#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
ADAMTSL4	54507	hgsc.bcm.edu	37	1	150532541	150532541	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr1:150532541C>A	ENST00000369038.2	+	17	3295	c.3094C>A	c.(3094-3096)Caa>Aaa	p.Q1032K	ADAMTSL4_ENST00000271643.4_Missense_Mutation_p.Q1032K|ADAMTSL4_ENST00000369039.5_Missense_Mutation_p.Q1055K|RP11-54A4.2_ENST00000442435.2_RNA			Q6UY14	ATL4_HUMAN	ADAMTS-like 4	1032	PLAC. {ECO:0000255|PROSITE- ProRule:PRU00233}.				apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|positive regulation of apoptotic process (GO:0043065)	interstitial matrix (GO:0005614)	metalloendopeptidase activity (GO:0004222)|protease binding (GO:0002020)			breast(1)|cervix(1)|endometrium(6)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(3)	32	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			CCCAGATGATCAATGCAAGGA	0.597											OREG0013787	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q1032K		Atlas-SNP	.											.	ADAMTSL4	101	.	0			c.C3094A						.						148.0	139.0	142.0					1																	150532541		2203	4300	6503	SO:0001583	missense	54507	exon19			GATGATCAATGCA	BC027478	CCDS955.1, CCDS30852.1, CCDS72908.1	1q21.2	2008-02-05	2005-12-01	2005-12-01	ENSG00000143382	ENSG00000143382			19706	protein-coding gene	gene with protein product		610113	"""thrombospondin repeat containing 1"""	TSRC1		12706885	Standard	NM_019032		Approved	DKFZP434K1772	uc001eux.3	Q6UY14	OTTHUMG00000034863	ENST00000369038.2:c.3094C>A	chr1.hg19:g.150532541C>A	ENSP00000358034:p.Gln1032Lys	185.0	0.0	1733	188.0	46.0	NM_019032	B2RTT0|F8WAD0|Q5T5F7|Q6IPM6|Q8N643|Q9HBS6	Missense_Mutation	SNP	ENST00000369038.2	hg19	CCDS955.1	.	.	.	.	.	.	.	.	.	.	C	10.95	1.496385	0.26861	.	.	ENSG00000143382	ENST00000271643;ENST00000369039;ENST00000369038	T;T;T	0.39229	1.09;1.09;1.09	4.73	3.8	0.43715	PLAC (2);	.	.	.	.	T	0.07188	0.0182	N	0.02539	-0.55	0.33920	D	0.640772	B;B;B	0.31351	0.32;0.012;0.27	B;B;B	0.31101	0.124;0.022;0.059	T	0.11179	-1.0598	9	0.33141	T	0.24	.	7.7469	0.28875	0.1867:0.6328:0.1805:0.0	.	993;1055;1032	B7ZMJ3;F8WAD0;Q6UY14	.;.;ATL4_HUMAN	K	1032;1055;1032	ENSP00000271643:Q1032K;ENSP00000358035:Q1055K;ENSP00000358034:Q1032K	ENSP00000271643:Q1032K	Q	+	1	0	ADAMTSL4	148799165	0.992000	0.36948	0.951000	0.38953	0.946000	0.59487	3.127000	0.50484	1.175000	0.42826	0.561000	0.74099	CAA	.	.		0.597	ADAMTSL4-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084395.4	NM_019032	
SLC35F3	148641	hgsc.bcm.edu	37	1	234041461	234041461	+	Silent	SNP	C	C	T			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr1:234041461C>T	ENST00000366618.3	+	2	385	c.240C>T	c.(238-240)atC>atT	p.I80I		NM_173508.2	NP_775779.1	Q8IY50	S35F3_HUMAN	solute carrier family 35, member F3	0					thiamine transport (GO:0015888)	integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|urinary_tract(1)	32	Ovarian(103;0.0454)	all_cancers(173;0.145)|Prostate(94;0.0885)	OV - Ovarian serous cystadenocarcinoma(106;0.00531)			TCCTGCGCATCACTGGCTACT	0.582																																					p.I80I		Atlas-SNP	.											.	SLC35F3	81	.	0			c.C240T						.						61.0	57.0	58.0					1																	234041461		2203	4300	6503	SO:0001819	synonymous_variant	148641	exon2			GCGCATCACTGGC		CCDS1600.1, CCDS73050.1	1q42.3	2013-05-22			ENSG00000183780	ENSG00000183780		"""Solute carriers"""	23616	protein-coding gene	gene with protein product							Standard	XM_005273070		Approved	FLJ37712	uc001hvy.1	Q8IY50	OTTHUMG00000037929	ENST00000366618.3:c.240C>T	chr1.hg19:g.234041461C>T		230.0	0.0		292.0	75.0	NM_173508	Q5TDD6|Q8N9C9	Silent	SNP	ENST00000366618.3	hg19	CCDS1600.1																																																																																			.	.		0.582	SLC35F3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092579.2	NM_173508	
SCN3A	6328	hgsc.bcm.edu	37	2	165946841	165946841	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr2:165946841T>C	ENST00000360093.3	-	28	6313	c.5822A>G	c.(5821-5823)aAa>aGa	p.K1941R	SCN3A_ENST00000409101.3_Missense_Mutation_p.K1892R|SCN3A_ENST00000465043.1_5'Flank|SCN3A_ENST00000283254.7_Missense_Mutation_p.K1941R|SCN3A_ENST00000540861.1_Missense_Mutation_p.K424R|AC013463.2_ENST00000431341.1_RNA	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	1941					membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CATGTCTTGTTTTATAGGTAA	0.348																																					p.K1941R		Atlas-SNP	.											.	SCN3A	544	.	0			c.A5822G						.						93.0	92.0	92.0					2																	165946841		2203	4300	6503	SO:0001583	missense	6328	exon28			TCTTGTTTTATAG	AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10590	protein-coding gene	gene with protein product		182391	"""sodium channel, voltage-gated, type III, alpha polypeptide"""			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.5822A>G	chr2.hg19:g.165946841T>C	ENSP00000353206:p.Lys1941Arg	271.0	0.0		335.0	84.0	NM_006922	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Missense_Mutation	SNP	ENST00000360093.3	hg19		.	.	.	.	.	.	.	.	.	.	T	5.697	0.313120	0.10789	.	.	ENSG00000153253	ENST00000360093;ENST00000283254;ENST00000409101;ENST00000540861	D;D;D;D	0.96940	-3.95;-3.95;-3.9;-4.18	6.03	6.03	0.97812	.	0.000000	0.64402	D	0.000002	D	0.92110	0.7499	L	0.31578	0.945	0.44562	D	0.997529	B;B;B	0.20261	0.011;0.011;0.043	B;B;B	0.20577	0.009;0.009;0.03	D	0.88047	0.2785	10	0.25751	T	0.34	.	10.8274	0.46640	0.0:0.0699:0.0:0.9301	.	1892;1892;1941	Q9NY46-2;Q9NY46-4;Q9NY46-3	.;.;.	R	1941;1941;1892;424	ENSP00000353206:K1941R;ENSP00000283254:K1941R;ENSP00000386726:K1892R;ENSP00000439920:K424R	ENSP00000283254:K1941R	K	-	2	0	SCN3A	165655087	1.000000	0.71417	1.000000	0.80357	0.397000	0.30659	3.240000	0.51368	2.308000	0.77769	0.533000	0.62120	AAA	.	.		0.348	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922	
MYH15	22989	hgsc.bcm.edu	37	3	108203986	108203986	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr3:108203986A>G	ENST00000273353.3	-	12	1182	c.1126T>C	c.(1126-1128)Ttt>Ctt	p.F376L		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	376	Myosin motor.					cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						TTCTGTTTAAATTTCATATTT	0.398																																					p.F376L		Atlas-SNP	.											.	MYH15	223	.	0			c.T1126C						.						134.0	124.0	127.0					3																	108203986		1867	4103	5970	SO:0001583	missense	22989	exon12			GTTTAAATTTCAT	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"""Myosins / Myosin superfamily : Class II"""	31073	protein-coding gene	gene with protein product		609929	"""myosin, heavy polypeptide 15"""			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.1126T>C	chr3.hg19:g.108203986A>G	ENSP00000273353:p.Phe376Leu	173.0	0.0		150.0	38.0	NM_014981		Missense_Mutation	SNP	ENST00000273353.3	hg19	CCDS43127.1	.	.	.	.	.	.	.	.	.	.	A	29.0	4.968019	0.92855	.	.	ENSG00000144821	ENST00000273353	D	0.89939	-2.59	6.05	4.87	0.63330	Myosin head, motor domain (2);	.	.	.	.	D	0.95655	0.8587	M	0.93507	3.425	0.52099	D	0.999945	D	0.89917	1.0	D	0.97110	1.0	D	0.96062	0.9039	9	0.87932	D	0	.	13.328	0.60471	0.8681:0.1319:0.0:0.0	.	376	Q9Y2K3	MYH15_HUMAN	L	376	ENSP00000273353:F376L	ENSP00000273353:F376L	F	-	1	0	MYH15	109686676	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.354000	0.79424	1.077000	0.40990	0.528000	0.53228	TTT	.	.		0.398	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988	
PLEKHG4B	153478	hgsc.bcm.edu	37	5	161903	161903	+	Silent	SNP	C	C	T			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr5:161903C>T	ENST00000283426.6	+	10	1475	c.1425C>T	c.(1423-1425)tcC>tcT	p.S475S		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	475							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		TACAGCAATCCTGCCAGAAAG	0.577																																					p.S475S		Atlas-SNP	.											.	PLEKHG4B	167	.	0			c.C1425T						.						75.0	71.0	73.0					5																	161903		2203	4300	6503	SO:0001819	synonymous_variant	153478	exon10			GCAATCCTGCCAG	BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"""Pleckstrin homology (PH) domain containing"""	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.1425C>T	chr5.hg19:g.161903C>T		129.0	0.0		111.0	16.0	NM_052909		Silent	SNP	ENST00000283426.6	hg19	CCDS34124.1																																																																																			.	.		0.577	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909	
ITGA1	3672	hgsc.bcm.edu	37	5	52193327	52193327	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr5:52193327T>C	ENST00000282588.6	+	10	1590	c.1132T>C	c.(1132-1134)Tct>Cct	p.S378P		NM_181501.1	NP_852478.1	P56199	ITA1_HUMAN	integrin, alpha 1	378					activation of MAPK activity (GO:0000187)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular extravasation (GO:0045123)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neutrophil chemotaxis (GO:0030593)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|vasodilation (GO:0042311)	acrosomal vesicle (GO:0001669)|basal part of cell (GO:0045178)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha1-beta1 complex (GO:0034665)|integrin complex (GO:0008305)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)|protein phosphatase binding (GO:0019903)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(19)|ovary(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(810;5.05e-05)|Breast(144;0.0851)				AATGGAAATGTCTCAGACTGG	0.383																																					p.S378P		Atlas-SNP	.											.	ITGA1	112	.	0			c.T1132C						.						89.0	84.0	85.0					5																	52193327		2203	4300	6503	SO:0001583	missense	3672	exon10			GAAATGTCTCAGA	X68742	CCDS3955.1	5q11.1	2010-03-23			ENSG00000213949	ENSG00000213949		"""CD molecules"", ""Integrins"""	6134	protein-coding gene	gene with protein product		192968				8428973, 11937138	Standard	NM_181501		Approved	VLA1, CD49a	uc003jou.3	P56199	OTTHUMG00000131163	ENST00000282588.6:c.1132T>C	chr5.hg19:g.52193327T>C	ENSP00000282588:p.Ser378Pro	94.0	0.0		90.0	15.0	NM_181501	B2RNU0	Missense_Mutation	SNP	ENST00000282588.6	hg19	CCDS3955.1	.	.	.	.	.	.	.	.	.	.	T	28.4	4.921172	0.92249	.	.	ENSG00000213949	ENST00000282588	T	0.67345	-0.26	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.81735	0.4885	M	0.76328	2.33	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.83324	-0.0016	10	0.62326	D	0.03	.	16.4447	0.83919	0.0:0.0:0.0:1.0	.	378	P56199	ITA1_HUMAN	P	378	ENSP00000282588:S378P	ENSP00000282588:S378P	S	+	1	0	ITGA1	52229084	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.857000	0.69525	2.284000	0.76573	0.528000	0.53228	TCT	.	.		0.383	ITGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253855.3	NM_181501	
