#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_ACHILLES_Lineage_Results_Top_Genes	i_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	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_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	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_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	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_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	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_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
CEP104	9731	broad.mit.edu	37	1	3761888	3761888	+	Missense_Mutation	SNP	C	C	G			TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr1:3761888C>G	ENST00000378230.3	-	5	778	c.454G>C	c.(454-456)Gga>Cga	p.G152R	CEP104_ENST00000378223.3_Missense_Mutation_p.G152R	NM_014704.3	NP_055519.1	O60308	CE104_HUMAN	centrosomal protein 104kDa	152						centriole (GO:0005814)	glutamate binding (GO:0016595)|glycine binding (GO:0016594)|thienylcyclohexylpiperidine binding (GO:0016596)			breast(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(14)|lung(8)|prostate(1)|skin(3)	39						GCAGGGTCTCCAATGATATTT	0.294																																						uc001aky.2																			0				breast(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(14)|lung(8)|prostate(1)|skin(3)	39						c.(454-456)Gga>Cga		Homo sapiens centrosomal protein 104kDa (CEP104), mRNA.							84.0	95.0	92.0					1																	3761888		2201	4300	6501	SO:0001583	missense	9731					centriole	binding	g.chr1:3761888C>G	AB011134	CCDS30571.1	1p36.32	2014-02-20	2011-05-06	2011-05-06	ENSG00000116198	ENSG00000116198			24866	protein-coding gene	gene with protein product	"""glycine, glutamate, thienylcyclohexylpiperidine binding protein"""		"""KIAA0562"""	KIAA0562		7488117, 21399614	Standard	NM_014704		Approved	GlyBP, RP1-286D6.4	uc001aky.2	O60308	OTTHUMG00000003507	ENST00000378230.3:c.454G>C	1.37:g.3761888C>G	ENSP00000367476:p.Gly152Arg					CEP104_uc010nzm.1_Non-coding_Transcript|CEP104_uc001akz.3_Missense_Mutation_p.G152R	p.G152R	NM_014704	NP_055519	O60308	CE104_HUMAN			4	813	-			152					Q5JSQ3|Q5SR24|Q5SR25|Q6PKF5|Q86W32|Q86X14	Missense_Mutation	SNP	ENST00000378230.3	37	c.454G>C	CCDS30571.1	.	.	.	.	.	.	.	.	.	.	C	17.21	3.330623	0.60743	.	.	ENSG00000116198	ENST00000378230;ENST00000428079;ENST00000378223	D;D	0.85773	-2.03;-2.03	5.29	4.37	0.52481	Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	D	0.92861	0.7729	M	0.87682	2.9	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.93864	0.7156	10	0.87932	D	0	.	14.3281	0.66534	0.1495:0.8505:0.0:0.0	.	152;152	O60308-3;O60308	.;CE104_HUMAN	R	152;94;152	ENSP00000367476:G152R;ENSP00000367468:G152R	ENSP00000367468:G152R	G	-	1	0	CEP104	3751748	1.000000	0.71417	1.000000	0.80357	0.521000	0.34408	7.211000	0.77933	1.209000	0.43321	-0.181000	0.13052	GGA		0.294	CEP104-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009747.3	NM_014704	
ABCA4	24	broad.mit.edu	37	1	94466600	94466600	+	Missense_Mutation	SNP	C	C	T			TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr1:94466600C>T	ENST00000370225.3	-	46	6430	c.6344G>A	c.(6343-6345)aGc>aAc	p.S2115N	ABCA4_ENST00000465352.1_5'Flank|ABCA4_ENST00000536513.1_Missense_Mutation_p.S385N|ABCA4_ENST00000535881.1_Missense_Mutation_p.S234N	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	2115	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				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)		TCTGATGATGCTCACGATGAC	0.632																																						uc001dqh.3																			0				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						c.