#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
AGTRAP	57085	hgsc.bcm.edu	37	1	11808647	11808647	+	Missense_Mutation	SNP	G	G	T	rs141868096		TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr1:11808647G>T	ENST00000314340.5	+	4	398	c.344G>T	c.(343-345)gGt>gTt	p.G115V	AGTRAP_ENST00000491346.1_Splice_Site|AGTRAP_ENST00000510878.1_Missense_Mutation_p.V80L|AGTRAP_ENST00000400895.2_Silent_p.G147G|AGTRAP_ENST00000376627.2_Silent_p.G159G|AGTRAP_ENST00000376629.4_Splice_Site|AGTRAP_ENST00000452018.2_Splice_Site|AGTRAP_ENST00000376637.3_Splice_Site	NM_020350.4	NP_065083.3	Q6RW13	ATRAP_HUMAN	angiotensin II receptor-associated protein	115	Interaction with AGTR1.				regulation of blood pressure (GO:0008217)|response to hypoxia (GO:0001666)	cell cortex (GO:0005938)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	angiotensin type II receptor activity (GO:0004945)		AGTRAP/BRAF(2)	endometrium(1)|lung(3)|prostate(1)	5	Ovarian(185;0.249)	Lung NSC(185;4.15e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.46e-06)|COAD - Colon adenocarcinoma(227;0.000256)|BRCA - Breast invasive adenocarcinoma(304;0.0003)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0649)		GAGCGCGGGGGTGAGCTCCTG	0.662																																					p.G115V		Atlas-SNP	.											.	AGTRAP	9	.	0			c.G344T						.						57.0	48.0	51.0					1																	11808647		2203	4300	6503	SO:0001583	missense	57085	exon4			GCGGGGGTGAGCT	AF165187	CCDS136.1, CCDS30585.1, CCDS30586.1, CCDS41248.1, CCDS44056.1	1p36.22	2008-02-05			ENSG00000177674	ENSG00000177674			13539	protein-coding gene	gene with protein product		608729				11733189	Standard	NM_001040194		Approved	ATRAP	uc001asv.3	Q6RW13	OTTHUMG00000002230	ENST00000314340.5:c.344G>T	chr1.hg19:g.11808647G>T	ENSP00000319713:p.Gly115Val	31.0	0.0		26.0	11.0	NM_020350	A8MVQ5|Q5SNV4|Q5SNV5|Q96AC0|Q96PL4|Q9NRW9	Missense_Mutation	SNP	ENST00000314340.5	hg19	CCDS136.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	18.33|18.33|18.33	3.601366|3.601366|3.601366	0.66445|0.66445|0.66445	.|.|.	.|.|.	ENSG00000177674|ENSG00000177674|ENSG00000177674	ENST00000376637;ENST00000376629;ENST00000452018|ENST00000314340|ENST00000510878	.|T|.	.|0.69685|.	.|-0.42|.	3.93|3.93|3.93	3.93|3.93|3.93	0.45458|0.45458|0.45458	.|.|.	.|0.000000|.	.|0.64402|.	.|U|.	.|0.000001|.	.|T|T	.|0.48554|0.48554	.|0.1506|0.1506	.|.|.	.|.|.	.|.|.	0.28240|0.28240|0.28240	N|N|N	0.925738|0.925738|0.925738	.|D|.	.|0.89917|.	.|1.0|.	.|D|.	.|0.97110|.	.|1.0|.	.|T|T	.|0.41324|0.41324	.|-0.9515|-0.9515	.|8|4	.|.|.	.|.|.	.|.|.	.|-2.2315|-2.2315	13.8422|13.8422|13.8422	0.63446|0.63446|0.63446	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.|.	.|115|.	.|Q6RW13|.	.|ATRAP_HUMAN|.	.|V|L	-1|115|80	.|ENSP00000319713:G115V|.	.|.|.	.|G|V	+|+|+	.|2|1	.|0|0	AGTRAP|AGTRAP|AGTRAP	11731234|11731234|11731234	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.898000|0.898000|0.898000	0.35279|0.35279|0.35279	0.891000|0.891000|0.891000	0.51852|0.51852|0.51852	8.330000|8.330000|8.330000	0.90019|0.90019|0.90019	2.208000|2.208000|2.208000	0.71279|0.71279|0.71279	0.462000|0.462000|0.462000	0.41574|0.41574|0.41574	.|GGT|GTG	.	G|1.000;A|0.000		0.662	AGTRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006335.1	NM_020350	
TMEM39B	55116	hgsc.bcm.edu	37	1	32566142	32566142	+	Silent	SNP	C	C	T	rs373923538		TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr1:32566142C>T	ENST00000336294.5	+	8	1361	c.1215C>T	c.(1213-1215)gaC>gaT	p.D405D	TMEM39B_ENST00000487305.1_3'UTR|TMEM39B_ENST00000427288.1_Silent_p.D290D|TMEM39B_ENST00000456834.2_3'UTR|TMEM39B_ENST00000373634.4_Silent_p.D206D	NM_018056.2	NP_060526.2	Q9GZU3	TM39B_HUMAN	transmembrane protein 39B	405						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|lung(5)|ovary(1)|prostate(2)	11		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				TCCCCTCTGACGTCTCCCACT	0.592																																					p.D405D		Atlas-SNP	.											.	TMEM39B	66	.	0			c.C1215T						.	C		0,4406		0,0,2203	80.0	69.0	72.0		1215	-10.0	0.0	1		72	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	TMEM39B	NM_018056.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		405/493	32566142	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	55116	exon8			CTCTGACGTCTCC	AL136695	CCDS351.2	1p35.1	2008-02-05			ENSG00000121775	ENSG00000121775			25510	protein-coding gene	gene with protein product						12477932	Standard	NM_018056		Approved	FLJ10315	uc010ogv.2	Q9GZU3	OTTHUMG00000004020	ENST00000336294.5:c.1215C>T	chr1.hg19:g.32566142C>T		113.0	0.0		88.0	9.0	NM_018056	B4DKN8|B4DQE6|B4DTN8|D3DPP4|Q6IA44	Silent	SNP	ENST00000336294.5	hg19	CCDS351.2																																																																																			.	.		0.592	TMEM39B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011489.2	NM_018056	
INADL	10207	hgsc.bcm.edu	37	1	62299331	62299331	+	Silent	SNP	C	C	T			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr1:62299331C>T	ENST00000371158.2	+	17	2100	c.1986C>T	c.(1984-1986)gaC>gaT	p.D662D	INADL_ENST00000316485.6_Silent_p.D662D	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	662					cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						TTCAGGTTGACCACAATATGG	0.363																																					p.D662D		Atlas-SNP	.											.	INADL	179	.	0			c.C1986T						.						110.0	104.0	106.0					1																	62299331		2203	4300	6503	SO:0001819	synonymous_variant	10207	exon17			GGTTGACCACAAT	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.1986C>T	chr1.hg19:g.62299331C>T		164.0	0.0		195.0	36.0	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Silent	SNP	ENST00000371158.2	hg19	CCDS617.2																																																																																			.	.		0.363	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605	
ADCY10	55811	hgsc.bcm.edu	37	1	167825481	167825481	+	Missense_Mutation	SNP	C	C	T			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr1:167825481C>T	ENST00000367851.4	-	17	2277	c.2093G>A	c.(2092-2094)gGt>gAt	p.G698D	ADCY10_ENST00000367848.1_Missense_Mutation_p.G606D|ADCY10_ENST00000545172.1_Missense_Mutation_p.G545D	NM_018417.4	NP_060887.2	Q96PN6	ADCYA_HUMAN	adenylate cyclase 10 (soluble)	698					cAMP biosynthetic process (GO:0006171)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|spermatogenesis (GO:0007283)	apical part of cell (GO:0045177)|axon (GO:0030424)|basal part of cell (GO:0045178)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)			autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(26)|ovary(2)|prostate(4)|skin(6)|stomach(1)|urinary_tract(1)	63						CTGTACTGCACCAATGACAAT	0.458																																					p.G698D		Atlas-SNP	.											.	ADCY10	175	.	0			c.G2093A						.						309.0	259.0	276.0					1																	167825481		2203	4300	6503	SO:0001583	missense	55811	exon17			ACTGCACCAATGA	AF271058	CCDS1265.1, CCDS53426.1, CCDS72977.1	1q24	2013-02-04			ENSG00000143199	ENSG00000143199	4.6.1.1	"""Adenylate cyclases"""	21285	protein-coding gene	gene with protein product	"""soluble adenylyl cyclase"", ""Hypercalciuria, absorptive, 2"""	605205					Standard	XM_006711449		Approved	SAC, Sacy, SACI, HCA2, RP1-313L4.2	uc001ger.3	Q96PN6	OTTHUMG00000034573	ENST00000367851.4:c.2093G>A	chr1.hg19:g.167825481C>T	ENSP00000356825:p.Gly698Asp	188.0	0.0		278.0	13.0	NM_018417	B4DZF0|F5GWS5|O95558|Q5R329|Q5R330|Q8WXV4|Q9NNX0	Missense_Mutation	SNP	ENST00000367851.4	hg19	CCDS1265.1	.	.	.	.	.	.	.	.	.	.	C	13.07	2.126709	0.37533	.	.	ENSG00000143199	ENST00000545172;ENST00000367851;ENST00000367848	T;T;T	0.34275	1.37;1.38;1.38	5.16	5.16	0.70880	.	0.110120	0.41938	D	0.000798	T	0.45577	0.1349	M	0.68317	2.08	0.30578	N	0.762778	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.975;0.946	T	0.34675	-0.9819	9	0.21014	T	0.42	-17.3898	14.1528	0.65398	0.0:1.0:0.0:0.0	.	545;606;698	F5GWS5;Q96PN6-2;Q96PN6	.;.;ADCYA_HUMAN	D	545;698;606	ENSP00000441992:G545D;ENSP00000356825:G698D;ENSP00000356822:G606D	ENSP00000356822:G606D	G	-	2	0	ADCY10	166092105	0.023000	0.18921	0.070000	0.20053	0.003000	0.03518	1.668000	0.37481	2.421000	0.82119	0.563000	0.77884	GGT	.	.		0.458	ADCY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083663.1	NM_018417	
ZNF648	127665	hgsc.bcm.edu	37	1	182026606	182026606	+	Silent	SNP	T	T	C			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr1:182026606T>C	ENST00000339948.3	-	2	747	c.540A>G	c.(538-540)gtA>gtG	p.V180V		NM_001009992.1	NP_001009992.1	Q5T619	ZN648_HUMAN	zinc finger protein 648	180					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(7)|large_intestine(10)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	40						CGGACGTGTCTACACTTTTGT	0.582																																					p.V180V	NSCLC(71;908 1374 5429 20458 35642)	Atlas-SNP	.											.	ZNF648	111	.	0			c.A540G						.						65.0	68.0	67.0					1																	182026606		2203	4300	6503	SO:0001819	synonymous_variant	127665	exon2			CGTGTCTACACTT	AK128654	CCDS30952.1	1q25.3	2013-01-08			ENSG00000179930	ENSG00000179930		"""Zinc fingers, C2H2-type"""	18190	protein-coding gene	gene with protein product							Standard	NM_001009992		Approved	FLJ46813	uc001goz.3	Q5T619	OTTHUMG00000037302	ENST00000339948.3:c.540A>G	chr1.hg19:g.182026606T>C		73.0	0.0		83.0	25.0	NM_001009992	B2RP16	Silent	SNP	ENST00000339948.3	hg19	CCDS30952.1																																																																																			.	.		0.582	ZNF648-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090794.1	XM_060597	
ALMS1	7840	hgsc.bcm.edu	37	2	73613036	73613037	+	Missense_Mutation	DNP	GA	GA	CT	rs61156725|rs72319667|rs3074417	byFrequency	TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr2:73613036_73613037GA>CT	ENST00000264448.6	+	1	151_152	c.40_41GA>CT	c.(40-42)GAg>CTg	p.E14L	ALMS1_ENST00000409009.1_Missense_Mutation_p.E14L|ALMS1_ENST00000377715.1_Missense_Mutation_p.E14L	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	14	Glu-rich.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.E27_E28delEE(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CGAGCTggaggaggaggaggag	0.693																																					p.E14Q|p.E14V		Atlas-SNP	.											.	ALMS1	384	.	1	Deletion - In frame(1)	ovary(1)	c.G40C|c.A41T						.																																			SO:0001583	missense	7840	exon1			CTGGAGGAGGAGG|TGGAGGAGGAGGA	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	Exception_encountered	chr2.hg19:g.73613036_73613037delinsCT	ENSP00000264448:p.Glu14Leu	181.0|178.0	0.0		230.0|231.0	12.0|19.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1																																																																																			.	.		0.693	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
RGPD4	285190	hgsc.bcm.edu	37	2	108453116	108453116	+	Missense_Mutation	SNP	T	T	C			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr2:108453116T>C	ENST00000408999.3	+	2	208	c.131T>C	c.(130-132)cTt>cCt	p.L44P	RGPD4_ENST00000354986.4_Missense_Mutation_p.L44P	NM_182588.2	NP_872394.2	Q7Z3J3	RGPD4_HUMAN	RANBP2-like and GRIP domain containing 4	44					protein targeting to Golgi (GO:0000042)					breast(1)|endometrium(7)|kidney(4)|lung(23)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(3)	43						GAATATGATCTTGCTAAAAAG	0.249																																					p.L44P		Atlas-SNP	.											.	RGPD4	112	.	0			c.T131C						.																																			SO:0001583	missense	285190	exon2			ATGATCTTGCTAA	BX537861	CCDS46381.1	2q12.3	2013-01-10			ENSG00000196862	ENSG00000196862		"""Tetratricopeptide (TTC) repeat domain containing"""	32417	protein-coding gene	gene with protein product		612707				15710750, 15815621	Standard	NM_182588		Approved	RGP4, DKFZp686P0288	uc010ywk.2	Q7Z3J3	OTTHUMG00000153208	ENST00000408999.3:c.131T>C	chr2.hg19:g.108453116T>C	ENSP00000386810:p.Leu44Pro	381.0	1.0		383.0	103.0	NM_182588	B9A029	Missense_Mutation	SNP	ENST00000408999.3	hg19	CCDS46381.1	.	.	.	.	.	.	.	.	.	.	t	9.842	1.191238	0.21954	.	.	ENSG00000196862	ENST00000354986;ENST00000408999	T;T	0.37915	1.17;1.17	2.35	2.35	0.29111	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	.	.	.	.	T	0.49490	0.1560	L	0.53249	1.67	0.54753	D	0.999983	D	0.64830	0.994	D	0.79784	0.993	T	0.41233	-0.9520	9	0.40728	T	0.16	-21.0283	9.2374	0.37475	0.0:0.0:0.0:1.0	.	44	Q7Z3J3	RGPD4_HUMAN	P	44	ENSP00000347081:L44P;ENSP00000386810:L44P	ENSP00000347081:L44P	L	+	2	0	RGPD4	107819548	1.000000	0.71417	1.000000	0.80357	0.601000	0.36947	6.117000	0.71577	1.080000	0.41073	0.155000	0.16302	CTT	.	.		0.249	RGPD4-001	NOVEL	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330096.2	XM_496581	
PPIG	9360	hgsc.bcm.edu	37	2	170471112	170471112	+	Missense_Mutation	SNP	G	G	A			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr2:170471112G>A	ENST00000260970.3	+	9	645	c.425G>A	c.(424-426)gGa>gAa	p.G142E	PPIG_ENST00000462903.1_Missense_Mutation_p.G142E|PPIG_ENST00000409714.3_Missense_Mutation_p.G127E|PPIG_ENST00000448752.2_Missense_Mutation_p.G142E	NM_004792.2	NP_004783.2	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G (cyclophilin G)	142	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				protein folding (GO:0006457)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(17)|ovary(2)|stomach(1)|urinary_tract(1)	43					L-Proline(DB00172)	GTTGTTTTTGGACAAGTAATC	0.318																																					p.G142E		Atlas-SNP	.											.	PPIG	100	.	0			c.G425A						.						98.0	102.0	101.0					2																	170471112		2203	4300	6503	SO:0001583	missense	9360	exon9			TTTTTGGACAAGT	X99717	CCDS2235.1	2q31.1	2010-07-23	2006-01-12		ENSG00000138398	ENSG00000138398	6.1.1.16		14650	protein-coding gene	gene with protein product	"""SR-related CTD-associated factor 10"""	606093	"""peptidyl-prolyl isomerase G (cyclophilin G)"""			8973360, 9153302	Standard	NM_004792		Approved	CARS-Cyp, SRCyp, SCAF10	uc002uez.3	Q13427	OTTHUMG00000132206	ENST00000260970.3:c.425G>A	chr2.hg19:g.170471112G>A	ENSP00000260970:p.Gly142Glu	420.0	1.0		403.0	132.0	NM_004792	D3DPC5|D3DPC6|O00706|Q53R40|Q53SN4|Q96DG9	Missense_Mutation	SNP	ENST00000260970.3	hg19	CCDS2235.1	.	.	.	.	.	.	.	.	.	.	G	18.91	3.723290	0.68959	.	.	ENSG00000138398	ENST00000260970;ENST00000530133;ENST00000433207;ENST00000409714;ENST00000462903;ENST00000448752;ENST00000414307	D;D;D;D;D;D	0.87256	-2.23;-2.23;-2.23;-2.23;-2.23;-2.23	5.37	5.37	0.77165	Peptidyl-prolyl cis-trans isomerase, cyclophilin-type (4);Cyclophilin-like (1);	0.000000	0.85682	D	0.000000	D	0.96898	0.8987	H	0.99555	4.625	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	D	0.98847	1.0757	10	0.87932	D	0	-11.2017	19.1154	0.93336	0.0:0.0:1.0:0.0	.	138;127;127;142;142	C9JM79;E9PG73;Q2NKQ6;Q13427-2;Q13427	.;.;.;.;PPIG_HUMAN	E	142;142;138;127;142;142;142	ENSP00000260970:G142E;ENSP00000408683:G138E;ENSP00000386245:G127E;ENSP00000435987:G142E;ENSP00000407083:G142E;ENSP00000402222:G142E	ENSP00000260970:G142E	G	+	2	0	PPIG	170179358	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	9.869000	0.99810	2.511000	0.84671	0.491000	0.48974	GGA	.	.		0.318	PPIG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255264.2		
