#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Confidence	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_NTotCov	i_NVarCov	i_NVarRat	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_TVarRat	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	i_dbSNP_AF	i_dbSNP_PopFreq	i_dbSNP_Strength	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
TEKT2	27285	hgsc.bcm.edu	37	1	36552574	36552574	+	Silent	SNP	C	C	T			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr1:36552574C>T	ENST00000207457.3	+	6	802	c.675C>T	c.(673-675)aaC>aaT	p.N225N	ADPRHL2_ENST00000373178.4_5'Flank	NM_014466.2	NP_055281.2	Q9UIF3	TEKT2_HUMAN	tektin 2 (testicular)	225					cell projection organization (GO:0030030)|inner dynein arm assembly (GO:0036159)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|pancreas(1)|skin(2)	13		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GTCGGTTCAACAAGGACCGAG	0.592																																					p.N225N		Atlas-SNP	.											.	TEKT2	32	.	0			c.C675T						PASS	.						58.0	54.0	55.0					1																	36552574		2203	4300	6503	SO:0001819	synonymous_variant	27285	exon6			GTTCAACAAGGAC	AB033823	CCDS401.1	1p34.3	2008-02-05			ENSG00000092850	ENSG00000092850			11725	protein-coding gene	gene with protein product		608953				12029069, 11751288	Standard	NM_014466		Approved	TEKTB1	uc001bzr.3	Q9UIF3	OTTHUMG00000007629	ENST00000207457.3:c.675C>T	chr1.hg19:g.36552574C>T		65.0	0.0	.		47.0	17.0	.	NM_014466	A6NIS6|O60638	Silent	SNP	ENST00000207457.3	hg19	CCDS401.1																																																																																			.	.	.	none		0.592	TEKT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020200.1	NM_014466	
SLC35D1	23169	hgsc.bcm.edu	37	1	67519574	67519574	+	Silent	SNP	C	C	A			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr1:67519574C>A	ENST00000235345.5	-	1	208	c.123G>T	c.(121-123)ctG>ctT	p.L41L	SLC35D1_ENST00000506472.2_5'Flank	NM_015139.2	NP_055954.1	Q9NTN3	S35D1_HUMAN	solute carrier family 35 (UDP-GlcA/UDP-GalNAc transporter), member D1	41					carbohydrate transport (GO:0008643)|cellular glucuronidation (GO:0052695)|chondroitin sulfate biosynthetic process (GO:0030206)|embryonic skeletal system development (GO:0048706)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|UDP-glucuronate biosynthetic process (GO:0006065)|UDP-glucuronic acid transport (GO:0015787)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	UDP-glucuronic acid transmembrane transporter activity (GO:0005461)			endometrium(2)|kidney(1)|large_intestine(3)|lung(4)	10						CCAGCAGCTTCAGAAACACGG	0.612																																					p.L41L		Atlas-SNP	.											.	SLC35D1	22	.	0			c.G123T						PASS	.						47.0	50.0	49.0					1																	67519574		2203	4300	6503	SO:0001819	synonymous_variant	23169	exon1			CAGCTTCAGAAAC	AB044343	CCDS636.1	1p32-p31	2013-07-17	2013-07-17		ENSG00000116704	ENSG00000116704		"""Solute carriers"""	20800	protein-coding gene	gene with protein product		610804	"""solute carrier family 35 (UDP-glucuronic acid/UDP-N-acetylgalactosamine dual transporter), member D1"""			11322953	Standard	NM_015139		Approved	UGTREL7, KIAA0260	uc001ddk.2	Q9NTN3	OTTHUMG00000009360	ENST00000235345.5:c.123G>T	chr1.hg19:g.67519574C>A		194.0	0.0	.		115.0	35.0	.	NM_015139	A8K185|B7Z3X2|Q52LU5|Q92548	Silent	SNP	ENST00000235345.5	hg19	CCDS636.1																																																																																			.	.	.	none		0.612	SLC35D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025948.1	NM_015139	
ERICH3	127254	hgsc.bcm.edu	37	1	75037280	75037280	+	Missense_Mutation	SNP	C	C	A			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr1:75037280C>A	ENST00000326665.5	-	14	4332	c.4114G>T	c.(4114-4116)Gca>Tca	p.A1372S	C1orf173_ENST00000433746.2_5'UTR	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		1372	Glu-rich.									NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						GCTTTATTTGCTATTGTTTTC	0.522																																					p.A1372S		Atlas-SNP	.											.	C1orf173	380	.	0			c.G4114T						PASS	.						130.0	133.0	132.0					1																	75037280		2203	4300	6503	SO:0001583	missense	127254	exon14			TATTTGCTATTGT																												ENST00000326665.5:c.4114G>T	chr1.hg19:g.75037280C>A	ENSP00000322609:p.Ala1372Ser	149.0	0.0	.		97.0	37.0	.	NM_001002912	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Missense_Mutation	SNP	ENST00000326665.5	hg19	CCDS30755.1	.	.	.	.	.	.	.	.	.	.	C	8.132	0.783370	0.16189	.	.	ENSG00000178965	ENST00000326665	T	0.14516	2.5	5.0	3.1	0.35709	.	.	.	.	.	T	0.02688	0.0081	N	0.24115	0.695	0.09310	N	1	B	0.15473	0.013	B	0.16289	0.015	T	0.45789	-0.9237	9	0.18710	T	0.47	-4.6121	10.2042	0.43103	0.0:0.7597:0.0:0.2403	.	1372	Q5RHP9	CA173_HUMAN	S	1372	ENSP00000322609:A1372S	ENSP00000322609:A1372S	A	-	1	0	C1orf173	74809868	0.148000	0.22702	0.009000	0.14445	0.260000	0.26232	0.903000	0.28475	0.528000	0.28580	-1.134000	0.01955	GCA	.	.	.	none		0.522	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1		
ABCA4	24	hgsc.bcm.edu	37	1	94546179	94546179	+	Silent	SNP	G	G	A			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr1:94546179G>A	ENST00000370225.3	-	8	1040	c.954C>T	c.(952-954)atC>atT	p.I318I	ABCA4_ENST00000535735.1_Silent_p.I318I	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	318					phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		GGTCAGACAGGATGCCCATCA	0.542																																					p.I318I		Atlas-SNP	.											.	ABCA4	275	.	0			c.C954T						PASS	.						99.0	91.0	94.0					1																	94546179		2203	4300	6503	SO:0001819	synonymous_variant	24	exon8			AGACAGGATGCCC	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"""ATP binding cassette transporters / subfamily A"""	34	protein-coding gene	gene with protein product	"""Stargardt disease"""	601691	"""ATP-binding cassette transporter, retinal-specific"""	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.954C>T	chr1.hg19:g.94546179G>A		138.0	0.0	.		97.0	30.0	.	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Silent	SNP	ENST00000370225.3	hg19	CCDS747.1																																																																																			.	.	.	none		0.542	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350	
SLC30A7	148867	hgsc.bcm.edu	37	1	101387350	101387350	+	Missense_Mutation	SNP	A	A	G			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr1:101387350A>G	ENST00000370112.4	+	8	982	c.795A>G	c.(793-795)atA>atG	p.I265M	SLC30A7_ENST00000357650.4_Missense_Mutation_p.I265M	NM_001144884.1|NM_133496.4	NP_001138356.1|NP_598003.2	Q8NEW0	ZNT7_HUMAN	solute carrier family 30 (zinc transporter), member 7	265					cellular protein metabolic process (GO:0044267)|sequestering of zinc ion (GO:0032119)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	cation transmembrane transporter activity (GO:0008324)			endometrium(3)|large_intestine(2)|lung(10)	15		all_epithelial(167;0.000445)|all_lung(203;0.00645)|Lung NSC(277;0.0119)		Epithelial(280;0.0437)|all cancers(265;0.0498)|COAD - Colon adenocarcinoma(174;0.162)|Colorectal(144;0.19)|Lung(183;0.201)		GTCTGATGATAGCAGATCCTA	0.328																																					p.I265M	NSCLC(91;473 1491 3102 16827 21633)	Atlas-SNP	.											.	SLC30A7	33	.	0			c.A795G						PASS	.						166.0	157.0	160.0					1																	101387350		2202	4299	6501	SO:0001583	missense	148867	exon8			GATGATAGCAGAT	AF233345	CCDS776.1	1p21.1	2013-05-22			ENSG00000162695	ENSG00000162695		"""Solute carriers"""	19306	protein-coding gene	gene with protein product		611149				12446736	Standard	NM_133496		Approved	ZnTL2, ZNT7	uc001dto.2	Q8NEW0	OTTHUMG00000011815	ENST00000370112.4:c.795A>G	chr1.hg19:g.101387350A>G	ENSP00000359130:p.Ile265Met	59.0	0.0	.		31.0	11.0	.	NM_133496	B2R949|D3DT61|Q8TCH2	Missense_Mutation	SNP	ENST00000370112.4	hg19	CCDS776.1	.	.	.	.	.	.	.	.	.	.	A	18.12	3.552196	0.65311	.	.	ENSG00000162695	ENST00000370112;ENST00000357650	T;T	0.64803	-0.12;-0.12	5.62	4.46	0.54185	.	0.000000	0.85682	D	0.000000	T	0.69477	0.3115	M	0.83692	2.655	0.80722	D	1	D	0.76494	0.999	D	0.74023	0.982	T	0.72232	-0.4353	10	0.48119	T	0.1	-9.0402	7.9394	0.29950	0.721:0.1427:0.0:0.1363	.	265	Q8NEW0	ZNT7_HUMAN	M	265	ENSP00000359130:I265M;ENSP00000350278:I265M	ENSP00000350278:I265M	I	+	3	3	SLC30A7	101159938	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.388000	0.34442	0.920000	0.36970	0.533000	0.62120	ATA	.	.	.	none		0.328	SLC30A7-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032711.1	NM_133496	
HMCN1	83872	hgsc.bcm.edu	37	1	186043967	186043967	+	Missense_Mutation	SNP	G	G	T	rs561957484		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr1:186043967G>T	ENST00000271588.4	+	53	8463	c.8234G>T	c.(8233-8235)tGt>tTt	p.C2745F	HMCN1_ENST00000367492.2_Missense_Mutation_p.C2745F	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2745	Ig-like C2-type 25.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						CGATATACTTGTGTAGCATCT	0.348																																					p.C2745F		Atlas-SNP	.											.	HMCN1	797	.	0			c.G8234T						PASS	.						130.0	129.0	129.0					1																	186043967		2203	4300	6503	SO:0001583	missense	83872	exon53			ATACTTGTGTAGC	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.8234G>T	chr1.hg19:g.186043967G>T	ENSP00000271588:p.Cys2745Phe	104.0	0.0	.		97.0	4.0	.	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.610506	0.87258	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	D;D	0.89050	-2.46;-2.46	5.47	5.47	0.80525	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.97259	0.9104	H	0.99273	4.495	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.98221	1.0478	10	0.52906	T	0.07	.	19.3239	0.94253	0.0:0.0:1.0:0.0	.	2745	Q96RW7	HMCN1_HUMAN	F	2745	ENSP00000271588:C2745F;ENSP00000356462:C2745F	ENSP00000271588:C2745F	C	+	2	0	HMCN1	184310590	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	9.864000	0.99589	2.558000	0.86282	0.491000	0.48974	TGT	.	.	.	none		0.348	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
IRF2BP2	359948	hgsc.bcm.edu	37	1	234743060	234743060	+	Silent	SNP	G	G	A			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr1:234743060G>A	ENST00000366609.3	-	2	1617	c.1587C>T	c.(1585-1587)ttC>ttT	p.F529F	RP4-781K5.2_ENST00000436039.1_RNA|IRF2BP2_ENST00000366610.3_Silent_p.F513F|IRF2BP2_ENST00000491430.1_5'UTR	NM_182972.2	NP_892017.2	Q7Z5L9	I2BP2_HUMAN	interferon regulatory factor 2 binding protein 2	529	Cys-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	11	Ovarian(103;0.0303)	all_cancers(173;0.0236)|Prostate(94;0.0115)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)|Epithelial(3;6.2e-05)			AAGGGAAGCAGAACTTGTGCG	0.587																																					p.F529F		Atlas-SNP	.											.	IRF2BP2	37	.	0			c.C1587T						PASS	.						81.0	87.0	85.0					1																	234743060		2203	4300	6503	SO:0001819	synonymous_variant	359948	exon2			GAAGCAGAACTTG	AY278023	CCDS1602.1, CCDS41475.1	1q42.3	2008-02-05			ENSG00000168264	ENSG00000168264			21729	protein-coding gene	gene with protein product		615332				12799427	Standard	NM_182972		Approved	IRF-2BP2	uc001hwg.3	Q7Z5L9	OTTHUMG00000037981	ENST00000366609.3:c.1587C>T	chr1.hg19:g.234743060G>A		99.0	0.0	.		99.0	38.0	.	NM_182972	B1AM35|B1AM36|Q6P083|Q7Z5L8|Q8N351|Q8WUH8	Silent	SNP	ENST00000366609.3	hg19	CCDS1602.1																																																																																			.	.	.	none		0.587	IRF2BP2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000092705.1	NM_182972	
GRB14	2888	hgsc.bcm.edu	37	2	165477654	165477654	+	Missense_Mutation	SNP	C	C	G			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr2:165477654C>G	ENST00000263915.3	-	1	704	c.166G>C	c.(166-168)Ggg>Cgg	p.G56R		NM_004490.2	NP_004481.2	Q14449	GRB14_HUMAN	growth factor receptor-bound protein 14	56					blood coagulation (GO:0007596)|leukocyte migration (GO:0050900)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			breast(3)|endometrium(2)|large_intestine(6)|lung(10)|ovary(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	32						CCGCGGGTCCCGTCCGGAAGG	0.771																																					p.G56R		Atlas-SNP	.											.	GRB14	73	.	0			c.G166C						PASS	.						2.0	3.0	3.0					2																	165477654		1387	3094	4481	SO:0001583	missense	2888	exon1			GGGTCCCGTCCGG		CCDS2222.1	2q22-q24	2013-02-14			ENSG00000115290	ENSG00000115290		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	4565	protein-coding gene	gene with protein product		601524				8812444	Standard	XM_005246477		Approved		uc002ucl.3	Q14449	OTTHUMG00000132135	ENST00000263915.3:c.166G>C	chr2.hg19:g.165477654C>G	ENSP00000263915:p.Gly56Arg	2.0	0.0	.		53.0	30.0	.	NM_004490	B7Z7F9|Q7Z6I1	Missense_Mutation	SNP	ENST00000263915.3	hg19	CCDS2222.1	.	.	.	.	.	.	.	.	.	.	C	14.78	2.638721	0.47153	.	.	ENSG00000115290	ENST00000263915	T	0.23552	1.9	3.52	3.52	0.40303	.	0.650759	0.12693	N	0.447067	T	0.14570	0.0352	N	0.08118	0	0.80722	D	1	B	0.28055	0.199	B	0.28139	0.086	T	0.10660	-1.0620	10	0.66056	D	0.02	-0.5305	10.4807	0.44691	0.0:1.0:0.0:0.0	.	56	Q14449	GRB14_HUMAN	R	56	ENSP00000263915:G56R	ENSP00000263915:G56R	G	-	1	0	GRB14	165185900	0.128000	0.22383	0.967000	0.41034	0.993000	0.82548	1.792000	0.38754	1.822000	0.53115	0.585000	0.79938	GGG	.	.	.	none		0.771	GRB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255180.2		