(6343-6345)aGc>aAc		Homo sapiens ATP-binding cassette, sub-family A (ABC1), member 4 (ABCA4), mRNA.							121.0	109.0	113.0					1																	94466600		2203	4300	6503	SO:0001583	missense	24				phototransduction, visible light|visual perception	integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances	g.chr1:94466600C>T	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.6344G>A	1.37:g.94466600C>T	ENSP00000359245:p.Ser2115Asn						p.S2115N	NM_000350	NP_000341	P78363	ABCA4_HUMAN		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)	45	6448	-		all_lung(203;0.000757)|Lung NSC(277;0.00335)	2115			ABC transporter 2.		O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	ENST00000370225.3	37	c.6344G>A	CCDS747.1	.	.	.	.	.	.	.	.	.	.	C	13.48	2.251130	0.39797	.	.	ENSG00000198691	ENST00000546054;ENST00000370225;ENST00000536513;ENST00000535881	D;D;D	0.95272	-3.66;-3.66;-3.66	6.08	3.18	0.36537	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.251294	0.51477	N	0.000086	D	0.83403	0.5247	L	0.31157	0.91	0.80722	D	1	B	0.06786	0.001	B	0.11329	0.006	T	0.78191	-0.2300	10	0.33141	T	0.24	.	10.9317	0.47222	0.0:0.7428:0.0:0.2572	.	2115	P78363	ABCA4_HUMAN	N	907;2115;385;234	ENSP00000359245:S2115N;ENSP00000439707:S385N;ENSP00000443203:S234N	ENSP00000359245:S2115N	S	-	2	0	ABCA4	94239188	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.648000	0.46647	0.880000	0.35969	0.655000	0.94253	AGC		0.632	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350	
PPM1J	333926	broad.mit.edu	37	1	113252867	113252867	+	Missense_Mutation	SNP	C	C	T	rs113935705		TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr1:113252867C>T	ENST00000309276.6	-	10	1611	c.1436G>A	c.(1435-1437)cGt>cAt	p.R479H	RP11-426L16.10_ENST00000606505.1_Intron|RHOC_ENST00000339083.7_5'Flank|PPM1J_ENST00000359994.4_Missense_Mutation_p.R273H|RHOC_ENST00000369642.3_5'Flank|PPM1J_ENST00000464951.1_Missense_Mutation_p.R273H|RP11-426L16.10_ENST00000471038.2_Intron	NM_005167.5	NP_005158.5	Q5JR12	PPM1J_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1J	479	PP2C-like.				protein dephosphorylation (GO:0006470)		protein serine/threonine phosphatase activity (GO:0004722)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	14	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GTTGGGGAGACGCCAGCCACG	0.622													C|||	1	0.000199681	0.0	0.0	5008	,	,		17374	0.0		0.0	False		,,,				2504	0.001					uc001ect.1																			0				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	14						c.(1435-1437)cGt>cAt		Homo sapiens protein phosphatase, Mg2+/Mn2+ dependent, 1J (PPM1J), mRNA.		C	HIS/ARG	2,4404	2.1+/-5.4	0,2,2201	47.0	52.0	50.0		1436	4.9	1.0	1	dbSNP_132	50	0,8600		0,0,4300	no	missense	PPM1J	NM_005167.5	29	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging	479/506	113252867	2,13004	2203	4300	6503	SO:0001583	missense	333926							g.chr1:113252867C>T	AK093270	CCDS855.2	1p13.1	2012-04-17	2010-03-05		ENSG00000155367	ENSG00000155367	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	20785	protein-coding gene	gene with protein product	"""protein phosphatase 2C zeta"""	609957	"""protein phosphatase 1J (PP2C domain containing)"""			12633878	Standard	NM_005167		Approved	FLJ35951, MGC19531, DKFZp434P1514, PP2Czeta, PPP2CZ	uc001ect.1	Q5JR12	OTTHUMG00000012019	ENST00000309276.6:c.1436G>A	1.37:g.113252867C>T	ENSP00000308926:p.Arg479His					RHOC_uc001ecq.1_5'Flank|RHOC_uc001ecr.1_5'Flank|RHOC_uc009wgk.1_5'Flank|PPM1J_uc009wgl.1_Intron|PPM1J_uc001ecs.1_Missense_Mutation_p.R273H	p.R479H	NM_005167	NP_005158	Q5JR12	PPM1J_HUMAN		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)	9	1463	-	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)	479			PP2C-like.		