KIF1A	547	hgsc.bcm.edu	37	2	241700204	241700204	+	Missense_Mutation	SNP	G	G	T			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr2:241700204G>T	ENST00000320389.7	-	24	2453	c.2295C>A	c.(2293-2295)gaC>gaA	p.D765E	KIF1A_ENST00000498729.2_Missense_Mutation_p.D774E	NM_004321.6	NP_004312.2	Q12756	KIF1A_HUMAN	kinesin family member 1A	765					anterograde axon cargo transport (GO:0008089)|ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			NS(1)|central_nervous_system(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(25)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	66		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		GGGGCAGCAGGTCGGGTGGCA	0.632																																					p.D774E		Atlas-SNP	.											.	KIF1A	152	.	0			c.C2322A						.						43.0	49.0	47.0					2																	241700204		1957	4127	6084	SO:0001583	missense	547	exon25			CAGCAGGTCGGGT	AF004425	CCDS46561.1, CCDS58757.1	2q37.2	2014-09-17	2004-01-09	2004-01-14	ENSG00000130294	ENSG00000130294		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	888	protein-coding gene	gene with protein product		601255	"""axonal transport of synaptic vesicles"", ""chromosome 2 open reading frame 20"", ""spastic paraplegia 30 (autosomal recessive)"""	ATSV, C2orf20, SPG30		7539720, 10323250, 22258533	Standard	NM_001244008		Approved	UNC104	uc010fzk.3	Q12756	OTTHUMG00000151940	ENST00000320389.7:c.2295C>A	chr2.hg19:g.241700204G>T	ENSP00000322791:p.Asp765Glu	278.0	1.0		291.0	107.0	NM_001244008	B0I1S5|F5H045|O95068|Q13355|Q14752|Q2NKJ6|Q4LE42|Q53T78|Q59GH1|Q63Z40|Q6P1R9|Q7KZ57	Missense_Mutation	SNP	ENST00000320389.7	hg19	CCDS46561.1	.	.	.	.	.	.	.	.	.	.	G	6.888	0.533288	0.13188	.	.	ENSG00000130294	ENST00000320389;ENST00000498729;ENST00000373308;ENST00000404283	T;T;T	0.74315	-0.83;-0.83;-0.83	4.94	1.64	0.23874	.	0.000000	0.85682	U	0.000000	T	0.52322	0.1727	N	0.17474	0.49	0.53688	D	0.999972	B;B;B	0.26195	0.002;0.144;0.033	B;B;B	0.29785	0.009;0.107;0.041	T	0.44574	-0.9319	10	0.02654	T	1	.	10.4463	0.44497	0.3256:0.0:0.6744:0.0	.	774;774;765	F5H045;Q12756-2;Q12756	.;.;KIF1A_HUMAN	E	765;774;774;774	ENSP00000322791:D765E;ENSP00000438388:D774E;ENSP00000384231:D774E	ENSP00000322791:D765E	D	-	3	2	KIF1A	241348877	1.000000	0.71417	0.992000	0.48379	0.968000	0.65278	1.501000	0.35693	0.510000	0.28216	-0.324000	0.08512	GAC	.	.		0.632	KIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324536.3	NM_138483	
TRPC3	7222	hgsc.bcm.edu	37	4	122833233	122833233	+	Nonsense_Mutation	SNP	G	G	A			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr4:122833233G>A	ENST00000379645.3	-	5	1430	c.1357C>T	c.(1357-1359)Cga>Tga	p.R453*	TRPC3_ENST00000264811.5_Nonsense_Mutation_p.R380*|TRPC3_ENST00000513531.1_Nonsense_Mutation_p.R325*	NM_001130698.1	NP_001124170.1	Q13507	TRPC3_HUMAN	transient receptor potential cation channel, subfamily C, member 3	368					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|phototransduction (GO:0007602)|platelet activation (GO:0030168)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cardiac muscle hypertrophy in response to stress (GO:1903244)|response to ATP (GO:0033198)|response to calcium ion (GO:0051592)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(12)|lung(13)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						AAAGGGCTTCGCAGAATTTTC	0.413																																					p.R453X		Atlas-SNP	.											.	TRPC3	201	.	0			c.C1357T						.						53.0	62.0	59.0					4																	122833233		2203	4300	6503	SO:0001587	stop_gained	7222	exon5			GGCTTCGCAGAAT	Y13758	CCDS3725.1, CCDS47130.1	4q27	2011-12-14			ENSG00000138741	ENSG00000138741		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	12335	protein-coding gene	gene with protein product		602345				8646775, 16382100	Standard	NM_003305		Approved		uc003ieg.2	Q13507	OTTHUMG00000133069	ENST00000379645.3:c.1357C>T	chr4.hg19:g.122833233G>A	ENSP00000368966:p.Arg453*	68.0	0.0		53.0	17.0	NM_001130698	A7VJS1|E9PCJ9|O00593|Q15660|Q52M35|Q5G1L5	Nonsense_Mutation	SNP	ENST00000379645.3	hg19	CCDS47130.1	.	.	.	.	.	.	.	.	.	.	G	42	9.596350	0.99214	.	.	ENSG00000138741	ENST00000264811;ENST00000379645;ENST00000513531	.	.	.	5.21	4.34	0.51931	.	0.097830	0.44285	D	0.000467	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-46.5027	14.8638	0.70399	0.0:0.0:0.8551:0.1449	.	.	.	.	X	380;453;325	.	ENSP00000264811:R380X	R	-	1	2	TRPC3	123052683	1.000000	0.71417	0.999000	0.59377	0.987000	0.75469	4.759000	0.62227	1.144000	0.42321	0.455000	0.32223	CGA	.	.		0.413	TRPC3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364252.1	NM_003305	
CDH9	1007	hgsc.bcm.edu	37	5	26915756	26915756	+	Missense_Mutation	SNP	G	G	A			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr5:26915756G>A	ENST00000231021.4	-	3	677	c.505C>T	c.(505-507)Cct>Tct	p.P169S		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	169	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						GACATTTCAGGAACACTGGCA	0.348																																					p.P169S	Melanoma(8;187 585 15745 40864 52829)	Atlas-SNP	.											.	CDH9	305	.	0			c.C505T						.						73.0	73.0	73.0					5																	26915756		2203	4300	6503	SO:0001583	missense	1007	exon3			TTTCAGGAACACT	AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"""Cadherins / Major cadherins"""	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.505C>T	chr5.hg19:g.26915756G>A	ENSP00000231021:p.Pro169Ser	97.0	0.0		160.0	75.0	NM_016279	Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	hg19	CCDS3893.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.162476	0.78226	.	.	ENSG00000113100	ENST00000231021	T	0.52983	0.64	4.77	4.77	0.60923	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.56790	0.2009	L	0.43701	1.375	0.58432	D	0.999999	D	0.57899	0.981	P	0.58820	0.846	T	0.54214	-0.8327	9	.	.	.	.	16.74	0.85456	0.0:0.0:1.0:0.0	.	169	Q9ULB4	CADH9_HUMAN	S	169	ENSP00000231021:P169S	.	P	-	1	0	CDH9	26951513	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.703000	0.98714	2.352000	0.79861	0.650000	0.86243	CCT	.	.		0.348	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279	
ITGA2	3673	hgsc.bcm.edu	37	5	52370309	52370309	+	Splice_Site	SNP	T	T	C			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr5:52370309T>C	ENST00000296585.5	+	21	2807		c.e21+2			NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)						axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular response to hormone stimulus (GO:0032870)|collagen-activated signaling pathway (GO:0038065)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|hepatocyte differentiation (GO:0070365)|hypotonic response (GO:0006971)|integrin-mediated signaling pathway (GO:0007229)|mammary gland development (GO:0030879)|mesodermal cell differentiation (GO:0048333)|organ morphogenesis (GO:0009887)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell projection organization (GO:0031346)|positive regulation of collagen binding (GO:0033343)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA binding (GO:0043388)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|response to amine (GO:0014075)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to muscle activity (GO:0014850)|response to organic cyclic compound (GO:0014070)|skin morphogenesis (GO:0043589)|substrate-dependent cell migration (GO:0006929)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	axon terminus (GO:0043679)|basal part of cell (GO:0045178)|cell outer membrane (GO:0009279)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin alpha2-beta1 complex (GO:0034666)|integrin complex (GO:0008305)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(1)|lung(18)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	47		Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181)				GAACAACAGGTACAACTTGCA	0.438																																					.		Atlas-SNP	.											.	ITGA2	211	.	0			c.2664+2T>C						.						161.0	133.0	143.0					5																	52370309		2203	4300	6503	SO:0001630	splice_region_variant	3673	exon21			AACAGGTACAACT		CCDS3957.1	5q11.2	2010-03-23			ENSG00000164171	ENSG00000164171		"""CD molecules"", ""Integrins"""	6137	protein-coding gene	gene with protein product		192974		CD49B			Standard	NM_002203		Approved	CD49b	uc003joy.3	P17301	OTTHUMG00000131165	ENST00000296585.5:c.2664+2T>C	chr5.hg19:g.52370309T>C		91.0	0.0		137.0	6.0	NM_002203	Q14595	Splice_Site	SNP	ENST00000296585.5	hg19	CCDS3957.1	.	.	.	.	.	.	.	.	.	.	T	11.26	1.585762	0.28268	.	.	ENSG00000164171	ENST00000296585	.	.	.	5.01	5.01	0.66863	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.7407	0.62847	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	ITGA2	52406066	1.000000	0.71417	0.996000	0.52242	0.050000	0.14768	5.090000	0.64498	2.224000	0.72417	0.528000	0.53228	.	.	.		0.438	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253857.2	NM_002203	Intron
CATSPER3	347732	hgsc.bcm.edu	37	5	134343827	134343827	+	Missense_Mutation	SNP	A	A	T			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr5:134343827A>T	ENST00000282611.6	+	4	759	c.673A>T	c.(673-675)Acg>Tcg	p.T225S		NM_178019.2	NP_821138.1	Q86XQ3	CTSR3_HUMAN	cation channel, sperm associated 3	225					calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|endoplasmic reticulum (GO:0005783)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|stomach(1)|urinary_tract(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CAGCTTGGCCACGGTACTGTG	0.562																																					p.T225S		Atlas-SNP	.											.	CATSPER3	38	.	0			c.A673T						.						82.0	76.0	78.0					5																	134343827		2203	4300	6503	SO:0001583	missense	347732	exon4			TTGGCCACGGTAC	AF432876	CCDS4181.1	5q31.2	2011-07-05			ENSG00000152705	ENSG00000152705		"""Voltage-gated ion channels / Cation channels, sperm associated"""	20819	protein-coding gene	gene with protein product		609120				12646162, 12932298, 17227845, 16382101	Standard	NM_178019		Approved	CACRC	uc003lag.3	Q86XQ3	OTTHUMG00000129137	ENST00000282611.6:c.673A>T	chr5.hg19:g.134343827A>T	ENSP00000282611:p.Thr225Ser	101.0	0.0		137.0	10.0	NM_178019	Q86XS6	Missense_Mutation	SNP	ENST00000282611.6	hg19	CCDS4181.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.270117	0.80469	.	.	ENSG00000152705	ENST00000282611	D	0.98400	-4.91	4.46	4.46	0.54185	Ion transport (1);	0.000000	0.56097	D	0.000035	D	0.98566	0.9521	M	0.74258	2.255	0.38616	D	0.951025	D	0.76494	0.999	D	0.85130	0.997	D	0.99874	1.1101	9	.	.	.	-25.7976	11.9375	0.52882	1.0:0.0:0.0:0.0	.	225	Q86XQ3	CTSR3_HUMAN	S	225	ENSP00000282611:T225S	.	T	+	1	0	CATSPER3	134371726	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.599000	0.67592	1.950000	0.56595	0.460000	0.39030	ACG	.	.		0.562	CATSPER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251191.2	NM_178019	
PCDHA4	56144	hgsc.bcm.edu	37	5	140188506	140188506	+	Silent	SNP	C	C	T			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr5:140188506C>T	ENST00000530339.1	+	1	1734	c.1734C>T	c.(1732-1734)agC>agT	p.S578S	PCDHA1_ENST00000504120.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000356878.4_Silent_p.S578S|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Silent_p.S578S|PCDHA2_ENST00000526136.1_Intron	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	578					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGCAGTGAGCGAGCTGGTGC	0.662																																					p.S578S		Atlas-SNP	.											.	PCDHA4	419	.	0			c.C1734T						.						95.0	89.0	91.0					5																	140188506		2202	4299	6501	SO:0001819	synonymous_variant	56144	exon1			AGTGAGCGAGCTG	AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"""Cadherins / Protocadherins : Clustered"""	8670	other	complex locus constituent	"""ortholog of mouse CNR1, KIAA0345-like 10"""	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.1734C>T	chr5.hg19:g.140188506C>T		77.0	0.0		65.0	17.0	NM_031500	O75285|Q2M253	Silent	SNP	ENST00000530339.1	hg19	CCDS54916.1																																																																																			.	.		0.662	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907	
GRIA1	2890	hgsc.bcm.edu	37	5	153190694	153190694	+	Missense_Mutation	SNP	G	G	A			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr5:153190694G>A	ENST00000285900.5	+	16	2973	c.2630G>A	c.(2629-2631)cGg>cAg	p.R877Q	GRIA1_ENST00000518142.1_Missense_Mutation_p.R797Q|GRIA1_ENST00000518783.1_Missense_Mutation_p.R887Q|GRIA1_ENST00000340592.5_Missense_Mutation_p.R877Q|GRIA1_ENST00000521843.2_Missense_Mutation_p.R808Q|GRIA1_ENST00000448073.4_Missense_Mutation_p.R887Q	NM_000827.3|NM_001258019.1	NP_000818.2|NP_001244948.1	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1	877					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term memory (GO:0007616)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|axonal spine (GO:0044308)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|dendrite membrane (GO:0032590)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|neuron spine (GO:0044309)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|PDZ domain binding (GO:0030165)			NS(1)|breast(4)|endometrium(7)|kidney(3)|large_intestine(24)|liver(2)|lung(23)|ovary(4)|pancreas(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	81		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Perampanel(DB08883)|Sevoflurane(DB01236)	GAGAATGGTCGGGTGGTCAGC	0.592																																					p.R887Q		Atlas-SNP	.											.	GRIA1	321	.	0			c.G2660A						.						55.0	54.0	55.0					5																	153190694		2203	4300	6503	SO:0001583	missense	2890	exon16			ATGGTCGGGTGGT		CCDS4322.1, CCDS47318.1, CCDS58986.1, CCDS58987.1, CCDS58988.1, CCDS58989.1	5q33	2012-08-29			ENSG00000155511	ENSG00000155511		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4571	protein-coding gene	gene with protein product		138248		GLUR1		1652753, 1319477	Standard	NM_000827		Approved	GluA1, GLURA	uc011dcy.2	P42261	OTTHUMG00000130148	ENST00000285900.5:c.2630G>A	chr5.hg19:g.153190694G>A	ENSP00000285900:p.Arg877Gln	232.0	0.0		255.0	66.0	NM_001258021	B7Z2S0|B7Z2W8|B7Z3F6|B7Z9G9|D3DQI4|E7ESV8|Q2NKM6	Missense_Mutation	SNP	ENST00000285900.5	hg19	CCDS4322.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.288962	0.80914	.	.	ENSG00000155511	ENST00000285900;ENST00000544403;ENST00000518142;ENST00000340592;ENST00000521843;ENST00000544794;ENST00000518783;ENST00000448073	T;T;T;T;T;T;T	0.12984	2.68;2.64;2.69;2.64;2.63;2.66;2.66	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	T	0.25044	0.0608	L	0.41236	1.265	0.58432	D	0.999999	P;P;D;P;D	0.71674	0.918;0.918;0.998;0.951;0.997	B;B;P;B;P	0.56648	0.17;0.17;0.665;0.32;0.803	T	0.01004	-1.1484	10	0.87932	D	0	.	17.3487	0.87316	0.0:0.0:1.0:0.0	.	887;887;797;877;877	E7ESV8;B7Z9G9;B7Z3F6;P42261-2;P42261	.;.;.;.;GRIA1_HUMAN	Q	877;877;797;877;810;808;887;887	ENSP00000285900:R877Q;ENSP00000427920:R797Q;ENSP00000339343:R877Q;ENSP00000427864:R810Q;ENSP00000442108:R808Q;ENSP00000428994:R887Q;ENSP00000415569:R887Q	ENSP00000285900:R877Q	R	+	2	0	GRIA1	153170887	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.242000	0.95408	2.330000	0.79161	0.561000	0.74099	CGG	.	.		0.592	GRIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252456.3		