ATG9A	79065	hgsc.bcm.edu	37	2	220085516	220085516	+	Missense_Mutation	SNP	C	C	T			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr2:220085516C>T	ENST00000409618.1	-	15	2906	c.2467G>A	c.(2467-2469)Gtg>Atg	p.V823M	ATG9A_ENST00000396761.2_Missense_Mutation_p.V823M|ABCB6_ENST00000265316.3_5'Flank|ABCB6_ENST00000439002.2_5'Flank|ATG9A_ENST00000361242.4_Missense_Mutation_p.V823M|ATG9A_ENST00000409422.1_Missense_Mutation_p.V762M			Q7Z3C6	ATG9A_HUMAN	autophagy related 9A	823					autophagic vacuole assembly (GO:0000045)|late nucleophagy (GO:0044805)|mitochondrion degradation (GO:0000422)|piecemeal microautophagy of nucleus (GO:0034727)|protein localization to pre-autophagosomal structure (GO:0034497)|protein transport (GO:0015031)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)				endometrium(2)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|stomach(1)	13		Renal(207;0.0474)		Epithelial(149;1.37e-06)|all cancers(144;0.000222)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCTTCGGGCACGGGCTCAGGG	0.607																																					p.V823M		Atlas-SNP	.											.	ATG9A	50	.	0			c.G2467A						PASS	.						46.0	47.0	47.0					2																	220085516		1899	4124	6023	SO:0001583	missense	79065	exon15			CGGGCACGGGCTC	AK021732	CCDS42820.1	2q35	2014-02-12	2012-06-06	2005-09-11	ENSG00000198925	ENSG00000198925			22408	protein-coding gene	gene with protein product		612204	"""APG9 autophagy 9-like 1 (S. cerevisiae)"", ""ATG9 autophagy related 9 homolog A (S. cerevisiae)"""	APG9L1			Standard	NM_024085		Approved	FLJ22169	uc002vkf.1	Q7Z3C6	OTTHUMG00000154557	ENST00000409618.1:c.2467G>A	chr2.hg19:g.220085516C>T	ENSP00000386710:p.Val823Met	42.0	0.0	.		73.0	4.0	.	NM_001077198	Q3ZAQ6|Q6P0N7|Q7Z317|Q7Z320|Q8NDK6|Q8WU65|Q9BVL5|Q9H6L1|Q9HAG7	Missense_Mutation	SNP	ENST00000409618.1	hg19	CCDS42820.1	.	.	.	.	.	.	.	.	.	.	C	16.25	3.071397	0.55646	.	.	ENSG00000198925	ENST00000396761;ENST00000409618;ENST00000361242;ENST00000409422	T;T;T;T	0.72725	-0.68;-0.68;-0.68;-0.68	5.06	5.06	0.68205	.	0.064569	0.64402	D	0.000010	T	0.65984	0.2744	L	0.34521	1.04	0.46874	D	0.999238	D	0.58268	0.982	P	0.44732	0.459	T	0.70722	-0.4794	10	0.56958	D	0.05	-11.0302	18.6114	0.91286	0.0:1.0:0.0:0.0	.	823	Q7Z3C6	ATG9A_HUMAN	M	823;823;823;762	ENSP00000379983:V823M;ENSP00000386710:V823M;ENSP00000355173:V823M;ENSP00000386535:V762M	ENSP00000355173:V823M	V	-	1	0	ATG9A	219793760	0.997000	0.39634	0.956000	0.39512	0.708000	0.40852	3.656000	0.54467	2.627000	0.88993	0.655000	0.94253	GTG	.	.	.	none		0.607	ATG9A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335930.1	NM_024085	
DES	1674	hgsc.bcm.edu	37	2	220283244	220283245	+	Missense_Mutation	DNP	GG	GG	AT	rs1058253		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr2:220283244_220283245GG>AT	ENST00000373960.3	+	1	146_147	c.60_61GG>AT	c.(58-63)ggGGcc>ggATcc	p.A21S		NM_001927.3	NP_001918.3	P17661	DESM_HUMAN	desmin	21	Head.				cytoskeleton organization (GO:0007010)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart contraction (GO:0008016)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intermediate filament (GO:0005882)|neuromuscular junction (GO:0031594)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|identical protein binding (GO:0042802)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(10)|skin(1)	18		Renal(207;0.0183)		Epithelial(149;5.25e-07)|all cancers(144;0.000103)|Lung(261;0.00533)|LUSC - Lung squamous cell carcinoma(224;0.008)		CCTTCGGCGGGGCCCCGGGCTT	0.733																																					p.G20G|p.A21S		Atlas-SNP	.											.	DES	53	.	0			c.G60A|c.G61T						PASS	.																																			SO:0001583	missense	1674	exon1			CGGCGGGGCCCCG|GGCGGGGCCCCGG	AF521879	CCDS33383.1	2q35	2014-09-17			ENSG00000175084	ENSG00000175084		"""Intermediate filaments type III"""	2770	protein-coding gene	gene with protein product	"""intermediate filament protein"""	125660				2673923, 9736733	Standard	NM_001927		Approved	CMD1I, CSM1, CSM2	uc002vll.3	P17661	OTTHUMG00000058924	Exception_encountered	chr2.hg19:g.220283244_220283245delinsAT	ENSP00000363071:p.Ala21Ser	3.0	0.0	.		29.0|31.0	21.0|24.0	.	NM_001927	Q15787|Q549R7|Q549R8|Q549R9|Q8IZR1|Q8IZR6|Q8NES2|Q8NEU6|Q8TAC4|Q8TCX2|Q8TD99|Q9UHN5|Q9UJ80	Silent|Missense_Mutation	SNP	ENST00000373960.3	hg19	CCDS33383.1																																																																																			.	G|1.000;|0.000|.	.	alt|none		0.733	DES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130240.1	NM_001927	
KIF1A	547	hgsc.bcm.edu	37	2	241696843	241696843	+	Intron	SNP	C	C	A	rs537608637|rs10594016|rs533559120		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr2:241696843C>A	ENST00000320389.7	-	25	2714				KIF1A_ENST00000498729.2_Missense_Mutation_p.E917D	NM_004321.6	NP_004312.2	Q12756	KIF1A_HUMAN	kinesin family member 1A						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)		cctcctcatcctcctcctcct	0.682													C|||	1	0.000199681	0.0	0.0014	5008	,	,		8551	0.0		0.0	False		,,,				2504	0.0				p.E917D		Atlas-SNP	.											.	KIF1A	152	.	0			c.G2751T						PASS	.																																			SO:0001627	intron_variant	547	exon27			CTCATCCTCCTCC	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.2555+933G>T	chr2.hg19:g.241696843C>A		97.0	0.0	.		189.0	11.0	.	NM_001244008	B0I1S5|F5H045|O95068|Q13355|Q14752|Q2NKJ6|Q4LE42|Q53T78|Q59GH1|Q63Z40|Q6P1R9|Q7KZ57	Missense_Mutation	SNP	ENST00000320389.7	hg19	CCDS46561.1	.	.	.	.	.	.	.	.	.	.	C	8.327	0.825706	0.16749	.	.	ENSG00000130294	ENST00000498729;ENST00000373308;ENST00000404283	T;T	0.73047	-0.63;-0.71	4.04	3.16	0.36331	.	.	.	.	.	T	0.50429	0.1615	.	.	.	0.27599	N	0.949023	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.21690	-1.0238	8	0.08381	T	0.77	.	12.6857	0.56946	0.1669:0.833:0.0:0.0	.	917;917	F5H045;Q12756-2	.;.	D	917	ENSP00000438388:E917D;ENSP00000384231:E917D	ENSP00000362405:E917D	E	-	3	2	KIF1A	241345516	0.997000	0.39634	0.999000	0.59377	0.888000	0.51559	0.203000	0.17315	0.685000	0.31468	-0.372000	0.07161	GAG	.	.	.	none		0.682	KIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324536.3	NM_138483	
SETD2	29072	hgsc.bcm.edu	37	3	47164505	47164505	+	Silent	SNP	G	G	T			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr3:47164505G>T	ENST00000409792.3	-	3	1663	c.1621C>A	c.(1621-1623)Cga>Aga	p.R541R		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	541					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		GATGACCCTCGTCGGAATCCC	0.358			"""N, F, S, Mis"""		clear cell renal carcinoma																																p.R541R		Atlas-SNP	.		Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	SETD2	721	.	0			c.C1621A						PASS	.						100.0	100.0	100.0					3																	47164505		2200	4292	6492	SO:0001819	synonymous_variant	29072	exon3			ACCCTCGTCGGAA	AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"""Chromatin-modifying enzymes / K-methyltransferases"""	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.1621C>A	chr3.hg19:g.47164505G>T		42.0	0.0	.		77.0	4.0	.	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Silent	SNP	ENST00000409792.3	hg19	CCDS2749.2																																																																																			.	.	.	none		0.358	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159	
GMPPB	29925	hgsc.bcm.edu	37	3	49759370	49759370	+	Intron	SNP	C	C	T	rs71324991		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr3:49759370C>T	ENST00000480687.1	-	9	1068				GMPPB_ENST00000308375.6_Missense_Mutation_p.E327K|AMIGO3_ENST00000535833.1_Intron|AMIGO3_ENST00000320431.7_5'Flank|GMPPB_ENST00000308388.6_Intron			Q9Y5P6	GMPPB_HUMAN	GDP-mannose pyrophosphorylase B						cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|mannose-1-phosphate guanylyltransferase activity (GO:0004475)			endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|skin(1)	6				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		CCGCCCCTCTCCCCACCCAGC	0.632																																					p.E327K		Atlas-SNP	.											.	GMPPB	14	.	0			c.G979A						PASS	.						52.0	52.0	52.0					3																	49759370		2203	4300	6503	SO:0001627	intron_variant	29925	exon8			CCCTCTCCCCACC	AF135421	CCDS2802.1, CCDS2803.1	3p21.31	2008-02-05			ENSG00000173540	ENSG00000173540	2.7.7.22		22932	protein-coding gene	gene with protein product		615320					Standard	NM_013334		Approved	KIAA1851	uc003cxl.1	Q9Y5P6	OTTHUMG00000158151	ENST00000480687.1:c.951+27G>A	chr3.hg19:g.49759370C>T		81.0	0.0	.		113.0	67.0	.	NM_013334	A8K6N5|Q9H7U3	Missense_Mutation	SNP	ENST00000480687.1	hg19	CCDS2803.1	.	.	.	.	.	.	.	.	.	.	C	4.938	0.174300	0.09391	.	.	ENSG00000173540	ENST00000308375	T	0.72942	-0.7	4.7	1.73	0.24493	.	1.157320	0.06701	N	0.771475	T	0.53722	0.1814	.	.	.	0.32702	N	0.512756	B	0.02656	0.0	B	0.01281	0.0	T	0.51988	-0.8635	9	0.24483	T	0.36	-2.0563	5.6606	0.17667	0.0:0.442:0.3934:0.1645	.	327	Q9Y5P6-2	.	K	327	ENSP00000309092:E327K	ENSP00000309092:E327K	E	-	1	0	GMPPB	49734374	0.000000	0.05858	0.023000	0.16930	0.167000	0.22549	-0.551000	0.06027	0.524000	0.28502	0.655000	0.94253	GAG	.	C|0.500;T|0.500	0.500	weak		0.632	GMPPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350291.1	NM_013334	
UBA7	7318	hgsc.bcm.edu	37	3	49847782	49847782	+	Missense_Mutation	SNP	A	A	T			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr3:49847782A>T	ENST00000333486.3	-	13	1705	c.1547T>A	c.(1546-1548)cTg>cAg	p.L516Q	UBA7_ENST00000494212.1_5'Flank	NM_003335.2	NP_003326.2	P41226	UBA7_HUMAN	ubiquitin-like modifier activating enzyme 7	516	2 approximate repeats.				cellular protein modification process (GO:0006464)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|modification-dependent protein catabolic process (GO:0019941)|negative regulation of type I interferon production (GO:0032480)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ISG15 activating enzyme activity (GO:0019782)|ubiquitin activating enzyme activity (GO:0004839)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(15)|large_intestine(4)|lung(7)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;3.58e-06)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		GGTGGGATCCAGTGGGTAGGT	0.587																																					p.L516Q		Atlas-SNP	.											.	UBA7	64	.	0			c.T1547A						PASS	.						102.0	104.0	103.0					3																	49847782		2203	4300	6503	SO:0001583	missense	7318	exon13			GGATCCAGTGGGT	BC006378	CCDS2805.1	3p21	2007-11-30	2007-11-30	2007-11-30	ENSG00000182179	ENSG00000182179		"""Ubiquitin-like modifier activating enzymes"""	12471	protein-coding gene	gene with protein product	"""UBA1, ubiquitin-activating enzyme E1 homolog B (yeast)"", ""UBA7, ubiquitin-activating enzyme E1"""	191325	"""ubiquitin-activating enzyme E1-like"""	UBE1L		8327486	Standard	NM_003335		Approved	D8, UBE2, UBA1B	uc003cxr.3	P41226	OTTHUMG00000158267	ENST00000333486.3:c.1547T>A	chr3.hg19:g.49847782A>T	ENSP00000333266:p.Leu516Gln	270.0	0.0	.		254.0	148.0	.	NM_003335	Q9BRB2	Missense_Mutation	SNP	ENST00000333486.3	hg19	CCDS2805.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.249400	0.80024	.	.	ENSG00000182179	ENST00000333486	T	0.67345	-0.26	5.67	5.67	0.87782	UBA/THIF-type NAD/FAD binding fold (1);Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	0.331674	0.29631	N	0.011601	D	0.86180	0.5871	M	0.93854	3.465	0.52501	D	0.999951	D	0.76494	0.999	D	0.74674	0.984	D	0.89830	0.3995	10	0.87932	D	0	-8.7204	15.9043	0.79412	1.0:0.0:0.0:0.0	.	516	P41226	UBA7_HUMAN	Q	516	ENSP00000333266:L516Q	ENSP00000333266:L516Q	L	-	2	0	UBA7	49822786	1.000000	0.71417	0.352000	0.25734	0.711000	0.40976	8.947000	0.93000	2.169000	0.68431	0.459000	0.35465	CTG	.	.	.	none		0.587	UBA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350503.1	NM_003335	
IGF2BP2	10644	hgsc.bcm.edu	37	3	185542743	185542743	+	Missense_Mutation	SNP	C	C	G			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr3:185542743C>G	ENST00000382199.2	-	1	101	c.6G>C	c.(4-6)atG>atC	p.M2I	IGF2BP2_ENST00000346192.3_Missense_Mutation_p.M2I|IGF2BP2_ENST00000457616.2_Missense_Mutation_p.M2I	NM_006548.4	NP_006539.3	Q9Y6M1	IF2B2_HUMAN	insulin-like growth factor 2 mRNA binding protein 2	2					anatomical structure morphogenesis (GO:0009653)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|translation regulator activity (GO:0045182)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|skin(3)	20	all_cancers(143;5.84e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)			AAAGCTTGTTCATCATCCGTC	0.706																																					p.M2I		Atlas-SNP	.											.	IGF2BP2	69	.	0			c.G6C						PASS	.						22.0	24.0	24.0					3																	185542743		2202	4300	6502	SO:0001583	missense	10644	exon1			CTTGTTCATCATC	BC021290	CCDS3273.2, CCDS33903.1	3q27.2	2013-02-12			ENSG00000073792	ENSG00000073792		"""RNA binding motif (RRM) containing"""	28867	protein-coding gene	gene with protein product	"""IGF II mRNA binding protein 2"""	608289				10190901, 9891060	Standard	NM_001007225		Approved	IMP-2	uc003fpo.3	Q9Y6M1	OTTHUMG00000074025	ENST00000382199.2:c.6G>C	chr3.hg19:g.185542743C>G	ENSP00000371634:p.Met2Ile	88.0	0.0	.		169.0	34.0	.	NM_001007225	A0A4Z0|B3FTN2|B3FTN3|B3FTN4	Missense_Mutation	SNP	ENST00000382199.2	hg19	CCDS3273.2	.	.	.	.	.	.	.	.	.	.	C	25.2	4.612112	0.87258	.	.	ENSG00000073792	ENST00000382199;ENST00000457616;ENST00000346192	T;T;T	0.20332	2.11;2.31;2.08	2.43	2.43	0.29744	.	0.000000	0.64402	U	0.000001	T	0.47358	0.1441	M	0.85197	2.74	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.998	D;D;D	0.77557	0.978;0.99;0.965	T	0.56914	-0.7900	10	0.87932	D	0	-7.2297	11.9545	0.52974	0.0:1.0:0.0:0.0	.	2;2;2	F8W930;Q9Y6M1-1;Q9Y6M1	.;.;IF2B2_HUMAN	I	2	ENSP00000371634:M2I;ENSP00000410242:M2I;ENSP00000320204:M2I	ENSP00000320204:M2I	M	-	3	0	IGF2BP2	187025437	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.717000	0.74707	1.354000	0.45846	0.393000	0.25936	ATG	.	.	.	none		0.706	IGF2BP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000157087.2	NM_006548	
NKX3-2	579	hgsc.bcm.edu	37	4	13545664	13545664	+	Silent	SNP	G	G	A			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr4:13545664G>A	ENST00000382438.5	-	1	1010	c.375C>T	c.(373-375)ctC>ctT	p.L125L	AC006445.8_ENST00000501050.1_lincRNA	NM_001189.3	NP_001180.1	P78367	NKX32_HUMAN	NK3 homeobox 2	125					determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|intestinal epithelial cell development (GO:0060576)|middle ear morphogenesis (GO:0042474)|negative regulation of apoptotic process (GO:0043066)|negative regulation of chondrocyte differentiation (GO:0032331)|organ formation (GO:0048645)|pancreas development (GO:0031016)|skeletal system development (GO:0001501)|skeletal system morphogenesis (GO:0048705)|spleen development (GO:0048536)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(1)|large_intestine(1)|lung(4)|prostate(1)	7						CCGGCTGGCCGAGGCTCAAGG	0.721																																					p.L125L		Atlas-SNP	.											.	NKX3-2	15	.	0			c.C375T						PASS	.						3.0	4.0	4.0					4																	13545664		1713	3631	5344	SO:0001819	synonymous_variant	579	exon1			CTGGCCGAGGCTC	AF009801	CCDS3410.1	4p16.3	2012-03-09	2007-07-26	2007-07-26	ENSG00000109705	ENSG00000109705		"""Homeoboxes / ANTP class : NKL subclass"""	951	protein-coding gene	gene with protein product		602183	"""bagpipe homeobox homolog 1 (Drosophila)"""	BAPX1		9344671	Standard	NM_001189		Approved	NKX3B, NKX3.2	uc003gmx.2	P78367	OTTHUMG00000090657	ENST00000382438.5:c.375C>T	chr4.hg19:g.13545664G>A		3.0	0.0	.		29.0	18.0	.	NM_001189	Q2M2I7	Silent	SNP	ENST00000382438.5	hg19	CCDS3410.1																																																																																			.	.	.	none		0.721	NKX3-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207317.3		