B3KSB7|Q6DKJ7|Q96EZ7|Q9UF84	Missense_Mutation	SNP	ENST00000309276.6	37	c.1436G>A	CCDS855.2	.	.	.	.	.	.	.	.	.	.	C	22.2	4.252604	0.80135	4.54E-4	0.0	ENSG00000155367	ENST00000309276;ENST00000359994	T;T	0.34859	1.34;1.44	5.77	4.87	0.63330	Protein phosphatase 2C-like (4);	0.112676	0.64402	N	0.000013	T	0.55561	0.1928	M	0.90759	3.145	0.53005	D	0.999962	D;D	0.89917	1.0;1.0	D;D	0.72338	0.959;0.977	T	0.66015	-0.6028	10	0.72032	D	0.01	-3.8076	10.6168	0.45456	0.0:0.8525:0.0:0.1475	.	479;273	Q5JR12;Q5JR12-2	PPM1J_HUMAN;.	H	479;273	ENSP00000308926:R479H;ENSP00000353088:R273H	ENSP00000308926:R479H	R	-	2	0	PPM1J	113054390	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.803000	0.55560	1.465000	0.48006	0.561000	0.74099	CGT		0.622	PPM1J-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033251.1	NM_005167	
TCHH	7062	broad.mit.edu	37	1	152082812	152082812	+	Missense_Mutation	SNP	G	G	A			TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr1:152082812G>A	ENST00000368804.1	-	2	2880	c.2881C>T	c.(2881-2883)Cgg>Tgg	p.R961W		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	961	10 X 30 AA tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ttatccttcCGATATTGCCTT	0.562																																						uc009wne.1																			0				NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105						c.(2881-2883)Cgg>Tgg		Homo sapiens trichohyalin (TCHH), mRNA.							203.0	206.0	205.0					1																	152082812		1917	4129	6046	SO:0001583	missense	7062				keratinization	cytoskeleton	calcium ion binding	g.chr1:152082812G>A	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"""EF-hand domain containing"""	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.2881C>T	1.37:g.152082812G>A	ENSP00000357794:p.Arg961Trp					TCHH_uc001ezp.2_Missense_Mutation_p.R961W	p.R961W	NM_007113	NP_009044	Q07283	TRHY_HUMAN	LUSC - Lung squamous cell carcinoma(543;0.206)		2	3153	-	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		961			10 X 30 AA tandem repeats.		Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	37	c.2881C>T	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	g	5.506	0.278255	0.10403	.	.	ENSG00000159450	ENST00000368804	T	0.12465	2.68	2.85	0.787	0.18596	.	.	.	.	.	T	0.05960	0.0155	N	0.24115	0.695	0.09310	N	1	D	0.76494	0.999	P	0.59171	0.853	T	0.16958	-1.0385	9	0.72032	D	0.01	.	1.0859	0.01652	0.1463:0.2299:0.3895:0.2344	.	961	Q07283	TRHY_HUMAN	W	961	ENSP00000357794:R961W	ENSP00000357794:R961W	R	-	1	2	TCHH	150349436	0.003000	0.15002	0.002000	0.10522	0.020000	0.10135	-0.229000	0.09098	0.145000	0.18977	0.462000	0.41574	CGG		0.562	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113	
FLG	2312	broad.mit.edu	37	1	152278705	152278705	+	Missense_Mutation	SNP	C	C	T	rs369659011		TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr1:152278705C>T	ENST00000368799.1	-	3	8692	c.8657G>A	c.(8656-8658)cGc>cAc	p.R2886H	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2886	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GGATCCCTGGCGCCTGCTTCT	0.562									Ichthyosis																													uc001ezu.1																			0				autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424						c.(8656-8658)cGc>cAc		Homo sapiens filaggrin (FLG), mRNA.		