SYNGAP1	8831	hgsc.bcm.edu	37	6	33412344	33412344	+	Missense_Mutation	SNP	T	T	C			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr6:33412344T>C	ENST00000418600.2	+	16	3633	c.3532T>C	c.(3532-3534)Tac>Cac	p.Y1178H	SYNGAP1_ENST00000496374.1_3'UTR|SYNGAP1_ENST00000428982.2_Missense_Mutation_p.Y1119H|SYNGAP1_ENST00000293748.5_Missense_Mutation_p.Y1178H	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	1178					dendrite development (GO:0016358)|negative regulation of axonogenesis (GO:0050771)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|pattern specification process (GO:0007389)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|receptor clustering (GO:0043113)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of MAPK cascade (GO:0043408)|regulation of synapse structure and activity (GO:0050803)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Rab GTPase activator activity (GO:0005097)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(15)|ovary(7)|pancreas(1)|stomach(1)|urinary_tract(1)	43						GCGGGAAGAGTACAAGCTCAA	0.567																																					p.Y1178H		Atlas-SNP	.											.	SYNGAP1	202	.	0			c.T3532C						.						78.0	64.0	69.0					6																	33412344		2203	4300	6503	SO:0001583	missense	8831	exon16			GAAGAGTACAAGC	AB067525	CCDS34434.2	6p21.3	2010-06-25	2010-06-25		ENSG00000197283	ENSG00000197283			11497	protein-coding gene	gene with protein product		603384	"""synaptic Ras GTPase activating protein 1 homolog (rat)"""			9581761, 18323856	Standard	NM_006772		Approved	SYNGAP, RASA5, KIAA1938	uc011dri.2	Q96PV0	OTTHUMG00000031096	ENST00000418600.2:c.3532T>C	chr6.hg19:g.33412344T>C	ENSP00000403636:p.Tyr1178His	96.0	0.0		102.0	29.0	NM_006772	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Missense_Mutation	SNP	ENST00000418600.2	hg19	CCDS34434.2	.	.	.	.	.	.	.	.	.	.	T	17.17	3.320222	0.60634	.	.	ENSG00000197283	ENST00000293748;ENST00000418600;ENST00000449372;ENST00000428982	T;T;T	0.80994	-1.44;-1.44;-1.44	4.61	4.61	0.57282	.	0.150213	0.45606	D	0.000341	T	0.73265	0.3565	L	0.36672	1.1	0.34971	D	0.753149	D;D;D	0.65815	0.995;0.987;0.994	P;P;P	0.61658	0.892;0.693;0.827	T	0.70651	-0.4813	10	0.15499	T	0.54	.	12.0081	0.53272	0.0:0.0:0.0:1.0	.	1178;1178;1178	Q96PV0;Q96PV0-2;Q96PV0-4	SYGP1_HUMAN;.;.	H	1178;1178;1164;1119	ENSP00000293748:Y1178H;ENSP00000403636:Y1178H;ENSP00000412475:Y1119H	ENSP00000293748:Y1178H	Y	+	1	0	SYNGAP1	33520322	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.034000	0.76511	1.936000	0.56123	0.533000	0.62120	TAC	.	.		0.567	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407	
SNAP91	9892	hgsc.bcm.edu	37	6	84303250	84303250	+	Missense_Mutation	SNP	G	G	A			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr6:84303250G>A	ENST00000439399.2	-	18	1959	c.1643C>T	c.(1642-1644)aCc>aTc	p.T548I	SNAP91_ENST00000521743.1_Missense_Mutation_p.T548I|SNAP91_ENST00000195649.6_Missense_Mutation_p.T548I|SNAP91_ENST00000369694.2_Missense_Mutation_p.T548I|SNAP91_ENST00000520302.1_Missense_Mutation_p.T546I|SNAP91_ENST00000521485.1_Missense_Mutation_p.T548I|SNAP91_ENST00000428679.2_Missense_Mutation_p.T548I|SNAP91_ENST00000520213.1_Intron|SNAP91_ENST00000437520.1_Intron	NM_014841.2	NP_055656.1	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa	548	Ala-rich.|Thr-rich.				clathrin coat assembly (GO:0048268)|protein transport (GO:0015031)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|protein kinase binding (GO:0019901)			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(22)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)		agcggaggtggtggtagtggt	0.577																																					p.T548I		Atlas-SNP	.											.	SNAP91	199	.	0			c.C1643T						.						19.0	23.0	22.0					6																	84303250		2091	4148	6239	SO:0001583	missense	9892	exon17			GAGGTGGTGGTAG	AB014556	CCDS47455.1, CCDS56437.1, CCDS56438.1	6q15	2012-12-07	2012-12-07		ENSG00000065609	ENSG00000065609			14986	protein-coding gene	gene with protein product		607923	"""synaptosomal-associated protein, 91 kDa (mouse) homolog"", ""synaptosomal-associated protein, 91kDa homolog (mouse)"""			9734811, 12493563, 10436022	Standard	NM_014841		Approved	KIAA0656, AP180, CALM	uc003pka.3	O60641	OTTHUMG00000015114	ENST00000439399.2:c.1643C>T	chr6.hg19:g.84303250G>A	ENSP00000400459:p.Thr548Ile	138.0	0.0		142.0	43.0	NM_001242792	A8K0L7|E5RI02|Q5JX13|Q68DL9|Q6P9D3|Q9NTY7	Missense_Mutation	SNP	ENST00000439399.2	hg19	CCDS47455.1	.	.	.	.	.	.	.	.	.	.	G	14.89	2.671805	0.47781	.	.	ENSG00000065609	ENST00000521485;ENST00000369694;ENST00000439399;ENST00000195649;ENST00000428679;ENST00000520302;ENST00000521743	T;T;T;T;T;T;T	0.15372	2.46;2.45;2.45;2.46;2.46;2.43;2.45	5.3	5.3	0.74995	.	1.080100	0.07004	N	0.823920	T	0.07593	0.0191	N	0.14661	0.345	0.80722	D	1	P;B;P;B	0.41313	0.745;0.392;0.622;0.392	B;B;B;B	0.36418	0.224;0.11;0.149;0.11	T	0.40646	-0.9552	10	0.72032	D	0.01	-0.0231	18.5672	0.91120	0.0:0.0:1.0:0.0	.	429;546;548;546	B7Z2N2;E5RI02;O60641;E1P549	.;.;AP180_HUMAN;.	I	548;548;548;548;548;546;548	ENSP00000429776:T548I;ENSP00000358708:T548I;ENSP00000400459:T548I;ENSP00000195649:T548I;ENSP00000412492:T548I;ENSP00000428511:T546I;ENSP00000428215:T548I	ENSP00000195649:T548I	T	-	2	0	SNAP91	84359969	1.000000	0.71417	0.990000	0.47175	0.934000	0.57294	6.245000	0.72398	2.476000	0.83614	0.462000	0.41574	ACC	.	.		0.577	SNAP91-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375296.1		
FUCA2	2519	hgsc.bcm.edu	37	6	143823511	143823511	+	Missense_Mutation	SNP	G	G	A			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr6:143823511G>A	ENST00000002165.6	-	4	999	c.944C>T	c.(943-945)aCa>aTa	p.T315I	FUCA2_ENST00000367585.1_Intron|RP1-20N2.6_ENST00000589489.1_RNA|RP1-20N2.6_ENST00000591892.1_RNA|RP1-20N2.6_ENST00000593045.1_RNA|RP1-20N2.6_ENST00000589563.1_RNA|RP1-20N2.6_ENST00000610068.1_RNA|RP1-20N2.6_ENST00000593175.1_RNA|RP1-20N2.6_ENST00000590703.1_RNA|FUCA2_ENST00000438118.2_Intron|RP1-20N2.6_ENST00000591189.1_RNA|RP1-20N2.6_ENST00000415586.1_RNA	NM_032020.4	NP_114409.2	Q9BTY2	FUCO2_HUMAN	fucosidase, alpha-L- 2, plasma	315					fucose metabolic process (GO:0006004)|glycoside catabolic process (GO:0016139)|regulation of entry of bacterium into host cell (GO:2000535)|response to bacterium (GO:0009617)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-L-fucosidase activity (GO:0004560)|fucose binding (GO:0042806)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				OV - Ovarian serous cystadenocarcinoma(155;7.45e-06)|GBM - Glioblastoma multiforme(68;0.0142)		TTCTTCAATTGTAAGATAGTC	0.388																																					p.T315I		Atlas-SNP	.											.	FUCA2	28	.	0			c.C944T						.						164.0	153.0	156.0					6																	143823511		2203	4300	6503	SO:0001583	missense	2519	exon4			TCAATTGTAAGAT	BC003060	CCDS5200.1	6q24	2012-10-02			ENSG00000001036	ENSG00000001036	3.2.1.51		4008	protein-coding gene	gene with protein product		136820				6590153	Standard	NM_032020		Approved	MGC1314, dJ20N2.5	uc003qjm.3	Q9BTY2	OTTHUMG00000015728	ENST00000002165.6:c.944C>T	chr6.hg19:g.143823511G>A	ENSP00000002165:p.Thr315Ile	113.0	0.0		113.0	39.0	NM_032020	E9PEB6|Q7Z6V1|Q7Z6Y2|Q8NBK4	Missense_Mutation	SNP	ENST00000002165.6	hg19	CCDS5200.1	.	.	.	.	.	.	.	.	.	.	G	17.60	3.430817	0.62844	.	.	ENSG00000001036	ENST00000002165	T	0.59502	0.26	5.62	5.62	0.85841	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.143965	0.64402	D	0.000010	D	0.83589	0.5287	H	0.97611	4.04	0.53688	D	0.999974	D	0.64830	0.994	D	0.71656	0.974	D	0.89043	0.3450	10	0.87932	D	0	-9.7956	19.6689	0.95903	0.0:0.0:1.0:0.0	.	315	Q9BTY2	FUCO2_HUMAN	I	315	ENSP00000002165:T315I	ENSP00000002165:T315I	T	-	2	0	FUCA2	143865204	1.000000	0.71417	0.213000	0.23690	0.980000	0.70556	4.359000	0.59449	2.642000	0.89623	0.655000	0.94253	ACA	.	.		0.388	FUCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042521.2	NM_032020	
SUGCT	79783	hgsc.bcm.edu	37	7	40234654	40234654	+	Missense_Mutation	SNP	T	T	C			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr7:40234654T>C	ENST00000335693.4	+	6	523	c.500T>C	c.(499-501)aTc>aCc	p.I167T	C7orf10_ENST00000540834.1_Missense_Mutation_p.I160T|C7orf10_ENST00000401647.2_Missense_Mutation_p.I167T|C7orf10_ENST00000309930.5_Missense_Mutation_p.I167T	NM_001193313.1	NP_001180242.1	Q9HAC7	SUCHY_HUMAN		167					metabolic process (GO:0008152)	mitochondrion (GO:0005739)	succinate-hydroxymethylglutarate CoA-transferase activity (GO:0047369)			endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)	18						TATTGTTCCATCACAGGTATT	0.393																																					p.I167T		Atlas-SNP	.											.	C7orf10	99	.	0			c.T500C						.						270.0	266.0	267.0					7																	40234654		1902	4120	6022	SO:0001583	missense	79783	exon6			GTTCCATCACAGG																												ENST00000335693.4:c.500T>C	chr7.hg19:g.40234654T>C	ENSP00000338475:p.Ile167Thr	56.0	0.0		67.0	15.0	NM_001193313	A4D1W5|B4DR73|Q4KMW4|Q4KMW8|Q4KMZ0|Q8TE00|Q8TEY1	Missense_Mutation	SNP	ENST00000335693.4	hg19	CCDS55105.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	23.5|23.5	4.426576|4.426576	0.83667|0.83667	.|.	.|.	ENSG00000175600|ENSG00000175600	ENST00000309930;ENST00000401647;ENST00000335693;ENST00000540834|ENST00000416370	T;T;T;T|.	0.60171|.	0.21;0.21;0.21;2.5|.	5.81|5.81	5.81|5.81	0.92471|0.92471	CoA-transferase family III domain (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.85852|0.85852	0.5793|0.5793	M|M	0.93283|0.93283	3.4|3.4	0.50632|0.50632	D|D	0.999885|0.999885	D;D;D|.	0.54601|.	0.967;0.967;0.959|.	P;P;P|.	0.58391|.	0.838;0.838;0.749|.	D|D	0.89525|0.89525	0.3781|0.3781	10|5	0.87932|.	D|.	0|.	-14.1537|-14.1537	15.1388|15.1388	0.72595|0.72595	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	167;167;130|.	Q4KMW8;Q9HAC7;Q9HAC7-2|.	.;CG010_HUMAN;.|.	T|P	167;167;167;160|162	ENSP00000312054:I167T;ENSP00000385222:I167T;ENSP00000338475:I167T;ENSP00000445521:I160T|.	ENSP00000312054:I167T|.	I|S	+|+	2|1	0|0	C7orf10|C7orf10	40201179|40201179	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	6.548000|6.548000	0.73896|0.73896	2.210000|2.210000	0.71456|0.71456	0.533000|0.533000	0.62120|0.62120	ATC|TCA	.	.		0.393	C7orf10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000338388.1		
ZNF804B	219578	hgsc.bcm.edu	37	7	88966180	88966180	+	Nonsense_Mutation	SNP	T	T	A			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr7:88966180T>A	ENST00000333190.4	+	4	4493	c.3884T>A	c.(3883-3885)tTg>tAg	p.L1295*		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	1295							metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			ATTCCTACATTGTTTGGTCCT	0.443										HNSCC(36;0.09)																											p.L1295X		Atlas-SNP	.											.	ZNF804B	322	.	0			c.T3884A						.						203.0	189.0	194.0					7																	88966180		2203	4300	6503	SO:0001587	stop_gained	219578	exon4			CTACATTGTTTGG	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"""zinc finger 804B"""				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.3884T>A	chr7.hg19:g.88966180T>A	ENSP00000329638:p.Leu1295*	131.0	0.0		120.0	25.0	NM_181646	B2RTV2|Q7Z714|Q96MN7	Nonsense_Mutation	SNP	ENST00000333190.4	hg19	CCDS5613.1	.	.	.	.	.	.	.	.	.	.	T	44	11.041769	0.99507	.	.	ENSG00000182348	ENST00000333190	.	.	.	5.41	5.41	0.78517	.	0.126543	0.36002	N	0.002848	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.3995	15.6016	0.76628	0.0:0.0:0.0:1.0	.	.	.	.	X	1295	.	ENSP00000329638:L1295X	L	+	2	0	ZNF804B	88804116	1.000000	0.71417	0.958000	0.39756	0.495000	0.33615	7.181000	0.77682	2.258000	0.74832	0.533000	0.62120	TTG	.	.		0.443	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646	
TSGA13	114960	hgsc.bcm.edu	37	7	130356523	130356523	+	Silent	SNP	A	A	G			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr7:130356523A>G	ENST00000456951.1	-	8	1487	c.636T>C	c.(634-636)caT>caC	p.H212H	TSGA13_ENST00000356588.3_Silent_p.H212H|COPG2_ENST00000445977.2_5'Flank			Q96PP4	TSG13_HUMAN	testis specific, 13	212										endometrium(1)|kidney(3)|large_intestine(3)|lung(6)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	18	Melanoma(18;0.0435)					TATCTCTCTCATGGACTGGAG	0.433																																					p.H212H		Atlas-SNP	.											.	TSGA13	35	.	0			c.T636C						.						233.0	223.0	226.0					7																	130356523		2203	4300	6503	SO:0001819	synonymous_variant	114960	exon7			TCTCTCATGGACT	AK093329	CCDS5824.1	7q32	2008-02-04			ENSG00000213265	ENSG00000213265			12369	protein-coding gene	gene with protein product							Standard	NM_052933		Approved		uc003vqi.3	Q96PP4	OTTHUMG00000154999	ENST00000456951.1:c.636T>C	chr7.hg19:g.130356523A>G		92.0	0.0		109.0	41.0	NM_052933	B3KSC9	Silent	SNP	ENST00000456951.1	hg19	CCDS5824.1																																																																																			.	.		0.433	TSGA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337997.1	NM_052933	
PODXL	5420	hgsc.bcm.edu	37	7	131241029	131241029	+	Silent	SNP	G	G	C	rs11277659|rs547816245|rs532078953|rs79759078|rs571821675	byFrequency	TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr7:131241029G>C	ENST00000378555.3	-	1	337	c.90C>G	c.(88-90)ccC>ccG	p.P30P	PODXL_ENST00000541194.1_Silent_p.P30P|PODXL_ENST00000537928.1_Silent_p.P30P|PODXL_ENST00000465001.1_Intron|PODXL_ENST00000322985.9_Silent_p.P30P			O00592	PODXL_HUMAN	podocalyxin-like	30					cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					CATTCTGGGAGggcgacggcg	0.751																																					p.P30P		Atlas-SNP	.											.	PODXL	53	.	0			c.C90G						.						5.0	7.0	6.0					7																	131241029		1981	3946	5927	SO:0001819	synonymous_variant	5420	exon1			CTGGGAGGGCGAC		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.90C>G	chr7.hg19:g.131241029G>C		101.0	0.0		119.0	13.0	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Silent	SNP	ENST00000378555.3	hg19	CCDS34755.1																																																																																			.	.		0.751	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111	