ANKRD32	84250	hgsc.bcm.edu	37	5	94001726	94001726	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr5:94001726T>G	ENST00000265140.5	+	12	1948	c.1529T>G	c.(1528-1530)aTc>aGc	p.I510S		NM_032290.3	NP_115666.2	Q9BQI6	ANR32_HUMAN	ankyrin repeat domain 32	510						centrosome (GO:0005813)|nucleus (GO:0005634)				NS(1)|breast(2)|endometrium(2)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|skin(1)	13		all_cancers(142;1.51e-09)|all_epithelial(76;4.68e-12)|all_lung(232;5.94e-05)|Ovarian(174;0.000953)|Lung NSC(167;0.00105)|Colorectal(57;0.122)|Lung SC(612;0.152)		all cancers(79;3.88e-18)		GAAGTCCTTATCAGGTAAGGA	0.348																																					p.I510S		Atlas-SNP	.											.	ANKRD32	117	.	0			c.T1529G						.						150.0	119.0	128.0					5																	94001726		692	1591	2283	SO:0001583	missense	84250	exon12			TCCTTATCAGGTA	AL136560	CCDS4071.2	5q15	2013-01-10			ENSG00000133302	ENSG00000133302		"""Ankyrin repeat domain containing"""	25408	protein-coding gene	gene with protein product			"""BRCT domain containing 1"""	BRCTD1			Standard	NM_032290		Approved	DKFZp761C121, DKFZp564C0469	uc003kkr.4	Q9BQI6	OTTHUMG00000121133	ENST00000265140.5:c.1529T>G	chr5.hg19:g.94001726T>G	ENSP00000265140:p.Ile510Ser	43.0	0.0		60.0	5.0	NM_032290	B4DMG4|Q3B7K4|Q6NSA5|Q6PHW9|Q9Y402	Missense_Mutation	SNP	ENST00000265140.5	hg19	CCDS4071.2	.	.	.	.	.	.	.	.	.	.	T	14.23	2.472039	0.43942	.	.	ENSG00000133302	ENST00000265140	T	0.56103	0.48	5.25	5.25	0.73442	.	0.495502	0.16842	N	0.197281	T	0.42108	0.1188	L	0.29908	0.895	0.32464	N	0.543763	B	0.23058	0.079	B	0.26517	0.07	T	0.53954	-0.8365	10	0.87932	D	0	.	9.6422	0.39846	0.0:0.0783:0.0:0.9217	.	510	Q9BQI6	ANR32_HUMAN	S	510	ENSP00000265140:I510S	ENSP00000265140:I510S	I	+	2	0	ANKRD32	94027482	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	3.821000	0.55700	1.966000	0.57179	0.477000	0.44152	ATC	.	.		0.348	ANKRD32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241610.1	NM_032290	
MGAT4B	11282	hgsc.bcm.edu	37	5	179226059	179226059	+	Silent	SNP	G	G	A			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr5:179226059G>A	ENST00000292591.7	-	11	1562	c.1212C>T	c.(1210-1212)agC>agT	p.S404S	MGAT4B_ENST00000521305.1_5'Flank|MGAT4B_ENST00000337755.5_Silent_p.S419S|MIR1229_ENST00000408467.1_RNA	NM_014275.4	NP_055090.1	Q9UQ53	MGT4B_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme B	404					cellular protein metabolic process (GO:0044267)|N-glycan processing (GO:0006491)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	13	all_cancers(89;0.000201)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0525)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TCAGGCTCGTGCTCACCTCTG	0.622																																					p.S419S	GBM(13;414 434 4098 22176 23230)	Atlas-SNP	.											.	MGAT4B	41	.	0			c.C1257T						.						152.0	146.0	148.0					5																	179226059		2203	4300	6503	SO:0001819	synonymous_variant	11282	exon10			GCTCGTGCTCACC	AB000624	CCDS4448.1, CCDS4449.1	5q35	2013-02-25	2005-11-16		ENSG00000161013	ENSG00000161013	2.4.1.145	"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	7048	protein-coding gene	gene with protein product		604561	"""mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isoenzyme B"""			10372966	Standard	NM_014275		Approved	GnT-Ivb	uc003mks.3	Q9UQ53	OTTHUMG00000130912	ENST00000292591.7:c.1212C>T	chr5.hg19:g.179226059G>A		348.0	0.0		367.0	42.0	NM_054013	A8MPR0|Q86TF1|Q96GH4|Q9NSK6	Silent	SNP	ENST00000292591.7	hg19	CCDS4448.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.194|9.194	1.026686|1.026686	0.19512|0.19512	.|.	.|.	ENSG00000161013|ENSG00000161013	ENST00000520969;ENST00000518980|ENST00000518778;ENST00000520875	.|.	.|.	.|.	4.03|4.03	4.03|4.03	0.46877|0.46877	.|.	.|.	.|.	.|.	.|.	T|T	0.71324|0.71324	0.3326|0.3326	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.71981|0.71981	-0.4428|-0.4428	4|4	.|.	.|.	.|.	-26.1269|-26.1269	16.3834|16.3834	0.83489|0.83489	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	V|Y	101;150|229;185	.|.	.|.	A|H	-|-	2|1	0|0	MGAT4B|MGAT4B	179158665|179158665	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.695000|0.695000	0.40330|0.40330	3.682000|3.682000	0.54656|0.54656	2.072000|2.072000	0.62099|0.62099	0.561000|0.561000	0.74099|0.74099	GCA|CAC	.	.		0.622	MGAT4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253503.3	NM_014275	
BAG6	7917	hgsc.bcm.edu	37	6	31610883	31610883	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr6:31610883G>A	ENST00000375964.6	-	14	1989	c.1676C>T	c.(1675-1677)aCc>aTc	p.T559I	BAG6_ENST00000362049.6_Missense_Mutation_p.T553I|BAG6_ENST00000439687.2_Missense_Mutation_p.T552I|BAG6_ENST00000375976.4_Missense_Mutation_p.T553I|BAG6_ENST00000211379.5_Missense_Mutation_p.T553I|BAG6_ENST00000404765.2_Missense_Mutation_p.T589I|BAG6_ENST00000470875.1_5'UTR	NM_004639.3|NM_080703.2	NP_004630.3|NP_542434.1	P46379	BAG6_HUMAN	BCL2-associated athanogene 6	559	4 X 29 AA approximate repeats.|Pro-rich.				brain development (GO:0007420)|cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|embryo development (GO:0009790)|immune system process (GO:0002376)|internal peptidyl-lysine acetylation (GO:0018393)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|kidney development (GO:0001822)|lung development (GO:0030324)|negative regulation of apoptotic process (GO:0043066)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of proteolysis (GO:0045861)|protein stabilization (GO:0050821)|regulation of cell proliferation (GO:0042127)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)|tail-anchored membrane protein insertion into ER membrane (GO:0071816)|transport (GO:0006810)|ubiquitin-dependent protein catabolic process (GO:0006511)	BAT3 complex (GO:0071818)|cytosol (GO:0005829)|nucleus (GO:0005634)	polyubiquitin binding (GO:0031593)|proteasome binding (GO:0070628)|ribosome binding (GO:0043022)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(2)|pancreas(2)|skin(3)|urinary_tract(2)	36						CATACCTGGGGTCCCCTGAGC	0.602																																					p.T559I		Atlas-SNP	.											.	BAG6	73	.	0			c.C1676T						.						8.0	10.0	9.0					6																	31610883		2192	4274	6466	SO:0001583	missense	7917	exon14			CCTGGGGTCCCCT	M31294	CCDS4709.1, CCDS47403.1, CCDS56414.1, CCDS56415.1	6p21.3	2011-06-14	2010-12-09	2010-12-09	ENSG00000204463	ENSG00000204463			13919	protein-coding gene	gene with protein product		142590	"""HLA-B associated transcript 3"""	BAT3		2156268	Standard	NM_004639		Approved	G3, D6S52E	uc003nvf.4	P46379	OTTHUMG00000031171	ENST00000375964.6:c.1676C>T	chr6.hg19:g.31610883G>A	ENSP00000365131:p.Thr559Ile	14.0	0.0		12.0	5.0	NM_004639	A2ADJ7|A3KQ42|A3KQ44|A6NGY6|A6PWF7|B0UX84|B4DZ12|B4E3V4|E7EMZ4|F8VXY4|O95874|Q5HYL9|Q5SQ35|Q5SQ36|Q5SQ37|Q5SQ41|Q5SRP8|Q5SRP9|Q5STC1|Q5STX1|Q5STX3|Q96SA6|Q9BCN4	Missense_Mutation	SNP	ENST00000375964.6	hg19	CCDS47403.1	.	.	.	.	.	.	.	.	.	.	G	16.99	3.272818	0.59649	.	.	ENSG00000204463	ENST00000375976;ENST00000375964;ENST00000211379;ENST00000404765;ENST00000439687;ENST00000362049;ENST00000437771;ENST00000438149;ENST00000436214	T;T;T;T;T;T;T;T	0.52295	1.15;1.26;1.15;1.35;0.89;1.27;0.69;0.67	5.17	5.17	0.71159	.	0.304052	0.35615	N	0.003100	T	0.24122	0.0584	N	0.08118	0	0.42030	D	0.991025	B;P;B;P	0.44429	0.319;0.835;0.421;0.557	B;P;B;B	0.44477	0.104;0.451;0.107;0.154	T	0.27191	-1.0081	10	0.72032	D	0.01	.	16.5889	0.84759	0.0:0.0:1.0:0.0	.	552;553;559;553	E7EMZ4;F8VXY4;P46379;P46379-2	.;.;BAG6_HUMAN;.	I	553;559;553;589;552;553;589;147;167	ENSP00000365143:T553I;ENSP00000365131:T559I;ENSP00000211379:T553I;ENSP00000384494:T589I;ENSP00000402856:T552I;ENSP00000354875:T553I;ENSP00000397978:T589I;ENSP00000410280:T147I	ENSP00000211379:T553I	T	-	2	0	BAG6	31718862	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	2.556000	0.45862	2.600000	0.87896	0.650000	0.86243	ACC	.	.		0.602	BAG6-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_080703	