C	HIS/ARG	0,4108		0,0,2054	92.0	149.0	131.0		8657	-6.8	0.0	1		131	1,8555		0,1,4277	no	missense	FLG	NM_002016.1	29	0,1,6331	TT,TC,CC		0.0117,0.0,0.0079	benign	2886/4062	152278705	1,12663	2054	4278	6332	SO:0001583	missense	2312	Ichthyosis	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity	g.chr1:152278705C>T	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.8657G>A	1.37:g.152278705C>T	ENSP00000357789:p.Arg2886His						p.R2886H	NM_002016	NP_002007	P20930	FILA_HUMAN	LUSC - Lung squamous cell carcinoma(543;0.206)		2	8693	-	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		2886			Ser-rich.		Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	c.8657G>A	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	C	2.358	-0.347234	0.05208	0.0	1.17E-4	ENSG00000143631	ENST00000368799;ENST00000368796	T	0.01335	5.0	3.38	-6.77	0.01727	.	.	.	.	.	T	0.00328	0.0010	L	0.60455	1.87	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.51772	-0.8663	9	0.06625	T	0.88	.	3.5086	0.07700	0.1189:0.4835:0.126:0.2716	.	2886	P20930	FILA_HUMAN	H	2886;148	ENSP00000357789:R2886H	ENSP00000357786:R148H	R	-	2	0	FLG	150545329	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.617000	0.00881	-2.651000	0.00424	-3.074000	0.00066	CGC		0.562	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
USH2A	7399	broad.mit.edu	37	1	216595382	216595382	+	Silent	SNP	G	G	A			TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr1:216595382G>A	ENST00000307340.3	-	2	683	c.297C>T	c.(295-297)gcC>gcT	p.A99A	USH2A_ENST00000366942.3_Silent_p.A99A|USH2A_ENST00000366943.2_Silent_p.A99A	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	99					hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		CTGAGAAAAGGGCAGTGTAGG	0.453										HNSCC(13;0.011)																												uc001hku.1																			0		p.A99V(2)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527						c.(295-297)gcC>gcT		Homo sapiens Usher syndrome 2A (autosomal recessive, mild) (USH2A), transcript variant 2, mRNA.							117.0	110.0	112.0					1																	216595382		2203	4300	6503	SO:0001819	synonymous_variant	7399				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding	g.chr1:216595382G>A	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.297C>T	1.37:g.216595382G>A		HNSCC(13;0.011)				USH2A_uc001hkv.3_Silent_p.A99A	p.A99A	NM_206933	NP_996816	O75445	USH2A_HUMAN		OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)	1	684	-			99					Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	37	c.297C>T	CCDS31025.1																																																																																				0.453	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
COG2	22796	broad.mit.edu	37	1	230798959	230798959	+	Frame_Shift_Del	DEL	A	A	-	rs141422644	byFrequency	TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr1:230798959delA	ENST00000366669.4	+	4	488	c.373delA	c.(373-375)aaafs	p.K127fs	COG2_ENST00000366668.3_Frame_Shift_Del_p.K127fs|COG2_ENST00000535166.1_Frame_Shift_Del_p.K11fs|COG2_ENST00000534989.1_Frame_Shift_Del_p.K68fs	NM_001145036.1|NM_007357.2	NP_001138508.1|NP_031383.1	Q14746	COG2_HUMAN	component of oligomeric golgi complex 2	127					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	cytosol (GO:0005829)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|Golgi transport complex (GO:0017119)	protein transporter activity (GO:0008565)			NS(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|urinary_tract(3)	27	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				GGACATTAGGAAAAAAAAGGT	0.348																																						uc001htw.3																			0				NS(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|urinary_tract(3)	27						c.