PTP4A3	11156	hgsc.bcm.edu	37	8	142432342	142432342	+	Start_Codon_SNP	SNP	T	T	C			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr8:142432342T>C	ENST00000521578.1	+	2	947	c.2T>C	c.(1-3)aTg>aCg	p.M1T	PTP4A3_ENST00000329397.1_Start_Codon_SNP_p.M1T|PTP4A3_ENST00000524028.1_Start_Codon_SNP_p.M1T|PTP4A3_ENST00000520105.1_Start_Codon_SNP_p.M1T|PTP4A3_ENST00000349124.1_Start_Codon_SNP_p.M1T			O75365	TP4A3_HUMAN	protein tyrosine phosphatase type IVA, member 3	1					peptidyl-tyrosine dephosphorylation (GO:0035335)	endosome (GO:0005768)|plasma membrane (GO:0005886)	prenylated protein tyrosine phosphatase activity (GO:0004727)			endometrium(2)|large_intestine(1)|lung(3)	6	all_cancers(97;2.55e-15)|all_epithelial(106;1.39e-13)|Lung NSC(106;2.07e-05)|all_lung(105;2.89e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0474)			GGAGGCGCCATGGCTCGGATG	0.627																																					p.M1T		Atlas-SNP	.											.	PTP4A3	19	.	0			c.T2C						.						62.0	67.0	65.0					8																	142432342		2201	4297	6498	SO:0001582	initiator_codon_variant	11156	exon1			GCGCCATGGCTCG	AF041434	CCDS6382.1, CCDS6383.1	8q24.3	2011-06-09				ENSG00000184489		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PRLs"""	9636	protein-coding gene	gene with protein product		606449					Standard	NM_032611		Approved	PRL-3, PRL-R, PRL3	uc003ywg.1	O75365		ENST00000521578.1:c.2T>C	chr8.hg19:g.142432342T>C	ENSP00000428976:p.Met1Thr	112.0	0.0		127.0	45.0	NM_032611	Q8IVN5|Q99849|Q9BTW5	Missense_Mutation	SNP	ENST00000521578.1	hg19	CCDS6383.1	.	.	.	.	.	.	.	.	.	.	T	13.88	2.367876	0.42003	.	.	ENSG00000184489	ENST00000521578;ENST00000520105;ENST00000523147;ENST00000329397;ENST00000349124;ENST00000524028	D;T;D;T	0.95035	-3.59;0.86;-3.59;0.86	4.89	4.89	0.63831	.	0.092739	0.64402	D	0.000001	D	0.92893	0.7739	.	.	.	0.27200	N	0.9602	P;P	0.39071	0.634;0.658	B;B	0.40825	0.153;0.341	D	0.89364	0.3670	9	0.87932	D	0	-10.3615	13.3283	0.60473	0.0:0.0:0.0:1.0	.	1;1	O75365-2;O75365	.;TP4A3_HUMAN	T	1	ENSP00000428976:M1T;ENSP00000428758:M1T;ENSP00000332274:M1T;ENSP00000331730:M1T	ENSP00000332274:M1T	M	+	2	0	PTP4A3	142501524	1.000000	0.71417	0.996000	0.52242	0.515000	0.34225	5.963000	0.70372	1.839000	0.53478	0.402000	0.26972	ATG	.	.		0.627	PTP4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378977.1	NM_032611	Missense_Mutation
SCRIB	23513	hgsc.bcm.edu	37	8	144873558	144873558	+	Splice_Site	SNP	C	C	T			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr8:144873558C>T	ENST00000320476.3	-	35	4754		c.e35+1		RP11-429J17.8_ENST00000532625.1_RNA|RP11-429J17.8_ENST00000527139.1_RNA|RP11-429J17.8_ENST00000534089.1_RNA|SCRIB_ENST00000546337.1_5'Flank|SCRIB_ENST00000356994.2_Splice_Site|SCRIB_ENST00000377533.3_Splice_Site	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein						activation of Rac GTPase activity (GO:0032863)|apoptotic process involved in morphogenesis (GO:0060561)|astrocyte cell migration (GO:0043615)|asymmetric protein localization (GO:0008105)|auditory receptor cell stereocilium organization (GO:0060088)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cochlear nucleus development (GO:0021747)|establishment of apical/basal cell polarity (GO:0035089)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of mitotic cell cycle (GO:0045930)|neural tube closure (GO:0001843)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of receptor recycling (GO:0001921)|protein localization to adherens junction (GO:0071896)|single organismal cell-cell adhesion (GO:0016337)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle targeting (GO:0016080)|viral process (GO:0016032)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)|Scrib-APC-beta-catenin complex (GO:0034750)				NS(1)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(20)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	42	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			CCCCAACTCACCAGGGCTGGG	0.667																																					.	Pancreas(51;966 1133 10533 14576 29674)	Atlas-SNP	.											.	SCRIB	192	.	0			c.4822+1G>A						.						25.0	23.0	23.0					8																	144873558		2195	4298	6493	SO:0001630	splice_region_variant	23513	exon37			AACTCACCAGGGC	AY062238	CCDS6411.1, CCDS6412.1	8q24.3	2013-03-05	2013-03-05		ENSG00000180900	ENSG00000180900			30377	protein-coding gene	gene with protein product		607733	"""scribbled homolog (Drosophila)"""			11027293, 14681682	Standard	NM_182706		Approved	KIAA0147, SCRB1, Vartul	uc003yzo.1	Q14160	OTTHUMG00000165154	ENST00000320476.3:c.4747+1G>A	chr8.hg19:g.144873558C>T		265.0	0.0		228.0	145.0	NM_182706	Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Splice_Site	SNP	ENST00000320476.3	hg19	CCDS6411.1	.	.	.	.	.	.	.	.	.	.	C	11.71	1.719434	0.30503	.	.	ENSG00000180900	ENST00000356994;ENST00000320476;ENST00000526832;ENST00000377533	.	.	.	4.24	4.24	0.50183	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.9849	0.53142	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SCRIB	144945546	0.000000	0.05858	0.968000	0.41197	0.459000	0.32528	0.384000	0.20668	2.209000	0.71365	0.486000	0.48141	.	.	.		0.667	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000382215.1	NM_015356	Intron
A1CF	29974	hgsc.bcm.edu	37	10	52601663	52601663	+	Missense_Mutation	SNP	T	T	A			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr10:52601663T>A	ENST00000373993.1	-	3	368	c.324A>T	c.(322-324)gaA>gaT	p.E108D	A1CF_ENST00000395495.1_Missense_Mutation_p.E108D|A1CF_ENST00000373997.3_Missense_Mutation_p.E108D|A1CF_ENST00000374001.2_Missense_Mutation_p.E108D|A1CF_ENST00000373995.3_Missense_Mutation_p.E116D|A1CF_ENST00000395489.2_Missense_Mutation_p.E101D|A1CF_ENST00000282641.2_Missense_Mutation_p.E108D			Q9NQ94	A1CF_HUMAN	APOBEC1 complementation factor	108	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cytidine to uridine editing (GO:0016554)|gene expression (GO:0010467)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|protein stabilization (GO:0050821)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			NS(1)|breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(14)|prostate(2)|skin(3)	29						CATTCTTGGCTTCCACTTTAT	0.318																																					p.E116D		Atlas-SNP	.											.	A1CF	190	.	0			c.A348T						.						159.0	147.0	151.0					10																	52601663		2201	4299	6500	SO:0001583	missense	29974	exon6			CTTGGCTTCCACT	AF271790	CCDS7241.1, CCDS7242.1, CCDS7243.1, CCDS73133.1	10q21.1	2013-02-12			ENSG00000148584	ENSG00000148584		"""RNA binding motif (RRM) containing"""	24086	protein-coding gene	gene with protein product						11815617, 11072063	Standard	NM_014576		Approved	ACF, ASP, ACF64, ACF65, APOBEC1CF	uc001jjj.3	Q9NQ94	OTTHUMG00000018240	ENST00000373993.1:c.324A>T	chr10.hg19:g.52601663T>A	ENSP00000363105:p.Glu108Asp	85.0	0.0		72.0	28.0	NM_001198820	A1L4F2|A8K7G7|B7ZM14|Q5SZQ0|Q9NQ93|Q9NQX8|Q9NQX9|Q9NXC9|Q9NZD3	Missense_Mutation	SNP	ENST00000373993.1	hg19	CCDS7242.1	.	.	.	.	.	.	.	.	.	.	T	10.73	1.432096	0.25813	.	.	ENSG00000148584	ENST00000374001;ENST00000373993;ENST00000373997;ENST00000373995;ENST00000282641;ENST00000395495;ENST00000395488;ENST00000395489;ENST00000414883	T;T;T;T;T;T;T;T	0.39056	1.1;1.1;1.1;2.56;1.1;2.56;2.56;2.56	5.76	0.87	0.19102	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.090773	0.85682	N	0.000000	T	0.11965	0.0291	N	0.02120	-0.675	0.49299	D	0.99977	B;B;B;B	0.17038	0.001;0.0;0.02;0.001	B;B;B;B	0.16722	0.003;0.004;0.016;0.003	T	0.06041	-1.0849	10	0.16896	T	0.51	-11.4567	1.0491	0.01576	0.1459:0.221:0.1512:0.4818	.	101;108;108;116	F8W9F8;Q9NQ94;Q9NQ94-2;Q9NQ94-4	.;A1CF_HUMAN;.;.	D	108;108;108;116;108;108;91;101;108	ENSP00000363113:E108D;ENSP00000363105:E108D;ENSP00000363109:E108D;ENSP00000363107:E116D;ENSP00000282641:E108D;ENSP00000378873:E108D;ENSP00000378868:E101D;ENSP00000397953:E108D	ENSP00000282641:E108D	E	-	3	2	A1CF	52271669	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	1.086000	0.30853	0.431000	0.26258	0.383000	0.25322	GAA	.	.		0.318	A1CF-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048086.2	NM_014576	
PRKG1	5592	hgsc.bcm.edu	37	10	54042052	54042052	+	Missense_Mutation	SNP	T	T	C			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr10:54042052T>C	ENST00000401604.2	+	14	1834	c.1640T>C	c.(1639-1641)cTa>cCa	p.L547P	PRKG1-AS1_ENST00000452247.2_RNA|PRKG1_ENST00000373980.4_Missense_Mutation_p.L562P|PRKG1_ENST00000373985.1_Missense_Mutation_p.L535P|PRKG1_ENST00000373975.2_Missense_Mutation_p.L265P|PRKG1-AS1_ENST00000426785.2_RNA			Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I	547	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|dendrite development (GO:0016358)|forebrain development (GO:0030900)|negative regulation of platelet aggregation (GO:0090331)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|regulation of GTPase activity (GO:0043087)|relaxation of vascular smooth muscle (GO:0060087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	53		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		CTGGGAATCCTAATGTATGAA	0.453																																					p.L562P		Atlas-SNP	.											.	PRKG1	167	.	0			c.T1685C						.						100.0	88.0	92.0					10																	54042052		2203	4300	6503	SO:0001583	missense	5592	exon14			GAATCCTAATGTA		CCDS7244.1	10q11.2	2009-07-10			ENSG00000185532	ENSG00000185532	2.7.11.1		9414	protein-coding gene	gene with protein product		176894		PRKGR1B, PRKG1B		2792381, 1544322	Standard	NM_001098512		Approved	PGK, PKG	uc001jjo.3	Q13976	OTTHUMG00000018248	ENST00000401604.2:c.1640T>C	chr10.hg19:g.54042052T>C	ENSP00000384200:p.Leu547Pro	140.0	0.0		137.0	49.0	NM_006258	A5YM56|B3KSF3|E2PU10|P14619|Q5JP05|Q5JSJ6|Q6P5T7	Missense_Mutation	SNP	ENST00000401604.2	hg19	CCDS44399.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.484595	0.84854	.	.	ENSG00000185532	ENST00000401604;ENST00000373985;ENST00000373980;ENST00000332193;ENST00000373975	T;T;T	0.68765	-0.35;-0.35;-0.35	5.63	5.63	0.86233	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.85915	0.5808	M	0.92169	3.28	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.998;0.999	D	0.89359	0.3666	10	0.87932	D	0	-9.8148	15.791	0.78364	0.0:0.0:0.0:1.0	.	265;562;547	B3KSF3;Q13976-2;Q13976	.;.;KGP1_HUMAN	P	547;535;562;265;159	ENSP00000384200:L547P;ENSP00000363097:L535P;ENSP00000363092:L562P	ENSP00000327642:L265P	L	+	2	0	PRKG1	53712058	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.990000	0.88215	2.270000	0.75569	0.460000	0.39030	CTA	.	.		0.453	PRKG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
SLIT1	6585	hgsc.bcm.edu	37	10	98924583	98924583	+	Missense_Mutation	SNP	G	G	A			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr10:98924583G>A	ENST00000266058.4	-	2	507	c.262C>T	c.(262-264)Cgg>Tgg	p.R88W	ARHGAP19-SLIT1_ENST00000453547.2_Silent_p.C513C|SLIT1_ENST00000371041.3_Missense_Mutation_p.R88W|SLIT1_ENST00000456008.2_5'UTR|SLIT1_ENST00000371070.4_Missense_Mutation_p.R88W	NM_003061.2	NP_003052.2	O75093	SLIT1_HUMAN	slit homolog 1 (Drosophila)	88					axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|dorsal/ventral axon guidance (GO:0033563)|establishment of nucleus localization (GO:0040023)|forebrain morphogenesis (GO:0048853)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of synapse assembly (GO:0051964)|retinal ganglion cell axon guidance (GO:0031290)|spinal cord development (GO:0021510)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(37)|ovary(5)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	78		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		CACAGCACCCGCAGCTGCTTG	0.612																																					p.R88W		Atlas-SNP	.											.	SLIT1	154	.	0			c.C262T						.						140.0	121.0	128.0					10																	98924583		2203	4300	6503	SO:0001583	missense	6585	exon2			GCACCCGCAGCTG	AB011537	CCDS7453.1	10q23.3-q24	2008-08-01	2001-11-28		ENSG00000187122	ENSG00000187122			11085	protein-coding gene	gene with protein product		603742	"""slit (Drosophila) homolog 1"""	SLIL1		9693030, 9813312	Standard	NM_003061		Approved	slit1, MEGF4, Slit-1, SLIT3	uc001kmw.2	O75093	OTTHUMG00000018843	ENST00000266058.4:c.262C>T	chr10.hg19:g.98924583G>A	ENSP00000266058:p.Arg88Trp	52.0	0.0		69.0	18.0	NM_003061	Q5T0V1|Q8WWZ2|Q9UIL7	Missense_Mutation	SNP	ENST00000266058.4	hg19	CCDS7453.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.080403	0.76528	.	.	ENSG00000187122	ENST00000266058;ENST00000371057;ENST00000371054;ENST00000371070;ENST00000314867;ENST00000456008;ENST00000371041	T;T;T;T	0.59083	0.29;0.29;0.29;0.29	4.79	4.79	0.61399	.	0.000000	0.85682	D	0.000000	T	0.70666	0.3250	L	0.58583	1.82	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.996;0.95	T	0.73081	-0.4095	10	0.87932	D	0	.	11.9031	0.52694	0.0:0.0:0.8255:0.1745	.	88;88;88	E7EWQ8;O75093-2;O75093	.;.;SLIT1_HUMAN	W	88;88;88;88;71;88;88	ENSP00000266058:R88W;ENSP00000360109:R88W;ENSP00000315005:R71W;ENSP00000360080:R88W	ENSP00000266058:R88W	R	-	1	2	SLIT1	98914573	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.616000	0.54174	2.474000	0.83562	0.561000	0.74099	CGG	.	.		0.612	SLIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049636.1	NM_003061	
SMPD1	6609	hgsc.bcm.edu	37	11	6411944	6411944	+	Missense_Mutation	SNP	T	T	C	rs550067660	byFrequency	TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr11:6411944T>C	ENST00000342245.4	+	1	284	c.116T>C	c.(115-117)cTg>cCg	p.L39P	SMPD1_ENST00000533196.1_3'UTR|SMPD1_ENST00000356761.2_Missense_Mutation_p.L39P|SMPD1_ENST00000527275.1_Missense_Mutation_p.L39P|SMPD1_ENST00000299397.3_Missense_Mutation_p.L39P	NM_000543.4|NM_001007593.2	NP_000534.3|NP_001007594.2	P17405	ASM_HUMAN	sphingomyelin phosphodiesterase 1, acid lysosomal	39					cell death (GO:0008219)|ceramide biosynthetic process (GO:0046513)|glycosphingolipid metabolic process (GO:0006687)|negative regulation of MAP kinase activity (GO:0043407)|nervous system development (GO:0007399)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein dephosphorylation (GO:0035307)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)|sphingomyelin metabolic process (GO:0006684)|termination of signal transduction (GO:0023021)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lamellar body (GO:0042599)|lysosomal lumen (GO:0043202)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)			breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(3)	23		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;4.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)	Amlodipine(DB00381)|Chlorpromazine(DB00477)|Desipramine(DB01151)	gtgctggcgctggcgctggcg	0.711																																					p.L39P		Atlas-SNP	.											.	SMPD1	108	.	0			c.T116C						.						14.0	18.0	17.0					11																	6411944		2190	4281	6471	SO:0001583	missense	6609	exon1			TGGCGCTGGCGCT	AB209775	CCDS31409.1, CCDS44531.1, CCDS31409.2	11p15.4-p15.1	2010-04-28	2008-02-04		ENSG00000166311	ENSG00000166311	3.1.4.12		11120	protein-coding gene	gene with protein product	"""acid sphingomyelinase"""	607608				1711683	Standard	NM_000543		Approved	ASM	uc001mcw.3	P17405	OTTHUMG00000165453	ENST00000342245.4:c.116T>C	chr11.hg19:g.6411944T>C	ENSP00000340409:p.Leu39Pro	114.0	0.0		117.0	39.0	NM_000543	A8K8M3|E9PKS3|P17406|Q13811|Q16837|Q16841	Missense_Mutation	SNP	ENST00000342245.4	hg19	CCDS44531.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.414709	0.83449	.	.	ENSG00000166311	ENST00000299397;ENST00000356761;ENST00000342245;ENST00000527275	T;T;T;T	0.11063	2.81;2.81;2.83;2.83	4.97	3.76	0.43208	.	.	.	.	.	T	0.12390	0.0301	N	0.08118	0	0.35645	D	0.811284	D;D;D	0.69078	0.995;0.997;0.995	P;D;P	0.65010	0.854;0.931;0.854	T	0.24404	-1.0161	9	0.72032	D	0.01	.	8.3318	0.32191	0.0:0.0:0.1998:0.8002	.	39;39;37	E9PKS3;G3XAB5;P17405	.;.;ASM_HUMAN	P	39	ENSP00000299397:L39P;ENSP00000349203:L39P;ENSP00000340409:L39P;ENSP00000435350:L39P	ENSP00000299397:L39P	L	+	2	0	SMPD1	6368520	0.415000	0.25416	0.956000	0.39512	0.093000	0.18481	0.928000	0.28831	1.982000	0.57802	0.460000	0.39030	CTG	.	.		0.711	SMPD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384205.1	NM_000543	