LFNG	3955	hgsc.bcm.edu	37	7	2566469	2566469	+	Splice_Site	SNP	G	G	T			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr7:2566469G>T	ENST00000222725.5	+	7	1007		c.e7-1		LFNG_ENST00000402506.1_Splice_Site|LFNG_ENST00000402045.1_Splice_Site|LFNG_ENST00000359574.3_Splice_Site|LFNG_ENST00000338732.3_Splice_Site|MIR4648_ENST00000580107.1_RNA	NM_001040167.1	NP_001035257.1	Q8NES3	LFNG_HUMAN	LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase						compartment pattern specification (GO:0007386)|female meiotic division (GO:0007143)|metabolic process (GO:0008152)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|ovarian follicle development (GO:0001541)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of protein binding (GO:0032092)|regulation of Notch signaling pathway (GO:0008593)|regulation of somitogenesis (GO:0014807)|somitogenesis (GO:0001756)	extracellular region (GO:0005576)|integral component of Golgi membrane (GO:0030173)|vesicle (GO:0031982)	metal ion binding (GO:0046872)|O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity (GO:0033829)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1)|urinary_tract(2)	6		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;2.54e-14)		GCTCCCCACAGGTGACGCTGA	0.677																																					.		Atlas-SNP	.											.	LFNG	57	.	0			c.775-1G>T						.						26.0	28.0	27.0					7																	2566469		2199	4298	6497	SO:0001630	splice_region_variant	3955	exon8			CCCACAGGTGACG	BC014851	CCDS34586.1, CCDS34587.1, CCDS55081.1, CCDS55082.1	7p22.3	2013-02-19	2006-11-13		ENSG00000106003	ENSG00000106003	2.4.1.222	"""Beta 3-glycosyltransferases"""	6560	protein-coding gene	gene with protein product		602576	"""lunatic fringe (Drosophila) homolog"", ""lunatic fringe homolog (Drosophila)"""			9878264, 9187150	Standard	NM_001166355		Approved	SCDO3	uc003smf.3	Q8NES3	OTTHUMG00000152043	ENST00000222725.5:c.988-1G>T	chr7.hg19:g.2566469G>T		86.0	0.0		65.0	4.0	NM_001166355	B3KTY6|B5MCR5|O00589|Q96C39|Q9UJW5	Splice_Site	SNP	ENST00000222725.5	hg19	CCDS34587.1	.	.	.	.	.	.	.	.	.	.	G	14.50	2.553078	0.45487	.	.	ENSG00000106003	ENST00000402506;ENST00000402045;ENST00000338732;ENST00000222725;ENST00000359574	.	.	.	4.46	4.46	0.54185	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.1069	0.86666	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	LFNG	2532995	1.000000	0.71417	0.984000	0.44739	0.700000	0.40528	9.205000	0.95048	2.007000	0.58848	0.561000	0.74099	.	.	.		0.677	LFNG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325021.1	NM_002304	Intron
FOCAD	54914	hgsc.bcm.edu	37	9	20740268	20740268	+	Silent	SNP	C	C	T			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr9:20740268C>T	ENST00000380249.1	+	7	685	c.321C>T	c.(319-321)caC>caT	p.H107H	FOCAD_ENST00000338382.6_Silent_p.H107H	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	107						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)											CCATTATGCACTTACTACAAA	0.303																																					p.H107H		Atlas-SNP	.											.	.	.	.	0			c.C321T						.						78.0	80.0	79.0					9																	20740268		2203	4297	6500	SO:0001819	synonymous_variant	54914	exon7			TATGCACTTACTA	AB058700	CCDS34993.1	9p21	2012-03-23	2012-03-23	2012-03-23	ENSG00000188352	ENSG00000188352			23377	protein-coding gene	gene with protein product		614606	"""KIAA1797"""	KIAA1797		22427331	Standard	XM_006716794		Approved	FLJ20375	uc003zog.1	Q5VW36	OTTHUMG00000066930	ENST00000380249.1:c.321C>T	chr9.hg19:g.20740268C>T		232.0	0.0		226.0	53.0	NM_017794	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Silent	SNP	ENST00000380249.1	hg19	CCDS34993.1																																																																																			.	.		0.303	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794	
PAX5	5079	hgsc.bcm.edu	37	9	37002701	37002701	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr9:37002701C>T	ENST00000358127.4	-	5	622	c.548G>A	c.(547-549)gGc>gAc	p.G183D	PAX5_ENST00000446742.1_Missense_Mutation_p.G117D|PAX5_ENST00000520154.1_Missense_Mutation_p.G183D|PAX5_ENST00000522003.1_Missense_Mutation_p.G75D|PAX5_ENST00000523145.1_Missense_Mutation_p.G75D|PAX5_ENST00000523241.1_Missense_Mutation_p.G183D|PAX5_ENST00000377852.2_Missense_Mutation_p.G183D|PAX5_ENST00000377847.2_Missense_Mutation_p.G183D|RP11-297B17.3_ENST00000509911.2_RNA|PAX5_ENST00000520281.1_Intron|PAX5_ENST00000414447.1_Intron|PAX5_ENST00000377853.2_Missense_Mutation_p.G183D	NM_001280554.1|NM_001280556.1|NM_016734.1	NP_001267483.1|NP_001267485.1|NP_057953.1	Q02548	PAX5_HUMAN	paired box 5	183			G -> S (in ALL3; confers susceptibility to ALL3; reduced transcription factor activity). {ECO:0000269|PubMed:24013638}.|G -> V. {ECO:0000269|PubMed:24013638}.		humoral immune response (GO:0006959)|multicellular organismal development (GO:0007275)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|skeletal muscle cell differentiation (GO:0035914)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.?(40)	PAX5/JAK2(18)	NS(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(151)|kidney(1)|lung(10)|prostate(1)|skin(1)	171		all_cancers(2;3.46e-10)|Acute lymphoblastic leukemia(2;7.09e-56)|all_hematologic(2;6.65e-44)		GBM - Glioblastoma multiforme(29;0.0108)		GCCCAGGATGCCGCTGATGGA	0.677			"""T, Mis, D, F, S"""	"""IGH@, ETV6, PML, FOXP1, ZNF521, ELN"""	"""NHL, ALL, B-ALL"""																																p.G183D		Atlas-SNP	.		Dom	yes		9	9p13	5079	paired box gene 5 (B-cell lineage specific activator protein)		L	.	PAX5	250	.	40	Unknown(40)	haematopoietic_and_lymphoid_tissue(40)	c.G548A						.						48.0	37.0	41.0					9																	37002701		2202	4296	6498	SO:0001583	missense	5079	exon5			AGGATGCCGCTGA		CCDS6607.1, CCDS65039.1, CCDS65040.1, CCDS65041.1, CCDS65042.1, CCDS65043.1, CCDS65044.1, CCDS65045.1, CCDS65046.1, CCDS65047.1, CCDS65048.1	9p13.2	2011-06-20	2007-07-12		ENSG00000196092	ENSG00000196092		"""Paired boxes"", ""Homeoboxes / PRD class"""	8619	protein-coding gene	gene with protein product	"""B-cell lineage specific activator"""	167414	"""paired box gene 5 (B-cell lineage specific activator protein)"", ""paired box gene 5 (B-cell lineage specific activator)"""			1516825, 8431641	Standard	NM_016734		Approved	BSAP	uc003zzo.1	Q02548	OTTHUMG00000019907	ENST00000358127.4:c.548G>A	chr9.hg19:g.37002701C>T	ENSP00000350844:p.Gly183Asp	182.0	0.0		132.0	6.0	NM_016734	A3QVP6|A3QVP7|A3QVP8|C0KTF6|C0KTF7|C0KTF8|C0KTF9|C0KTG0|O75933|Q5SFM2|Q6S728|Q6S729|Q6S730|Q6S731|Q6S732	Missense_Mutation	SNP	ENST00000358127.4	hg19	CCDS6607.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	31|31	5.097231|5.097231	0.94197|0.94197	.|.	.|.	ENSG00000196092|ENSG00000196092	ENST00000522932|ENST00000358127;ENST00000377849;ENST00000377853;ENST00000377852;ENST00000523241;ENST00000520154;ENST00000446742;ENST00000522003;ENST00000523145;ENST00000377847	.|D;D;D;D;D;D;D;D;D	.|0.98234	.|-4.29;-4.29;-4.31;-4.8;-4.79;-3.97;-2.13;-2.71;-4.81	5.15|5.15	5.15|5.15	0.70609|0.70609	.|.	.|0.316779	.|0.32258	.|N	.|0.006354	D|D	0.98896|0.98896	0.9626|0.9626	M|M	0.76938|0.76938	2.355|2.355	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D;D	.|0.89917	.|1.0;1.0;0.965;0.999;1.0;1.0;1.0	.|D;D;P;D;D;D;D	.|0.87578	.|0.998;0.992;0.806;0.98;0.998;0.992;0.992	D|D	0.99858|0.99858	1.1080|1.1080	5|10	.|0.72032	.|D	.|0.01	.|.	18.9629|18.9629	0.92684|0.92684	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|117;183;183;183;183;183;183	.|C0KTF9;C0KTF6;E7ERW5;E7EQT0;Q6S730;Q6S731;Q02548	.|.;.;.;.;.;.;PAX5_HUMAN	T|D	17|183;75;183;183;183;183;117;75;75;183	.|ENSP00000350844:G183D;ENSP00000367084:G183D;ENSP00000367083:G183D;ENSP00000429637:G183D;ENSP00000429291:G183D;ENSP00000404687:G117D;ENSP00000429359:G75D;ENSP00000429197:G75D;ENSP00000367078:G183D	.|ENSP00000350844:G183D	A|G	-|-	1|2	0|0	PAX5|PAX5	36992701|36992701	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.902000|0.902000	0.53008|0.53008	6.942000|6.942000	0.75928|0.75928	2.553000|2.553000	0.86117|0.86117	0.555000|0.555000	0.69702|0.69702	GCA|GGC	.	.		0.677	PAX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052433.1		
KRAS	3845	hgsc.bcm.edu	37	12	25380255	25380255	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr12:25380255C>A	ENST00000256078.4	-	3	266	c.203G>T	c.(202-204)aGg>aTg	p.R68M	AC087239.1_ENST00000594112.1_5'Flank|KRAS_ENST00000557334.1_Intron|KRAS_ENST00000311936.3_Missense_Mutation_p.R68M	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	68					actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)		UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			GTACTGGTCCCTCATTGCACT	0.408		119	Mis		"""pancreatic, colorectal, lung, thyroid, AML, others"""				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											p.R68M	Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	Atlas-SNP	.		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"""L, E, M, O"""	.	KRAS	30930	.	0			c.G203T						.						119.0	107.0	111.0					12																	25380255		2203	4300	6503	SO:0001583	missense	3845	exon3	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	TGGTCCCTCATTG	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"""v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog"", ""v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"""	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.203G>T	chr12.hg19:g.25380255C>A	ENSP00000256078:p.Arg68Met	144.0	0.0		151.0	34.0	NM_004985	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	hg19	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	31	5.062554	0.93898	.	.	ENSG00000133703	ENST00000311936;ENST00000256078	T;T	0.80909	-1.43;-0.63	5.77	5.77	0.91146	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.92014	0.7470	M	0.89785	3.06	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.92760	0.6223	10	0.87932	D	0	.	19.3504	0.94381	0.0:1.0:0.0:0.0	.	68;68	P01116-2;P01116	.;RASK_HUMAN	M	68	ENSP00000308495:R68M;ENSP00000256078:R68M	ENSP00000256078:R68M	R	-	2	0	KRAS	25271522	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.805000	0.86005	2.885000	0.99019	0.655000	0.94253	AGG	.	.		0.408	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360	