NIPAL1	152519	hgsc.bcm.edu	37	4	48037862	48037862	+	Silent	SNP	T	T	C			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr4:48037862T>C	ENST00000295461.5	+	6	972	c.906T>C	c.(904-906)aaT>aaC	p.N302N		NM_207330.1	NP_997213.1	Q6NVV3	NIPA3_HUMAN	NIPA-like domain containing 1	302						integral component of membrane (GO:0016021)	magnesium ion transmembrane transporter activity (GO:0015095)			endometrium(2)|large_intestine(1)|lung(3)|skin(2)	8						ACACCTTTAATACCTCTCTTG	0.423																																					p.N302N		Atlas-SNP	.											.	NIPAL1	29	.	0			c.T906C						PASS	.						138.0	122.0	127.0					4																	48037862		2203	4300	6503	SO:0001819	synonymous_variant	152519	exon6			CTTTAATACCTCT	BC067881	CCDS3479.1	4p12	2009-03-24		2009-03-24	ENSG00000163293	ENSG00000163293			27194	protein-coding gene	gene with protein product				NPAL1			Standard	NM_207330		Approved	DKFZp686A06115	uc003gxw.3	Q6NVV3	OTTHUMG00000128622	ENST00000295461.5:c.906T>C	chr4.hg19:g.48037862T>C		201.0	0.0	.		145.0	58.0	.	NM_207330	B3KTB0|Q68DA9	Silent	SNP	ENST00000295461.5	hg19	CCDS3479.1																																																																																			.	.	.	none		0.423	NIPAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250491.4	NM_207330	
MAP3K1	4214	hgsc.bcm.edu	37	5	56170960	56170960	+	Silent	SNP	G	G	T			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr5:56170960G>T	ENST00000399503.3	+	10	1788	c.1788G>T	c.(1786-1788)ctG>ctT	p.L596L		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	596					activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		GGGCCCTGCTGTTGGCAAATG	0.552																																					p.L596L		Atlas-SNP	.											.	MAP3K1	355	.	0			c.G1788T						PASS	.						88.0	87.0	87.0					5																	56170960		1908	4114	6022	SO:0001819	synonymous_variant	4214	exon10			CCTGCTGTTGGCA	U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6848	protein-coding gene	gene with protein product		600982	"""mitogen-activated protein kinase kinase kinase 1"""	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	ENST00000399503.3:c.1788G>T	chr5.hg19:g.56170960G>T		96.0	0.0	.		72.0	4.0	.	NM_005921		Silent	SNP	ENST00000399503.3	hg19	CCDS43318.1																																																																																			.	.	.	none		0.552	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066	
MSH3	4437	hgsc.bcm.edu	37	5	79970928	79970928	+	Missense_Mutation	SNP	A	A	T			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr5:79970928A>T	ENST00000265081.6	+	7	1234	c.1154A>T	c.(1153-1155)aAc>aTc	p.N385I		NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	385					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		AAAAAGGGCAACATTTTTATT	0.333								Mismatch excision repair (MMR)																													p.N385I	Melanoma(88;1010 1399 13793 26548 36275)	Atlas-SNP	.											.	MSH3	129	.	0			c.A1154T						PASS	.						148.0	152.0	151.0					5																	79970928		2203	4300	6503	SO:0001583	missense	4437	exon7			AGGGCAACATTTT	U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"""Divergent upstream protein"", ""Mismatch repair protein 1"""	600887	"""mutS (E. coli) homolog 3"", ""mutS homolog 3 (E. coli)"""				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.1154A>T	chr5.hg19:g.79970928A>T	ENSP00000265081:p.Asn385Ile	148.0	0.0	.		98.0	41.0	.	NM_002439	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Missense_Mutation	SNP	ENST00000265081.6	hg19	CCDS34195.1	.	.	.	.	.	.	.	.	.	.	A	8.987	0.976749	0.18812	.	.	ENSG00000113318	ENST00000265081;ENST00000535995	D	0.88664	-2.41	5.6	-5.6	0.02497	DNA mismatch repair protein MutS, connector (2);	0.642828	0.16451	N	0.213870	T	0.79405	0.4440	L	0.53249	1.67	0.09310	N	1	B	0.33318	0.408	B	0.34138	0.176	T	0.67783	-0.5581	9	.	.	.	-1.1852	2.0942	0.03664	0.3478:0.3369:0.2064:0.1089	.	385	P20585	MSH3_HUMAN	I	385;376	ENSP00000265081:N385I	.	N	+	2	0	MSH3	80006684	0.010000	0.17322	0.000000	0.03702	0.294000	0.27393	0.093000	0.15086	-0.822000	0.04306	-0.367000	0.07326	AAC	.	.	.	none		0.333	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439	
KDM3B	51780	hgsc.bcm.edu	37	5	137717257	137717257	+	Missense_Mutation	SNP	A	A	C			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr5:137717257A>C	ENST00000314358.5	+	6	958	c.758A>C	c.(757-759)gAt>gCt	p.D253A		NM_016604.3	NP_057688	Q7LBC6	KDM3B_HUMAN	lysine (K)-specific demethylase 3B	253					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(15)|liver(2)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	65						ATGCTGATGGATAATTCAGCG	0.433																																					p.D253A		Atlas-SNP	.											.	KDM3B	177	.	0			c.A758C						PASS	.						134.0	117.0	123.0					5																	137717257		2203	4300	6503	SO:0001583	missense	51780	exon6			TGATGGATAATTC	AF251039	CCDS34242.1	5q31	2011-07-01	2009-04-06	2009-04-06	ENSG00000120733	ENSG00000120733		"""Chromatin-modifying enzymes / K-demethylases"""	1337	protein-coding gene	gene with protein product		609373	"""chromosome 5 open reading frame 7"", ""jumonji domain containing 1B"""	C5orf7, JMJD1B		15138608	Standard	NM_016604		Approved	KIAA1082, NET22	uc003lcy.1	Q7LBC6	OTTHUMG00000163469	ENST00000314358.5:c.758A>C	chr5.hg19:g.137717257A>C	ENSP00000326563:p.Asp253Ala	87.0	0.0	.		72.0	25.0	.	NM_016604	A6H8X7|Q9BVH6|Q9BW93|Q9BZ52|Q9NYF4|Q9UPS0	Missense_Mutation	SNP	ENST00000314358.5	hg19	CCDS34242.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.253034	0.80135	.	.	ENSG00000120733	ENST00000314358;ENST00000545151	T	0.68025	-0.3	4.79	4.79	0.61399	.	0.104922	0.64402	D	0.000006	T	0.70876	0.3274	N	0.24115	0.695	0.80722	D	1	D	0.71674	0.998	D	0.75484	0.986	T	0.75357	-0.3346	10	0.72032	D	0.01	-8.6271	14.278	0.66194	1.0:0.0:0.0:0.0	.	253	Q7LBC6	KDM3B_HUMAN	A	253;43	ENSP00000326563:D253A	ENSP00000326563:D253A	D	+	2	0	KDM3B	137745156	1.000000	0.71417	0.996000	0.52242	0.876000	0.50452	6.004000	0.70709	1.905000	0.55150	0.460000	0.39030	GAT	.	.	.	none		0.433	KDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373597.1	NM_016604	
CASP8AP2	9994	hgsc.bcm.edu	37	6	90573643	90573643	+	RNA	SNP	T	T	C			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr6:90573643T>C	ENST00000551025.1	+	0	3652									caspase 8 associated protein 2											NS(1)|endometrium(7)|kidney(6)|large_intestine(12)|lung(21)|ovary(2)|urinary_tract(2)	51		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		TAATTCAGATTATTGTGGTAT	0.403																																					p.Y739H	Colon(187;1656 2025 17045 31481 39901)	Atlas-SNP	.											.	CASP8AP2	108	.	0			c.T2215C						PASS	.						69.0	67.0	67.0					6																	90573643		1866	4106	5972			9994	exon7			TCAGATTATTGTG	AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"""FLICE-associated huge protein"""	606880	"""CASP8 associated protein 2"""			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		chr6.hg19:g.90573643T>C		113.0	0.0	.		68.0	5.0	.	NM_001137667		Missense_Mutation	SNP	ENST00000551025.1	hg19																																																																																				.	.	.	none		0.403	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667	
REPS1	85021	hgsc.bcm.edu	37	6	139262487	139262487	+	Missense_Mutation	SNP	A	A	T			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr6:139262487A>T	ENST00000450536.2	-	8	1694	c.1120T>A	c.(1120-1122)Ttg>Atg	p.L374M	REPS1_ENST00000415951.2_Missense_Mutation_p.L374M|REPS1_ENST00000409812.2_Missense_Mutation_p.L374M|REPS1_ENST00000367663.4_Missense_Mutation_p.L374M|REPS1_ENST00000258062.5_Missense_Mutation_p.L374M			Q96D71	REPS1_HUMAN	RALBP1 associated Eps domain containing 1	374	EH 2. {ECO:0000255|PROSITE- ProRule:PRU00077}.				receptor-mediated endocytosis (GO:0006898)	coated pit (GO:0005905)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|SH3 domain binding (GO:0017124)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(2)	19				GBM - Glioblastoma multiforme(68;0.000434)|OV - Ovarian serous cystadenocarcinoma(155;0.000548)		GAATCTTCCAAATCAATCAGT	0.388																																					p.L374M		Atlas-SNP	.											.	REPS1	58	.	0			c.T1120A						PASS	.						167.0	170.0	169.0					6																	139262487		2203	4300	6503	SO:0001583	missense	85021	exon8			CTTCCAAATCAAT		CCDS5193.2, CCDS47488.1, CCDS69212.1, CCDS69213.1	6q24.1	2013-01-10			ENSG00000135597	ENSG00000135597		"""EF-hand domain containing"""	15578	protein-coding gene	gene with protein product		614825					Standard	XM_005267177		Approved		uc011edr.2	Q96D71	OTTHUMG00000015685	ENST00000450536.2:c.1120T>A	chr6.hg19:g.139262487A>T	ENSP00000392065:p.Leu374Met	76.0	0.0	.		64.0	12.0	.	NM_001128617	B7ZBZ8|B7ZBZ9|B7ZC00|J3KP76|Q5JWJ5|Q5JWJ6|Q5JWJ7|Q8NDR7|Q8WU62|Q9BXY9	Missense_Mutation	SNP	ENST00000450536.2	hg19		.	.	.	.	.	.	.	.	.	.	A	18.47	3.630297	0.67015	.	.	ENSG00000135597	ENST00000450536;ENST00000367663;ENST00000529597;ENST00000409812;ENST00000258062;ENST00000415951;ENST00000367668	T;T;T;T;T;T	0.35789	1.31;1.35;1.33;1.34;1.29;1.36	5.91	4.76	0.60689	.	0.000000	0.85682	D	0.000000	T	0.23014	0.0556	N	0.08118	0	0.80722	D	1	D;D;D;P;P	0.89917	1.0;1.0;1.0;0.82;0.872	D;D;D;P;B	0.80764	0.992;0.981;0.994;0.451;0.393	T	0.23904	-1.0175	10	0.45353	T	0.12	-6.2792	8.9289	0.35657	0.8584:0.0:0.1416:0.0	.	374;322;374;374;374	Q96D71-3;B2R7D3;Q96D71-2;Q96D71;E9PMG1	.;.;.;REPS1_HUMAN;.	M	374;374;360;374;374;374;322	ENSP00000392065:L374M;ENSP00000356635:L374M;ENSP00000434251:L360M;ENSP00000386699:L374M;ENSP00000258062:L374M;ENSP00000397941:L374M	ENSP00000258062:L374M	L	-	1	2	REPS1	139304180	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.783000	0.47766	1.074000	0.40909	0.533000	0.62120	TTG	.	.	.	none		0.388	REPS1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000042447.3		
PDE1C	5137	hgsc.bcm.edu	37	7	31862809	31862809	+	Missense_Mutation	SNP	C	C	A			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr7:31862809C>A	ENST00000396191.1	-	14	1915	c.1460G>T	c.(1459-1461)gGt>gTt	p.G487V	PDE1C_ENST00000396193.1_Missense_Mutation_p.G547V|PDE1C_ENST00000321453.7_Missense_Mutation_p.G487V|PDE1C_ENST00000396184.3_Missense_Mutation_p.G487V|PDE1C_ENST00000479980.1_5'Flank|PDE1C_ENST00000396182.2_Missense_Mutation_p.G487V	NM_001191057.1	NP_001177986.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	487	Catalytic. {ECO:0000250}.				activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)	cytosol (GO:0005829)	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(38)|prostate(4)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	81			GBM - Glioblastoma multiforme(11;0.216)		Caffeine(DB00201)	TCCCTCTGAACCAGAGGTCTT	0.443																																					p.G547V		Atlas-SNP	.											.	PDE1C	465	.	0			c.G1640T						PASS	.						107.0	96.0	100.0					7																	31862809		2203	4300	6503	SO:0001583	missense	5137	exon15			TCTGAACCAGAGG	U40371	CCDS5437.1, CCDS55099.1, CCDS55100.1	7p15.1-p14.3	2008-05-15	2002-08-29		ENSG00000154678	ENSG00000154678	3.1.4.17	"""Phosphodiesterases"""	8776	protein-coding gene	gene with protein product		602987	"""phosphodiesterase 1C, calmodulin-dependent (70kD)"""			8557689	Standard	XM_005249769		Approved	Hcam3	uc003tco.2	Q14123	OTTHUMG00000023836	ENST00000396191.1:c.1460G>T	chr7.hg19:g.31862809C>A	ENSP00000379494:p.Gly487Val	100.0	0.0	.		117.0	38.0	.	NM_001191058	B3KPC6|E9PE92|Q14124|Q8NB10	Missense_Mutation	SNP	ENST00000396191.1	hg19	CCDS55099.1	.	.	.	.	.	.	.	.	.	.	C	17.54	3.415990	0.62511	.	.	ENSG00000154678	ENST00000396193;ENST00000396191;ENST00000321453;ENST00000396184;ENST00000396182	T;T;T;T;T	0.72505	-0.66;-0.66;-0.66;-0.63;-0.63	5.91	5.91	0.95273	.	0.634852	0.16753	N	0.200964	T	0.76730	0.4028	L	0.29908	0.895	0.80722	D	1	B;B;D	0.65815	0.081;0.23;0.995	B;B;P	0.60949	0.056;0.082;0.881	T	0.76537	-0.2923	10	0.54805	T	0.06	.	19.9003	0.96983	0.0:1.0:0.0:0.0	.	487;547;487	Q14123-2;E9PE92;Q14123	.;.;PDE1C_HUMAN	V	547;487;487;487;487	ENSP00000379496:G547V;ENSP00000379494:G487V;ENSP00000318105:G487V;ENSP00000379487:G487V;ENSP00000379485:G487V	ENSP00000318105:G487V	G	-	2	0	PDE1C	31829334	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.060000	0.76692	2.808000	0.96608	0.655000	0.94253	GGT	.	.	.	none		0.443	PDE1C-006	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328458.1		
CSMD1	64478	hgsc.bcm.edu	37	8	2824167	2824167	+	Missense_Mutation	SNP	A	A	G			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr8:2824167A>G	ENST00000520002.1	-	59	9583	c.9028T>C	c.(9028-9030)Tac>Cac	p.Y3010H	CSMD1_ENST00000602557.1_Missense_Mutation_p.Y3010H|CSMD1_ENST00000400186.3_Intron|CSMD1_ENST00000537824.1_Missense_Mutation_p.Y3009H|CSMD1_ENST00000602723.1_Intron|CSMD1_ENST00000542608.1_Intron			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	3010	Sushi 23. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		GAGGTCTTGTAGCCTTCCCAG	0.547																																					p.Y3009H		Atlas-SNP	.											.	CSMD1	1469	.	0			c.T9025C						PASS	.						72.0	76.0	75.0					8																	2824167		2071	4221	6292	SO:0001583	missense	64478	exon58			TCTTGTAGCCTTC			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14026	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 24"""	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.9028T>C	chr8.hg19:g.2824167A>G	ENSP00000430733:p.Tyr3010His	211.0	0.0	.		122.0	50.0	.	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.86|18.86	3.714217|3.714217	0.68730|0.68730	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000335551|ENST00000520002;ENST00000318252;ENST00000537824	.|T;T	.|0.40756	.|1.02;1.02	5.46|5.46	5.46|5.46	0.80206|0.80206	.|Complement control module (2);Sushi/SCR/CCP (3);	.|0.079141	.|0.53938	.|D	.|0.000060	T|T	0.69495|0.69495	0.3117|0.3117	M|M	0.87827|0.87827	2.91|2.91	0.80722|0.80722	D|D	1|1	.|D;D	.|0.76494	.|0.999;0.999	.|D;D	.|0.83275	.|0.996;0.992	T|T	0.76113|0.76113	-0.3078|-0.3078	5|10	.|0.87932	.|D	.|0	.|.	15.5456|15.5456	0.76097|0.76097	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|3010;3010	.|E5RIG2;Q96PZ7	.|.;CSMD1_HUMAN	P|H	2426|3010;2871;3009	.|ENSP00000430733:Y3010H;ENSP00000441462:Y3009H	.|ENSP00000320445:Y2871H	L|Y	-|-	2|1	0|0	CSMD1|CSMD1	2811574|2811574	1.000000|1.000000	0.71417|0.71417	0.807000|0.807000	0.32361|0.32361	0.329000|0.329000	0.28539|0.28539	9.116000|9.116000	0.94341|0.94341	2.068000|2.068000	0.61886|0.61886	0.533000|0.533000	0.62120|0.62120	CTA|TAC	.	.	.	none		0.547	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