EHF	26298	hgsc.bcm.edu	37	11	34680176	34680176	+	Missense_Mutation	SNP	G	G	A			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr11:34680176G>A	ENST00000533754.1	+	8	921	c.704G>A	c.(703-705)gGc>gAc	p.G235D	EHF_ENST00000531794.1_Missense_Mutation_p.G257D|EHF_ENST00000257831.3_Missense_Mutation_p.G235D|EHF_ENST00000450654.2_Missense_Mutation_p.G212D|EHF_ENST00000530286.1_Missense_Mutation_p.G235D					ets homologous factor										NFIA/EHF(2)	autonomic_ganglia(1)|cervix(1)|endometrium(3)|kidney(3)|lung(8)|upper_aerodigestive_tract(1)	17		all_hematologic(20;0.117)	Epithelial(1;0.055)|all cancers(1;0.137)|STAD - Stomach adenocarcinoma(6;0.235)			CGATCTGAGGGCGTCTTCAGG	0.488																																					p.G257D		Atlas-SNP	.											.	EHF	38	.	0			c.G770A						.						89.0	93.0	92.0					11																	34680176		2202	4298	6500	SO:0001583	missense	26298	exon8			CTGAGGGCGTCTT	AF170583	CCDS7894.1, CCDS55752.1, CCDS55753.1	11p12	2008-07-18				ENSG00000135373			3246	protein-coding gene	gene with protein product	"""epithelium-specific ets factor 3"", ""ESE3 transcription factor"""	605439				10527851	Standard	NM_012153		Approved	ESE3, ESEJ	uc021qfu.1	Q9NZC4		ENST00000533754.1:c.704G>A	chr11.hg19:g.34680176G>A	ENSP00000435837:p.Gly235Asp	144.0	0.0		156.0	45.0	NM_001206616		Missense_Mutation	SNP	ENST00000533754.1	hg19	CCDS7894.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.922457	0.92319	.	.	ENSG00000135373	ENST00000257831;ENST00000450654;ENST00000530286;ENST00000533754;ENST00000531794	T;T;T;T;T	0.15834	2.39;2.39;2.39;2.39;2.39	5.7	5.7	0.88788	Winged helix-turn-helix transcription repressor DNA-binding (1);Ets (4);	0.000000	0.85682	D	0.000000	T	0.57036	0.2026	H	0.94734	3.575	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.998;1.0	T	0.69131	-0.5226	10	0.87932	D	0	.	19.8388	0.96673	0.0:0.0:1.0:0.0	.	257;212;235	E9PSB2;Q9NZC4-2;Q9NZC4	.;.;EHF_HUMAN	D	235;212;235;235;257	ENSP00000257831:G235D;ENSP00000399733:G212D;ENSP00000433508:G235D;ENSP00000435837:G235D;ENSP00000435835:G257D	ENSP00000257831:G235D	G	+	2	0	EHF	34636752	1.000000	0.71417	1.000000	0.80357	0.837000	0.47467	9.869000	0.99810	2.695000	0.91970	0.561000	0.74099	GGC	.	.		0.488	EHF-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000389855.1	NM_012153	
SF3B2	10992	hgsc.bcm.edu	37	11	65828119	65828119	+	Missense_Mutation	SNP	A	A	G			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr11:65828119A>G	ENST00000322535.6	+	14	1745	c.1696A>G	c.(1696-1698)Atc>Gtc	p.I566V	SF3B2_ENST00000528302.1_Missense_Mutation_p.I549V	NM_006842.2	NP_006833.2	Q13435	SF3B2_HUMAN	splicing factor 3b, subunit 2, 145kDa	566					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	41						CAAAATTGACATCGACTACCA	0.493																																					p.I566V		Atlas-SNP	.											.	SF3B2	85	.	0			c.A1696G						.						145.0	127.0	133.0					11																	65828119		2201	4295	6496	SO:0001583	missense	10992	exon14			ATTGACATCGACT	U41371	CCDS31612.1	11q13	2010-07-21	2002-08-29		ENSG00000087365	ENSG00000087365			10769	protein-coding gene	gene with protein product		605591	"""splicing factor 3b, subunit 2, 145kD"""			8566756	Standard	XM_005273726		Approved	SAP145, SF3b1, Cus1, SF3b145	uc001ogy.1	Q13435	OTTHUMG00000166751	ENST00000322535.6:c.1696A>G	chr11.hg19:g.65828119A>G	ENSP00000318861:p.Ile566Val	136.0	0.0		144.0	49.0	NM_006842	A8K485|B4DT19|Q7L4T5|Q7Z627|Q969K1|Q96CM6|Q9BWD2	Missense_Mutation	SNP	ENST00000322535.6	hg19	CCDS31612.1	.	.	.	.	.	.	.	.	.	.	A	25.6	4.653305	0.88056	.	.	ENSG00000087365	ENST00000528302;ENST00000322535;ENST00000355456	.	.	.	5.82	5.82	0.92795	Domain of unknown function DUF382 (1);	0.000000	0.85682	D	0.000000	T	0.72486	0.3466	M	0.80183	2.485	0.80722	D	1	P	0.37083	0.581	P	0.45946	0.498	T	0.75811	-0.3186	9	0.66056	D	0.02	-21.0583	14.1327	0.65266	1.0:0.0:0.0:0.0	.	566	Q13435	SF3B2_HUMAN	V	549;566;470	.	ENSP00000318861:I566V	I	+	1	0	SF3B2	65584695	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.319000	0.89992	2.221000	0.72209	0.528000	0.53228	ATC	.	.		0.493	SF3B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391352.2		
MYO7A	4647	hgsc.bcm.edu	37	11	76909563	76909563	+	Missense_Mutation	SNP	G	G	A			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr11:76909563G>A	ENST00000409709.3	+	34	4737	c.4465G>A	c.(4465-4467)Gtc>Atc	p.V1489I	MYO7A_ENST00000458637.2_Missense_Mutation_p.V1489I|MYO7A_ENST00000409619.2_Missense_Mutation_p.V1478I	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	1489	FERM 1. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						CAAGAACGACGTCATCGTGGC	0.607																																					p.V1489I		Atlas-SNP	.											MYO7A,NS,carcinoma,0,1	MYO7A	164	.	0			c.G4465A						.						73.0	81.0	78.0					11																	76909563		2084	4188	6272	SO:0001583	missense	4647	exon34			AACGACGTCATCG	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"""A-kinase anchor proteins"", ""Myosins / Myosin superfamily : Class VII"""	7606	protein-coding gene	gene with protein product		276903	"""myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"""	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.4465G>A	chr11.hg19:g.76909563G>A	ENSP00000386331:p.Val1489Ile	54.0	0.0		44.0	15.0	NM_000260	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Missense_Mutation	SNP	ENST00000409709.3	hg19	CCDS53683.1	.	.	.	.	.	.	.	.	.	.	G	12.23	1.876425	0.33162	.	.	ENSG00000137474	ENST00000409709;ENST00000458637;ENST00000409619;ENST00000545136;ENST00000358342;ENST00000343356;ENST00000341717;ENST00000458169;ENST00000544424	D;D;D;D	0.91351	-2.83;-2.83;-2.83;-2.83	5.06	5.06	0.68205	FERM domain (1);	0.067374	0.64402	D	0.000017	D	0.89677	0.6784	M	0.78049	2.395	0.80722	D	1	P;P;B	0.43662	0.545;0.814;0.343	B;B;B	0.35413	0.161;0.202;0.086	D	0.89739	0.3932	10	0.34782	T	0.22	.	18.6167	0.91305	0.0:0.0:1.0:0.0	.	1478;1489;1489	B9A011;F8VUN5;Q13402	.;.;MYO7A_HUMAN	I	1489;1489;1478;700;1488;1458;1365;670;142	ENSP00000386331:V1489I;ENSP00000392185:V1489I;ENSP00000386635:V1478I;ENSP00000417017:V670I	ENSP00000345075:V1365I	V	+	1	0	MYO7A	76587211	1.000000	0.71417	0.556000	0.28293	0.082000	0.17680	4.164000	0.58190	2.624000	0.88883	0.655000	0.94253	GTC	.	.		0.607	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260	
APOA4	337	hgsc.bcm.edu	37	11	116692001	116692001	+	Missense_Mutation	SNP	G	G	C			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr11:116692001G>C	ENST00000357780.3	-	3	887	c.773C>G	c.(772-774)gCc>gGc	p.A258G		NM_000482.3	NP_000473.2	P06727	APOA4_HUMAN	apolipoprotein A-IV	258	13 X 22 AA approximate tandem repeats.				cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|chylomicron assembly (GO:0034378)|chylomicron remodeling (GO:0034371)|high-density lipoprotein particle remodeling (GO:0034375)|hydrogen peroxide catabolic process (GO:0042744)|innate immune response in mucosa (GO:0002227)|leukocyte cell-cell adhesion (GO:0007159)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|multicellular organismal lipid catabolic process (GO:0044240)|negative regulation of plasma lipoprotein particle oxidation (GO:0034445)|phosphatidylcholine metabolic process (GO:0046470)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of triglyceride catabolic process (GO:0010898)|protein-lipid complex assembly (GO:0065005)|regulation of cholesterol transport (GO:0032374)|regulation of intestinal cholesterol absorption (GO:0030300)|removal of superoxide radicals (GO:0019430)|response to lipid hydroperoxide (GO:0006982)|response to stilbenoid (GO:0035634)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|very-low-density lipoprotein particle remodeling (GO:0034372)	blood microparticle (GO:0072562)|chylomicron (GO:0042627)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	antioxidant activity (GO:0016209)|cholesterol transporter activity (GO:0017127)|copper ion binding (GO:0005507)|lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)|phosphatidylcholine binding (GO:0031210)|phosphatidylcholine-sterol O-acyltransferase activator activity (GO:0060228)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(2)|lung(10)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Breast(348;0.0126)|Medulloblastoma(222;0.0425)|all_hematologic(158;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|Epithelial(105;1.62e-05)|all cancers(92;0.000165)|OV - Ovarian serous cystadenocarcinoma(223;0.148)		CTCGGCACTGGCCGAGATCCT	0.642																																					p.A258G		Atlas-SNP	.											.	APOA4	51	.	0			c.C773G						.						51.0	55.0	54.0					11																	116692001		2201	4292	6493	SO:0001583	missense	337	exon3			GCACTGGCCGAGA		CCDS31681.1	11q23.3	2013-01-24			ENSG00000110244	ENSG00000110244		"""Apolipoproteins"""	602	protein-coding gene	gene with protein product		107690					Standard	NM_000482		Approved		uc001pps.1	P06727	OTTHUMG00000046110	ENST00000357780.3:c.773C>G	chr11.hg19:g.116692001G>C	ENSP00000350425:p.Ala258Gly	61.0	0.0		40.0	18.0	NM_000482	A8MSL6|Q14CW8|Q6Q787	Missense_Mutation	SNP	ENST00000357780.3	hg19	CCDS31681.1	.	.	.	.	.	.	.	.	.	.	G	11.63	1.696713	0.30142	.	.	ENSG00000110244	ENST00000357780	T	0.74421	-0.84	4.96	-0.127	0.13510	Apolipoprotein/apolipophorin (1);	0.715917	0.12970	N	0.424246	T	0.82006	0.4943	M	0.83852	2.665	0.09310	N	1	D	0.58970	0.984	P	0.60345	0.873	T	0.71097	-0.4691	10	0.30854	T	0.27	-7.5352	9.7132	0.40258	0.0:0.3156:0.471:0.2134	.	258	P06727	APOA4_HUMAN	G	258	ENSP00000350425:A258G	ENSP00000350425:A258G	A	-	2	0	APOA4	116197211	0.045000	0.20229	0.000000	0.03702	0.026000	0.11368	2.350000	0.44063	0.097000	0.17492	0.563000	0.77884	GCC	.	.		0.642	APOA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106279.2	NM_000482	
LDHB	3945	hgsc.bcm.edu	37	12	21799847	21799847	+	Missense_Mutation	SNP	A	A	C			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr12:21799847A>C	ENST00000396076.1	-	3	565	c.233T>G	c.(232-234)aTt>aGt	p.I78S	LDHB_ENST00000350669.1_Missense_Mutation_p.I78S	NM_001174097.1	NP_001167568.1	P07195	LDHB_HUMAN	lactate dehydrogenase B	78					cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|lactate metabolic process (GO:0006089)|NAD metabolic process (GO:0019674)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	L-lactate dehydrogenase activity (GO:0004459)|NAD binding (GO:0051287)			breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	26						ATCTGCCACAATTTTAGGTGT	0.373																																					p.I78S		Atlas-SNP	.											.	LDHB	47	.	0			c.T233G						.						119.0	106.0	111.0					12																	21799847		2203	4300	6503	SO:0001583	missense	3945	exon3			GCCACAATTTTAG		CCDS8691.1	12p12.2-p12.1	2012-10-02			ENSG00000111716	ENSG00000111716	1.1.1.27		6541	protein-coding gene	gene with protein product		150100					Standard	NM_002300		Approved		uc001rfe.3	P07195	OTTHUMG00000133760	ENST00000396076.1:c.233T>G	chr12.hg19:g.21799847A>C	ENSP00000379386:p.Ile78Ser	55.0	0.0		62.0	17.0	NM_002300		Missense_Mutation	SNP	ENST00000396076.1	hg19	CCDS8691.1	.	.	.	.	.	.	.	.	.	.	A	18.46	3.629126	0.67015	.	.	ENSG00000111716	ENST00000396076;ENST00000350669;ENST00000396075;ENST00000450584;ENST00000539782	D;D;D;D;D	0.90900	-2.75;-2.75;-2.75;-2.75;-2.75	4.96	4.96	0.65561	Lactate/malate dehydrogenase, N-terminal (1);NAD(P)-binding domain (1);	0.045811	0.85682	D	0.000000	D	0.94974	0.8374	M	0.89287	3.02	0.80722	D	1	P	0.39737	0.685	P	0.53266	0.722	D	0.95668	0.8721	10	0.72032	D	0.01	.	14.6699	0.68937	1.0:0.0:0.0:0.0	.	78	P07195	LDHB_HUMAN	S	78	ENSP00000379386:I78S;ENSP00000229319:I78S;ENSP00000379385:I78S;ENSP00000398015:I78S;ENSP00000442680:I78S	ENSP00000229319:I78S	I	-	2	0	LDHB	21691114	1.000000	0.71417	1.000000	0.80357	0.845000	0.48019	9.157000	0.94714	1.858000	0.53909	0.460000	0.39030	ATT	.	.		0.373	LDHB-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258220.2	NM_002300	
R3HDM2	22864	hgsc.bcm.edu	37	12	57674222	57674222	+	Silent	SNP	C	C	T			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr12:57674222C>T	ENST00000347140.3	-	14	1611	c.1221G>A	c.(1219-1221)caG>caA	p.Q407Q	R3HDM2_ENST00000413953.2_Silent_p.Q134Q|R3HDM2_ENST00000403821.2_Silent_p.Q407Q|RP11-123K3.4_ENST00000548184.1_3'UTR|R3HDM2_ENST00000402412.1_Silent_p.Q421Q|R3HDM2_ENST00000441731.2_Silent_p.Q68Q|R3HDM2_ENST00000358907.2_Silent_p.Q407Q			Q9Y2K5	R3HD2_HUMAN	R3H domain containing 2	407	Gln-rich.					nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	22						gctgctgctgctgttgctgct	0.567																																					p.Q407Q		Atlas-SNP	.											.	R3HDM2	125	.	0			c.G1221A						.						104.0	93.0	97.0					12																	57674222		2203	4300	6503	SO:0001819	synonymous_variant	22864	exon12			CTGCTGCTGTTGC	AB023219	CCDS8937.2	12q13.3	2012-11-19			ENSG00000179912	ENSG00000179912			29167	protein-coding gene	gene with protein product							Standard	NM_014925		Approved	KIAA1002	uc009zpm.1	Q9Y2K5	OTTHUMG00000171568	ENST00000347140.3:c.1221G>A	chr12.hg19:g.57674222C>T		64.0	0.0		79.0	5.0	NM_014925	Q2M1T9|Q3ZCT5	Silent	SNP	ENST00000347140.3	hg19	CCDS8937.2	.	.	.	.	.	.	.	.	.	.	C	12.71	2.018308	0.35606	.	.	ENSG00000179912	ENST00000466401	.	.	.	4.49	1.62	0.23740	.	.	.	.	.	T	0.51719	0.1691	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.36768	-0.9734	4	.	.	.	1.0729	5.4164	0.16376	0.0:0.5998:0.1455:0.2548	.	.	.	.	N	5	.	.	S	-	2	0	R3HDM2	55960489	0.030000	0.19436	0.992000	0.48379	0.921000	0.55340	-1.132000	0.03235	0.156000	0.19299	-0.294000	0.09567	AGC	.	.		0.567	R3HDM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326570.2	NM_014925	
FAM216A	29902	hgsc.bcm.edu	37	12	110924510	110924510	+	Missense_Mutation	SNP	G	G	A			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr12:110924510G>A	ENST00000377673.5	+	5	1120	c.608G>A	c.(607-609)aGa>aAa	p.R203K		NM_013300.2	NP_037432.2	Q8WUB2	F216A_HUMAN	family with sequence similarity 216, member A	203																	CGGCCAGTGAGAAACAAAGAA	0.468																																					p.R203K		Atlas-SNP	.											.	.	.	.	0			c.G608A						.						81.0	87.0	85.0					12																	110924510		2203	4300	6503	SO:0001583	missense	29902	exon5			CAGTGAGAAACAA	U79274	CCDS31899.1	12q24.11	2012-02-07	2012-02-07	2012-02-07	ENSG00000204856	ENSG00000204856			30180	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 24"""	C12orf24			Standard	NM_013300		Approved	HSU79274	uc001tqu.4	Q8WUB2	OTTHUMG00000169526	ENST00000377673.5:c.608G>A	chr12.hg19:g.110924510G>A	ENSP00000366901:p.Arg203Lys	81.0	0.0		119.0	26.0	NM_013300	A6NH30|Q99776	Missense_Mutation	SNP	ENST00000377673.5	hg19	CCDS31899.1	.	.	.	.	.	.	.	.	.	.	G	18.96	3.733588	0.69189	.	.	ENSG00000204856	ENST00000377673;ENST00000538285;ENST00000548869;ENST00000546396	T	0.57907	0.37	4.32	3.43	0.39272	.	0.000000	0.44688	D	0.000437	T	0.34308	0.0893	N	0.24115	0.695	0.80722	D	1	P;P;P	0.45957	0.496;0.869;0.869	B;B;B	0.38842	0.196;0.283;0.283	T	0.21348	-1.0248	10	0.87932	D	0	-7.5831	7.9714	0.30130	0.1118:0.0:0.8882:0.0	.	203;203;203	B4DJX7;F5GZE4;Q8WUB2	.;.;CL024_HUMAN	K	203;203;109;12	ENSP00000366901:R203K	ENSP00000366901:R203K	R	+	2	0	C12orf24	109408893	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	2.253000	0.43205	1.038000	0.40049	0.467000	0.42956	AGA	.	.		0.468	FAM216A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404616.1	NM_013300	