SYT16	83851	hgsc.bcm.edu	37	14	62547559	62547559	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr14:62547559A>G	ENST00000430451.2	+	4	1198	c.1001A>G	c.(1000-1002)gAc>gGc	p.D334G	RP11-355I22.5_ENST00000553990.1_lincRNA|SYT16_ENST00000446982.2_Missense_Mutation_p.T364A	NM_031914.2	NP_114120.2	Q17RD7	SYT16_HUMAN	synaptotagmin XVI	334					exocytosis (GO:0006887)					central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	35				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)		CAGGAACAGGACAGGACCAAT	0.488																																					p.D334G		Atlas-SNP	.											.	SYT16	144	.	0			c.A1001G						.						15.0	15.0	15.0					14																	62547559		1972	4155	6127	SO:0001583	missense	83851	exon4			AACAGGACAGGAC	BC040924	CCDS45121.1	14q23.2	2014-07-02	2005-07-15	2005-07-15	ENSG00000139973	ENSG00000139973		"""Synaptotagmins"""	23142	protein-coding gene	gene with protein product	"""synaptotagmin XIV-related"", "" chr14 synaptotagmin"""	610950	"""synaptotagmin XIV-like"""	SYT14L		11543631	Standard	NM_031914		Approved	yt14r, CHR14SYT, Strep14	uc001xfu.1	Q17RD7	OTTHUMG00000171106	ENST00000430451.2:c.1001A>G	chr14.hg19:g.62547559A>G	ENSP00000394700:p.Asp334Gly	214.0	0.0		159.0	39.0	NM_031914	B4DZH2|B7ZL60|C9J8I3|Q707N2|Q7Z441|Q8IUU0|Q9BQR8	Missense_Mutation	SNP	ENST00000430451.2	hg19	CCDS45121.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	8.226|8.226	0.803502|0.803502	0.16467|0.16467	.|.	.|.	ENSG00000139973|ENSG00000139973	ENST00000430451|ENST00000446982	T|T	0.04194|0.32272	3.68|1.46	5.27|5.27	2.92|2.92	0.33932|0.33932	.|.	0.721021|.	0.13603|.	N|.	0.375717|.	T|T	0.18841|0.18841	0.0452|0.0452	N|N	0.19112|0.19112	0.55|0.55	0.09310|0.09310	N|N	1|1	B|B	0.02656|0.13145	0.0|0.007	B|B	0.01281|0.09377	0.0|0.004	T|T	0.21075|0.21075	-1.0256|-1.0256	10|9	0.46703|0.72032	T|D	0.11|0.01	-26.0138|-26.0138	5.8678|5.8678	0.18786|0.18786	0.7175:0.1393:0.1432:0.0|0.7175:0.1393:0.1432:0.0	.|.	334|364	Q17RD7|B4DZH2	SYT16_HUMAN|.	G|A	334|364	ENSP00000394700:D334G|ENSP00000388023:T364A	ENSP00000394700:D334G|ENSP00000388023:T364A	D|T	+|+	2|1	0|0	SYT16|SYT16	61617312|61617312	0.082000|0.082000	0.21442|0.21442	0.559000|0.559000	0.28332|0.28332	0.277000|0.277000	0.26821|0.26821	1.197000|1.197000	0.32211|0.32211	0.453000|0.453000	0.26858|0.26858	0.533000|0.533000	0.62120|0.62120	GAC|ACA	.	.		0.488	SYT16-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000411700.1	NM_031914	
UNC79	57578	hgsc.bcm.edu	37	14	94038399	94038399	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr14:94038399A>T	ENST00000393151.2	+	15	1915	c.1915A>T	c.(1915-1917)Aat>Tat	p.N639Y	UNC79_ENST00000555664.1_Missense_Mutation_p.N639Y|UNC79_ENST00000256339.4_Missense_Mutation_p.N462Y|UNC79_ENST00000553484.1_Missense_Mutation_p.N639Y			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	639					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						AGTCCCAGATAATCAGTTAAA	0.398																																					p.N462Y		Atlas-SNP	.											.	UNC79	366	.	0			c.A1384T						.						55.0	57.0	56.0					14																	94038399		2203	4300	6503	SO:0001583	missense	57578	exon15			CCAGATAATCAGT	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"""KIAA1409"""	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.1915A>T	chr14.hg19:g.94038399A>T	ENSP00000376858:p.Asn639Tyr	62.0	0.0		42.0	15.0	NM_020818	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	hg19		.	.	.	.	.	.	.	.	.	.	A	13.02	2.112003	0.37242	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.18502	2.21;2.21;2.21;2.21	5.73	4.56	0.56223	.	0.346019	0.29178	N	0.012905	T	0.09992	0.0245	N	0.08118	0	0.25971	N	0.9825	B	0.28998	0.23	B	0.26864	0.074	T	0.17319	-1.0373	10	0.62326	D	0.03	-6.924	13.1509	0.59488	0.8569:0.1431:0.0:0.0	.	639	C9JQL1	.	Y	462;639;639;639;639	ENSP00000256339:N462Y;ENSP00000450868:N639Y;ENSP00000451360:N639Y;ENSP00000376858:N639Y	ENSP00000256339:N462Y	N	+	1	0	KIAA1409	93108152	1.000000	0.71417	0.273000	0.24645	0.899000	0.52679	3.159000	0.50731	0.956000	0.37904	0.528000	0.53228	AAT	.	.		0.398	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395	
SNAI3	333929	hgsc.bcm.edu	37	16	88747899	88747899	+	Silent	SNP	G	G	T	rs531621935	byFrequency	TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr16:88747899G>T	ENST00000332281.5	-	2	386	c.300C>A	c.(298-300)gcC>gcA	p.A100A	SNAI3-AS1_ENST00000563261.1_RNA	NM_178310.3	NP_840101.1	Q3KNW1	SNAI3_HUMAN	snail family zinc finger 3	100					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	copper ion binding (GO:0005507)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|central_nervous_system(1)|kidney(1)|lung(1)|ovary(1)|skin(1)	6				BRCA - Breast invasive adenocarcinoma(80;0.048)		GTACAATGGCGGCCCGGCTGG	0.687																																					p.A100A	Colon(27;366 710 19748 23199 27567)	Atlas-SNP	.											.	SNAI3	23	.	0			c.C300A						.						57.0	67.0	64.0					16																	88747899		2198	4299	6497	SO:0001819	synonymous_variant	333929	exon2			AATGGCGGCCCGG	BC041461	CCDS32505.1	16q24.3	2013-05-23	2013-05-23			ENSG00000185669		"""Snail homologs"", ""Zinc fingers, C2H2-type"""	18411	protein-coding gene	gene with protein product		612741	"""zinc finger protein 293"", ""snail homolog 3 (Drosophila)"""	ZNF293		12579345	Standard	NM_178310		Approved	SMUC, Zfp293	uc002flj.3	Q3KNW1		ENST00000332281.5:c.300C>A	chr16.hg19:g.88747899G>T		94.0	0.0		88.0	4.0	NM_178310	Q86SU5	Silent	SNP	ENST00000332281.5	hg19	CCDS32505.1																																																																																			.	.		0.687	SNAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422582.1		
PTPRM	5797	hgsc.bcm.edu	37	18	7888162	7888162	+	Silent	SNP	C	C	T			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr18:7888162C>T	ENST00000332175.8	+	3	1292	c.255C>T	c.(253-255)ctC>ctT	p.L85L	PTPRM_ENST00000400053.4_Silent_p.L23L|PTPRM_ENST00000580170.1_Silent_p.L85L|PTPRM_ENST00000400060.4_Silent_p.L85L	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	85	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				CCCACCTGCTCTTACCCCAAC	0.463																																					p.L85L		Atlas-SNP	.											.	PTPRM	185	.	0			c.C255T						.						157.0	162.0	161.0					18																	7888162		2203	4300	6503	SO:0001819	synonymous_variant	5797	exon3			CCTGCTCTTACCC	X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.255C>T	chr18.hg19:g.7888162C>T		186.0	0.0		147.0	37.0	NM_001105244	A7MBN1|D3DUH8|J3QL11	Silent	SNP	ENST00000332175.8	hg19	CCDS11840.1																																																																																			.	.		0.463	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1		
ZNF519	162655	hgsc.bcm.edu	37	18	14105585	14105585	+	Silent	SNP	C	C	T			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr18:14105585C>T	ENST00000590202.1	-	3	1106	c.954G>A	c.(952-954)aaG>aaA	p.K318K	ZNF519_ENST00000589498.1_Intron|RP11-411B10.3_ENST00000592926.1_RNA|ZNF519_ENST00000589203.1_Intron	NM_145287.3	NP_660330.2	Q8TB69	ZN519_HUMAN	zinc finger protein 519	318					negative regulation of transcription during meiosis (GO:0051038)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|urinary_tract(1)	18						ACTTGAAAGGCTTCTCTCCAG	0.393																																					p.K318K		Atlas-SNP	.											ZNF519,NS,carcinoma,0,1	ZNF519	53	.	0			c.G954A						.						82.0	84.0	83.0					18																	14105585		2203	4300	6503	SO:0001819	synonymous_variant	162655	exon3			GAAAGGCTTCTCT	BC024227	CCDS32797.1	18p11.21	2014-06-18			ENSG00000175322	ENSG00000175322		"""Zinc fingers, C2H2-type"", ""-"""	30574	protein-coding gene	gene with protein product	"""similar to Zinc finger protein 85 (Zinc finger protein HPF4) (HTF1)"""					12477932	Standard	NM_145287		Approved	HsT2362, FLJ36809	uc002kst.2	Q8TB69	OTTHUMG00000182055	ENST00000590202.1:c.954G>A	chr18.hg19:g.14105585C>T		64.0	0.0		78.0	4.0	NM_145287		Silent	SNP	ENST00000590202.1	hg19	CCDS32797.1																																																																																			.	.		0.393	ZNF519-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459037.1	NM_145287	
ZNF426	79088	hgsc.bcm.edu	37	19	9643591	9643591	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr19:9643591G>C	ENST00000535489.1	-	4	591	c.255C>G	c.(253-255)atC>atG	p.I85M	ZNF426_ENST00000593003.1_Missense_Mutation_p.I47M|ZNF426_ENST00000589289.1_Missense_Mutation_p.I85M|ZNF426_ENST00000253115.2_Missense_Mutation_p.I85M			Q9BUY5	ZN426_HUMAN	zinc finger protein 426	85	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(3)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	20						TGGGTTTGATGATCTGACCTC	0.408																																					p.I85M		Atlas-SNP	.											ZNF426,colon,carcinoma,0,1	ZNF426	56	.	0			c.C255G						.						130.0	113.0	119.0					19																	9643591		2203	4300	6503	SO:0001583	missense	79088	exon6			TTTGATGATCTGA	AK095759	CCDS12215.1, CCDS74279.1	19p13.2	2013-01-08				ENSG00000130818		"""Zinc fingers, C2H2-type"", ""-"""	20725	protein-coding gene	gene with protein product							Standard	NM_024106		Approved	MGC2663	uc002mlq.3	Q9BUY5		ENST00000535489.1:c.255C>G	chr19.hg19:g.9643591G>C	ENSP00000439017:p.Ile85Met	96.0	0.0		97.0	21.0	NM_024106	B3KTL2	Missense_Mutation	SNP	ENST00000535489.1	hg19	CCDS12215.1	.	.	.	.	.	.	.	.	.	.	G	8.902	0.956519	0.18507	.	.	ENSG00000130818	ENST00000545189;ENST00000253115;ENST00000535489	T;T	0.00864	5.6;5.6	1.9	-3.81	0.04294	Krueppel-associated box (3);	.	.	.	.	T	0.00695	0.0023	L	0.35487	1.065	0.09310	N	1	B;B	0.24186	0.099;0.099	B;B	0.12837	0.008;0.008	T	0.46707	-0.9172	9	0.36615	T	0.2	.	0.0214	0.00003	0.3038:0.2151:0.1805:0.3005	.	72;85	Q59EH4;Q9BUY5	.;ZN426_HUMAN	M	72;85;85	ENSP00000253115:I85M;ENSP00000439017:I85M	ENSP00000253115:I85M	I	-	3	3	ZNF426	9504591	0.000000	0.05858	0.000000	0.03702	0.917000	0.54804	-4.119000	0.00291	-1.544000	0.01721	0.313000	0.20887	ATC	.	.		0.408	ZNF426-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449905.1	NM_024106	