(373-375)aaafs		Homo sapiens component of oligomeric golgi complex 2 (COG2), transcript variant 1, mRNA.																																				SO:0001589	frameshift_variant	22796				Golgi organization|intra-Golgi vesicle-mediated transport|intracellular protein transport|oligosaccharide biosynthetic process|protein glycosylation	Golgi membrane|Golgi stack|Golgi transport complex	protein binding|protein transporter activity	g.chr1:230798959delA	Z34975	CCDS1584.1, CCDS44329.1	1q42.2	2008-02-05	2002-05-28	2002-05-31	ENSG00000135775	ENSG00000135775		"""Components of oligomeric golgi complex"""	6546	protein-coding gene	gene with protein product		606974	"""low density lipoprotein receptor defect C complementing"""	LDLC		7962052	Standard	NM_007357		Approved		uc001htw.3	Q14746	OTTHUMG00000037753	ENST00000366669.4:c.373delA	1.37:g.230798959delA	ENSP00000355629:p.Lys127fs					COG2_uc001htx.3_Frame_Shift_Del_p.K125fs|COG2_uc010pwc.2_5'UTR	p.K125fs	NM_007357	NP_031383	Q14746	COG2_HUMAN			3	524	+	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)	125					Q86U99	Frame_Shift_Del	DEL	ENST00000366669.4	37	c.373delA	CCDS1584.1																																																																																				0.348	COG2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092087.1	NM_007357	
OR2G2	81470	broad.mit.edu	37	1	247752222	247752222	+	Silent	SNP	C	C	A			TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr1:247752222C>A	ENST00000320065.1	+	1	561	c.561C>A	c.(559-561)ctC>ctA	p.L187L	RP11-978I15.10_ENST00000446347.1_RNA|RP11-978I15.10_ENST00000435333.1_RNA	NM_001001915.1	NP_001001915.1	Q8NGZ5	OR2G2_HUMAN	olfactory receptor, family 2, subfamily G, member 2	187						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(4)|large_intestine(3)|lung(30)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			TCCCTGTGCTCATCAAGCTGG	0.537																																						uc010pyy.2																			0				endometrium(4)|kidney(4)|large_intestine(3)|lung(30)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						c.(559-561)ctC>ctA		Homo sapiens olfactory receptor, family 2, subfamily G, member 2 (OR2G2), mRNA.							182.0	177.0	179.0					1																	247752222		2203	4300	6503	SO:0001819	synonymous_variant	81470				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr1:247752222C>A	BK004472	CCDS31092.1	1q44	2012-08-09	2008-05-23		ENSG00000177489	ENSG00000177489		"""GPCR / Class A : Olfactory receptors"""	15007	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily G, member 2"", ""olfactory receptor, family 2, subfamily G, member 2 pseudogene"""				Standard	NM_001001915		Approved		uc010pyy.2	Q8NGZ5	OTTHUMG00000040575	ENST00000320065.1:c.561C>A	1.37:g.247752222C>A							p.L187L	NM_001001915	NP_001001915	Q8NGZ5	OR2G2_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.017)		0	561	+	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		187					Q5JQT2|Q6IEZ0	Silent	SNP	ENST00000320065.1	37	c.561C>A	CCDS31092.1																																																																																				0.537	OR2G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097623.1		