KL	9365	hgsc.bcm.edu	37	13	33591317	33591317	+	Missense_Mutation	SNP	G	G	A			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr13:33591317G>A	ENST00000380099.3	+	1	747	c.739G>A	c.(739-741)Ggc>Agc	p.G247S	KL_ENST00000487852.1_3'UTR|KL_ENST00000426690.2_Intron	NM_004795.3	NP_004786.2	Q9UEF7	KLOT_HUMAN	klotho	247	Glycosyl hydrolase-1 1.				acute inflammatory response (GO:0002526)|aging (GO:0007568)|calcium ion homeostasis (GO:0055074)|carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-glucosidase activity (GO:0008422)|beta-glucuronidase activity (GO:0004566)|fibroblast growth factor binding (GO:0017134)|signal transducer activity (GO:0004871)|vitamin D binding (GO:0005499)			breast(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|skin(5)	41	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		GGCCTGGCACGGCTACGCCAC	0.692																																					p.G247S		Atlas-SNP	.											.	KL	106	.	0			c.G739A						.						17.0	16.0	16.0					13																	33591317		2101	4091	6192	SO:0001583	missense	9365	exon1			TGGCACGGCTACG	AB005142	CCDS9347.1	13q12	2008-02-05			ENSG00000133116	ENSG00000133116			6344	protein-coding gene	gene with protein product		604824				9464267	Standard	NM_004795		Approved		uc001uus.3	Q9UEF7	OTTHUMG00000017408	ENST00000380099.3:c.739G>A	chr13.hg19:g.33591317G>A	ENSP00000369442:p.Gly247Ser	36.0	0.0		66.0	20.0	NM_004795	Q5VZ95|Q96KV5|Q96KW5|Q9UEI9|Q9Y4F0	Missense_Mutation	SNP	ENST00000380099.3	hg19	CCDS9347.1	.	.	.	.	.	.	.	.	.	.	G	29.5	5.011954	0.93346	.	.	ENSG00000133116	ENST00000380099	T	0.35048	1.33	4.55	4.55	0.56014	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	T	0.62221	0.2410	M	0.78456	2.415	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.66602	-0.5882	10	0.54805	T	0.06	-26.5644	17.4992	0.87727	0.0:0.0:1.0:0.0	.	247	Q9UEF7	KLOT_HUMAN	S	247	ENSP00000369442:G247S	ENSP00000369442:G247S	G	+	1	0	KL	32489317	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.256000	0.95535	2.357000	0.79964	0.563000	0.77884	GGC	.	.		0.692	KL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045987.1		
NFATC4	4776	hgsc.bcm.edu	37	14	24845611	24845611	+	Missense_Mutation	SNP	C	C	T			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr14:24845611C>T	ENST00000250373.4	+	9	2309	c.2168C>T	c.(2167-2169)cCc>cTc	p.P723L	NFATC4_ENST00000554966.1_Missense_Mutation_p.P736L|NFATC4_ENST00000554591.1_Missense_Mutation_p.P786L|NFATC4_ENST00000555393.1_Missense_Mutation_p.P11L|NFATC4_ENST00000555453.1_Missense_Mutation_p.P711L|NFATC4_ENST00000413692.2_Missense_Mutation_p.P786L|NFATC4_ENST00000556279.1_Missense_Mutation_p.P755L|NFATC4_ENST00000539237.2_Missense_Mutation_p.P755L|NFATC4_ENST00000422617.3_Missense_Mutation_p.P711L|NFATC4_ENST00000554661.1_Missense_Mutation_p.P653L|NFATC4_ENST00000554050.1_Missense_Mutation_p.P723L|NFATC4_ENST00000555802.1_Missense_Mutation_p.P11L|NFATC4_ENST00000554473.1_Missense_Mutation_p.P258L|NFATC4_ENST00000556759.1_Missense_Mutation_p.P258L|NFATC4_ENST00000554344.1_Missense_Mutation_p.P653L|NFATC4_ENST00000555167.1_Missense_Mutation_p.P258L|NFATC4_ENST00000553708.1_Missense_Mutation_p.P723L|NFATC4_ENST00000424781.2_Missense_Mutation_p.P736L|NFATC4_ENST00000553469.1_Missense_Mutation_p.P755L|NFATC4_ENST00000557451.1_Missense_Mutation_p.P653L|NFATC4_ENST00000556169.1_Missense_Mutation_p.P711L|NFATC4_ENST00000557767.1_Missense_Mutation_p.P11L|NFATC4_ENST00000553879.1_Missense_Mutation_p.P653L|NFATC4_ENST00000555590.1_Missense_Mutation_p.P736L	NM_004554.4	NP_004545.2	Q14934	NFAC4_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4	723	Pro-rich.				cellular respiration (GO:0045333)|cellular response to lithium ion (GO:0071285)|cellular response to UV (GO:0034644)|heart development (GO:0007507)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of synaptic plasticity (GO:0048167)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	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 negative regulation of transcription (GO:0001078)|transcription coactivator activity (GO:0003713)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(7)|liver(4)|lung(12)|ovary(1)|skin(2)	34				GBM - Glioblastoma multiforme(265;0.018)		CCCCCCTACCCCTCCTATCCC	0.617																																					p.P786L		Atlas-SNP	.											.	NFATC4	115	.	0			c.C2357T						.						61.0	68.0	65.0					14																	24845611		2203	4300	6503	SO:0001583	missense	4776	exon10			CCTACCCCTCCTA	BC053855	CCDS9629.1, CCDS45089.1, CCDS55909.1, CCDS55910.1, CCDS55911.1, CCDS73625.1	14q11.2	2009-11-24			ENSG00000100968	ENSG00000100968		"""Nuclear factor of activated T-cells"""	7778	protein-coding gene	gene with protein product		602699				7749981	Standard	NM_004554		Approved	NFAT3	uc010tok.2	Q14934	OTTHUMG00000029351	ENST00000250373.4:c.2168C>T	chr14.hg19:g.24845611C>T	ENSP00000250373:p.Pro723Leu	101.0	0.0		127.0	23.0	NM_001198967	B4DDG5|B4DY55|B5B2U7|B5B2U8|B5B2U9|B5B2V0|B5B2V1|B5B2V2|B5B2V3|B5B2V4|B5B2V5|B5B2V7|B5B2V8|B5B2V9|B5B2W0|B5B2W1|B5B2W2|B5B2W3|B5B2W4|B5B2W5|B5B2W6|B5B2W7|B5B2W8|B5B2W9|B5B2X0|Q7Z598|Q96H68	Missense_Mutation	SNP	ENST00000250373.4	hg19	CCDS9629.1	.	.	.	.	.	.	.	.	.	.	C	14.90	2.674926	0.47781	.	.	ENSG00000100968	ENST00000413692;ENST00000554591;ENST00000555590;ENST00000554966;ENST00000424781;ENST00000539237;ENST00000556279;ENST00000553469;ENST00000554050;ENST00000250373;ENST00000553708;ENST00000553879;ENST00000554344;ENST00000554661;ENST00000556169;ENST00000557451;ENST00000422617;ENST00000555453;ENST00000554473;ENST00000556759;ENST00000555167;ENST00000557767;ENST00000555393;ENST00000555802	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.51325	3.16;3.02;3.19;3.03;3.21;3.2;3.18;3.01;3.03;3.18;3.18;2.88;2.88;2.77;2.7;2.9;2.88;2.86;1.38;1.51;1.48;0.79;0.71	5.13	5.13	0.70059	.	0.213578	0.33895	N	0.004445	T	0.29028	0.0721	N	0.14661	0.345	0.47441	D	0.999426	B;B;B;B;B;B;B;B;B;B;B;B;B	0.26547	0.065;0.007;0.027;0.027;0.027;0.027;0.027;0.152;0.152;0.007;0.027;0.152;0.016	B;B;B;B;B;B;B;B;B;B;B;B;B	0.24006	0.023;0.015;0.025;0.035;0.025;0.025;0.025;0.05;0.05;0.015;0.035;0.05;0.011	T	0.10200	-1.0640	10	0.12103	T	0.63	-6.9713	13.9397	0.64048	0.0:1.0:0.0:0.0	.	711;711;755;755;736;736;736;786;786;711;755;786;723	Q14934-17;Q14934-9;Q14934-14;Q14934-4;Q14934-15;Q14934-6;Q14934-7;Q14934-2;Q14934-3;Q14934-10;Q14934-5;Q14934-11;Q14934	.;.;.;.;.;.;.;.;.;.;.;.;NFAC4_HUMAN	L	786;786;736;736;736;755;755;755;723;723;723;653;653;653;711;653;711;711;258;258;258;11;11;11	ENSP00000388910:P786L;ENSP00000452039:P786L;ENSP00000451224:P736L;ENSP00000450644:P736L;ENSP00000388668:P736L;ENSP00000439350:P755L;ENSP00000452270:P755L;ENSP00000451502:P755L;ENSP00000451151:P723L;ENSP00000250373:P723L;ENSP00000450590:P723L;ENSP00000452349:P653L;ENSP00000450469:P653L;ENSP00000450733:P653L;ENSP00000451454:P711L;ENSP00000451284:P653L;ENSP00000396788:P711L;ENSP00000450686:P711L;ENSP00000450810:P258L;ENSP00000451183:P258L;ENSP00000451395:P258L;ENSP00000451801:P11L;ENSP00000451590:P11L	ENSP00000250373:P723L	P	+	2	0	NFATC4	23915451	0.994000	0.37717	1.000000	0.80357	0.993000	0.82548	3.423000	0.52756	2.667000	0.90743	0.561000	0.74099	CCC	.	.		0.617	NFATC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073206.6	NM_004554	
GPHN	10243	hgsc.bcm.edu	37	14	67525478	67525478	+	Silent	SNP	T	T	A			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr14:67525478T>A	ENST00000315266.5	+	10	2141	c.1020T>A	c.(1018-1020)ctT>ctA	p.L340L	GPHN_ENST00000459628.1_Silent_p.L355L|GPHN_ENST00000543237.1_Silent_p.L386L|GPHN_ENST00000544752.2_3'UTR|GPHN_ENST00000305960.9_Silent_p.L309L|GPHN_ENST00000478722.1_Silent_p.L373L	NM_001024218.1	NP_001019389.1	Q9NQX3	GEPH_HUMAN	gephyrin	340	MPT adenylyltransferase.				establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycine receptor clustering (GO:0072579)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|molybdopterin adenylyltransferase activity (GO:0061598)|molybdopterin molybdotransferase activity (GO:0061599)|transferase activity (GO:0016740)			large_intestine(8)|liver(1)|ovary(2)|stomach(1)	12		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		CTCCGGTGCTTGGGACAGAAA	0.398			T	MLL	AL																																p.L373L		Atlas-SNP	.		Dom	yes		14	14q24	10243	gephyrin (GPH)		L	.	GPHN	79	.	0			c.T1119A						.						173.0	166.0	168.0					14																	67525478		2203	4300	6503	SO:0001819	synonymous_variant	10243	exon11			GGTGCTTGGGACA	AB037806	CCDS9777.1, CCDS32103.1	14q23.3	2008-04-22			ENSG00000171723	ENSG00000171723			15465	protein-coding gene	gene with protein product		603930				1319186, 10325225, 18403029	Standard	XM_005267250		Approved	KIAA1385	uc001xix.3	Q9NQX3	OTTHUMG00000029785	ENST00000315266.5:c.1020T>A	chr14.hg19:g.67525478T>A		45.0	0.0		51.0	17.0	NM_020806	Q9H4E9|Q9P2G2	Silent	SNP	ENST00000315266.5	hg19	CCDS32103.1																																																																																			.	.		0.398	GPHN-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000074299.2	NM_020806	
CIITA	4261	hgsc.bcm.edu	37	16	10989526	10989526	+	Splice_Site	SNP	A	A	T	rs200879588		TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr16:10989526A>T	ENST00000324288.8	+	3	333	c.200A>T	c.(199-201)gAa>gTa	p.E67V	CIITA_ENST00000537380.1_3'UTR|CIITA_ENST00000381835.5_Splice_Site_p.E67V	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	67	Asp/Glu-rich (acidic).				aging (GO:0007568)|cellular response to electrical stimulus (GO:0071257)|cellular response to exogenous dsRNA (GO:0071360)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to antibiotic (GO:0046677)|response to interferon-gamma (GO:0034341)|transcription, DNA-templated (GO:0006351)	cell surface (GO:0009986)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|GTP binding (GO:0005525)|kinase activity (GO:0016301)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transferase activity, transferring acyl groups (GO:0016746)			central_nervous_system(1)|large_intestine(7)|ovary(1)|skin(1)|stomach(2)	12						TTCCTCCCAGAACCCGACACA	0.552			T	"""FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"""	"""PMBL, Hodgkin Lymphona, """																																p.E67V		Atlas-SNP	.		Dom	yes		16	16p13	4261	"""class II, major histocompatibility complex, transactivator"""		L	.	CIITA	92	.	0			c.A200T						.						77.0	75.0	75.0					16																	10989526		2197	4300	6497	SO:0001630	splice_region_variant	4261	exon3			TCCCAGAACCCGA	U18259	CCDS10544.1, CCDS66943.1, CCDS73826.1	16p13	2014-09-17	2005-08-12	2005-08-12	ENSG00000179583	ENSG00000179583		"""Nucleotide-binding domain and leucine rich repeat containing"""	7067	protein-coding gene	gene with protein product	"""NLR family, acid domain containing"", ""nucleotide-binding oligomerization domain, leucine rich repeat and acid domain containing"""	600005	"""MHC class II transactivator"""	MHC2TA		8402893	Standard	NM_000246		Approved	C2TA, NLRA	uc002dai.4	P33076	OTTHUMG00000129753	ENST00000324288.8:c.200-1A>T	chr16.hg19:g.10989526A>T		121.0	0.0		120.0	32.0	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Missense_Mutation	SNP	ENST00000324288.8	hg19	CCDS10544.1	.	.	.	.	.	.	.	.	.	.	A	19.86	3.904970	0.72868	.	.	ENSG00000179583	ENST00000324288;ENST00000381835;ENST00000388910;ENST00000537380	T;T	0.77489	-1.1;1.25	4.78	4.78	0.61160	.	0.326457	0.21745	N	0.069773	T	0.82235	0.4993	L	0.48642	1.525	0.31959	N	0.608646	D;D;P;P;D;D	0.76494	0.999;0.997;0.954;0.954;0.987;0.993	D;P;P;P;P;P	0.70487	0.969;0.829;0.572;0.572;0.809;0.776	T	0.83045	-0.0155	9	.	.	.	.	10.7295	0.46087	1.0:0.0:0.0:0.0	.	67;67;67;67;67;67	F5H2J4;E9PFE0;A0N0N9;P33076;F2Z2G8;Q96KL4	.;.;.;C2TA_HUMAN;.;.	V	67	ENSP00000316328:E67V;ENSP00000371257:E67V	.	E	+	2	0	CIITA	10897027	0.996000	0.38824	0.840000	0.33206	0.833000	0.47200	4.088000	0.57678	1.801000	0.52704	0.533000	0.62120	GAA	.	A|0.999;G|0.001		0.552	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246	Missense_Mutation
POLR3E	55718	hgsc.bcm.edu	37	16	22325438	22325438	+	Missense_Mutation	SNP	A	A	G			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr16:22325438A>G	ENST00000299853.5	+	8	678	c.511A>G	c.(511-513)Aag>Gag	p.K171E	POLR3E_ENST00000359210.4_Missense_Mutation_p.K171E|POLR3E_ENST00000564209.1_Missense_Mutation_p.K171E|POLR3E_ENST00000418581.2_Missense_Mutation_p.K135E	NM_001258033.1|NM_001258035.1|NM_018119.3	NP_001244962.1|NP_001244964.1|NP_060589.1	Q9NVU0	RPC5_HUMAN	polymerase (RNA) III (DNA directed) polypeptide E (80kD)	171					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	centrosome (GO:0005813)|cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA-directed RNA polymerase activity (GO:0003899)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27				GBM - Glioblastoma multiforme(48;0.012)		AGACGATGTTAAGCAGATCAC	0.617																																					p.K171E		Atlas-SNP	.											.	POLR3E	62	.	0			c.A511G						.						61.0	49.0	53.0					16																	22325438		2197	4300	6497	SO:0001583	missense	55718	exon8			GATGTTAAGCAGA	AY092085	CCDS10605.1, CCDS58432.1, CCDS58433.1, CCDS58434.1, CCDS73845.1	16p12	2013-01-21			ENSG00000058600	ENSG00000058600		"""RNA polymerase subunits"""	30347	protein-coding gene	gene with protein product						10819331, 10521666	Standard	NM_018119		Approved	RPC5, SIN, FLJ10509	uc002dkk.4	Q9NVU0	OTTHUMG00000094779	ENST00000299853.5:c.511A>G	chr16.hg19:g.22325438A>G	ENSP00000299853:p.Lys171Glu	67.0	0.0		79.0	4.0	NM_001258033	B4DL24|B4DUP6|H3BT11|Q9BWF7|Q9H8W8|Q9H907|Q9P276	Missense_Mutation	SNP	ENST00000299853.5	hg19	CCDS10605.1	.	.	.	.	.	.	.	.	.	.	A	34	5.292316	0.95546	.	.	ENSG00000058600	ENST00000299853;ENST00000359210;ENST00000418581	T;T;T	0.44881	0.91;0.91;0.91	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.61073	0.2318	L	0.56769	1.78	0.80722	D	1	D;P;D;D;D;D	0.67145	0.996;0.926;0.993;0.995;0.996;0.991	D;P;D;D;D;D	0.69479	0.964;0.802;0.951;0.919;0.951;0.919	T	0.63637	-0.6592	10	0.87932	D	0	-35.7917	16.0282	0.80558	1.0:0.0:0.0:0.0	.	115;135;171;171;171;171	B4DDR0;B4DL24;B4DUP6;Q9NVU0-2;Q9NVU0;Q9NVU0-3	.;.;.;.;RPC5_HUMAN;.	E	171;171;135	ENSP00000299853:K171E;ENSP00000352140:K171E;ENSP00000399254:K135E	ENSP00000299853:K171E	K	+	1	0	POLR3E	22232939	1.000000	0.71417	0.992000	0.48379	0.934000	0.57294	8.636000	0.91010	2.268000	0.75426	0.454000	0.30748	AAG	.	.		0.617	POLR3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211590.1	NM_018119	