ZNF585A	199704	hgsc.bcm.edu	37	19	37643714	37643714	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr19:37643714A>C	ENST00000356958.4	-	5	1345	c.1087T>G	c.(1087-1089)Ttt>Gtt	p.F363V	ZNF585A_ENST00000392157.2_Missense_Mutation_p.F308V|ZNF585A_ENST00000292841.5_Missense_Mutation_p.F308V|ZNF585A_ENST00000588723.1_Intron|ZNF585A_ENST00000355533.2_Missense_Mutation_p.F308V			Q6P3V2	Z585A_HUMAN	zinc finger protein 585A	363					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(4)|central_nervous_system(1)|endometrium(2)|large_intestine(17)|lung(11)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CTGTAGGTAAAGGCCTTCCCA	0.418																																					p.F308V		Atlas-SNP	.											.	ZNF585A	117	.	0			c.T922G						.						91.0	90.0	90.0					19																	37643714		2203	4298	6501	SO:0001583	missense	199704	exon6			AGGTAAAGGCCTT	AK074345	CCDS12499.1, CCDS74353.1	19q13.13	2013-01-08				ENSG00000196967		"""Zinc fingers, C2H2-type"", ""-"""	26305	protein-coding gene	gene with protein product						12477932	Standard	NM_199126		Approved	FLJ23765	uc002ofn.1	Q6P3V2		ENST00000356958.4:c.1087T>G	chr19.hg19:g.37643714A>C	ENSP00000349440:p.Phe363Val	180.0	0.0		207.0	45.0	NM_199126	Q8TE95|Q96MV3	Missense_Mutation	SNP	ENST00000356958.4	hg19		.	.	.	.	.	.	.	.	.	.	A	13.85	2.358830	0.41801	.	.	ENSG00000196967	ENST00000356958;ENST00000292841;ENST00000392157;ENST00000355533	T;T;T;T	0.41758	0.99;0.99;0.99;0.99	2.83	2.83	0.33086	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.38326	N	0.001726	T	0.66177	0.2763	M	0.90309	3.105	0.40621	D	0.981766	D	0.71674	0.998	D	0.79784	0.993	T	0.71928	-0.4444	10	0.87932	D	0	.	9.0963	0.36640	1.0:0.0:0.0:0.0	.	363	Q6P3V2	Z585A_HUMAN	V	363;308;308;308	ENSP00000349440:F363V;ENSP00000292841:F308V;ENSP00000375998:F308V;ENSP00000347724:F308V	ENSP00000292841:F308V	F	-	1	0	ZNF585A	42335554	1.000000	0.71417	0.995000	0.50966	0.266000	0.26442	8.306000	0.89962	1.295000	0.44724	0.459000	0.35465	TTT	.	.		0.418	ZNF585A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000457980.2	NM_152655	
MAP3K10	4294	hgsc.bcm.edu	37	19	40698304	40698304	+	Silent	SNP	G	G	A			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr19:40698304G>A	ENST00000253055.3	+	1	654	c.366G>A	c.(364-366)gtG>gtA	p.V122V	MAP3K10_ENST00000593906.1_3'UTR	NM_002446.3	NP_002437.2	Q02779	M3K10_HUMAN	mitogen-activated protein kinase kinase kinase 10	122	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|JNK cascade (GO:0007254)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of apoptotic process (GO:0043065)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|protein autophosphorylation (GO:0046777)|signal transduction (GO:0007165)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|bHLH transcription factor binding (GO:0043425)|JUN kinase kinase kinase activity (GO:0004706)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription corepressor activity (GO:0003714)			NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	24						GCGAGGAGGTGGCAGTCAAGG	0.667																																					p.V122V		Atlas-SNP	.											.	MAP3K10	70	.	0			c.G366A						.						32.0	38.0	36.0					19																	40698304		2203	4299	6502	SO:0001819	synonymous_variant	4294	exon1			GGAGGTGGCAGTC	X90846	CCDS12549.1	19q13.2	2014-08-12			ENSG00000130758		2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6849	protein-coding gene	gene with protein product	"""MKN28 kinase"", ""mixed lineage kinase 2"", ""MKN28 derived nonreceptor_type serine/threonine kinase"""	600137		MLK2		8536694, 7731697	Standard	NM_002446		Approved	MST, MEKK10	uc002ona.3	Q02779	OTTHUMG00000182591	ENST00000253055.3:c.366G>A	chr19.hg19:g.40698304G>A		38.0	0.0		31.0	14.0	NM_002446	Q12761|Q14871	Silent	SNP	ENST00000253055.3	hg19	CCDS12549.1																																																																																			.	.		0.667	MAP3K10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462552.1	NM_002446	
HRC	3270	hgsc.bcm.edu	37	19	49657886	49657886	+	Silent	SNP	C	C	T			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr19:49657886C>T	ENST00000252825.4	-	1	795	c.609G>A	c.(607-609)gaG>gaA	p.E203E	HRC_ENST00000595625.1_Silent_p.E203E	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	203	4 X tandem repeats, acidic.|6 X approximate tandem repeats.|Glu-rich (acidic).				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		TGGAGGcctcctcttcctcct	0.572																																					p.E203E	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											.	HRC	85	.	0			c.G609A						.						123.0	91.0	102.0					19																	49657886		2203	4300	6503	SO:0001819	synonymous_variant	3270	exon1			GGCCTCCTCTTCC		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"""histidine-rich calcium-binding protein"""			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.609G>A	chr19.hg19:g.49657886C>T		294.0	0.0		353.0	19.0	NM_002152	Q504Y6	Silent	SNP	ENST00000252825.4	hg19	CCDS12759.1																																																																																			.	.		0.572	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152	
HRC	3270	hgsc.bcm.edu	37	19	49657916	49657916	+	Silent	SNP	T	T	C	rs7409255		TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr19:49657916T>C	ENST00000252825.4	-	1	765	c.579A>G	c.(577-579)gaA>gaG	p.E193E	HRC_ENST00000595625.1_Silent_p.E193E	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	193	4 X tandem repeats, acidic.|6 X approximate tandem repeats.|Glu-rich (acidic).				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		cctcctcctcttcTCCTTCAT	0.557																																					p.E193E	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											.	HRC	85	.	0			c.A579G						.						119.0	95.0	103.0					19																	49657916		2203	4300	6503	SO:0001819	synonymous_variant	3270	exon1			CTCCTCTTCTCCT		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"""histidine-rich calcium-binding protein"""			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.579A>G	chr19.hg19:g.49657916T>C		284.0	0.0		287.0	43.0	NM_002152	Q504Y6	Silent	SNP	ENST00000252825.4	hg19	CCDS12759.1																																																																																			.	.		0.557	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152	
HRC	3270	hgsc.bcm.edu	37	19	49657923	49657923	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr19:49657923T>C	ENST00000252825.4	-	1	758	c.572A>G	c.(571-573)gAa>gGa	p.E191G	HRC_ENST00000595625.1_Missense_Mutation_p.E191G	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	191	4 X tandem repeats, acidic.|6 X approximate tandem repeats.				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		ctcttcTCCTTCATCATCTTC	0.562																																					p.E191G	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											.	HRC	85	.	0			c.A572G						.						125.0	99.0	108.0					19																	49657923		2203	4300	6503	SO:0001583	missense	3270	exon1			TCTCCTTCATCAT		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"""histidine-rich calcium-binding protein"""			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.572A>G	chr19.hg19:g.49657923T>C	ENSP00000252825:p.Glu191Gly	289.0	0.0		273.0	17.0	NM_002152	Q504Y6	Missense_Mutation	SNP	ENST00000252825.4	hg19	CCDS12759.1	.	.	.	.	.	.	.	.	.	.	t	12.02	1.813186	0.32053	.	.	ENSG00000130528	ENST00000252825;ENST00000434964	T	0.07327	3.2	2.91	1.86	0.25419	.	.	.	.	.	T	0.07728	0.0194	L	0.58428	1.81	0.18873	N	0.999988	B	0.02656	0.0	B	0.04013	0.001	T	0.41770	-0.9490	9	0.22109	T	0.4	-0.1912	2.7058	0.05162	0.2254:0.1385:0.0:0.6361	.	191	P23327	SRCH_HUMAN	G	191;161	ENSP00000252825:E191G	ENSP00000252825:E191G	E	-	2	0	HRC	54349735	0.229000	0.23729	0.215000	0.23724	0.196000	0.23810	0.207000	0.17395	0.305000	0.22832	0.375000	0.23000	GAA	.	.		0.562	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152	
ZNF841	284371	hgsc.bcm.edu	37	19	52569235	52569235	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr19:52569235A>T	ENST00000426391.2	-	5	2103	c.1552T>A	c.(1552-1554)Ttc>Atc	p.F518I	ZNF841_ENST00000594295.1_Missense_Mutation_p.F634I|ZNF841_ENST00000359973.2_Intron|ZNF841_ENST00000389534.4_Missense_Mutation_p.F634I|CTC-471J1.2_ENST00000569091.1_RNA|ZNF432_ENST00000598446.1_Intron			Q6ZN19	ZN841_HUMAN	zinc finger protein 841	518					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|kidney(3)|lung(3)	11						TAGTAACTGAAGACCTTGCCG	0.438																																					p.F634I		Atlas-SNP	.											.	ZNF841	183	.	0			c.T1900A						.						121.0	104.0	109.0					19																	52569235		692	1591	2283	SO:0001583	missense	284371	exon7			AACTGAAGACCTT	AK131409	CCDS46161.1	19q13.41	2013-01-08			ENSG00000197608	ENSG00000197608		"""Zinc fingers, C2H2-type"", ""-"""	27611	protein-coding gene	gene with protein product							Standard	NM_001136499		Approved	LOC284371	uc010ydh.1	Q6ZN19		ENST00000426391.2:c.1552T>A	chr19.hg19:g.52569235A>T	ENSP00000415453:p.Phe518Ile	199.0	0.0		220.0	20.0	NM_001136499	B9EG58|Q6ZN82|Q6ZP71|Q8N9U7	Missense_Mutation	SNP	ENST00000426391.2	hg19		.	.	.	.	.	.	.	.	.	.	A	24.0	4.487668	0.84854	.	.	ENSG00000197608	ENST00000389534;ENST00000426391	T;T	0.47528	0.84;0.84	1.75	1.75	0.24633	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.71074	0.3297	M	0.93854	3.465	0.80722	D	1	D;D	0.71674	0.961;0.998	D;D	0.70935	0.958;0.971	T	0.74012	-0.3801	9	0.87932	D	0	.	8.2942	0.31976	1.0:0.0:0.0:0.0	.	634;518	Q6ZN19-3;Q6ZN19	.;ZN841_HUMAN	I	634;518	ENSP00000374185:F634I;ENSP00000415453:F518I	ENSP00000374185:F634I	F	-	1	0	ZNF841	57261047	0.350000	0.24878	0.001000	0.08648	0.819000	0.46315	4.733000	0.62036	0.795000	0.33922	0.260000	0.18958	TTC	.	.		0.438	ZNF841-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000462435.1	XM_209155	