NEFL	4747	hgsc.bcm.edu	37	8	24813800	24813800	+	RNA	SNP	G	G	A			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr8:24813800G>A	ENST00000221169.5	-	0	824				CTD-2168K21.2_ENST00000607735.1_RNA			P07196	NFL_HUMAN	neurofilament, light polypeptide						anterograde axon cargo transport (GO:0008089)|axon transport of mitochondrion (GO:0019896)|cell death (GO:0008219)|intermediate filament organization (GO:0045109)|locomotion (GO:0040011)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of neuron apoptotic process (GO:0043524)|neurofilament bundle assembly (GO:0033693)|neuromuscular process controlling balance (GO:0050885)|neuron projection morphogenesis (GO:0048812)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of axonogenesis (GO:0050772)|protein polymerization (GO:0051258)|regulation of axon diameter (GO:0031133)|response to corticosterone (GO:0051412)|response to peptide hormone (GO:0043434)|response to toxic substance (GO:0009636)|retrograde axon cargo transport (GO:0008090)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|neurofilament (GO:0005883)	identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|protein C-terminus binding (GO:0008022)|structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)	21		Ovarian(32;0.00965)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)		GCTGATGGCGGCTACCTGGCT	0.637																																					p.A77V		Atlas-SNP	.											.	NEFL	47	.	0			c.C230T						PASS	.						30.0	33.0	32.0					8																	24813800		2172	4272	6444			4747	exon1			ATGGCGGCTACCT		CCDS75712.1	8p21.2	2014-09-17	2008-09-19		ENSG00000104725	ENSG00000277586		"""Intermediate filaments type IV"""	7739	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 110"""	162280	"""neurofilament, light polypeptide 68kDa"""			17620486, 3145240	Standard	NM_006158		Approved	NFL, CMT1F, CMT2E, NF68, PPP1R110	uc003xee.4	P07196	OTTHUMG00000134284		chr8.hg19:g.24813800G>A		174.0	0.0	.		173.0	13.0	.	NM_006158	B9ZVN2|Q16154|Q8IU72	Missense_Mutation	SNP	ENST00000221169.5	hg19																																																																																				.	.	.	none		0.637	NEFL-001	KNOWN	sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000258943.4	NM_006158	
MATN2	4147	hgsc.bcm.edu	37	8	99039960	99039960	+	Missense_Mutation	SNP	G	G	T			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr8:99039960G>T	ENST00000520016.1	+	13	2383	c.2259G>T	c.(2257-2259)agG>agT	p.R753S	MATN2_ENST00000524308.1_Missense_Mutation_p.R712S|MATN2_ENST00000522025.2_Missense_Mutation_p.R469S|MATN2_ENST00000521689.1_Missense_Mutation_p.R753S|RPL30_ENST00000518164.1_Intron|MATN2_ENST00000254898.5_Missense_Mutation_p.R753S			O00339	MATN2_HUMAN	matrilin 2	753	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(2)|urinary_tract(1)	31	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			AAGGGGCCAGGCCCCTTTCCA	0.562																																					p.R753S		Atlas-SNP	.											.	MATN2	165	.	0			c.G2259T						PASS	.						41.0	42.0	42.0					8																	99039960		1887	4109	5996	SO:0001583	missense	4147	exon14			GGCCAGGCCCCTT	U69263	CCDS55264.1, CCDS55265.1	8q22.1-q22.2	2008-05-15							6908	protein-coding gene	gene with protein product		602108				9083061, 11852232	Standard	XM_005250920		Approved		uc003yic.3	O00339		ENST00000520016.1:c.2259G>T	chr8.hg19:g.99039960G>T	ENSP00000430487:p.Arg753Ser	124.0	0.0	.		137.0	52.0	.	NM_002380	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Missense_Mutation	SNP	ENST00000520016.1	hg19	CCDS55264.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	18.65|18.65|18.65	3.670245|3.670245|3.670245	0.67814|0.67814|0.67814	.|.|.	.|.|.	ENSG00000132561|ENSG00000132561|ENSG00000132561	ENST00000518154|ENST00000519582|ENST00000521689;ENST00000254898;ENST00000378716;ENST00000524308;ENST00000522025;ENST00000520016	.|.|D;D;D;D;D	.|.|0.87571	.|.|-2.27;-2.27;-2.27;-2.27;-2.27	5.24|5.24|5.24	4.34|4.34|4.34	0.51931|0.51931|0.51931	.|.|von Willebrand factor, type A (3);	.|.|0.000000	.|.|0.64402	.|.|D	.|.|0.000002	D|D|D	0.94548|0.94548|0.94548	0.8244|0.8244|0.8244	H|H|H	0.95187|0.95187|0.95187	3.635|3.635|3.635	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|.|D;D;D	.|.|0.89917	.|.|1.0;1.0;1.0	.|.|D;D;D	.|.|0.91635	.|.|0.999;0.999;0.999	D|D|D	0.94271|0.94271|0.94271	0.7511|0.7511|0.7511	5|5|10	.|.|0.87932	.|.|D	.|.|0	-23.5915|-23.5915|-23.5915	8.2515|8.2515|8.2515	0.31724|0.31724|0.31724	0.2672:0.0:0.7328:0.0|0.2672:0.0:0.7328:0.0|0.2672:0.0:0.7328:0.0	.|.|.	.|.|753;753;753	.|.|E9PF03;O00339-2;O00339	.|.|.;.;MATN2_HUMAN	S|V|S	536|9|753;753;712;712;469;753	.|.|ENSP00000429977:R753S;ENSP00000254898:R753S;ENSP00000430221:R712S;ENSP00000429010:R469S;ENSP00000430487:R753S	.|.|ENSP00000254898:R753S	A|G|R	+|+|+	1|2|3	0|0|2	MATN2|MATN2|MATN2	99109136|99109136|99109136	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.934000|0.934000|0.934000	0.57294|0.57294|0.57294	3.500000|3.500000|3.500000	0.53318|0.53318|0.53318	1.272000|1.272000|1.272000	0.44329|0.44329|0.44329	0.555000|0.555000|0.555000	0.69702|0.69702|0.69702	GCC|GGC|AGG	.	.	.	none		0.562	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1		
FOCAD	54914	hgsc.bcm.edu	37	9	20988333	20988333	+	Missense_Mutation	SNP	G	G	A			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr9:20988333G>A	ENST00000380249.1	+	43	5273	c.4909G>A	c.(4909-4911)Gtt>Att	p.V1637I	FOCAD_ENST00000338382.6_Missense_Mutation_p.V1637I|FOCAD_ENST00000605086.1_Missense_Mutation_p.V1073I	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	1637						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)											CATTTCAGGCGTTTTGAAGAG	0.378																																					p.V1637I		Atlas-SNP	.											.	.	.	.	0			c.G4909A						PASS	.						144.0	133.0	137.0					9																	20988333		2203	4300	6503	SO:0001583	missense	54914	exon43			TCAGGCGTTTTGA	AB058700	CCDS34993.1	9p21	2012-03-23	2012-03-23	2012-03-23	ENSG00000188352	ENSG00000188352			23377	protein-coding gene	gene with protein product		614606	"""KIAA1797"""	KIAA1797		22427331	Standard	XM_006716794		Approved	FLJ20375	uc003zog.1	Q5VW36	OTTHUMG00000066930	ENST00000380249.1:c.4909G>A	chr9.hg19:g.20988333G>A	ENSP00000369599:p.Val1637Ile	103.0	0.0	.		91.0	8.0	.	NM_017794	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Missense_Mutation	SNP	ENST00000380249.1	hg19	CCDS34993.1	.	.	.	.	.	.	.	.	.	.	G	17.54	3.415680	0.62511	.	.	ENSG00000188352	ENST00000380249;ENST00000338382	T;T	0.22945	1.93;1.93	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.52597	0.1744	M	0.72118	2.19	0.80722	D	1	D	0.76494	0.999	D	0.67382	0.951	T	0.36383	-0.9750	10	0.45353	T	0.12	-28.3855	20.8794	0.99867	0.0:0.0:1.0:0.0	.	1637	Q5VW36	K1797_HUMAN	I	1637	ENSP00000369599:V1637I;ENSP00000344307:V1637I	ENSP00000344307:V1637I	V	+	1	0	KIAA1797	20978333	1.000000	0.71417	0.317000	0.25265	0.044000	0.14063	5.911000	0.69939	2.941000	0.99782	0.655000	0.94253	GTT	.	.	.	none		0.378	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794	
TOPORS	10210	hgsc.bcm.edu	37	9	32541932	32541932	+	Missense_Mutation	SNP	C	C	T			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr9:32541932C>T	ENST00000360538.2	-	3	2707	c.2591G>A	c.(2590-2592)aGc>aAc	p.S864N	TOPORS_ENST00000379858.1_Missense_Mutation_p.S799N	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	864	Interaction with TOP1.|Interaction with UBE2I.|Lys-rich.				cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of apoptotic process (GO:0043066)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein localization to nucleus (GO:0034504)|protein monoubiquitination (GO:0006513)|protein sumoylation (GO:0016925)|regulation of cell proliferation (GO:0042127)|retina layer formation (GO:0010842)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|gamma-tubulin complex (GO:0000930)|midbody (GO:0030496)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|PML body (GO:0016605)|spindle pole (GO:0000922)|ubiquitin ligase complex (GO:0000151)	antigen binding (GO:0003823)|DNA binding (GO:0003677)|DNA topoisomerase binding (GO:0044547)|SUMO ligase activity (GO:0019789)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		TACACTTAGGCTCCGGGTCTT	0.358																																					p.S864N		Atlas-SNP	.											.	TOPORS	127	.	0			c.G2591A						PASS	.						203.0	207.0	205.0					9																	32541932		2203	4300	6503	SO:0001583	missense	10210	exon3			CTTAGGCTCCGGG	AF098300	CCDS6527.1, CCDS56566.1	9p21	2013-01-09	2010-09-17		ENSG00000197579	ENSG00000197579		"""RING-type (C3HC4) zinc fingers"""	21653	protein-coding gene	gene with protein product		609507	"""retinitis pigmentosa 31 (autosomal dominant)"", ""topoisomerase I binding, arginine/serine-rich"""	RP31		10352183, 12083797, 17924349	Standard	NM_005802		Approved	TP53BPL, LUN	uc003zrb.3	Q9NS56	OTTHUMG00000019743	ENST00000360538.2:c.2591G>A	chr9.hg19:g.32541932C>T	ENSP00000353735:p.Ser864Asn	72.0	0.0	.		38.0	11.0	.	NM_005802	O43273|Q6P987|Q9NS55|Q9UNR9	Missense_Mutation	SNP	ENST00000360538.2	hg19	CCDS6527.1	.	.	.	.	.	.	.	.	.	.	C	16.72	3.202662	0.58234	.	.	ENSG00000197579	ENST00000360538;ENST00000379858	T;T	0.34072	1.38;1.44	5.91	5.91	0.95273	.	0.000000	0.64402	D	0.000011	T	0.52468	0.1736	L	0.32530	0.975	0.39310	D	0.965069	D	0.89917	1.0	D	0.83275	0.996	T	0.53982	-0.8361	10	0.87932	D	0	-9.414	19.0572	0.93070	0.0:1.0:0.0:0.0	.	864	Q9NS56	TOPRS_HUMAN	N	864;799	ENSP00000353735:S864N;ENSP00000369187:S799N	ENSP00000353735:S864N	S	-	2	0	TOPORS	32531932	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.479000	0.60236	2.803000	0.96430	0.650000	0.86243	AGC	.	.	.	none		0.358	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802	
FCN2	2220	hgsc.bcm.edu	37	9	137777085	137777085	+	Splice_Site	SNP	G	G	T	rs529779645	byFrequency	TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr9:137777085G>T	ENST00000291744.6	+	5	312	c.302G>T	c.(301-303)gGc>gTc	p.G101V	FCN2_ENST00000350339.2_Splice_Site_p.G63V	NM_004108.2	NP_004099.2	Q15485	FCN2_HUMAN	ficolin (collagen/fibrinogen domain containing lectin) 2	101	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)|opsonization (GO:0008228)	blood microparticle (GO:0072562)|collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	antigen binding (GO:0003823)|calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|urinary_tract(2)	20		Myeloproliferative disorder(178;0.0333)		OV - Ovarian serous cystadenocarcinoma(145;3.58e-08)|Epithelial(140;6.41e-08)|all cancers(34;3.96e-07)		CCCTTCCCAGGCCCGCGTACC	0.667																																					p.G101V		Atlas-SNP	.											.	FCN2	55	.	0			c.G302T						PASS	.						53.0	52.0	52.0					9																	137777085		2203	4300	6503	SO:0001630	splice_region_variant	2220	exon5			TCCCAGGCCCGCG	D49353	CCDS6983.1	9q34	2013-09-12	2013-09-12		ENSG00000160339	ENSG00000160339		"""Fibrinogen C domain containing"""	3624	protein-coding gene	gene with protein product	"""hucolin"", ""collagen/fibrinogen domain-containing protein 2"", ""ficolin B"", ""serum lectin p35"", ""L-ficolin"""	601624	"""ficolin (collagen/fibrinogen domain-containing lectin) 2 (hucolin)"""			8884275	Standard	XM_006717015		Approved	P35, FCNL, EBP-37, ficolin-2	uc004cfg.1	Q15485	OTTHUMG00000020892	ENST00000291744.6:c.302-1G>T	chr9.hg19:g.137777085G>T		54.0	0.0	.		45.0	16.0	.	NM_004108	A6NFG7|A8K478|Q6IS69|Q7M4P4|Q9UC57	Missense_Mutation	SNP	ENST00000291744.6	hg19	CCDS6983.1	.	.	.	.	.	.	.	.	.	.	G	6.759	0.508916	0.12883	.	.	ENSG00000160339	ENST00000350339;ENST00000291744	T;T	0.19394	2.15;2.15	3.59	2.66	0.31614	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (3);	.	.	.	.	T	0.40815	0.1132	M	0.89353	3.025	0.30440	N	0.776243	P;P	0.49696	0.927;0.763	P;P	0.51701	0.462;0.677	T	0.48258	-0.9051	8	.	.	.	.	9.7179	0.40284	0.0:0.4147:0.5853:0.0	.	63;101	Q15485-2;Q15485	.;FCN2_HUMAN	V	63;101	ENSP00000291741:G63V;ENSP00000291744:G101V	.	G	+	2	0	FCN2	136916906	0.229000	0.23729	0.063000	0.19743	0.018000	0.09664	0.409000	0.21082	0.444000	0.26612	0.462000	0.41574	GGC	.	.	.	none		0.667	FCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054960.1	NM_004108	Missense_Mutation
SOHLH1	402381	hgsc.bcm.edu	37	9	138594140	138594140	+	5'Flank	SNP	C	C	G			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr9:138594140C>G	ENST00000298466.5	-	0	0				KCNT1_ENST00000371757.2_Silent_p.G12G|SOHLH1_ENST00000425225.1_5'Flank|KCNT1_ENST00000487664.1_Silent_p.G12G|KCNT1_ENST00000298480.5_Silent_p.G12G	NM_001012415.2	NP_001012415	Q5JUK2	SOLH1_HUMAN	spermatogenesis and oogenesis specific basic helix-loop-helix 1						oogenesis (GO:0048477)|ovarian follicle development (GO:0001541)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)|lung(5)|prostate(1)	12		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.66e-07)|Epithelial(140;1.11e-06)|all cancers(34;6.45e-05)		ccccggggggcgtctgccggg	0.731																																					p.G12G		Atlas-SNP	.											.	KCNT1	139	.	0			c.C36G						PASS	.						12.0	16.0	15.0					9																	138594140		2168	4247	6415	SO:0001631	upstream_gene_variant	57582	exon1			GGGGGGCGTCTGC	BC031861	CCDS35174.1, CCDS48054.1	9q34.3	2013-05-21	2006-03-16	2006-03-16	ENSG00000165643	ENSG00000165643		"""Basic helix-loop-helix proteins"""	27845	protein-coding gene	gene with protein product	"""spermatogenesis associated 27"""	610224	"""chromosome 9 open reading frame 157"""	C9orf157		12477932	Standard	NM_001012415		Approved	NOHLH, TEB2, bA100C15.3, bHLHe80, SPATA27	uc010nbe.3	Q5JUK2	OTTHUMG00000020915		chr9.hg19:g.138594140C>G	Exception_encountered	1.0	0.0	.		23.0	14.0	.	NM_001272003	C9JG81|Q5EE14|Q5EGC2|Q8NEE3	Silent	SNP	ENST00000298466.5	hg19	CCDS35174.1																																																																																			.	.	.	none		0.731	SOHLH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055018.2	NM_001012415	
