCGCCGC	0.726																																					p.V331fs		Atlas-INDEL	.											.	HOOK2	73	.	0			c.992delT						.						3.0	3.0	3.0					19																	12880808		1798	3738	5536	SO:0001589	frameshift_variant	29911	exon11			.	AF044924	CCDS42507.1, CCDS42508.1	19p13.2	2013-08-21	2013-08-21						19885	protein-coding gene	gene with protein product		607824	"""hook homolog 2 (Drosophila)"""			9927460	Standard	NM_013312		Approved	HK2	uc002muy.2	Q96ED9		ENST00000397668.3:c.991delG	chr19.hg19:g.12880808delC	ENSP00000380785:p.Val331fs	41.0	0.0		59.0	13.0	NM_001100176	O60562	Frame_Shift_Del	DEL	ENST00000397668.3	hg19	CCDS42508.1																																																																																			.	.		0.726	HOOK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451008.1	NM_013312	