ZNF83	55769	hgsc.bcm.edu	37	19	53117500	53117500	+	Silent	SNP	T	T	C			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr19:53117500T>C	ENST00000597597.1	-	2	2571	c.318A>G	c.(316-318)ttA>ttG	p.L106L	ZNF83_ENST00000601257.1_Intron|ZNF83_ENST00000600714.1_Intron|ZNF83_ENST00000541777.2_Silent_p.L106L|ZNF83_ENST00000544146.1_Silent_p.L106L|ZNF83_ENST00000391789.4_Silent_p.L106L|ZNF83_ENST00000594682.2_3'UTR|ZNF83_ENST00000536937.1_Silent_p.L106L|ZNF83_ENST00000545872.1_Silent_p.L106L|ZNF83_ENST00000301096.3_Silent_p.L106L			P51522	ZNF83_HUMAN	zinc finger protein 83	106					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	18				OV - Ovarian serous cystadenocarcinoma(262;0.00841)|GBM - Glioblastoma multiforme(134;0.0244)		TAGTAAAATGTAAGCCTTGAT	0.333																																					p.L106L		Atlas-SNP	.											.	ZNF83	73	.	0			c.A318G						.						70.0	70.0	70.0					19																	53117500		2203	4300	6503	SO:0001819	synonymous_variant	55769	exon3			AAAATGTAAGCCT	M27877	CCDS12854.1	19q13.3	2013-01-08	2006-05-12			ENSG00000167766		"""Zinc fingers, C2H2-type"""	13158	protein-coding gene	gene with protein product		194558	"""zinc finger protein 83 (HPF1)"", ""zinc finger protein 816B"""	ZNF816B		8088807	Standard	NM_018300		Approved	FLJ11015, HPF1	uc010epy.3	P51522		ENST00000597597.1:c.318A>G	chr19.hg19:g.53117500T>C		219.0	0.0		232.0	31.0	NM_018300	A8MT75|Q3ZCX0|Q6PI08	Silent	SNP	ENST00000597597.1	hg19	CCDS12854.1																																																																																			.	.		0.333	ZNF83-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463700.1	NM_018300	
SYNJ1	8867	hgsc.bcm.edu	37	21	34017978	34017978	+	Silent	SNP	T	T	C	rs368850131	byFrequency	TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr21:34017978T>C	ENST00000322229.7	-	24	3368	c.3369A>G	c.(3367-3369)ccA>ccG	p.P1123P	SYNJ1_ENST00000357345.3_Silent_p.P1123P|SYNJ1_ENST00000382491.3_Silent_p.P1118P|SYNJ1_ENST00000382499.2_Silent_p.P1162P|SYNJ1_ENST00000433931.2_Silent_p.P1162P			O43426	SYNJ1_HUMAN	synaptojanin 1	1123	Pro-rich.				cell death (GO:0008219)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of synaptic vesicle uncoating (GO:1903390)|regulation of synaptic vesicle membrane organization (GO:1901632)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)	cytosol (GO:0005829)	inositol-polyphosphate 5-phosphatase activity (GO:0004445)|nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|lung(11)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	57						GAGGTCTCTGTGGGGGAGCCG	0.577													T|||	6	0.00119808	0.0008	0.0014	5008	,	,		11289	0.0		0.004	False		,,,				2504	0.0				p.P1162P		Atlas-SNP	.											.	SYNJ1	253	.	0			c.A3486G						.	T	,,,	3,4355		0,3,2176	6.0	8.0	7.0		3369,3354,3486,3486	-2.6	1.0	21		7	22,8474		0,22,4226	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SYNJ1	NM_001160302.1,NM_001160306.1,NM_003895.3,NM_203446.2	,,,	0,25,6402	CC,CT,TT		0.2589,0.0688,0.1945	,,,	1123/1296,1118/1527,1162/1613,1162/1351	34017978	25,12829	2179	4248	6427	SO:0001819	synonymous_variant	8867	exon25			TCTCTGTGGGGGA	AF009040	CCDS33539.1, CCDS33540.1, CCDS33539.2, CCDS33540.2, CCDS54483.1	21q22.2	2008-06-23			ENSG00000159082	ENSG00000159082			11503	protein-coding gene	gene with protein product		604297				9428629, 10773674	Standard	NM_203446		Approved	INPP5G	uc002yqh.2	O43426	OTTHUMG00000064926	ENST00000322229.7:c.3369A>G	chr21.hg19:g.34017978T>C		4.0	0.0		10.0	7.0	NM_203446	O43425|O94984|Q4KMR1	Silent	SNP	ENST00000322229.7	hg19	CCDS54484.1	.	.	.	.	.	.	.	.	.	.	T	10.76	1.441088	0.25900	6.88E-4	0.002589	ENSG00000159082	ENST00000438952;ENST00000416083	.	.	.	5.55	-2.63	0.06133	.	.	.	.	.	T	0.49406	0.1555	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41928	-0.9481	4	.	.	.	.	5.8028	0.18424	0.0:0.2566:0.233:0.5104	.	.	.	.	A	15;18	.	.	T	-	1	0	SYNJ1	32939849	0.974000	0.33945	0.979000	0.43373	0.816000	0.46133	-0.063000	0.11655	-0.461000	0.06993	-0.441000	0.05720	ACA	.	.		0.577	SYNJ1-201	KNOWN	basic|CCDS	protein_coding	protein_coding			
TMPRSS2	7113	hgsc.bcm.edu	37	21	42851169	42851169	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr21:42851169C>T	ENST00000332149.5	-	7	747	c.613G>A	c.(613-615)Gga>Aga	p.G205R	TMPRSS2_ENST00000398585.3_Missense_Mutation_p.G242R|TMPRSS2_ENST00000458356.1_Missense_Mutation_p.G205R	NM_005656.3	NP_005647.3	O15393	TMPS2_HUMAN	transmembrane protease, serine 2	205	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				positive regulation of viral entry into host cell (GO:0046598)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)		TMPRSS2/ETV1(34)|TMPRSS2/ETV5_ENST00000306376(5)|TMPRSS2/ERG(3582)|TMPRSS2/ETV4(13)	central_nervous_system(1)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	4		Prostate(19;4.48e-07)|all_epithelial(19;0.031)				CTGGTGGATCCGCTGTCATCC	0.348			T	"""ERG, ETV1, ETV4, ETV5"""	prostate																																p.G242R		Atlas-SNP	.		Dom	yes		21	21q22.3	7113	"""transmembrane protease, serine 2"""		E	.	TMPRSS2	148	.	0			c.G724A						.						138.0	138.0	138.0					21																	42851169		2203	4300	6503	SO:0001583	missense	7113	exon7			TGGATCCGCTGTC	U75329	CCDS33564.1, CCDS54486.1	21q22.3	2010-04-13			ENSG00000184012	ENSG00000184012		"""Serine peptidases / Transmembrane"""	11876	protein-coding gene	gene with protein product		602060				9325052	Standard	NM_005656		Approved	PRSS10	uc010gor.3	O15393	OTTHUMG00000086762	ENST00000332149.5:c.613G>A	chr21.hg19:g.42851169C>T	ENSP00000330330:p.Gly205Arg	82.0	0.0		90.0	4.0	NM_001135099	A8K6Z8|B2R8E5|B7Z459|D3DSJ2|F8WES1|Q6GTK7|Q9BXX1	Missense_Mutation	SNP	ENST00000332149.5	hg19	CCDS33564.1	.	.	.	.	.	.	.	.	.	.	C	10.36	1.327559	0.24080	.	.	ENSG00000184012	ENST00000332149;ENST00000398585;ENST00000458356;ENST00000454499;ENST00000424093	T;T;T;T;T	0.63255	-0.03;-0.03;-0.03;-0.03;-0.03	5.43	5.43	0.79202	Speract/scavenger receptor (1);Speract/scavenger receptor-related (2);	0.264721	0.30979	N	0.008486	T	0.75280	0.3828	M	0.74881	2.28	0.09310	N	0.999998	D;D	0.76494	0.999;0.999	P;D	0.65010	0.906;0.931	T	0.67473	-0.5662	10	0.21540	T	0.41	.	14.7197	0.69297	0.0:1.0:0.0:0.0	.	242;205	F8WES1;O15393	.;TMPS2_HUMAN	R	205;242;205;205;165	ENSP00000330330:G205R;ENSP00000381588:G242R;ENSP00000391216:G205R;ENSP00000389006:G205R;ENSP00000397846:G165R	ENSP00000330330:G205R	G	-	1	0	TMPRSS2	41773039	0.000000	0.05858	0.214000	0.23707	0.001000	0.01503	0.744000	0.26245	2.553000	0.86117	0.549000	0.68633	GGA	.	.		0.348	TMPRSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195189.1		
MT-ATP6	4508	hgsc.bcm.edu	37	M	8533	8533	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chrM:8533G>A	ENST00000361899.2	+	1	7	c.7G>A	c.(7-9)Gaa>Aaa	p.E3K	MT-ND3_ENST00000361227.2_5'Flank|MT-TA_ENST00000387392.1_RNA|MT-TN_ENST00000387400.1_RNA|MT-CO3_ENST00000362079.2_5'Flank|MT-TR_ENST00000387439.1_RNA|MT-ATP8_ENST00000361851.1_Silent_p.T56T|MT-ND4_ENST00000361381.2_5'Flank|MT-TD_ENST00000387419.1_RNA|MT-TW_ENST00000387382.1_RNA|MT-TC_ENST00000387405.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-ND4L_ENST00000361335.1_5'Flank|MT-TS1_ENST00000387416.2_RNA|MT-TY_ENST00000387409.1_RNA			P00846	ATP6_HUMAN	mitochondrially encoded ATP synthase 6	3					ATP catabolic process (GO:0006200)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|proton-transporting ATP synthase complex, coupling factor F(o) (GO:0045263)	hydrogen ion transmembrane transporter activity (GO:0015078)|transmembrane transporter activity (GO:0022857)			breast(2)|endometrium(7)|kidney(8)|prostate(1)	18						CCAAAATGAACGAAAATCTGT	0.413																																					p.E3K		Atlas-SNP	.											.	.	.	.	0			c.G7A						.																																			SO:0001583	missense	0	exon1			ATGAACGAAAATC			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198899	ENSG00000198899		"""Mitochondrial respiratory chain complex / Complex V"", ""ATPases / F-type"""	7414	protein-coding gene	gene with protein product		516060	"""ATP synthase 6"", ""spicular retinitis pigmentosa with dementia, seizures, ataxia, proximal muscle weakness and sensory deficit"""	MTATP6, RP		7219534	Standard			Approved	ATP6, ATPase-6, Su6m		P00846		ENST00000361899.2:c.7G>A	chrM.hg19:g.8533G>A	ENSP00000354632:p.Glu3Lys	23.0	0.0		58.0	4.0	ENST00000361899	Q34772|Q5S8W5|Q5S9E7|Q5S9I6|Q5SA31|Q6RPB7|Q6VHC0|Q6VHE0|Q6WQF4|Q7YCC1|Q7YCF8|Q7YCG1|Q85KU8|Q85KX1|Q85L05|Q8HNQ4|Q8HNQ8|Q8WCX6|Q9B2U5|Q9B2Z2	Missense_Mutation	SNP	ENST00000361899.2	hg19																																																																																				.	.		0.413	MT-ATP6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024031	