ATMIN	23300	hgsc.bcm.edu	37	16	81075037	81075037	+	Missense_Mutation	SNP	G	G	A			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr16:81075037G>A	ENST00000299575.4	+	2	437	c.413G>A	c.(412-414)tGc>tAc	p.C138Y	ATMIN_ENST00000564241.1_5'UTR|ATMIN_ENST00000539819.1_3'UTR|ATMIN_ENST00000566488.1_5'UTR	NM_015251.2	NP_056066.2	O43313	ATMIN_HUMAN	ATM interactor	138					cellular response to DNA damage stimulus (GO:0006974)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dynein binding (GO:0045502)|metal ion binding (GO:0046872)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	20						ATTGAAGGCTGCCCCAGAGGC	0.403																																					p.C138Y		Atlas-SNP	.											.	ATMIN	50	.	0			c.G413A						.						124.0	128.0	127.0					16																	81075037		2202	4300	6502	SO:0001583	missense	23300	exon2			AAGGCTGCCCCAG	BC002701	CCDS32494.1, CCDS73917.1	16q23.2	2013-01-07			ENSG00000166454	ENSG00000166454		"""Zinc fingers, C2H2-type"""	29034	protein-coding gene	gene with protein product	"""ATM/ATR-Substrate Chk2-Interacting Zn++-finger protein"", ""ATM INteracting protein"""	614693				15933716, 17525732, 19001856	Standard	XM_005255866		Approved	ASCIZ, KIAA0431, ZNF822	uc002ffz.1	O43313	OTTHUMG00000176469	ENST00000299575.4:c.413G>A	chr16.hg19:g.81075037G>A	ENSP00000299575:p.Cys138Tyr	374.0	0.0		267.0	122.0	NM_015251	A8K4H8|Q68DC9	Missense_Mutation	SNP	ENST00000299575.4	hg19	CCDS32494.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.884502	0.91814	.	.	ENSG00000166454	ENST00000299575	T	0.67698	-0.28	5.51	5.51	0.81932	Zinc finger, C2H2-like (1);	0.000000	0.85682	D	0.000000	T	0.76212	0.3956	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.78048	-0.2356	10	0.87932	D	0	-12.6354	19.7859	0.96437	0.0:0.0:1.0:0.0	.	138	O43313	ATMIN_HUMAN	Y	138	ENSP00000299575:C138Y	ENSP00000299575:C138Y	C	+	2	0	ATMIN	79632538	1.000000	0.71417	0.998000	0.56505	0.942000	0.58702	9.720000	0.98763	2.746000	0.94184	0.655000	0.94253	TGC	.	.		0.403	ATMIN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432140.1	NM_015251	
EPN2	22905	hgsc.bcm.edu	37	17	19186882	19186882	+	Silent	SNP	C	C	G			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr17:19186882C>G	ENST00000314728.5	+	3	934	c.450C>G	c.(448-450)acC>acG	p.T150T	EPN2_ENST00000395626.1_Silent_p.T150T|EPN2_ENST00000347697.2_Silent_p.T150T|EPN2_ENST00000575595.1_Intron|EPN2_ENST00000395620.2_Silent_p.T150T|EPN2_ENST00000395618.3_Intron|EPN2_ENST00000571254.1_Silent_p.T150T	NM_014964.4	NP_055779.2	O95208	EPN2_HUMAN	epsin 2	150					embryonic organ development (GO:0048568)|endocytosis (GO:0006897)|in utero embryonic development (GO:0001701)|Notch signaling pathway (GO:0007219)	clathrin coat of endocytic vesicle (GO:0030128)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	lipid binding (GO:0008289)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	19	all_cancers(12;3.11e-05)|all_epithelial(12;0.00121)|Hepatocellular(7;0.00345)|Breast(13;0.143)					CTCTCAAAACCAAAGAGCGCA	0.602																																					p.T150T		Atlas-SNP	.											.	EPN2	52	.	0			c.C450G						.						51.0	52.0	52.0					17																	19186882		2203	4300	6503	SO:0001819	synonymous_variant	22905	exon3			CAAAACCAAAGAG	AB028988	CCDS11203.1, CCDS11204.1, CCDS42277.1	17p11.2	2012-11-19			ENSG00000072134	ENSG00000072134			18639	protein-coding gene	gene with protein product	"""Eps15 binding protein"""	607263				10567358	Standard	NM_014964		Approved	KIAA1065, EHB21	uc002gvd.4	O95208	OTTHUMG00000178447	ENST00000314728.5:c.450C>G	chr17.hg19:g.19186882C>G		88.0	0.0		92.0	26.0	NM_148921	A8MTV8|B3KRX8|E9PBC2|O95207|Q52LD0|Q9H7Z2|Q9UPT7	Silent	SNP	ENST00000314728.5	hg19	CCDS11203.1																																																																																			.	.		0.602	EPN2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132283.3	NM_014964	
NF1	4763	hgsc.bcm.edu	37	17	29588781	29588781	+	Missense_Mutation	SNP	G	G	A			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr17:29588781G>A	ENST00000358273.4	+	35	5013	c.4630G>A	c.(4630-4632)Gca>Aca	p.A1544T	NF1_ENST00000356175.3_Missense_Mutation_p.A1523T	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	1544					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		AACACTTCTTGCATACCTGGG	0.408			"""D, Mis, N, F, S, O"""		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																											p.A1544T		Atlas-SNP	.	yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	.	NF1	1586	.	12	Whole gene deletion(8)|Unknown(4)	soft_tissue(7)|autonomic_ganglia(2)|central_nervous_system(2)|lung(1)	c.G4630A						.						118.0	104.0	109.0					17																	29588781		2203	4300	6503	SO:0001583	missense	4763	exon35	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	CTTCTTGCATACC		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"""neurofibromatosis"", ""von Recklinghausen disease"", ""Watson disease"""	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.4630G>A	chr17.hg19:g.29588781G>A	ENSP00000351015:p.Ala1544Thr	192.0	0.0		304.0	86.0	NM_001042492	O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	ENST00000358273.4	hg19	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	G	36	5.690594	0.96793	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735	D;D;D	0.81579	-1.51;-1.51;-1.51	5.68	5.68	0.88126	Rho GTPase activation protein (1);Armadillo-type fold (1);Ras GTPase-activating protein (1);	0.054740	0.64402	D	0.000001	D	0.87051	0.6081	L	0.46157	1.445	0.80722	D	1	D;P;D	0.58620	0.973;0.844;0.983	P;P;D	0.70016	0.729;0.501;0.967	D	0.87090	0.2172	10	0.59425	D	0.04	.	18.7806	0.91930	0.0:0.0:1.0:0.0	.	573;1523;1544	Q59FX3;P21359-2;P21359	.;.;NF1_HUMAN	T	1544;1523;1189	ENSP00000351015:A1544T;ENSP00000348498:A1523T;ENSP00000389907:A1189T	ENSP00000348498:A1523T	A	+	1	0	NF1	26612907	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.196000	0.94978	2.681000	0.91329	0.650000	0.86243	GCA	.	.		0.408	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267	
SUZ12	23512	hgsc.bcm.edu	37	17	30321616	30321616	+	Missense_Mutation	SNP	A	A	G			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr17:30321616A>G	ENST00000322652.5	+	13	1700	c.1471A>G	c.(1471-1473)Atc>Gtc	p.I491V	SUZ12_ENST00000580398.1_Missense_Mutation_p.I468V	NM_015355.2	NP_056170.2	Q15022	SUZ12_HUMAN	SUZ12 polycomb repressive complex 2 subunit	491					histone ubiquitination (GO:0016574)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|histone methyltransferase activity (GO:0042054)|metal ion binding (GO:0046872)|methylated histone binding (GO:0035064)|RNA binding (GO:0003723)|sequence-specific DNA binding (GO:0043565)		SSH2/SUZ12(2)|JAZF1/SUZ12(133)	breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|lung(5)|skin(1)	21		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.041)|Ovarian(249;0.182)|Breast(31;0.231)				AGATGTTTCTATCAATGAGTG	0.358			T	JAZF1	endometrial stromal tumours																																p.I491V		Atlas-SNP	.		Dom	yes		17	17q11.2	23512	suppressor of zeste 12 homolog (Drosophila)		M	.	SUZ12	61	.	0			c.A1471G						.						98.0	87.0	91.0					17																	30321616		2203	4300	6503	SO:0001583	missense	23512	exon13			GTTTCTATCAATG	D63881	CCDS11270.1	17q21	2013-06-05	2013-06-05		ENSG00000178691	ENSG00000178691		"""Zinc fingers, C2H2-type"""	17101	protein-coding gene	gene with protein product		606245	"""suppressor of zeste 12 homolog (Drosophila)"""			8590280, 11371647, 18784248	Standard	NM_015355		Approved	JJAZ1, KIAA0160, CHET9	uc002hgs.2	Q15022	OTTHUMG00000132813	ENST00000322652.5:c.1471A>G	chr17.hg19:g.30321616A>G	ENSP00000316578:p.Ile491Val	84.0	0.0		126.0	60.0	NM_015355	Q96BD9	Missense_Mutation	SNP	ENST00000322652.5	hg19	CCDS11270.1	.	.	.	.	.	.	.	.	.	.	a	12.60	1.986490	0.35036	.	.	ENSG00000178691	ENST00000322652	T	0.44083	0.93	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	T	0.37812	0.1017	L	0.46157	1.445	0.54753	D	0.999984	B;B	0.25521	0.059;0.128	B;B	0.23716	0.023;0.048	T	0.15578	-1.0432	10	0.33141	T	0.24	-7.7038	14.8417	0.70230	1.0:0.0:0.0:0.0	.	491;491	A8K1U9;Q15022	.;SUZ12_HUMAN	V	491	ENSP00000316578:I491V	ENSP00000316578:I491V	I	+	1	0	SUZ12	27345729	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.572000	0.82409	1.894000	0.54839	0.523000	0.50628	ATC	.	.		0.358	SUZ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256260.2	NM_015355	
PSMC5	5705	hgsc.bcm.edu	37	17	61908427	61908427	+	Missense_Mutation	SNP	G	G	A			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr17:61908427G>A	ENST00000310144.6	+	8	1019	c.711G>A	c.(709-711)atG>atA	p.M237I	PSMC5_ENST00000580864.1_Missense_Mutation_p.M229I|PSMC5_ENST00000581882.1_Missense_Mutation_p.M229I|FTSJ3_ENST00000580295.1_5'Flank|PSMC5_ENST00000375812.4_Missense_Mutation_p.M229I	NM_002805.5	NP_002796.4	P62195	PRS8_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 5	237	May mediate interaction with PRPF9. {ECO:0000250|UniProtKB:P62196}.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of inclusion body assembly (GO:0090261)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|nuclear proteasome complex (GO:0031595)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|thyrotropin-releasing hormone receptor binding (GO:0031531)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			endometrium(3)|kidney(2)|large_intestine(8)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	20						TGTTTGTCATGGCACGGGAAC	0.562																																					p.M237I		Atlas-SNP	.											.	PSMC5	41	.	0			c.G711A						.						81.0	78.0	79.0					17																	61908427		2203	4300	6503	SO:0001583	missense	5705	exon8			TGTCATGGCACGG	L38810	CCDS11645.1, CCDS56043.1	17q23.3	2010-04-21			ENSG00000087191	ENSG00000087191		"""Proteasome (prosome, macropain) subunits"", ""ATPases / AAA-type"""	9552	protein-coding gene	gene with protein product		601681				9473509, 9048938	Standard	NM_002805		Approved	SUG1, p45/SUG, TBP10, p45, S8, TRIP1, SUG-1	uc002jcb.3	P62195		ENST00000310144.6:c.711G>A	chr17.hg19:g.61908427G>A	ENSP00000310572:p.Met237Ile	74.0	0.0		109.0	45.0	NM_002805	A8K3Z3|A8K763|O35051|O43208|P47210|P52915|P52916	Missense_Mutation	SNP	ENST00000310144.6	hg19	CCDS11645.1	.	.	.	.	.	.	.	.	.	.	G	18.88	3.716511	0.68844	.	.	ENSG00000087191	ENST00000310144;ENST00000375812	D;D	0.92699	-3.09;-3.09	5.64	5.64	0.86602	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.87645	0.6229	N	0.05574	-0.02	0.80722	D	1	B;B	0.30889	0.299;0.167	B;B	0.40782	0.34;0.14	D	0.86779	0.1978	10	0.62326	D	0.03	.	17.243	0.87019	0.0:0.0:1.0:0.0	.	229;237	A8K3Z3;P62195	.;PRS8_HUMAN	I	237;229	ENSP00000310572:M237I;ENSP00000364970:M229I	ENSP00000310572:M237I	M	+	3	0	PSMC5	59262159	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	9.592000	0.98245	2.937000	0.99478	0.650000	0.86243	ATG	.	.		0.562	PSMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444404.1	NM_002805	
EEF2	1938	hgsc.bcm.edu	37	19	3980917	3980917	+	Missense_Mutation	SNP	G	G	C			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr19:3980917G>C	ENST00000309311.6	-	8	1160	c.1072C>G	c.(1072-1074)Ctg>Gtg	p.L358V	EEF2_ENST00000600720.1_5'Flank|SNORD37_ENST00000384048.1_RNA	NM_001961.3	NP_001952.1	P13639	EF2_HUMAN	eukaryotic translation elongation factor 2	358	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|hematopoietic progenitor cell differentiation (GO:0002244)|positive regulation of gene expression (GO:0010628)|positive regulation of translation (GO:0045727)|translation (GO:0006412)|translational elongation (GO:0006414)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation activator activity (GO:0008494)|translation elongation factor activity (GO:0003746)			endometrium(4)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|GBM - Glioblastoma multiforme(1328;0.0223)|STAD - Stomach adenocarcinoma(1328;0.18)		GGGGAGGGCAGGTGGATGGTG	0.692																																					p.L358V	Colon(165;1804 1908 4071 6587 18799)	Atlas-SNP	.											.	EEF2	57	.	0			c.C1072G						.																																			SO:0001583	missense	1938	exon8			AGGGCAGGTGGAT	Z11692	CCDS12117.1	19p13.3	2012-09-20			ENSG00000167658	ENSG00000167658			3214	protein-coding gene	gene with protein product	"""polypeptidyl-tRNA translocase"""	130610		EF2		2610926, 6427766	Standard	NM_001961		Approved	EEF-2	uc002lze.3	P13639		ENST00000309311.6:c.1072C>G	chr19.hg19:g.3980917G>C	ENSP00000307940:p.Leu358Val	39.0	0.0		62.0	18.0	NM_001961	B2RMP5|D6W618|Q58J86	Missense_Mutation	SNP	ENST00000309311.6	hg19	CCDS12117.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.127675	0.77549	.	.	ENSG00000167658	ENST00000543343;ENST00000309311	T	0.34275	1.37	5.4	4.36	0.52297	.	0.141721	0.48286	D	0.000197	T	0.56156	0.1966	M	0.75615	2.305	0.80722	D	1	D	0.69078	0.997	D	0.79108	0.992	T	0.58476	-0.7630	10	0.66056	D	0.02	-33.3889	8.8252	0.35050	0.1724:0.0:0.8276:0.0	.	358	P13639	EF2_HUMAN	V	358	ENSP00000307940:L358V	ENSP00000307940:L358V	L	-	1	2	EEF2	3931917	1.000000	0.71417	0.996000	0.52242	0.891000	0.51852	4.014000	0.57145	1.243000	0.43853	0.561000	0.74099	CTG	.	.		0.692	EEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457615.2	NM_001961	
ARHGEF18	23370	hgsc.bcm.edu	37	19	7528790	7528790	+	Silent	SNP	A	A	C			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr19:7528790A>C	ENST00000359920.6	+	12	2411	c.2158A>C	c.(2158-2160)Agg>Cgg	p.R720R	CTD-2207O23.3_ENST00000593531.1_Silent_p.P677P|ARHGEF18_ENST00000319670.9_Silent_p.R562R	NM_001130955.1	NP_001124427.1	Q6ZSZ5	ARHGI_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 18	720					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transforming growth factor beta receptor signaling pathway (GO:0007179)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	23		Renal(5;0.0902)				AGGCCCGCCCAGGAGGGCTGA	0.682																																					p.R720R		Atlas-SNP	.											.	ARHGEF18	129	.	0			c.A2158C						.						21.0	22.0	22.0					19																	7528790		2192	4285	6477	SO:0001819	synonymous_variant	23370	exon12			CCGCCCAGGAGGG	AK074372	CCDS12177.1, CCDS45946.1	19p13.3	2013-01-10	2009-06-12			ENSG00000104880		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	17090	protein-coding gene	gene with protein product	"""Rho-specific guanine nucleotide exchange factor p114"""		"""rho/rac guanine nucleotide exchange factor (GEF) 18"""			9628581, 11318610	Standard	NM_015318		Approved	P114-RhoGEF, KIAA0521, MGC15913	uc002mgi.3	Q6ZSZ5		ENST00000359920.6:c.2158A>C	chr19.hg19:g.7528790A>C		208.0	0.0		231.0	12.0	NM_001130955	A8MV62|B5ME81|O60274|Q6DD92	Silent	SNP	ENST00000359920.6	hg19	CCDS45946.1																																																																																			.	.		0.682	ARHGEF18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000436340.1	NM_015318	