ANK3	288	hgsc.bcm.edu	37	10	61829169	61829169	+	Missense_Mutation	SNP	C	C	T			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr10:61829169C>T	ENST00000280772.2	-	37	11661	c.11470G>A	c.(11470-11472)Gtg>Atg	p.V3824M	ANK3_ENST00000503366.1_Intron|ANK3_ENST00000355288.2_Intron|ANK3_ENST00000373827.2_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	3824					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						GAGACTTTCACTGGGTTATCT	0.378																																					p.V3824M		Atlas-SNP	.											.	ANK3	703	.	0			c.G11470A						PASS	.						241.0	236.0	238.0					10																	61829169		2203	4300	6503	SO:0001583	missense	288	exon37			CTTTCACTGGGTT	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"""Ankyrin repeat domain containing"""	494	protein-coding gene	gene with protein product	"""ankyrin-3, node of Ranvier"", ""ankyrin-G"""	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.11470G>A	chr10.hg19:g.61829169C>T	ENSP00000280772:p.Val3824Met	76.0	0.0	.		57.0	23.0	.	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	hg19	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	C	12.81	2.048577	0.36181	.	.	ENSG00000151150	ENST00000280772	T	0.43688	0.94	4.99	3.09	0.35607	.	0.226364	0.22221	N	0.062959	T	0.22666	0.0547	N	0.14661	0.345	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.04537	-1.0944	10	0.45353	T	0.12	.	5.5172	0.16914	0.0:0.6224:0.1464:0.2312	.	3824	Q12955	ANK3_HUMAN	M	3824	ENSP00000280772:V3824M	ENSP00000280772:V3824M	V	-	1	0	ANK3	61499175	0.975000	0.34042	1.000000	0.80357	0.979000	0.70002	0.968000	0.29357	0.581000	0.29539	0.650000	0.86243	GTG	.	.	.	none		0.378	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987	
MMRN2	79812	hgsc.bcm.edu	37	10	88703695	88703695	+	Silent	SNP	G	G	A			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr10:88703695G>A	ENST00000372027.5	-	6	1167	c.846C>T	c.(844-846)gcC>gcT	p.A282A	MMRN2_ENST00000488950.1_5'UTR	NM_024756.2	NP_079032.2	Q9H8L6	MMRN2_HUMAN	multimerin 2	282					angiogenesis (GO:0001525)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|stomach(1)	19						AGTCAGCCCTGGCCACGGCAC	0.602																																					p.A282A		Atlas-SNP	.											.	MMRN2	49	.	0			c.C846T						PASS	.						62.0	58.0	59.0					10																	88703695		2203	4300	6503	SO:0001819	synonymous_variant	79812	exon6			AGCCCTGGCCACG	AK023527	CCDS7379.1	10q23.31	2004-03-10	2004-03-02	2004-03-02	ENSG00000173269	ENSG00000173269		"""EMI domain containing"""	19888	protein-coding gene	gene with protein product		608925	"""elastin microfibril interfacer 3"""	EMILIN3		11559704	Standard	NM_024756		Approved	EndoGlyx-1, FLJ13465	uc001kea.3	Q9H8L6	OTTHUMG00000018663	ENST00000372027.5:c.846C>T	chr10.hg19:g.88703695G>A		109.0	0.0	.		89.0	41.0	.	NM_024756	Q504V7|Q6P2N2	Silent	SNP	ENST00000372027.5	hg19	CCDS7379.1																																																																																			.	.	.	none		0.602	MMRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049179.2	NM_024756	
RRP12	23223	hgsc.bcm.edu	37	10	99160073	99160073	+	Missense_Mutation	SNP	C	C	T			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr10:99160073C>T	ENST00000370992.4	-	2	469	c.358G>A	c.(358-360)Gcc>Acc	p.A120T	RP11-452K12.7_ENST00000422848.1_RNA|RRP12_ENST00000414986.1_Missense_Mutation_p.A120T|RRP12_ENST00000315563.6_Missense_Mutation_p.A120T	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	120						integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		TCCTTGTGGGCAGCCGAGTTG	0.582																																					p.A120T		Atlas-SNP	.											.	RRP12	97	.	0			c.G358A						PASS	.						119.0	119.0	119.0					10																	99160073		2203	4300	6503	SO:0001583	missense	23223	exon2			TGTGGGCAGCCGA		CCDS7457.1, CCDS44467.1, CCDS60605.1	10q24.2	2006-11-06	2006-11-06	2006-11-06	ENSG00000052749	ENSG00000052749			29100	protein-coding gene	gene with protein product			"""KIAA0690"""	KIAA0690		9734811	Standard	NM_015179		Approved		uc001knf.3	Q5JTH9	OTTHUMG00000018855	ENST00000370992.4:c.358G>A	chr10.hg19:g.99160073C>T	ENSP00000360031:p.Ala120Thr	112.0	0.0	.		75.0	22.0	.	NM_001145114	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Missense_Mutation	SNP	ENST00000370992.4	hg19	CCDS7457.1	.	.	.	.	.	.	.	.	.	.	C	14.00	2.406058	0.42715	.	.	ENSG00000052749	ENST00000370992;ENST00000315563;ENST00000414986	T;T;T	0.64260	-0.09;1.52;1.51	5.7	4.8	0.61643	Armadillo-type fold (1);	0.208574	0.49916	D	0.000127	T	0.51295	0.1666	L	0.40543	1.245	0.80722	D	1	P;P;B	0.45715	0.787;0.865;0.001	B;B;B	0.39503	0.158;0.301;0.005	T	0.48246	-0.9052	10	0.13108	T	0.6	-11.1652	15.9236	0.79592	0.1366:0.8634:0.0:0.0	.	120;120;120	E9PCK7;Q5JTH9-2;Q5JTH9	.;.;RRP12_HUMAN	T	120	ENSP00000360031:A120T;ENSP00000324315:A120T;ENSP00000414863:A120T	ENSP00000324315:A120T	A	-	1	0	RRP12	99150063	0.992000	0.36948	0.983000	0.44433	0.965000	0.64279	3.045000	0.49838	1.429000	0.47314	-0.361000	0.07541	GCC	.	.	.	none		0.582	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179	
STK32C	282974	hgsc.bcm.edu	37	10	134036392	134036392	+	Silent	SNP	C	C	T			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr10:134036392C>T	ENST00000368622.1	-	9	1122	c.741G>A	c.(739-741)aaG>aaA	p.K247K	STK32C_ENST00000368625.4_Silent_p.K377K					serine/threonine kinase 32C											breast(1)|endometrium(2)|large_intestine(2)|lung(15)|ovary(2)|skin(1)	23		all_cancers(35;2.72e-11)|all_epithelial(44;2.33e-08)|Lung NSC(174;0.000855)|all_lung(145;0.00146)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.112)|Melanoma(40;0.124)|Glioma(114;0.203)		Epithelial(32;3.99e-05)|all cancers(32;5.58e-05)|OV - Ovarian serous cystadenocarcinoma(35;9.96e-05)|BRCA - Breast invasive adenocarcinoma(275;0.222)		GCTCCACCCTCTTCTCGCTCA	0.711																																					p.K364K		Atlas-SNP	.											.	STK32C	61	.	0			c.G1092A						PASS	.						20.0	22.0	21.0					10																	134036392		2183	4281	6464	SO:0001819	synonymous_variant	282974	exon9			CACCCTCTTCTCG	AK057849	CCDS7666.1	10q26.3	2004-07-22			ENSG00000165752	ENSG00000165752			21332	protein-coding gene	gene with protein product							Standard	NM_173575		Approved	PKE, MGC23665, YANK3	uc001lle.1	Q86UX6	OTTHUMG00000019285	ENST00000368622.1:c.741G>A	chr10.hg19:g.134036392C>T		2.0	0.0	.		51.0	19.0	.	NM_173575		Silent	SNP	ENST00000368622.1	hg19																																																																																				.	.	.	none		0.711	STK32C-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000051068.2	NM_173575	
SLC22A18	5002	hgsc.bcm.edu	37	11	2937874	2937874	+	Missense_Mutation	SNP	G	G	T			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr11:2937874G>T	ENST00000380574.1	+	6	990	c.559G>T	c.(559-561)Gct>Tct	p.A187S	SLC22A18_ENST00000312221.5_Missense_Mutation_p.A187S|SLC22A18_ENST00000449793.2_Missense_Mutation_p.A89S|SLC22A18_ENST00000347936.2_Missense_Mutation_p.A187S			Q96BI1	S22AI_HUMAN	solute carrier family 22, member 18	187					drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|excretion (GO:0007588)|organic cation transport (GO:0015695)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|symporter activity (GO:0015293)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(2)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	8		all_epithelial(84;0.000124)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)|all_lung(207;0.198)		BRCA - Breast invasive adenocarcinoma(625;0.00256)|LUSC - Lung squamous cell carcinoma(625;0.192)		GGCCATCCTGGCTGCCCTGGC	0.687																																					p.A187S		Atlas-SNP	.											.	SLC22A18	20	.	0			c.G559T						PASS	.						41.0	44.0	43.0					11																	2937874		2202	4299	6501	SO:0001583	missense	5002	exon6			ATCCTGGCTGCCC	AF028738	CCDS7740.1	11p15.5	2013-05-22	2008-01-11	2004-01-21	ENSG00000110628	ENSG00000110628		"""Solute carriers"""	10964	protein-coding gene	gene with protein product		602631	"""solute carrier family 22 (organic cation transporter), member 1-like"""	ORCTL2, BWSCR1A, IMPT1, SLC22A1L		9499412, 9520460	Standard	NM_183233		Approved	BWR1A, TSSC5, ITM	uc001lwx.3	Q96BI1	OTTHUMG00000010037	ENST00000380574.1:c.559G>T	chr11.hg19:g.2937874G>T	ENSP00000369948:p.Ala187Ser	57.0	0.0	.		124.0	50.0	.	NM_002555	O14906|O43562|O60485|O60680|Q7LDS5|Q7LGF7	Missense_Mutation	SNP	ENST00000380574.1	hg19	CCDS7740.1	.	.	.	.	.	.	.	.	.	.	G	14.16	2.451570	0.43531	.	.	ENSG00000110628	ENST00000347936;ENST00000312221;ENST00000449793;ENST00000380574	T;T;T;T	0.81163	0.34;0.34;-1.46;0.34	3.77	2.8	0.32819	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.460037	0.20295	N	0.095157	D	0.84316	0.5445	M	0.62723	1.935	0.09310	N	1	D;D	0.59357	0.97;0.985	P;P	0.61070	0.681;0.883	T	0.74343	-0.3696	10	0.59425	D	0.04	-12.6812	8.7536	0.34633	0.0:0.0:0.7726:0.2273	.	89;187	E9PRM7;Q96BI1	.;S22AI_HUMAN	S	187;187;89;187	ENSP00000307859:A187S;ENSP00000311139:A187S;ENSP00000392072:A89S;ENSP00000369948:A187S	ENSP00000311139:A187S	A	+	1	0	SLC22A18	2894450	0.031000	0.19500	0.002000	0.10522	0.012000	0.07955	1.338000	0.33873	0.814000	0.34374	0.491000	0.48974	GCT	.	.	.	none		0.687	SLC22A18-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027770.1	NM_183233	
MARS	4141	hgsc.bcm.edu	37	12	57894254	57894254	+	Silent	SNP	G	G	C			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr12:57894254G>C	ENST00000262027.5	+	10	1376	c.1242G>C	c.(1240-1242)cgG>cgC	p.R414R	MARS_ENST00000447721.2_3'UTR|MARS_ENST00000315473.5_Silent_p.R180R	NM_004990.3	NP_004981.2	P56192	SYMC_HUMAN	methionyl-tRNA synthetase	414					gene expression (GO:0010467)|methionyl-tRNA aminoacylation (GO:0006431)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|methionine-tRNA ligase activity (GO:0004825)|tRNA binding (GO:0000049)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	33			GBM - Glioblastoma multiforme(3;4.27e-41)		L-Methionine(DB00134)	AGGAGGCTCGGGGTGACCAGT	0.562																																					p.R414R		Atlas-SNP	.											.	MARS	84	.	0			c.G1242C						PASS	.						147.0	115.0	126.0					12																	57894254		2203	4300	6503	SO:0001819	synonymous_variant	4141	exon10			GGCTCGGGGTGAC	X94754	CCDS8942.1	12q13.3	2014-05-06	2007-02-26		ENSG00000166986	ENSG00000166986	6.1.1.10	"""Aminoacyl tRNA synthetases / Class I"""	6898	protein-coding gene	gene with protein product	"""methionine tRNA ligase 1, cytoplasmic"""	156560				10448063, 24482476	Standard	NM_004990		Approved	MetRS, SPG70	uc001sog.3	P56192	OTTHUMG00000169996	ENST00000262027.5:c.1242G>C	chr12.hg19:g.57894254G>C		213.0	0.0	.		187.0	44.0	.	NM_004990	B3KVK7|Q14895|Q53H14|Q96A15|Q96BZ0|Q9NSE0	Silent	SNP	ENST00000262027.5	hg19	CCDS8942.1																																																																																			.	.	.	none		0.562	MARS-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407014.1	NM_004990	
NBEA	26960	hgsc.bcm.edu	37	13	35770159	35770159	+	Missense_Mutation	SNP	G	G	T			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr13:35770159G>T	ENST00000400445.3	+	31	5620	c.5086G>T	c.(5086-5088)Ggc>Tgc	p.G1696C	NBEA_ENST00000310336.4_Missense_Mutation_p.G1696C|NBEA_ENST00000540320.1_Missense_Mutation_p.G1696C|NBEA_ENST00000379939.2_Missense_Mutation_p.G1693C	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	1696					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		AACAAGTACAGGCCCTGATGC	0.433																																					p.G1696C		Atlas-SNP	.											.	NBEA	340	.	0			c.G5086T						PASS	.						79.0	78.0	78.0					13																	35770159		1906	4130	6036	SO:0001583	missense	26960	exon31			AGTACAGGCCCTG	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"""A-kinase anchor proteins"", ""WD repeat domain containing"""	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.5086G>T	chr13.hg19:g.35770159G>T	ENSP00000383295:p.Gly1696Cys	100.0	0.0	.		111.0	57.0	.	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.376162	0.82682	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336;ENST00000422518	T;T;T;T	0.64085	-0.08;-0.08;-0.08;-0.08	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	T	0.76688	0.4022	M	0.68317	2.08	0.80722	D	1	D;D	0.89917	0.999;1.0	P;D	0.80764	0.846;0.994	T	0.77742	-0.2474	10	0.72032	D	0.01	.	13.6145	0.62099	0.0706:0.0:0.9294:0.0	.	1696;1693	Q8NFP9;Q5T321	NBEA_HUMAN;.	C	1696;1696;1693;1696;323	ENSP00000440951:G1696C;ENSP00000383295:G1696C;ENSP00000369271:G1693C;ENSP00000308534:G1696C	ENSP00000308534:G1696C	G	+	1	0	NBEA	34668159	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.455000	0.80726	2.843000	0.97960	0.585000	0.79938	GGC	.	.	.	none		0.433	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678	
FSIP1	161835	hgsc.bcm.edu	37	15	40056080	40056080	+	Silent	SNP	C	C	T			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr15:40056080C>T	ENST00000350221.3	-	5	710	c.501G>A	c.(499-501)gaG>gaA	p.E167E		NM_152597.4	NP_689810.3	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	167										NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	23		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)		TTTCCATCTCCTCTTTACTTT	0.299																																					p.E167E		Atlas-SNP	.											.	FSIP1	53	.	0			c.G501A						PASS	.						51.0	57.0	55.0					15																	40056080		2201	4293	6494	SO:0001819	synonymous_variant	161835	exon5			CATCTCCTCTTTA	BC045191	CCDS10050.1	15q14	2012-11-19			ENSG00000150667	ENSG00000150667			21674	protein-coding gene	gene with protein product		615795				14702039	Standard	NM_152597		Approved	FLJ35989	uc001zki.3	Q8NA03	OTTHUMG00000172456	ENST00000350221.3:c.501G>A	chr15.hg19:g.40056080C>T		155.0	0.0	.		121.0	49.0	.	NM_152597	Q6X2C8|Q86Y89	Silent	SNP	ENST00000350221.3	hg19	CCDS10050.1																																																																																			.	.	.	none		0.299	FSIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252118.2	NM_152597	