MT-ND5	4540	hgsc.bcm.edu	37	M	13577	13577	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chrM:13577T>C	ENST00000361567.2	+	1	1241	c.1241T>C	c.(1240-1242)aTc>aCc	p.I414T	MT-CYB_ENST00000361789.2_5'Flank|MT-TH_ENST00000387441.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-TP_ENST00000387461.2_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	414					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						TATTACTCTCATCGCTACCTC	0.448																																					p.I414T		Atlas-SNP	.											.	.	.	.	0			c.T1241C						.																																			SO:0001583	missense	0	exon1			CTCTCATCGCTAC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.1241T>C	chrM.hg19:g.13577T>C	ENSP00000354813:p.Ile414Thr	58.0	0.0		84.0	6.0	ENST00000361567	Q34773|Q8WCY3	Missense_Mutation	SNP	ENST00000361567.2	hg19																																																																																				.	.		0.448	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
MT-ND6	4541	hgsc.bcm.edu	37	M	14226	14226	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chrM:14226G>A	ENST00000361681.2	-	1	447	c.448C>T	c.(448-450)Cgt>Tgt	p.R150C	MT-CYB_ENST00000361789.2_5'Flank|MT-TH_ENST00000387441.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-TP_ENST00000387461.2_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA			P03923	NU6M_HUMAN	mitochondrially encoded NADH dehydrogenase 6	150					cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|respiratory chain (GO:0070469)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(10)|kidney(17)|urinary_tract(1)	29						TACTAATCAACGCCCATAATC	0.413																																					p.R150C		Atlas-SNP	.											.	.	.	.	0			c.C448T						.																																			SO:0001583	missense	0	exon1			ATCAACGCCCATA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198695	ENSG00000198695	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7462	protein-coding gene	gene with protein product	"""complex I ND6 subunit"", ""NADH-ubiquinone oxidoreductase chain 6"""	516006	"""NADH dehydrogenase 6"""	MTND6			Standard			Approved	NAD6, ND6		P03923		ENST00000361681.2:c.448C>T	chrM.hg19:g.14226G>A	ENSP00000354665:p.Arg150Cys	34.0	0.0		67.0	9.0	ENST00000361681	Q34774|Q8HG30	Missense_Mutation	SNP	ENST00000361681.2	hg19																																																																																				.	.		0.413	MT-ND6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024037	
MT-CYB	4519	hgsc.bcm.edu	37	M	15297	15297	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chrM:15297T>C	ENST00000361789.2	+	1	551	c.551T>C	c.(550-552)aTc>aCc	p.I184T	MT-ND6_ENST00000361681.2_5'Flank|MT-TE_ENST00000387459.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-TP_ENST00000387461.2_RNA|MT-TL2_ENST00000387456.1_RNA			P00156	CYB_HUMAN	mitochondrially encoded cytochrome b	184					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(6)|endometrium(25)|kidney(33)|prostate(1)	65						CTTTCACTTCATCTTACCCTT	0.483											OREG0007583	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.I184T		Atlas-SNP	.											.	.	.	.	0			c.T551C						.																																			SO:0001583	missense	0	exon1			ACTTCATCTTGCC			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198727	ENSG00000198727		"""Cytochrome b genes"", ""Mitochondrial respiratory chain complex / Complex III"""	7427	protein-coding gene	gene with protein product		516020	"""cytochrome b"""	MTCYB			Standard			Approved	COB, CYTB, UQCR3		P00156		ENST00000361789.2:c.551T>C	chrM.hg19:g.15297T>C	ENSP00000354554:p.Ile184Thr	49.0	0.0	585	102.0	11.0	ENST00000361789	Q34786|Q8HBR6|Q8HNQ0|Q8HNQ1|Q8HNQ9|Q8HNR4|Q8HNR7|Q8W7V8|Q8WCV9|Q8WCY2|Q8WCY7|Q8WCY8|Q9B1A6|Q9B1B6|Q9B1B8|Q9B1D4|Q9B1X6|Q9B2V0|Q9B2V8|Q9B2W0|Q9B2W3|Q9B2W8|Q9B2X1|Q9B2X7|Q9B2X9|Q9B2Y3|Q9B2Z0|Q9B2Z4|Q9T6H6|Q9T9Y0|Q9TEH4	Missense_Mutation	SNP	ENST00000361789.2	hg19																																																																																				.	.		0.483	MT-CYB-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024038	
PIGQ	9091	hgsc.bcm.edu	37	16	633549	633549	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr16:633549delC	ENST00000026218.5	+	10	2286	c.2198delC	c.(2197-2199)accfs	p.T733fs	PIGQ_ENST00000321878.5_3'UTR	NM_148920.2	NP_683721.1	Q9BRB3	PIGQ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Q	733					C-terminal protein lipidation (GO:0006501)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of membrane (GO:0016021)	phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13		Hepatocellular(780;0.00335)				CAGTCGCTGACCCCCGTCCCC	0.627																																					p.T733fs		Atlas-Indel,Pindel	.											.	PIGQ	43	.	0			c.2197delA						.						38.0	39.0	39.0					16																	633549		2200	4300	6500	SO:0001589	frameshift_variant	9091	exon10			.	AB003723	CCDS10411.1, CCDS10412.1	16p13.3	2013-03-28	2006-06-28		ENSG00000007541	ENSG00000007541		"""Phosphatidylinositol glycan anchor biosynthesis"""	14135	protein-coding gene	gene with protein product		605754	"""phosphatidylinositol glycan, class Q"""			9463366, 9729469	Standard	NM_004204		Approved	hGPI1, GPI1	uc002cho.3	Q9BRB3	OTTHUMG00000168047	ENST00000026218.5:c.2198delC	chr16.hg19:g.633549delC	ENSP00000026218:p.Thr733fs	93.0	0.0		112.0	19.0	NM_148920	A2IDE1|D3DU52|O14927|Q96G00|Q96S22|Q9UJH4	Frame_Shift_Del	DEL	ENST00000026218.5	hg19	CCDS10411.1																																																																																			.	.		0.627	PIGQ-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000239270.2	NM_004204	
MUC5B	727897	hgsc.bcm.edu	37	11	1263483	1263484	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr11:1263483_1263484delAG	ENST00000529681.1	+	31	5431_5432	c.5373_5374delAG	c.(5371-5376)acagagfs	p.E1792fs	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Frame_Shift_Del_p.E1795fs	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1792	7 X Cys-rich subdomain repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		GTGAGTGGACAGAGTGGTTTGA	0.594																																					p.1791_1791del		Atlas-Indel,Pindel	.											.	MUC5B	473	.	0			c.5372_5373del						.																																			SO:0001589	frameshift_variant	727897	exon31			.	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.5373_5374delAG	chr11.hg19:g.1263485_1263486delAG	ENSP00000436812:p.Glu1792fs	290.0	0.0		234.0	42.0	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Frame_Shift_Del	DEL	ENST00000529681.1	hg19	CCDS44515.2																																																																																			.	.		0.594	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
CPS1	1373	hgsc.bcm.edu	37	2	211507320	211507322	+	In_Frame_Del	DEL	TGA	TGA	-			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	TGA	TGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr2:211507320_211507322delTGA	ENST00000233072.5	+	25	3268_3270	c.3072_3074delTGA	c.(3070-3075)tttgat>ttt	p.D1025del	CPS1_ENST00000430249.2_In_Frame_Del_p.D1031del|CPS1_ENST00000451903.2_In_Frame_Del_p.D574del|CPS1_ENST00000497121.1_3'UTR	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	1025					anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	GCACAGACTTTGATGAGTGTGAC	0.414																																					p.1030_1031del		Atlas-Indel,Pindel	.											.	CPS1	485	.	0			c.3089_3091del						.																																			SO:0001651	inframe_deletion	1373	exon26			.	AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"""carbamoyl-phosphate synthetase 1, mitochondrial"""				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.3072_3074delTGA	chr2.hg19:g.211507323_211507325delTGA	ENSP00000233072:p.Asp1025del	383.0	0.0		299.0	24.0	NM_001122633	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	In_Frame_Del	DEL	ENST00000233072.5	hg19	CCDS2393.1																																																																																			.	.		0.414	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5		
CASP8	841	hgsc.bcm.edu	37	2	202131436	202131437	+	Frame_Shift_Ins	INS	-	-	AG			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr2:202131436_202131437insAG	ENST00000432109.2	+	3	416_417	c.227_228insAG	c.(226-231)attaccfs	p.T77fs	CASP8_ENST00000323492.7_Frame_Shift_Ins_p.T77fs|CASP8_ENST00000358485.4_Frame_Shift_Ins_p.T136fs|CASP8_ENST00000392258.3_Frame_Shift_Ins_p.T77fs|CASP8_ENST00000264275.5_Frame_Shift_Ins_p.T77fs|CASP8_ENST00000264274.9_Frame_Shift_Ins_p.T77fs|CASP8_ENST00000392259.2_Frame_Shift_Ins_p.T77fs|CASP8_ENST00000392266.3_Frame_Shift_Ins_p.T77fs	NM_033355.3	NP_203519.1	Q14790	CASP8_HUMAN	caspase 8, apoptosis-related cysteine peptidase	77	DED 1. {ECO:0000255|PROSITE- ProRule:PRU00065}.				activation of cysteine-type endopeptidase activity (GO:0097202)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|B cell activation (GO:0042113)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic cyclic compound (GO:0071407)|execution phase of apoptosis (GO:0097194)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|heart development (GO:0007507)|hepatocyte apoptotic process (GO:0097284)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|macrophage differentiation (GO:0030225)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|natural killer cell activation (GO:0030101)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of necroptotic process (GO:0060546)|neural tube formation (GO:0001841)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of proteolysis (GO:0045862)|protein heterooligomerization (GO:0051291)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of thymocyte apoptotic process (GO:0070243)|response to antibiotic (GO:0046677)|response to cobalt ion (GO:0032025)|response to cold (GO:0009409)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|syncytiotrophoblast cell differentiation involved in labyrinthine layer development (GO:0060715)|T cell activation (GO:0042110)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRAIL-activated apoptotic signaling pathway (GO:0036462)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	CD95 death-inducing signaling complex (GO:0031265)|cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|membrane raft (GO:0045121)|microtubule organizing center (GO:0005815)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|Noc1p-Noc2p complex (GO:0030690)|nucleus (GO:0005634)|ripoptosome (GO:0097342)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type endopeptidase activity involved in apoptotic process (GO:0097153)|cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097199)|cysteine-type peptidase activity (GO:0008234)|death effector domain binding (GO:0035877)|peptidase activity (GO:0008233)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)			breast(5)|cervix(2)|endometrium(6)|large_intestine(11)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(9)|urinary_tract(3)	52						GATTTGCTGATTACCTACCTAA	0.46										HNSCC(4;0.00038)																											p.I135fs	Melanoma(82;831 1348 20716 36952 40159)	Atlas-INDEL	.											