MUC16	94025	hgsc.bcm.edu	37	19	9075042	9075042	+	Missense_Mutation	SNP	G	G	C			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr19:9075042G>C	ENST00000397910.4	-	3	12607	c.12404C>G	c.(12403-12405)aCc>aGc	p.T4135S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4137	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AAAGAGAGTGGTCTTCTCTGA	0.502																																					p.T4135S		Atlas-SNP	.											.	MUC16	4315	.	0			c.C12404G						.						142.0	133.0	136.0					19																	9075042		2062	4189	6251	SO:0001583	missense	94025	exon3			AGAGTGGTCTTCT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.12404C>G	chr19.hg19:g.9075042G>C	ENSP00000381008:p.Thr4135Ser	154.0	0.0		131.0	6.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	8.820	0.937406	0.18206	.	.	ENSG00000181143	ENST00000397910	T	0.27720	1.65	1.93	-1.97	0.07503	.	.	.	.	.	T	0.11580	0.0282	N	0.04018	-0.295	.	.	.	B	0.27166	0.17	B	0.28709	0.093	T	0.24621	-1.0155	8	0.87932	D	0	.	0.7984	0.01070	0.1625:0.235:0.3636:0.2388	.	4135	B5ME49	.	S	4135	ENSP00000381008:T4135S	ENSP00000381008:T4135S	T	-	2	0	MUC16	8936042	0.000000	0.05858	0.002000	0.10522	0.653000	0.38743	-0.281000	0.08456	-0.390000	0.07774	0.313000	0.20887	ACC	.	.		0.502	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
MYT1	4661	hgsc.bcm.edu	37	20	62843408	62843408	+	Silent	SNP	C	C	T			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr20:62843408C>T	ENST00000328439.1	+	9	1798	c.1434C>T	c.(1432-1434)gcC>gcT	p.A478A	MYT1_ENST00000536311.1_Silent_p.A478A|MYT1_ENST00000360149.4_Silent_p.A180A	NM_004535.2	NP_004526.1	Q99640	PMYT1_HUMAN	myelin transcription factor 1	0	Interaction with CDC2-CCNB1.|Interaction with PIN1.				G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(12)|liver(1)|lung(17)|ovary(5)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					CAGTCTTAGCCATGCATGAGA	0.607																																					p.A478A	GBM(59;481 1041 20555 21139 33705)	Atlas-SNP	.											.	MYT1	152	.	0			c.C1434T						.						147.0	133.0	138.0					20																	62843408		2203	4300	6503	SO:0001819	synonymous_variant	4661	exon9			CTTAGCCATGCAT	M96980	CCDS13558.1	20q13.33	2014-03-24			ENSG00000196132	ENSG00000196132		"""Zinc fingers, C2HC-type containing"""	7622	protein-coding gene	gene with protein product	"""neural zinc finger transcription factor 2"""	600379		PLPB1		1280325, 9268380	Standard	NM_004535		Approved	MTF1, MYTI, ZC2HC4A, NZF2	uc002yii.3	Q01538	OTTHUMG00000149988	ENST00000328439.1:c.1434C>T	chr20.hg19:g.62843408C>T		31.0	0.0		26.0	9.0	NM_004535	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Silent	SNP	ENST00000328439.1	hg19	CCDS13558.1																																																																																			.	.		0.607	MYT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080297.1	NM_004535	
BACE2	25825	hgsc.bcm.edu	37	21	42551226	42551226	+	Intron	SNP	G	G	C			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr21:42551226G>C	ENST00000330333.6	+	1	775				PLAC4_ENST00000414699.1_RNA|PLAC4_ENST00000440221.2_RNA|PLAC4_ENST00000536486.1_RNA|BACE2_ENST00000328735.6_Intron|BACE2_ENST00000347667.5_Intron|PLAC4_ENST00000430327.2_RNA|BACE2-IT1_ENST00000433378.1_RNA	NM_012105.3	NP_036237.2	Q9Y5Z0	BACE2_HUMAN	beta-site APP-cleaving enzyme 2						membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(2)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14		Prostate(19;1.57e-07)|all_epithelial(19;0.0251)				tgaggattgagggtgtcaggg	0.602																																					p.P110P		Atlas-SNP	.											.	.	.	.	0			c.C330G						.						152.0	132.0	139.0					21																	42551226		2190	4254	6444	SO:0001627	intron_variant	191585	exon1			GATTGAGGGTGTC	AF117892	CCDS13668.1, CCDS13669.1, CCDS13670.1	21q22.3	2011-08-11			ENSG00000182240	ENSG00000182240			934	protein-coding gene	gene with protein product		605668		AEPLC		10965118, 10830953	Standard	NM_138991		Approved	CEAP1, DRAP, ALP56	uc002yyw.3	Q9Y5Z0	OTTHUMG00000086742	ENST00000330333.6:c.312+10724G>C	chr21.hg19:g.42551226G>C		145.0	0.0		143.0	40.0	NM_182832	A8K7P1|Q5DIH8|Q8N2D4|Q9H2V8|Q9NZL1|Q9NZL2|Q9UJT6	Silent	SNP	ENST00000330333.6	hg19	CCDS13668.1																																																																																			.	.		0.602	BACE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195056.1		
PLA2G6	8398	hgsc.bcm.edu	37	22	38525570	38525570	+	Splice_Site	SNP	C	C	G			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr22:38525570C>G	ENST00000332509.3	-	8	1261		c.e8-1		PLA2G6_ENST00000402064.1_Splice_Site|PLA2G6_ENST00000335539.3_Splice_Site|PLA2G6_ENST00000490473.1_5'Flank	NM_003560.2	NP_003551.2	O60733	PLPL9_HUMAN	phospholipase A2, group VI (cytosolic, calcium-independent)						cardiolipin acyl-chain remodeling (GO:0035965)|cardiolipin biosynthetic process (GO:0032049)|cell death (GO:0008219)|chemotaxis (GO:0006935)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|glycerophospholipid biosynthetic process (GO:0046474)|innate immune response (GO:0045087)|lipid catabolic process (GO:0016042)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phospholipid metabolic process (GO:0006644)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of ceramide biosynthetic process (GO:2000304)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of exocytosis (GO:0045921)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of vasodilation (GO:0045909)|regulation of store-operated calcium channel activity (GO:1901339)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)|urinary bladder smooth muscle contraction (GO:0014832)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	calcium-independent phospholipase A2 activity (GO:0047499)|phospholipase A2 activity (GO:0004623)			breast(2)|endometrium(6)|kidney(1)|large_intestine(4)|liver(1)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	24	Melanoma(58;0.045)				Quinacrine(DB01103)	CGTTGTCTTTCTGTTGGAGAT	0.557																																					.		Atlas-SNP	.											.	PLA2G6	54	.	0			c.1078-1G>C						.						132.0	115.0	121.0					22																	38525570		2203	4300	6503	SO:0001630	splice_region_variant	8398	exon9			GTCTTTCTGTTGG	AF064594	CCDS13967.1, CCDS33645.1	22q13.1	2013-01-10			ENSG00000184381	ENSG00000184381	3.1.1.4	"""Patatin-like phospholipase domain containing"", ""Parkinson disease"", ""Ankyrin repeat domain containing"""	9039	protein-coding gene	gene with protein product	"""neurodegeneration with brain iron accumulation 2"""	603604				9417066, 16799181, 19029121	Standard	NM_001199562		Approved	iPLA2, PNPLA9, PARK14, iPLA2beta, NBIA2	uc003aux.1	O60733	OTTHUMG00000151246	ENST00000332509.3:c.1078-1G>C	chr22.hg19:g.38525570C>G		129.0	0.0		119.0	33.0	NM_001199562	A8K597|B0QYE8|O75645|Q8N452|Q9UG29|Q9UIT0|Q9Y671	Splice_Site	SNP	ENST00000332509.3	hg19	CCDS13967.1	.	.	.	.	.	.	.	.	.	.	C	17.18	3.323836	0.60634	.	.	ENSG00000184381	ENST00000332509;ENST00000419848;ENST00000335539;ENST00000402064;ENST00000335538;ENST00000396860;ENST00000452794;ENST00000451461;ENST00000427114;ENST00000427453;ENST00000452542	.	.	.	5.34	4.32	0.51571	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.408	0.67096	0.0:0.9282:0.0:0.0718	.	.	.	.	.	-1	.	.	.	-	.	.	PLA2G6	36855516	1.000000	0.71417	0.996000	0.52242	0.868000	0.49771	6.783000	0.75078	1.372000	0.46190	0.655000	0.94253	.	.	.		0.557	PLA2G6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321860.1	NM_001004426	Intron
CACNA1I	8911	hgsc.bcm.edu	37	22	40080333	40080333	+	Missense_Mutation	SNP	G	G	A			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr22:40080333G>A	ENST00000402142.3	+	36	5857	c.5857G>A	c.(5857-5859)Gcc>Acc	p.A1953T	CACNA1I_ENST00000404898.1_Missense_Mutation_p.A1918T|CACNA1I_ENST00000336649.4_Missense_Mutation_p.A1959T|CACNA1I_ENST00000401624.1_Missense_Mutation_p.A1953T|CACNA1I_ENST00000407673.1_Missense_Mutation_p.A1918T|CACNA1I_ENST00000400164.3_Missense_Mutation_p.A1918T	NM_021096.3	NP_066919.2	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type, alpha 1I subunit	1953					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|signal transduction (GO:0007165)|sleep (GO:0030431)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(2)|lung(27)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Melanoma(58;0.0749)				Cinnarizine(DB00568)|Flunarizine(DB04841)|Paramethadione(DB00617)|Spironolactone(DB00421)|Verapamil(DB00661)|Zonisamide(DB00909)	CTCCCCGGATGCCTCCAGCCC	0.642																																					p.A1953T		Atlas-SNP	.											.	CACNA1I	264	.	0			c.G5857A						.						43.0	50.0	48.0					22																	40080333		2034	4156	6190	SO:0001583	missense	8911	exon36			CCGGATGCCTCCA	AF129133	CCDS46710.1, CCDS46711.1	22q13.1	2012-03-07	2007-02-16		ENSG00000100346	ENSG00000100346		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1396	protein-coding gene	gene with protein product		608230				10454147, 16382099	Standard	NM_021096		Approved	Cav3.3	uc003ayd.3	Q9P0X4	OTTHUMG00000151096	ENST00000402142.3:c.5857G>A	chr22.hg19:g.40080333G>A	ENSP00000385019:p.Ala1953Thr	80.0	0.0		80.0	18.0	NM_021096	B0QY12|B0QY13|B0QY14|O95504|Q5JZ88|Q7Z6S9|Q8NFX6|Q9NZC8|Q9UH15|Q9UH30|Q9ULU9|Q9UNE6	Missense_Mutation	SNP	ENST00000402142.3	hg19	CCDS46710.1	.	.	.	.	.	.	.	.	.	.	G	7.192	0.591814	0.13812	.	.	ENSG00000100346	ENST00000402142;ENST00000404898;ENST00000401624;ENST00000407673;ENST00000336649;ENST00000400164	D;D;D;D;D;D	0.96716	-4.03;-4.0;-4.1;-4.07;-4.05;-3.96	5.05	4.03	0.46877	.	4.434490	0.00481	N	0.000123	D	0.90731	0.7091	N	0.08118	0	0.09310	N	1	B;B;B;B	0.06786	0.0;0.0;0.001;0.001	B;B;B;B	0.08055	0.001;0.001;0.003;0.001	T	0.80919	-0.1167	10	0.14656	T	0.56	.	8.8533	0.35212	0.225:0.0:0.775:0.0	.	1918;1953;1918;1953	Q9P0X4-3;Q9P0X4-2;Q9P0X4-4;Q9P0X4	.;.;.;CAC1I_HUMAN	T	1953;1918;1953;1918;1959;1918	ENSP00000385019:A1953T;ENSP00000384093:A1918T;ENSP00000383887:A1953T;ENSP00000385680:A1918T;ENSP00000337829:A1959T;ENSP00000383028:A1918T	ENSP00000337829:A1959T	A	+	1	0	CACNA1I	38410279	0.002000	0.14202	0.694000	0.30210	0.562000	0.35680	0.644000	0.24766	2.334000	0.79466	0.561000	0.74099	GCC	.	.		0.642	CACNA1I-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321290.1	NM_001003406	
MXRA5	25878	hgsc.bcm.edu	37	X	3235461	3235461	+	Silent	SNP	G	G	C			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chrX:3235461G>C	ENST00000217939.6	-	6	6415	c.6261C>G	c.(6259-6261)acC>acG	p.T2087T		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	2087	Ig-like C2-type 5.					extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				GGCGGATCTGGGTACCGTCCC	0.647																																					p.T2087T		Atlas-SNP	.											.	MXRA5	815	.	0			c.C6261G						.						32.0	28.0	29.0					X																	3235461		2194	4288	6482	SO:0001819	synonymous_variant	25878	exon6			GATCTGGGTACCG	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7539	protein-coding gene	gene with protein product	"""adlican"""					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.6261C>G	chrX.hg19:g.3235461G>C		69.0	0.0		61.0	34.0	NM_015419	Q6P1M7|Q9Y3Y8	Silent	SNP	ENST00000217939.6	hg19	CCDS14124.1																																																																																			.	.		0.647	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419	
NXF5	55998	hgsc.bcm.edu	37	X	101092559	101092559	+	Silent	SNP	A	A	T			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chrX:101092559A>T	ENST00000361708.2	-	15	1346	c.987T>A	c.(985-987)ccT>ccA	p.P329P	NXF5_ENST00000473265.2_Silent_p.P329P|NXF5_ENST00000537026.1_Silent_p.P329P			Q9H1B4	NXF5_HUMAN	nuclear RNA export factor 5	329	NTF2; truncated.				mRNA export from nucleus (GO:0006406)|multicellular organismal development (GO:0007275)|RNA transport (GO:0050658)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(2)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|skin(1)	30						GCTGAGTTTCAGGCAATGCAC	0.547																																					p.P329P		Atlas-SNP	.											.	NXF5	65	.	0			c.T987A						.						201.0	158.0	173.0					X																	101092559		2203	4300	6503	SO:0001819	synonymous_variant	55998	exon15			AGTTTCAGGCAAT	AJ277654	CCDS14491.1, CCDS14491.2	Xq22	2008-07-28			ENSG00000126952	ENSG00000126952			8075	protein-coding gene	gene with protein product		300319				11566096	Standard	NM_032946		Approved		uc011mrk.1	Q9H1B4	OTTHUMG00000022042	ENST00000361708.2:c.987T>A	chrX.hg19:g.101092559A>T		241.0	0.0		249.0	177.0	NM_032946	A2RRM0|B1AV82|B1AV83|B1AV84|B1AV85|Q9H1B0|Q9H1B1|Q9H1B2|Q9H1B3	Silent	SNP	ENST00000361708.2	hg19																																																																																				.	.		0.547	NXF5-201	KNOWN	basic	protein_coding	protein_coding			
LENG9	94059	hgsc.bcm.edu	37	19	54974339	54974339	+	Frame_Shift_Del	DEL	C	C	-			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr19:54974339delC	ENST00000333834.4	-	1	555	c.437delG	c.(436-438)cgcfs	p.R146fs		NM_198988.1	NP_945339.2	Q96B70	LENG9_HUMAN	leukocyte receptor cluster (LRC) member 9	146							catalytic activity (GO:0003824)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)	11	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.134)		GAAGCGCACGCGGTGCTGGGG	0.731																																					p.R146fs		Atlas-INDEL	.											.	LENG9	46	.	0			c.438delC						.						5.0	7.0	6.0					19																	54974339		2071	4126	6197	SO:0001589	frameshift_variant	94059	exon1			.	AF211976		19q13.4	2014-05-06			ENSG00000182909	ENSG00000275183			16306	protein-coding gene	gene with protein product						10941842	Standard	NM_198988		Approved		uc010yez.2	Q96B70	OTTHUMG00000188273	ENST00000333834.4:c.437delG	chr19.hg19:g.54974339delC	ENSP00000331647:p.Arg146fs	92.0	0.0		92.0	31.0	NM_198988	B2VAM3	Frame_Shift_Del	DEL	ENST00000333834.4	hg19	CCDS12895.2																																																																																			.	.		0.731	LENG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140806.3	NM_198988	
RBL2	5934	hgsc.bcm.edu	37	16	53487516	53487517	+	Frame_Shift_Ins	INS	-	-	A			TCGA-ZP-A9CZ-01A-11D-A382-10	TCGA-ZP-A9CZ-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	6d66d5db-1afc-4794-a21f-f14592ef7ea3	c0e67191-8b7f-4693-b0aa-d62f5f00ad42	g.chr16:53487516_53487517insA	ENST00000262133.6	+	6	1056_1057	c.919_920insA	c.(919-921)gaafs	p.E307fs	RBL2_ENST00000379935.4_3'UTR|RBL2_ENST00000544545.1_Frame_Shift_Ins_p.E91fs	NM_005611.3	NP_005602.3	Q08999	RBL2_HUMAN	retinoblastoma-like 2	307					chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						GAAACTTTATGAAAAAAAGGTT	0.337																																					p.E307fs		Atlas-INDEL	.											.	RBL2	115	.	0			c.919_920insA						.																																			SO:0001589	frameshift_variant	5934	exon6			.	X74594	CCDS10748.1	16q12.2	2014-03-11	2014-03-11		ENSG00000103479	ENSG00000103479			9894	protein-coding gene	gene with protein product		180203				8361765, 8643454	Standard	NM_005611		Approved	Rb2, p130	uc002ehi.4	Q08999	OTTHUMG00000133198	ENST00000262133.6:c.926dupA	chr16.hg19:g.53487523_53487523dupA	ENSP00000262133:p.Glu307fs	224.0	0.0		145.0	71.0	NM_005611	B7Z913|Q15073|Q16084|Q8NE70|Q92812	Frame_Shift_Ins	INS	ENST00000262133.6	hg19	CCDS10748.1																																																																																			.	.		0.337	RBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256908.3	NM_005611	