NDUFAF1	51103	hgsc.bcm.edu	37	15	41689069	41689069	+	Silent	SNP	G	G	A			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr15:41689069G>A	ENST00000260361.4	-	2	570	c.189C>T	c.(187-189)caC>caT	p.H63H		NM_016013.3	NP_057097.2	Q9Y375	CIA30_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 1	63					mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|mitochondrial respiratory chain complex I (GO:0005747)	unfolded protein binding (GO:0051082)			endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	12		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;8e-17)|GBM - Glioblastoma multiforme(113;1.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.114)		CTTCTTTCTGGTGATCTCCTT	0.423																																					p.H63H		Atlas-SNP	.											.	NDUFAF1	39	.	0			c.C189T						PASS	.						118.0	121.0	120.0					15																	41689069		2203	4300	6503	SO:0001819	synonymous_variant	51103	exon2			TTTCTGGTGATCT	AF151823	CCDS10075.1	15q11.2-q21.3	2012-10-12	2012-05-08		ENSG00000137806	ENSG00000137806		"""Mitochondrial respiratory chain complex assembly factors"""	18828	protein-coding gene	gene with protein product		606934				11935339, 10810093	Standard	NM_016013		Approved	CIA30, CGI-65	uc001znx.3	Q9Y375	OTTHUMG00000130340	ENST00000260361.4:c.189C>T	chr15.hg19:g.41689069G>A		77.0	0.0	.		60.0	24.0	.	NM_016013	Q9BVZ5	Silent	SNP	ENST00000260361.4	hg19	CCDS10075.1																																																																																			.	.	.	none		0.423	NDUFAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252692.2	NM_016013	
TICRR	90381	hgsc.bcm.edu	37	15	90167321	90167321	+	Silent	SNP	G	G	A			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr15:90167321G>A	ENST00000268138.7	+	20	3885	c.3780G>A	c.(3778-3780)acG>acA	p.T1260T	KIF7_ENST00000558928.1_Intron|TICRR_ENST00000560985.1_Silent_p.T1259T			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	1260	Pro-rich.				cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|formation of translation preinitiation complex (GO:0001731)|mitotic DNA replication checkpoint (GO:0033314)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)	chromatin binding (GO:0003682)										TCATGGGCACGCCTCAGAATC	0.542																																					p.T1260T		Atlas-SNP	.											.	.	.	.	0			c.G3780A						PASS	.						66.0	70.0	69.0					15																	90167321		2200	4299	6499	SO:0001819	synonymous_variant	90381	exon20			GGGCACGCCTCAG	AK123612	CCDS10352.2	15q26.1	2012-07-11	2012-07-11	2012-07-11	ENSG00000140534	ENSG00000140534			28704	protein-coding gene	gene with protein product	"""TOPBP1-interacting replication-stimulating protein"", ""SLD3 homolog (S. cerevisiae)"""	613298	"""chromosome 15 open reading frame 42"""	C15orf42		20116089, 20080954	Standard	NM_152259		Approved	MGC45866, FLJ41618, Treslin, SLD3	uc002boe.3	Q7Z2Z1	OTTHUMG00000149648	ENST00000268138.7:c.3780G>A	chr15.hg19:g.90167321G>A		49.0	0.0	.		39.0	17.0	.	NM_152259	B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Silent	SNP	ENST00000268138.7	hg19	CCDS10352.2																																																																																			.	.	.	none		0.542	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259	
ANKS3	124401	hgsc.bcm.edu	37	16	4748510	4748510	+	Missense_Mutation	SNP	G	G	T			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr16:4748510G>T	ENST00000304283.4	-	14	1936	c.1642C>A	c.(1642-1644)Cgc>Agc	p.R548S	ANKS3_ENST00000585773.1_Missense_Mutation_p.R475S|ANKS3_ENST00000446014.2_Missense_Mutation_p.R419S	NM_133450.3	NP_597707.1	Q6ZW76	ANKS3_HUMAN	ankyrin repeat and sterile alpha motif domain containing 3	548										endometrium(5)|kidney(4)|large_intestine(3)|lung(5)|prostate(1)|stomach(1)	19						TCGCGGGCGCGGTCCTGCTCC	0.736																																					p.R548S		Atlas-SNP	.											.	ANKS3	44	.	0			c.C1642A						PASS	.						6.0	7.0	6.0					16																	4748510		2086	4135	6221	SO:0001583	missense	124401	exon14			GGGCGCGGTCCTG	AK057329	CCDS10520.1, CCDS73820.1	16p13.3	2013-01-10			ENSG00000168096	ENSG00000168096		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	29422	protein-coding gene	gene with protein product						11853319	Standard	NM_133450		Approved	KIAA1977, FLJ32345, FLJ32767	uc002cxj.2	Q6ZW76	OTTHUMG00000129478	ENST00000304283.4:c.1642C>A	chr16.hg19:g.4748510G>T	ENSP00000304586:p.Arg548Ser	1.0	0.0	.		25.0	17.0	.	NM_133450	B4DWU4|D3DUE2|Q8TF25	Missense_Mutation	SNP	ENST00000304283.4	hg19	CCDS10520.1	.	.	.	.	.	.	.	.	.	.	G	13.71	2.318757	0.41096	.	.	ENSG00000168096	ENST00000304283;ENST00000446014	T;T	0.31510	1.49;3.24	5.46	-6.97	0.01616	.	1.035280	0.07528	N	0.911661	T	0.04815	0.0130	N	0.00289	-1.7	0.09310	N	0.999993	B	0.02656	0.0	B	0.01281	0.0	T	0.30001	-0.9993	10	0.08837	T	0.75	0.351	3.7451	0.08545	0.0874:0.2626:0.181:0.469	.	548	Q6ZW76	ANKS3_HUMAN	S	548;419	ENSP00000304586:R548S;ENSP00000406796:R419S	ENSP00000304586:R548S	R	-	1	0	ANKS3	4688511	0.000000	0.05858	0.001000	0.08648	0.091000	0.18340	-0.450000	0.06803	-1.265000	0.02449	-0.371000	0.07208	CGC	.	.	.	none		0.736	ANKS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251642.3	NM_133450	
GRIN2A	2903	hgsc.bcm.edu	37	16	10273887	10273887	+	Missense_Mutation	SNP	G	G	C			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr16:10273887G>C	ENST00000396573.2	-	3	691	c.382C>G	c.(382-384)Cat>Gat	p.H128D	GRIN2A_ENST00000330684.3_Missense_Mutation_p.H128D|GRIN2A_ENST00000404927.2_Missense_Mutation_p.H128D|GRIN2A_ENST00000562109.1_Missense_Mutation_p.H128D|GRIN2A_ENST00000396575.2_Missense_Mutation_p.H128D	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	128					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GCGCCCCCATGAATGCCCAAG	0.597																																					p.H128D		Atlas-SNP	.											.	GRIN2A	366	.	0			c.C382G						PASS	.						56.0	52.0	53.0					16																	10273887		2197	4300	6497	SO:0001583	missense	2903	exon3			CCCCATGAATGCC		CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.382C>G	chr16.hg19:g.10273887G>C	ENSP00000379818:p.His128Asp	145.0	0.0	.		158.0	42.0	.	NM_000833	O00669|Q17RZ6	Missense_Mutation	SNP	ENST00000396573.2	hg19	CCDS10539.1	.	.	.	.	.	.	.	.	.	.	G	19.62	3.862300	0.71949	.	.	ENSG00000183454	ENST00000396573;ENST00000404927;ENST00000330684;ENST00000396575	D;D;D;D	0.85861	-2.04;-2.04;-2.04;-2.04	4.54	4.54	0.55810	Extracellular ligand-binding receptor (1);	0.062818	0.64402	D	0.000007	D	0.91068	0.7189	M	0.75447	2.3	0.80722	D	1	D;P;P	0.67145	0.996;0.879;0.803	D;P;P	0.64776	0.929;0.677;0.479	D	0.91402	0.5144	9	.	.	.	.	16.2901	0.82747	0.0:0.0:1.0:0.0	.	128;128;128	Q547U9;Q17RZ6;Q12879	.;.;NMDE1_HUMAN	D	128	ENSP00000379818:H128D;ENSP00000385872:H128D;ENSP00000332549:H128D;ENSP00000379820:H128D	.	H	-	1	0	GRIN2A	10181388	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	7.938000	0.87678	2.088000	0.63022	0.561000	0.74099	CAT	.	.	.	none		0.597	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3		
DBNDD1	79007	hgsc.bcm.edu	37	16	90072805	90072805	+	Missense_Mutation	SNP	G	G	T			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr16:90072805G>T	ENST00000002501.6	-	4	546	c.415C>A	c.(415-417)Ccc>Acc	p.P139T	DBNDD1_ENST00000568838.1_Missense_Mutation_p.P259T|DBNDD1_ENST00000304733.3_Missense_Mutation_p.P159T|DBNDD1_ENST00000392973.3_Missense_Mutation_p.P145T	NM_001042610.1	NP_001036075.1	Q9H9R9	DBND1_HUMAN	dysbindin (dystrobrevin binding protein 1) domain containing 1	139						cytoplasm (GO:0005737)				kidney(1)|large_intestine(1)|lung(1)	3		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0275)		TGCCGCTCGGGGTCGCCTAGG	0.677																																					p.P159T		Atlas-SNP	.											.	DBNDD1	9	.	0			c.C475A						PASS	.						35.0	45.0	42.0					16																	90072805		2023	4188	6211	SO:0001583	missense	79007	exon4			GCTCGGGGTCGCC	AK090696	CCDS10991.2, CCDS42223.1, CCDS73931.1	16q24.3	2008-02-05			ENSG00000003249	ENSG00000003249			28455	protein-coding gene	gene with protein product						12477932	Standard	NM_001288708		Approved	MGC3101, FLJ12582	uc002fqe.1	Q9H9R9	OTTHUMG00000138984	ENST00000002501.6:c.415C>A	chr16.hg19:g.90072805G>T	ENSP00000002501:p.Pro139Thr	38.0	0.0	.		62.0	16.0	.	NM_024043	B4DQS3|Q69YT2|Q9BW25	Missense_Mutation	SNP	ENST00000002501.6	hg19	CCDS42223.1	.	.	.	.	.	.	.	.	.	.	G	12.61	1.990417	0.35131	.	.	ENSG00000003249	ENST00000304733;ENST00000002501;ENST00000392973	T;T	0.30448	1.53;1.53	5.64	0.925	0.19424	.	0.270724	0.37577	N	0.002024	T	0.18002	0.0432	L	0.46157	1.445	0.25250	N	0.989681	B;B	0.20052	0.023;0.041	B;B	0.15052	0.012;0.011	T	0.13098	-1.0522	10	0.16420	T	0.52	-4.1737	1.4458	0.02364	0.2704:0.1553:0.4171:0.1571	.	139;159	Q9H9R9;Q9H9R9-2	DBND1_HUMAN;.	T	159;139;259	ENSP00000306407:P159T;ENSP00000002501:P139T	ENSP00000002501:P139T	P	-	1	0	DBNDD1	88600306	1.000000	0.71417	0.003000	0.11579	0.131000	0.20780	1.604000	0.36804	0.321000	0.23259	0.491000	0.48974	CCC	.	.	.	none		0.677	DBNDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272872.1	NM_024043	
DNAH2	146754	hgsc.bcm.edu	37	17	7727530	7727530	+	Missense_Mutation	SNP	A	A	T			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr17:7727530A>T	ENST00000572933.1	+	76	13030	c.11570A>T	c.(11569-11571)cAc>cTc	p.H3857L	DNAH2_ENST00000389173.2_Missense_Mutation_p.H3857L			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	3857	AAA 6. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				CTGGCAGAGCACATGGGCATG	0.662																																					p.H3857L		Atlas-SNP	.											.	DNAH2	498	.	0			c.A11570T						PASS	.						63.0	56.0	59.0					17																	7727530		2203	4300	6503	SO:0001583	missense	146754	exon75			CAGAGCACATGGG	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"""Axonemal dyneins"""	2948	protein-coding gene	gene with protein product		603333	"""dynein, axonemal, heavy polypeptide 2"", ""dynein heavy chain domain 3"""	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.11570A>T	chr17.hg19:g.7727530A>T	ENSP00000458355:p.His3857Leu	27.0	0.0	.		100.0	56.0	.	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	hg19	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	A	13.72	2.321206	0.41096	.	.	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.08193	3.12	4.9	4.9	0.64082	Dynein heavy chain (1);	0.564059	0.19257	N	0.118766	T	0.05731	0.0150	N	0.11201	0.11	0.80722	D	1	B;B	0.14012	0.007;0.009	B;B	0.12156	0.004;0.007	T	0.38802	-0.9644	10	0.40728	T	0.16	.	13.4924	0.61405	1.0:0.0:0.0:0.0	.	3818;3857	Q9P225-2;Q9P225	.;DYH2_HUMAN	L	3818;3857	ENSP00000373825:H3857L	ENSP00000353818:H3818L	H	+	2	0	DNAH2	7668255	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	4.869000	0.63028	1.848000	0.53677	0.334000	0.21626	CAC	.	.	.	none		0.662	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877	
SPAG5	10615	hgsc.bcm.edu	37	17	26912886	26912886	+	Missense_Mutation	SNP	T	T	C			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr17:26912886T>C	ENST00000321765.5	-	7	2068	c.1736A>G	c.(1735-1737)gAt>gGt	p.D579G		NM_006461.3	NP_006452.3	Q96R06	SPAG5_HUMAN	sperm associated antigen 5	579	Interaction with KNSTRN.				chromosome segregation (GO:0007059)|mitotic sister chromatid segregation (GO:0000070)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|spindle organization (GO:0007051)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|microtubule plus-end (GO:0035371)|mitotic spindle (GO:0072686)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43	Lung NSC(42;0.00431)					CCTTACCGCATCCTTGCCTCT	0.498																																					p.D579G		Atlas-SNP	.											.	SPAG5	92	.	0			c.A1736G						PASS	.						225.0	197.0	206.0					17																	26912886		2203	4300	6503	SO:0001583	missense	10615	exon7			ACCGCATCCTTGC	AF063308	CCDS32594.1	17q11.2	2008-07-18			ENSG00000076382	ENSG00000076382			13452	protein-coding gene	gene with protein product	"""mitotic spindle coiled-coil related protein"", ""astrin"", ""mitotic spindle associated protein p126"""	615562				11549262	Standard	NM_006461		Approved	DEEPEST, MAP126, hMAP126	uc002hbq.3	Q96R06	OTTHUMG00000166586	ENST00000321765.5:c.1736A>G	chr17.hg19:g.26912886T>C	ENSP00000323300:p.Asp579Gly	74.0	0.0	.		79.0	48.0	.	NM_006461	O95213|Q9BWE8|Q9NT17|Q9UFE6	Missense_Mutation	SNP	ENST00000321765.5	hg19	CCDS32594.1	.	.	.	.	.	.	.	.	.	.	T	15.69	2.907625	0.52333	.	.	ENSG00000076382	ENST00000321765;ENST00000536674	.	.	.	5.82	3.52	0.40303	.	0.549745	0.17799	N	0.161643	T	0.25827	0.0629	L	0.29908	0.895	0.22096	N	0.999364	P	0.48294	0.908	B	0.39660	0.306	T	0.05099	-1.0906	9	0.56958	D	0.05	-1.7343	10.252	0.43375	0.0:0.0:0.3183:0.6817	.	579	Q96R06	SPAG5_HUMAN	G	579;76	.	ENSP00000323300:D579G	D	-	2	0	SPAG5	23937013	0.989000	0.36119	0.994000	0.49952	0.917000	0.54804	1.208000	0.32345	0.414000	0.25790	0.533000	0.62120	GAT	.	.	.	none		0.498	SPAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390564.2	NM_006461	
KRT13	3860	hgsc.bcm.edu	37	17	39658844	39658844	+	Silent	SNP	T	T	C			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr17:39658844T>C	ENST00000246635.3	-	6	1072	c.1026A>G	c.(1024-1026)aaA>aaG	p.K342K	KRT13_ENST00000587544.1_Silent_p.K342K|KRT13_ENST00000587118.1_5'Flank|KRT13_ENST00000336861.3_Silent_p.K342K|AC019349.5_ENST00000411759.1_RNA	NM_153490.2	NP_705694	P13646	K1C13_HUMAN	keratin 13	342	Coil 2.|Rod.				cellular response to retinoic acid (GO:0071300)|cytoskeleton organization (GO:0007010)|response to radiation (GO:0009314)|tongue morphogenesis (GO:0043587)	extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	33		Breast(137;0.000286)				CCAGCCCCGCTTTCTGGTGGA	0.627																																					p.K342K		Atlas-SNP	.											.	KRT13	72	.	0			c.A1026G						PASS	.						70.0	66.0	67.0					17																	39658844		2203	4300	6503	SO:0001819	synonymous_variant	3860	exon6			CCCCGCTTTCTGG		CCDS11396.1, CCDS11397.1	17q21.2	2013-06-20			ENSG00000171401	ENSG00000171401		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6415	protein-coding gene	gene with protein product	"""keratin, type I cytoskeletal 13"", ""cytokeratin 13"""	148065				16831889	Standard	NM_153490		Approved	K13, CK13, MGC3781, MGC161462	uc002hwu.1	P13646	OTTHUMG00000133434	ENST00000246635.3:c.1026A>G	chr17.hg19:g.39658844T>C		67.0	0.0	.		63.0	19.0	.	NM_002274	Q53G54|Q6AZK5|Q8N240	Silent	SNP	ENST00000246635.3	hg19	CCDS11396.1																																																																																			.	.	.	none		0.627	KRT13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257297.1	NM_153490	