.	CASP8	272	.	0			c.404_405insAG						.																																			SO:0001589	frameshift_variant	841	exon2			.	U60520	CCDS2342.1, CCDS2343.1, CCDS2345.1, CCDS42798.1, CCDS42799.1	2q33-q34	2014-09-17	2005-08-17		ENSG00000064012	ENSG00000064012		"""Caspases"""	1509	protein-coding gene	gene with protein product		601763	"""caspase 8, apoptosis-related cysteine protease"""			8681376, 8681377	Standard	NM_033355		Approved	MCH5, MACH, FLICE, Casp-8	uc002uxt.1	Q14790	OTTHUMG00000132821	Exception_encountered	chr2.hg19:g.202131436_202131437insAG	ENSP00000412523:p.Thr77fs	150.0	0.0		154.0	31.0	NM_001080125	O14676|Q14791|Q14792|Q14793|Q14794|Q14795|Q14796|Q15780|Q15806|Q53TT5|Q8TDI1|Q8TDI2|Q8TDI3|Q8TDI4|Q8TDI5|Q96T22|Q9C0K4|Q9UQ81	Frame_Shift_Ins	INS	ENST00000432109.2	hg19	CCDS2342.1																																																																																			.	.		0.460	CASP8-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000336853.2	NM_001228	
NEUROD1	4760	hgsc.bcm.edu	37	2	182542873	182542885	+	Frame_Shift_Del	DEL	CATGGGAGCTGTC	CATGGGAGCTGTC	-	rs145050582		TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	CATGGGAGCTGTC	CATGGGAGCTGTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr2:182542873_182542885delCATGGGAGCTGTC	ENST00000295108.3	-	2	1160_1172	c.703_715delGACAGCTCCCATG	c.(703-717)gacagctcccatgtcfs	p.DSSHV235fs	NEUROD1_ENST00000496876.1_Intron|CERKL_ENST00000479558.1_Intron	NM_002500.4	NP_002491.2	Q13562	NDF1_HUMAN	neuronal differentiation 1	235					amacrine cell differentiation (GO:0035881)|anterior/posterior pattern specification (GO:0009952)|cellular response to glucose stimulus (GO:0071333)|cerebellum development (GO:0021549)|dentate gyrus development (GO:0021542)|embryonic organ morphogenesis (GO:0048562)|endocrine pancreas development (GO:0031018)|enteroendocrine cell differentiation (GO:0035883)|glucose homeostasis (GO:0042593)|inner ear development (GO:0048839)|insulin secretion (GO:0030073)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neurogenesis (GO:0022008)|nitric oxide mediated signal transduction (GO:0007263)|nucleocytoplasmic transport (GO:0006913)|pancreatic A cell fate commitment (GO:0003326)|pancreatic PP cell fate commitment (GO:0003329)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell differentiation (GO:0045597)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle arrest (GO:0071156)|regulation of insulin secretion (GO:0050796)|regulation of intestinal epithelial structure maintenance (GO:0060730)|response to drug (GO:0042493)|response to glucose (GO:0009749)|signal transduction involved in regulation of gene expression (GO:0023019)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|protein heterodimerization activity (GO:0046982)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.H238H(1)		endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25			OV - Ovarian serous cystadenocarcinoma(117;0.088)			ACGTGGAAGACATGGGAGCTGTCCATGGTACCG	0.629											OREG0005604	type=TRANSCRIPTION FACTOR BINDING SITE|Gene=NEUROD1|TFbs=REST|Dataset=NRSF/REST ChIPSeq sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.235_239del		Atlas-INDEL	.											.	NEUROD1	67	.	1	Substitution - coding silent(1)	lung(1)	c.704_716del						.																																			SO:0001589	frameshift_variant	4760	exon2			.	U50823	CCDS2283.1	2q32	2013-05-21	2012-02-22		ENSG00000162992	ENSG00000162992		"""Basic helix-loop-helix proteins"""	7762	protein-coding gene	gene with protein product	"""beta-cell E-box transactivator 2"", ""neurogenic helix-loop-helix protein NEUROD"""	601724	"""neurogenic differentiation 1"""	NEUROD		7754368, 8786144	Standard	NM_002500		Approved	BETA2, BHF-1, NeuroD, bHLHa3, MODY6	uc002uof.4	Q13562	OTTHUMG00000132583	ENST00000295108.3:c.703_715delGACAGCTCCCATG	chr2.hg19:g.182542873_182542885delCATGGGAGCTGTC	ENSP00000295108:p.Asp235fs	142.0	0.0	1977	99.0	10.0	NM_002500	B2R9I8|F1T0E1|O00343|Q13340|Q5U095|Q96TH0|Q99455|Q9UEC8	Frame_Shift_Del	DEL	ENST00000295108.3	hg19	CCDS2283.1																																																																																			.	.		0.629	NEUROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255792.2	NM_002500	
AFF1	4299	hgsc.bcm.edu	37	4	88012960	88012963	+	Frame_Shift_Del	DEL	AGTT	AGTT	-			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	AGTT	AGTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr4:88012960_88012963delAGTT	ENST00000307808.6	+	6	1606_1609	c.1186_1189delAGTT	c.(1186-1191)agttctfs	p.SS396fs	AFF1_ENST00000544085.1_Frame_Shift_Del_p.SS34fs|AFF1_ENST00000395146.4_Frame_Shift_Del_p.SS403fs	NM_005935.2	NP_005926.1	P51825	AFF1_HUMAN	AF4/FMR2 family, member 1	396					positive regulation of transcription, DNA-templated (GO:0045893)	transcription elongation factor complex (GO:0008023)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|large_intestine(2)	3		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)		TCAGCATGTCAGTTCTGTAACCCA	0.275																																					p.402_403del		Atlas-Indel,Pindel	.											.	AFF1	102	.	0			c.1206_1209del						.																																			SO:0001589	frameshift_variant	4299	exon7			.	L22179	CCDS3616.1, CCDS54775.1	4q21.3	2009-08-04	2005-06-27	2005-06-27	ENSG00000172493	ENSG00000172493			7135	protein-coding gene	gene with protein product		159557	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 2"", ""pre-B-cell monocytic leukemia partner 1"""	PBM1, MLLT2		7689231, 1423625, 8353274	Standard	NM_005935		Approved	AF-4, AF4	uc011ccz.2	P51825	OTTHUMG00000130603	ENST00000307808.6:c.1186_1189delAGTT	chr4.hg19:g.88012960_88012963delAGTT	ENSP00000305689:p.Ser396fs	124.0	0.0		114.0	18.0	NM_001166693	B4DTU1|E9PBM3	Frame_Shift_Del	DEL	ENST00000307808.6	hg19	CCDS3616.1																																																																																			.	.		0.275	AFF1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253053.3	NM_005935	
ECE2	9718	hgsc.bcm.edu	37	3	184002776	184002810	+	Frame_Shift_Del	DEL	TTGAGTTCCTGTCTTTCTTGCTGTCACCATTGGAG	TTGAGTTCCTGTCTTTCTTGCTGTCACCATTGGAG	-			TCGA-DD-A4NB-01A-12D-A25V-10	TCGA-DD-A4NB-11A-11D-A25V-10	TTGAGTTCCTGTCTTTCTTGCTGTCACCATTGGAG	TTGAGTTCCTGTCTTTCTTGCTGTCACCATTGGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	5d58b984-e0b8-4237-a576-0e9d4079599e	861ea9b6-f62f-4d03-9672-dc9f8ce2695b	g.chr3:184002776_184002810delTTGAGTTCCTGTCTTTCTTGCTGTCACCATTGGAG	ENST00000402825.3	+	9	1385_1419	c.1385_1419delTTGAGTTCCTGTCTTTCTTGCTGTCACCATTGGAG	c.(1384-1419)cttgagttcctgtctttcttgctgtcaccattggagfs	p.LEFLSFLLSPLE462fs	EIF2B5_ENST00000444495.1_Intron|ECE2_ENST00000359140.4_Frame_Shift_Del_p.LEFLSFLLSPLE315fs|ECE2_ENST00000357474.5_Frame_Shift_Del_p.LEFLSFLLSPLE390fs|ECE2_ENST00000404464.3_Frame_Shift_Del_p.LEFLSFLLSPLE344fs	NM_014693.3	NP_055508.3	O60344	ECE2_HUMAN	endothelin converting enzyme 2	462	Endothelin-converting enzyme 2 region.				brain development (GO:0007420)|cardioblast differentiation (GO:0010002)|cell-cell signaling (GO:0007267)|heart development (GO:0007507)|peptide hormone processing (GO:0016486)	cytoplasmic vesicle membrane (GO:0030659)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|methyltransferase activity (GO:0008168)	p.S319F(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(13)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(4)	49	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			ATGGACTGGCTTGAGTTCCTGTCTTTCTTGCTGTCACCATTGGAGTTGAGTGACT	0.553											OREG0015945	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.462_473del		Pindel	.											.	ECE2	303	.	1	Substitution - Missense(1)	large_intestine(1)	c.1384_1418del						.																																			SO:0001589	frameshift_variant	9718	exon9			.	AF428263	CCDS3255.1, CCDS33899.1, CCDS3256.2, CCDS43179.1, CCDS46969.1	3q27.1	2007-07-26			ENSG00000145194	ENSG00000145194			13275	protein-coding gene	gene with protein product		610145				11718899	Standard	NM_032331		Approved	KIAA0604, MGC2408	uc003fni.4	O60344	OTTHUMG00000150551	ENST00000402825.3:c.1385_1419delTTGAGTTCCTGTCTTTCTTGCTGTCACCATTGGAG	chr3.hg19:g.184002776_184002810delTTGAGTTCCTGTCTTTCTTGCTGTCACCATTGGAG	ENSP00000384223:p.Leu462fs	475.0	0.0	1988	326.0	22.0	NM_014693	A5PLK8|Q6NTG7|Q6UW36|Q8NFD7|Q96NX3|Q96NX4|Q9BRZ8	Frame_Shift_Del	DEL	ENST00000402825.3	hg19	CCDS3256.2																																																																																			.	.		0.553	ECE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318874.3	NM_014693	