CBX4	8535	hgsc.bcm.edu	37	17	77807927	77807927	+	Missense_Mutation	SNP	A	A	G	rs200965379		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr17:77807927A>G	ENST00000269397.4	-	5	1691	c.1514T>C	c.(1513-1515)gTg>gCg	p.V505A		NM_003655.2	NP_003646.2	O00257	CBX4_HUMAN	chromobox homolog 4	505	Interaction with BMI1.|Poly-Ala.			V -> VAA (in Ref. 3; ACA49234). {ECO:0000305}.	chromatin modification (GO:0016568)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein sumoylation (GO:0016925)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|single-stranded RNA binding (GO:0003727)|SUMO binding (GO:0032183)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			tgccgccgccaccgccaccgc	0.711																																					p.V505A		Atlas-SNP	.											CBX4,uveal_tract,malignant_melanoma,0,1	CBX4	40	.	0			c.T1514C						PASS	.						15.0	21.0	19.0					17																	77807927		1776	3704	5480	SO:0001583	missense	8535	exon5			GCCGCCACCGCCA	AF013956	CCDS32758.1	17q25.3	2010-07-06	2010-06-24		ENSG00000141582	ENSG00000141582			1554	protein-coding gene	gene with protein product	"""NS5ATP1-binding protein 16"", ""Pc class 2 homolog (Drosophila)"""	603079	"""chromobox homolog 4 (Drosophila Pc class)"""			9315667	Standard	NM_003655		Approved	hPC2, PC2, NBP16	uc002jxe.3	O00257	OTTHUMG00000150415	ENST00000269397.4:c.1514T>C	chr17.hg19:g.77807927A>G	ENSP00000269397:p.Val505Ala	2.0	1.0	.		34.0	22.0	.	NM_003655	B1PJR7|Q6TPI8|Q96C04	Missense_Mutation	SNP	ENST00000269397.4	hg19	CCDS32758.1	.	.	.	.	.	.	.	.	.	.	a	0.008	-1.872700	0.00542	.	.	ENSG00000141582	ENST00000269397;ENST00000343048	.	.	.	0.575	0.575	0.17374	.	2.519730	0.02140	N	0.057046	T	0.20333	0.0489	N	0.08118	0	0.19775	N	0.999955	B	0.13594	0.008	B	0.04013	0.001	T	0.16217	-1.0410	8	0.32370	T	0.25	.	.	.	.	.	505	O00257	CBX4_HUMAN	A	505;235	.	ENSP00000269397:V505A	V	-	2	0	CBX4	75422522	0.000000	0.05858	0.005000	0.12908	0.005000	0.04900	0.179000	0.16840	0.475000	0.27415	0.158000	0.16466	GTG	.	.	.	weak		0.711	CBX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318007.1	NM_003655	
TMC2	117532	hgsc.bcm.edu	37	20	2592879	2592879	+	Missense_Mutation	SNP	C	C	G			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr20:2592879C>G	ENST00000358864.1	+	13	1651	c.1636C>G	c.(1636-1638)Ctg>Gtg	p.L546V	TMC2_ENST00000496948.1_3'UTR	NM_080751.2	NP_542789.2	Q8TDI7	TMC2_HUMAN	transmembrane channel-like 2	546					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						TCACTGGACTCTGTTTAACTA	0.512																																					p.L546V		Atlas-SNP	.											.	TMC2	121	.	0			c.C1636G						PASS	.						155.0	134.0	141.0					20																	2592879		2203	4300	6503	SO:0001583	missense	117532	exon13			TGGACTCTGTTTA	AF417580	CCDS13029.2	20p13	2010-08-05	2003-02-23		ENSG00000149488	ENSG00000149488			16527	protein-coding gene	gene with protein product		606707	"""transmembrane, cochlear expressed, 2"""	C20orf145		11850618, 12906855	Standard	XM_005260660		Approved	dJ686C3.3	uc002wgf.1	Q8TDI7	OTTHUMG00000031698	ENST00000358864.1:c.1636C>G	chr20.hg19:g.2592879C>G	ENSP00000351732:p.Leu546Val	63.0	0.0	.		78.0	10.0	.	NM_080751	Q5JXT0|Q5JXT1|Q6UWW4|Q6ZS41|Q8N9F3|Q9BYN2|Q9BYN3|Q9BYN4|Q9BYN5	Missense_Mutation	SNP	ENST00000358864.1	hg19	CCDS13029.2	.	.	.	.	.	.	.	.	.	.	C	14.67	2.603805	0.46423	.	.	ENSG00000149488	ENST00000358864	T	0.66099	-0.19	5.85	5.85	0.93711	.	0.076272	0.53938	D	0.000052	T	0.69540	0.3122	M	0.73962	2.25	0.49051	D	0.999745	B;P;P;P	0.41524	0.382;0.563;0.753;0.638	B;B;P;B	0.46299	0.091;0.139;0.511;0.313	T	0.64609	-0.6367	10	0.22706	T	0.39	-10.7732	18.0364	0.89305	0.0:1.0:0.0:0.0	.	377;378;546;546	B4DFB3;B7ZAE6;Q8TDI7-3;Q8TDI7	.;.;.;TMC2_HUMAN	V	546	ENSP00000351732:L546V	ENSP00000351732:L546V	L	+	1	2	TMC2	2540879	0.933000	0.31639	1.000000	0.80357	0.997000	0.91878	1.970000	0.40520	2.941000	0.99782	0.655000	0.94253	CTG	.	.	.	none		0.512	TMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077601.2		
PANK2	80025	hgsc.bcm.edu	37	20	3869791	3869791	+	Missense_Mutation	SNP	C	C	T			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr20:3869791C>T	ENST00000316562.4	+	1	50	c.44C>T	c.(43-45)gCg>gTg	p.A15V	PANK2_ENST00000497424.1_Intron|RP11-119B16.2_ENST00000451507.1_RNA|PANK2_ENST00000610179.1_5'Flank	NM_153638.2	NP_705902.2	Q9BZ23	PANK2_HUMAN	pantothenate kinase 2	15					aerobic respiration (GO:0009060)|cell death (GO:0008219)|coenzyme A biosynthetic process (GO:0015937)|coenzyme biosynthetic process (GO:0009108)|mitochondrion morphogenesis (GO:0070584)|pantothenate metabolic process (GO:0015939)|regulation of mitochondrial membrane potential (GO:0051881)|small molecule metabolic process (GO:0044281)|spermatid development (GO:0007286)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial intermembrane space (GO:0005758)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						CATTGGGCGGCGCCGCCATCA	0.701																																					p.A15V		Atlas-SNP	.											.	PANK2	37	.	0			c.C44T						PASS	.						19.0	14.0	16.0					20																	3869791		2183	4282	6465	SO:0001583	missense	80025	exon1			GGGCGGCGCCGCC	AK021791	CCDS13071.2, CCDS13072.1	20p13	2008-07-31	2008-07-31	2002-09-06	ENSG00000125779	ENSG00000125779	2.7.1.33		15894	protein-coding gene	gene with protein product	"""Hallervorden-Spatz syndrome"""	606157	"""neurodegeneration with brain iron accumulation 1 (Hallervorden-Spatz syndrome)"""	C20orf48, NBIA1		8944032, 11479594	Standard	XM_005260835		Approved	HSS, FLJ11729, PKAN, HARP	uc002wkc.3	Q9BZ23	OTTHUMG00000031768	ENST00000316562.4:c.44C>T	chr20.hg19:g.3869791C>T	ENSP00000313377:p.Ala15Val	85.0	0.0	.		113.0	34.0	.	NM_153638	B1AK33|B2Z3X0|D3DVZ0|Q5T7I2|Q5T7I4|Q7RTX5|Q8N7Q4|Q8TCR5|Q9BYW5|Q9HAF2	Missense_Mutation	SNP	ENST00000316562.4	hg19	CCDS13071.2	.	.	.	.	.	.	.	.	.	.	C	6.152	0.396211	0.11638	.	.	ENSG00000125779	ENST00000316562	D	0.97455	-4.39	4.57	-1.13	0.09775	.	0.546626	0.15407	N	0.263980	D	0.88691	0.6505	N	0.08118	0	0.21933	N	0.99946	B	0.06786	0.001	B	0.04013	0.001	T	0.80320	-0.1432	10	0.30854	T	0.27	-4.0E-4	4.3121	0.10976	0.0:0.4:0.1682:0.4318	.	15	Q9BZ23	PANK2_HUMAN	V	15	ENSP00000313377:A15V	ENSP00000313377:A15V	A	+	2	0	PANK2	3817791	0.959000	0.32827	0.677000	0.29947	0.004000	0.04260	-0.096000	0.11059	-0.135000	0.11495	-0.175000	0.13238	GCG	.	.	.	none		0.701	PANK2-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077793.2	NM_024960	
KRTAP19-5	337972	hgsc.bcm.edu	37	21	31874285	31874285	+	Missense_Mutation	SNP	C	C	T	rs370535457		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr21:31874285C>T	ENST00000334151.2	-	1	150	c.124G>A	c.(124-126)Gga>Aga	p.G42R		NM_181611.1	NP_853642.1	Q3LI72	KR195_HUMAN	keratin associated protein 19-5	42						intermediate filament (GO:0005882)				endometrium(1)|large_intestine(5)|lung(4)|pancreas(1)|prostate(1)	12						CCGTAGCCTCCGTAGCCACCG	0.572													C|||	1	0.000199681	0.0008	0.0	5008	,	,		17165	0.0		0.0	False		,,,				2504	0.0				p.G42R		Atlas-SNP	.											.	KRTAP19-5	32	.	0			c.G124A						PASS	.	C	ARG/GLY	1,4405	2.1+/-5.4	0,1,2202	128.0	122.0	124.0		124	-0.3	0.0	21		124	0,8600		0,0,4300	no	missense	KRTAP19-5	NM_181611.1	125	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	42/73	31874285	1,13005	2203	4300	6503	SO:0001583	missense	337972	exon1			AGCCTCCGTAGCC	AP001708	CCDS13597.1	21q22.1	2006-03-13			ENSG00000186977	ENSG00000186977		"""Keratin associated proteins"""	18940	protein-coding gene	gene with protein product						12359730	Standard	NM_181611		Approved	KAP19.5	uc011ada.2	Q3LI72	OTTHUMG00000057774	ENST00000334151.2:c.124G>A	chr21.hg19:g.31874285C>T	ENSP00000334985:p.Gly42Arg	172.0	0.0	.		48.0	34.0	.	NM_181611	A4IF22	Missense_Mutation	SNP	ENST00000334151.2	hg19	CCDS13597.1	.	.	.	.	.	.	.	.	.	.	C	12.38	1.920297	0.33908	2.27E-4	0.0	ENSG00000186977	ENST00000334151	T	0.11495	2.77	5.06	-0.26	0.12967	.	0.758211	0.10161	U	0.708309	T	0.07279	0.0184	.	.	.	0.09310	N	0.999999	P	0.48089	0.905	B	0.37480	0.251	T	0.30001	-0.9993	9	0.87932	D	0	-0.8878	4.9837	0.14180	0.0:0.5363:0.1489:0.3148	.	42	Q3LI72	KR195_HUMAN	R	42	ENSP00000334985:G42R	ENSP00000334985:G42R	G	-	1	0	KRTAP19-5	30796156	0.001000	0.12720	0.021000	0.16686	0.458000	0.32498	0.145000	0.16157	0.018000	0.15052	0.591000	0.81541	GGA	.	.	.	weak		0.572	KRTAP19-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128226.2		
TBL1X	6907	hgsc.bcm.edu	37	X	9683003	9683003	+	Missense_Mutation	SNP	C	C	T			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chrX:9683003C>T	ENST00000217964.7	+	17	2307	c.1667C>T	c.(1666-1668)gCc>gTc	p.A556V	TBL1X_ENST00000407597.2_Missense_Mutation_p.A556V|TBL1X_ENST00000424279.1_Missense_Mutation_p.A505V|TBL1X_ENST00000380961.1_Missense_Mutation_p.A505V|TBL1X_ENST00000536365.1_Missense_Mutation_p.A505V	NM_005647.3	NP_005638.1	O60907	TBL1X_HUMAN	transducin (beta)-like 1X-linked	556					canonical Wnt signaling pathway (GO:0060070)|cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|proteolysis (GO:0006508)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|histone binding (GO:0042393)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|cervix(1)|endometrium(5)|large_intestine(7)|lung(2)|ovary(1)|skin(2)	20		Hepatocellular(5;0.000888)				TGCTGGAACGCCCGAGGAGAC	0.592																																					p.A556V		Atlas-SNP	.											.	TBL1X	103	.	0			c.C1667T						PASS	.						86.0	62.0	70.0					X																	9683003		2203	4300	6503	SO:0001583	missense	6907	exon17			GGAACGCCCGAGG	Y12781	CCDS14133.1, CCDS48078.1	Xp22.3	2013-01-10	2002-05-22	2002-05-24	ENSG00000101849	ENSG00000101849		"""WD repeat domain containing"""	11585	protein-coding gene	gene with protein product		300196	"""transducin (beta)-like 1"""	TBL1		10330347	Standard	NM_005647		Approved	EBI	uc004csr.3	O60907	OTTHUMG00000021117	ENST00000217964.7:c.1667C>T	chrX.hg19:g.9683003C>T	ENSP00000217964:p.Ala556Val	272.0	0.0	.		178.0	81.0	.	NM_001139466	A8K044|A8K4J7|Q86UY2	Missense_Mutation	SNP	ENST00000217964.7	hg19	CCDS14133.1	.	.	.	.	.	.	.	.	.	.	C	17.08	3.297142	0.60086	.	.	ENSG00000101849	ENST00000407597;ENST00000424279;ENST00000536365;ENST00000380961;ENST00000217964	T;T;T;T;T	0.81247	-1.47;-1.47;-1.47;-1.47;-1.47	3.8	3.8	0.43715	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.116908	0.56097	D	0.000024	T	0.77994	0.4214	L	0.58101	1.795	0.44852	D	0.997864	B;B	0.29955	0.263;0.263	B;B	0.29598	0.104;0.104	T	0.80054	-0.1543	10	0.72032	D	0.01	.	15.6252	0.76851	0.0:1.0:0.0:0.0	.	519;556	Q59F53;O60907	.;TBL1X_HUMAN	V	556;505;505;505;556	ENSP00000385988:A556V;ENSP00000394097:A505V;ENSP00000445317:A505V;ENSP00000370348:A505V;ENSP00000217964:A556V	ENSP00000217964:A556V	A	+	2	0	TBL1X	9643003	1.000000	0.71417	0.958000	0.39756	0.937000	0.57800	4.399000	0.59703	1.667000	0.50832	0.429000	0.28392	GCC	.	.	.	none		0.592	TBL1X-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055709.1	NM_005647	
PHKA1	5255	hgsc.bcm.edu	37	X	71802352	71802352	+	Missense_Mutation	SNP	G	G	A			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chrX:71802352G>A	ENST00000373542.4	-	31	3553	c.3394C>T	c.(3394-3396)Ctt>Ttt	p.L1132F	PHKA1_ENST00000339490.3_Missense_Mutation_p.L1119F|PHKA1_ENST00000541944.1_Missense_Mutation_p.L1060F|PHKA1_ENST00000373539.3_Missense_Mutation_p.L1149F|PHKA1_ENST00000373545.3_Missense_Mutation_p.L1090F	NM_002637.3	NP_002628.2	P46020	KPB1_HUMAN	phosphorylase kinase, alpha 1 (muscle)	1132					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(2)|lung(18)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	52	Renal(35;0.156)					GTGAGGACAAGGATGGCTTCA	0.448																																					p.L1132F		Atlas-SNP	.											.	PHKA1	129	.	0			c.C3394T						PASS	.						114.0	86.0	96.0					X																	71802352		2203	4300	6503	SO:0001583	missense	5255	exon31			GGACAAGGATGGC		CCDS14421.1, CCDS48137.1, CCDS55453.1	Xq12-q13	2009-07-10			ENSG00000067177	ENSG00000067177	2.7.11.19		8925	protein-coding gene	gene with protein product		311870		PHKA			Standard	NM_002637		Approved		uc004eax.4	P46020	OTTHUMG00000022696	ENST00000373542.4:c.3394C>T	chrX.hg19:g.71802352G>A	ENSP00000362643:p.Leu1132Phe	417.0	1.0	.		293.0	86.0	.	NM_002637	B7ZL05|B7ZL07|Q2M3D7	Missense_Mutation	SNP	ENST00000373542.4	hg19	CCDS14421.1	.	.	.	.	.	.	.	.	.	.	G	15.39	2.819920	0.50633	.	.	ENSG00000067177	ENST00000373545;ENST00000373542;ENST00000541944;ENST00000339490;ENST00000373539	D;D;D;D;D	0.91464	-2.84;-2.85;-2.83;-2.82;-2.83	5.12	5.12	0.69794	.	0.000000	0.64402	D	0.000001	D	0.93216	0.7839	M	0.63428	1.95	0.48901	D	0.999723	D;P;P;D	0.76494	0.999;0.913;0.794;0.975	D;P;P;P	0.87578	0.998;0.459;0.66;0.835	D	0.92493	0.6002	10	0.46703	T	0.11	-11.3305	8.8082	0.34952	0.1046:0.0:0.8954:0.0	.	1060;1090;1119;1132	B7ZL07;A6NIT2;P46020-2;P46020	.;.;.;KPB1_HUMAN	F	1090;1132;1060;1119;1149	ENSP00000362646:L1090F;ENSP00000362643:L1132F;ENSP00000441251:L1060F;ENSP00000342469:L1119F;ENSP00000362640:L1149F	ENSP00000342469:L1119F	L	-	1	0	PHKA1	71719077	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.085000	0.30840	2.132000	0.65825	0.594000	0.82650	CTT	.	.	.	none		0.448	PHKA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058896.1		
GPR50	9248	hgsc.bcm.edu	37	X	150348665	150348665	+	Missense_Mutation	SNP	G	G	A			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chrX:150348665G>A	ENST00000218316.3	+	2	679	c.610G>A	c.(610-612)Gtg>Atg	p.V204M	AF003625.3_ENST00000602313.1_lincRNA|GPR50-AS1_ENST00000454196.1_RNA	NM_004224.3	NP_004215.2	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50	204					cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|identical protein binding (GO:0042802)|melatonin receptor activity (GO:0008502)			breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(6)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	38	Acute lymphoblastic leukemia(192;6.56e-05)					TCTCCTCATCGTGGGTTTCTG	0.532																																					p.V204M		Atlas-SNP	.											.	GPR50	195	.	0			c.G610A						PASS	.						230.0	203.0	212.0					X																	150348665		2123	4223	6346	SO:0001583	missense	9248	exon2			CTCATCGTGGGTT	U52219	CCDS44012.1	Xq28	2012-08-21			ENSG00000102195	ENSG00000102195		"""GPCR / Class A : Orphans"""	4506	protein-coding gene	gene with protein product		300207				9933574, 18400093	Standard	NM_004224		Approved	H9, Mel1c	uc010ntg.2	Q13585	OTTHUMG00000024166	ENST00000218316.3:c.610G>A	chrX.hg19:g.150348665G>A	ENSP00000218316:p.Val204Met	80.0	0.0	.		43.0	12.0	.	NM_004224	Q0VGG3|Q3ZAR0	Missense_Mutation	SNP	ENST00000218316.3	hg19	CCDS44012.1	.	.	.	.	.	.	.	.	.	.	G	17.71	3.456799	0.63401	.	.	ENSG00000102195	ENST00000535473;ENST00000218316	T	0.35048	1.33	4.33	4.33	0.51752	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.50684	0.1630	L	0.53729	1.69	0.47547	D	0.999454	D;P	0.69078	0.997;0.819	D;P	0.64321	0.924;0.668	T	0.47018	-0.9149	10	0.36615	T	0.2	-12.9108	13.7644	0.62986	0.0:0.0:1.0:0.0	.	157;204	F5H1S3;Q13585	.;MTR1L_HUMAN	M	157;204	ENSP00000218316:V204M	ENSP00000218316:V204M	V	+	1	0	GPR50	150099323	1.000000	0.71417	0.981000	0.43875	0.745000	0.42441	9.754000	0.98908	1.903000	0.55091	0.529000	0.55759	GTG	.	.	.	none		0.532	GPR50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060874.1	NM_004224	
RENBP	5973	hgsc.bcm.edu	37	X	153200791	153200791	+	Missense_Mutation	SNP	G	G	T			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chrX:153200791G>T	ENST00000393700.3	-	11	1312	c.1232C>A	c.(1231-1233)cCc>cAc	p.P411H	NAA10_ENST00000370015.4_5'Flank|RENBP_ENST00000369997.3_Missense_Mutation_p.P397H|NAA10_ENST00000370009.1_5'Flank|NAA10_ENST00000393712.3_5'Flank|RENBP_ENST00000412763.1_3'UTR|NAA10_ENST00000393710.3_5'Flank|NAA10_ENST00000464845.1_5'Flank	NM_002910.5	NP_002901.2	P51606	RENBP_HUMAN	renin binding protein	411					N-acetylglucosamine metabolic process (GO:0006044)|N-acetylmannosamine metabolic process (GO:0006051)|N-acetylneuraminate catabolic process (GO:0019262)|regulation of blood pressure (GO:0008217)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|endopeptidase inhibitor activity (GO:0004866)|N-acylglucosamine 2-epimerase activity (GO:0050121)			breast(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	20	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)				N-Acetyl-D-glucosamine(DB00141)	ggcgggggcggggCGGCTCAG	0.751																																					p.P411H		Atlas-SNP	.											.	RENBP	69	.	0			c.C1232A						PASS	.						2.0	3.0	2.0					X																	153200791		1563	2987	4550	SO:0001583	missense	5973	exon11			GGGGCGGGGCGGC		CCDS14738.2	Xq28	2013-09-23	2001-11-28		ENSG00000102032	ENSG00000102032			9959	protein-coding gene	gene with protein product	"""N-acylglucosamine 2-epimerase"", ""GlcNAc 2-epimerase"", ""N-acetyl-D-glucosamine 2-epimerase"""	312420	"""renin-binding protein"""			1618798	Standard	NM_002910		Approved	RNBP, RBP	uc004fjo.2	P51606	OTTHUMG00000024224	ENST00000393700.3:c.1232C>A	chrX.hg19:g.153200791G>T	ENSP00000377303:p.Pro411His	0.0	0.0	.		8.0	4.0	.	NM_002910	B4DNZ3|Q96BI6	Missense_Mutation	SNP	ENST00000393700.3	hg19	CCDS14738.2	.	.	.	.	.	.	.	.	.	.	g	13.98	2.398865	0.42512	.	.	ENSG00000102032	ENST00000393700;ENST00000369997;ENST00000451114	T;T	0.32988	1.43;1.43	3.76	-6.35	0.01975	Six-hairpin glycosidase-like (1);	2.963070	0.01364	U	0.012354	T	0.24890	0.0604	L	0.44542	1.39	0.09310	N	0.99999	B	0.02656	0.0	B	0.01281	0.0	T	0.19353	-1.0308	10	0.45353	T	0.12	1.1156	7.9104	0.29787	0.1647:0.1371:0.6982:0.0	.	411	P51606	RENBP_HUMAN	H	411;397;124	ENSP00000377303:P411H;ENSP00000359014:P397H	ENSP00000359014:P397H	P	-	2	0	RENBP	152853985	0.000000	0.05858	0.000000	0.03702	0.698000	0.40448	-1.269000	0.02834	-1.762000	0.01308	0.445000	0.29226	CCC	.	.	.	none		0.751	RENBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061103.3	NM_002910	
SREBF2	6721	hgsc.bcm.edu	37	22	42289217	42289217	+	Frame_Shift_Del	DEL	T	T	-			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr22:42289217delT	ENST00000361204.4	+	12	2471	c.2305delT	c.(2305-2307)tttfs	p.F770fs	SREBF2_ENST00000491541.1_3'UTR	NM_004599.2	NP_004590.2	Q12772	SRBP2_HUMAN	sterol regulatory element binding transcription factor 2	770					cellular lipid metabolic process (GO:0044255)|cellular response to laminar fluid shear stress (GO:0071499)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cholesterol homeostasis (GO:2000188)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|response to low-density lipoprotein particle (GO:0055098)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SREBP-SCAP-Insig complex (GO:0032937)	E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(6)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	38						GGGCCAGAAGTTTTTCATGGA	0.582																																					p.K768fs		Atlas-Indel,Pindel	.											.	SREBF2	99	.	0			c.2304delG						PASS	.						55.0	58.0	57.0					22																	42289217		2203	4300	6503	SO:0001589	frameshift_variant	6721	exon12			.	U02031	CCDS14023.1	22q13.2	2013-05-21			ENSG00000198911	ENSG00000198911		"""Basic helix-loop-helix proteins"""	11290	protein-coding gene	gene with protein product		600481				7903453	Standard	NM_004599		Approved	SREBP2, bHLHd2	uc003bbi.3	Q12772	OTTHUMG00000151261	ENST00000361204.4:c.2305delT	chr22.hg19:g.42289217delT	ENSP00000354476:p.Phe770fs	97.0	0.0	0		70.0	24.0	0.342857	NM_004599	Q05BD5|Q6GTH7|Q86V36|Q9UH04	Frame_Shift_Del	DEL	ENST00000361204.4	hg19	CCDS14023.1																																																																																			.	.	.	none		0.582	SREBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321956.1	NM_004599	
PLEC	5339	hgsc.bcm.edu	37	8	145024821	145024825	+	Frame_Shift_Del	DEL	CACCT	CACCT	-			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	CACCT	CACCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr8:145024821_145024825delCACCT	ENST00000322810.4	-	1	219_223	c.50_54delAGGTG	c.(49-54)gaggtgfs	p.EV17fs	PLEC_ENST00000436759.2_Intron|PLEC_ENST00000527096.1_Intron|PLEC_ENST00000356346.3_Intron|PLEC_ENST00000354958.2_Intron	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	17	Globular 1.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						CGCGGAAGAGCACCTCATAGATGGC	0.683																																					p.17_19del		Atlas-Indel,Pindel	.											.	PLEC	1144	.	0			c.51_55del						PASS	.																																			SO:0001589	frameshift_variant	5339	exon1			.	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.50_54delAGGTG	chr8.hg19:g.145024821_145024825delCACCT	ENSP00000323856:p.Glu17fs	3.0	0.0	0		46.0	17.0	0.369565	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Frame_Shift_Del	DEL	ENST00000322810.4	hg19	CCDS43772.1																																																																																			.	.	.	none		0.683	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
VAPB	9217	hgsc.bcm.edu	37	20	57009683	57009684	+	Frame_Shift_Ins	INS	-	-	C			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr20:57009683_57009684insC	ENST00000475243.1	+	3	575_576	c.237_238insC	c.(238-240)cccfs	p.P80fs	VAPB_ENST00000265619.2_Intron|VAPB_ENST00000395802.3_Intron	NM_004738.4	NP_004729.1	O95292	VAPB_HUMAN	VAMP (vesicle-associated membrane protein)-associated protein B and C	80	MSP. {ECO:0000255|PROSITE- ProRule:PRU00132}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell death (GO:0008219)|cellular calcium ion homeostasis (GO:0006874)|endoplasmic reticulum unfolded protein response (GO:0030968)|modulation by virus of host morphology or physiology (GO:0019048)|positive regulation of viral genome replication (GO:0045070)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	beta-tubulin binding (GO:0048487)|enzyme binding (GO:0019899)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|structural molecule activity (GO:0005198)			kidney(2)|lung(3)|prostate(1)	6	Lung NSC(12;0.000615)|all_lung(29;0.00186)		BRCA - Breast invasive adenocarcinoma(13;6.2e-12)|Epithelial(14;3.7e-08)|all cancers(14;3.88e-07)			TCGATTATGATCCCAATGAGAA	0.361																																					p.D79fs		Atlas-Indel,Pindel	.											.	VAPB	21	.	0			c.237_238insC						PASS	.																																			SO:0001589	frameshift_variant	9217	exon3			.	AF086628	CCDS33498.1, CCDS56198.1	20q13	2014-09-17			ENSG00000124164	ENSG00000124164			12649	protein-coding gene	gene with protein product		605704				9920726	Standard	NM_004738		Approved	VAP-B, VAP-C, ALS8	uc002xza.3	O95292	OTTHUMG00000032840	ENST00000475243.1:c.240dupC	chr20.hg19:g.57009686_57009686dupC	ENSP00000417175:p.Pro80fs	89.0	0.0	0		79.0	21.0	0.265823	NM_004738	A2A2F2|O95293|Q9P0H0	Frame_Shift_Ins	INS	ENST00000475243.1	hg19	CCDS33498.1																																																																																			.	.	.	none		0.361	VAPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079875.2		
IGFLR1	79713	hgsc.bcm.edu	37	19	36230984	36230986	+	In_Frame_Del	DEL	CGG	CGG	-	rs200340760		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	CGG	CGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr19:36230984_36230986delCGG	ENST00000592537.1	-	4	446_448	c.346_348delCCG	c.(346-348)ccgdel	p.P116del	AD000671.6_ENST00000589807.1_3'UTR|IGFLR1_ENST00000587101.1_5'UTR|IGFLR1_ENST00000246532.1_In_Frame_Del_p.P116del|KMT2B_ENST00000607650.1_RNA|IGFLR1_ENST00000588992.1_Intron|IGFLR1_ENST00000592889.1_Intron|IGFLR1_ENST00000344990.3_Intron			Q9H665	IGFR1_HUMAN	IGF-like family receptor 1	116						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|kidney(3)|large_intestine(1)|lung(8)|prostate(1)	15						TGGCAGGGACCGGCCTCTGGGGA	0.621																																					p.116_117del		Atlas-INDEL	.											.	IGFLR1	28	.	0			c.347_349del						PASS	.																																			SO:0001651	inframe_deletion	79713	exon4			.	AK026226	CCDS12472.1	19q13.12	2012-10-02	2011-04-04	2011-04-04	ENSG00000126246	ENSG00000126246			23620	protein-coding gene	gene with protein product		614143	"""U2(RNU2) small nuclear RNA auxiliary factor 1-like 4"", ""transmembrane protein 149"""	U2AF1L4, TMEM149		21454693	Standard	NM_024660		Approved	FLJ22573	uc002obd.4	Q9H665		ENST00000592537.1:c.346_348delCCG	chr19.hg19:g.36230984_36230986delCGG	ENSP00000466181:p.Pro116del	44.0	0.0	0		34.0	11.0	0.323529	NM_024660	Q8N5X0	In_Frame_Del	DEL	ENST00000592537.1	hg19	CCDS12472.1																																																																																			.	.	.	none		0.621	IGFLR1-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459077.1	NM_024660	
SLC14A1	6563	hgsc.bcm.edu	37	18	43316457	43316458	+	Frame_Shift_Ins	INS	-	-	A			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr18:43316457_43316458insA	ENST00000321925.4	+	6	739_740	c.507_508insA	c.(508-510)aaafs	p.K170fs	SLC14A1_ENST00000535474.1_Frame_Shift_Ins_p.K38fs|SLC14A1_ENST00000586142.1_Frame_Shift_Ins_p.K170fs|RP11-116O18.3_ENST00000589510.1_RNA|SLC14A1_ENST00000402943.2_Frame_Shift_Ins_p.K65fs|SLC14A1_ENST00000415427.3_Frame_Shift_Ins_p.K226fs|RP11-116O18.3_ENST00000586213.1_RNA|SLC14A1_ENST00000589700.1_Frame_Shift_Ins_p.K170fs|SLC14A1_ENST00000591943.1_Intron|SLC14A1_ENST00000436407.3_Frame_Shift_Ins_p.K226fs|SLC14A1_ENST00000502059.2_Frame_Shift_Ins_p.K62fs	NM_001128588.3|NM_001146036.2|NM_015865.6	NP_001122060.3|NP_001139508.2|NP_056949.4	Q13336	UT1_HUMAN	solute carrier family 14 (urea transporter), member 1 (Kidd blood group)	170					transmembrane transport (GO:0055085)|urea transmembrane transport (GO:0071918)|urea transport (GO:0015840)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	urea channel activity (GO:0015265)|urea transmembrane transporter activity (GO:0015204)|water transmembrane transporter activity (GO:0005372)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(11)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	21						CCATGCTCAGCAAATGGGACCT	0.455																																					p.S225fs		Atlas-Indel,Pindel	.											.	SLC14A1	84	.	0			c.675_676insA						PASS	.																																			SO:0001589	frameshift_variant	6563	exon5			.	BC040128	CCDS11925.1, CCDS45860.1	18q11-q12	2014-07-19	2014-01-02		ENSG00000141469	ENSG00000141469		"""Blood group antigens"", ""Solute carriers"""	10918	protein-coding gene	gene with protein product		613868	"""Kidd blood group"", ""solute carrier family 14 (urea transporter), member 1"""	JK		7797558	Standard	NM_001146037		Approved	HsT1341, RACH1, RACH2	uc010dnk.3	Q13336	OTTHUMG00000132617	ENST00000321925.4:c.510dupA	chr18.hg19:g.43316460_43316460dupA	ENSP00000318546:p.Lys170fs	156.0	0.0	0		128.0	51.0	0.398438	NM_001146037	A8K0P3|B3KR62|B3KVX3|C9EHF2|Q86VM5	Frame_Shift_Ins	INS	ENST00000321925.4	hg19	CCDS11925.1																																																																																			.	.	.	none		0.455	SLC14A1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255860.2	NM_015865	
MIA3	375056	hgsc.bcm.edu	37	1	222803477	222803477	+	Frame_Shift_Del	DEL	A	A	-			TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	g.chr1:222803477delA	ENST00000344922.5	+	4	2940	c.2915delA	c.(2914-2916)gaafs	p.E972fs	MIA3_ENST00000344441.6_Frame_Shift_Del_p.E972fs|MIA3_ENST00000344507.1_Intron|MIA3_ENST00000470521.1_3'UTR	NM_198551.2	NP_940953.2	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	972					chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|exocytosis (GO:0006887)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|positive regulation of bone mineralization (GO:0030501)|positive regulation of leukocyte migration (GO:0002687)|protein transport (GO:0015031)|wound healing (GO:0042060)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.V974fs*4(1)		breast(5)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(15)|lung(37)|ovary(5)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|urinary_tract(1)	80				GBM - Glioblastoma multiforme(131;0.0199)		TATAATATGGAAAAAGTCCTA	0.428																																					p.E972fs		Atlas-Indel,Pindel	.											.,1	MIA3	167	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.2914delG						PASS	.						74.0	72.0	73.0					1																	222803477		1967	4169	6136	SO:0001589	frameshift_variant	375056	exon4			.		CCDS41470.1, CCDS73035.1	1p36.33	2012-12-13		2006-07-25	ENSG00000154305	ENSG00000154305			24008	protein-coding gene	gene with protein product	"""C219 reactive peptide"", ""transport and golgi organization"""	613455				15183315	Standard	XM_005273121		Approved	UNQ6077, FLJ39207, KIAA0268, TANGO	uc001hnl.3	Q5JRA6	OTTHUMG00000037543	ENST00000344922.5:c.2915delA	chr1.hg19:g.222803477delA	ENSP00000340900:p.Glu972fs	76.0	0.0	0		73.0	32.0	0.438356	NM_198551	A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580	Frame_Shift_Del	DEL	ENST00000344922.5	hg19	CCDS41470.1																																																																																			.	.	.	none		0.428	MIA3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091489.4	NM_198551	