BMI1	648	broad.mit.edu	37	10	22615480	22615480	+	Missense_Mutation	SNP	T	T	G			TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr10:22615480T>G	ENST00000376663.3	+	2	607	c.102T>G	c.(100-102)tgT>tgG	p.C34W	COMMD3-BMI1_ENST00000602390.1_Missense_Mutation_p.C177W	NM_005180.8	NP_005171.4	P35226	BMI1_HUMAN	BMI1 proto-oncogene, polycomb ring finger	34					chromatin modification (GO:0016568)|hemopoiesis (GO:0030097)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|regulation of gene expression (GO:0010468)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|ubiquitin ligase complex (GO:0000151)	RING-like zinc finger domain binding (GO:0071535)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|skin(2)|urinary_tract(1)	12						TAATAGAATGTCTACATTCCT	0.413																																						uc009xkg.3																			0											c.(529-531)tgT>tgG		Homo sapiens COMMD3-BMI1 readthrough (COMMD3-BMI1), mRNA.							209.0	186.0	194.0					10																	22615480		2203	4300	6503	SO:0001583	missense	648				hemopoiesis|negative regulation of transcription from RNA polymerase II promoter|positive regulation of fibroblast proliferation|positive regulation of ubiquitin-protein ligase activity|segment specification|transcription, DNA-dependent	cytoplasm|nucleolus|PcG protein complex|ubiquitin ligase complex	RING-like zinc finger domain binding|zinc ion binding	g.chr10:22615480T>G	BC011652	CCDS7138.1	10p13	2014-06-26	2014-06-26	2006-04-26	ENSG00000168283	ENSG00000168283		"""RING-type (C3HC4) zinc fingers"", ""Polycomb group ring fingers"""	1066	protein-coding gene	gene with protein product		164831	"""polycomb group ring finger 4"", ""B lymphoma Mo-MLV insertion region 1 homolog (mouse)"""	PCGF4		8268912	Standard	NM_005180		Approved	RNF51		P35226	OTTHUMG00000017807	ENST00000376663.3:c.102T>G	10.37:g.22615480T>G	ENSP00000365851:p.Cys34Trp					COMMD3-BMI1_uc001irh.3_Missense_Mutation_p.C34W	p.C177W	NM_001204062	NP_001190991	P35226	BMI1_HUMAN			5	566	+			34			Interaction with E4F1.		Q16030|Q5T8Z3|Q96F37	Missense_Mutation	SNP	ENST00000376663.3	37	c.531T>G	CCDS7138.1	.	.	.	.	.	.	.	.	.	.	T	15.45	2.836132	0.50951	.	.	ENSG00000168283	ENST00000417470;ENST00000376691;ENST00000376663;ENST00000442508;ENST00000456675;ENST00000416820;ENST00000443519	D;D;D;D	0.99741	-6.43;-6.43;-6.43;-6.6	5.67	3.35	0.38373	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type, conserved site (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.042632	0.85682	D	0.000000	D	0.99857	0.9933	H	0.99937	4.99	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97160	0.9837	10	0.87932	D	0	-3.8278	8.1708	0.31254	0.0:0.2331:0.0:0.7669	.	34;34	Q5U0M5;P35226	.;BMI1_HUMAN	W	34;18;34;34;34;34;11	ENSP00000365851:C34W;ENSP00000397912:C34W;ENSP00000399220:C34W;ENSP00000390768:C11W	ENSP00000365851:C34W	C	+	3	2	BMI1	22655486	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.885000	0.28227	0.445000	0.26639	0.528000	0.53228	TGT		0.413	BMI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047176.1	NM_005180	
WDR11	55717	broad.mit.edu	37	10	122622305	122622305	+	Silent	SNP	A	A	G			TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr10:122622305A>G	ENST00000263461.6	+	5	831	c.585A>G	c.(583-585)tcA>tcG	p.S195S		NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	0					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(9)|prostate(2)|skin(2)|stomach(5)	38						AGCCTCCCTCAGGCCCTGGGA	0.443																																						uc021pzt.1																			0		p.S195L(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(9)|prostate(2)|skin(2)|stomach(5)	38						c.(583-585)tcA>tcG		Homo sapiens WD repeat domain 11 (WDR11), mRNA.							132.0	146.0	141.0					10																	122622305		2203	4300	6503	SO:0001819	synonymous_variant	55717					integral to membrane		g.chr10:122622305A>G	AF320223	CCDS7619.1	10q26	2013-01-21	2010-01-06	2010-01-06	ENSG00000120008	ENSG00000120008		"""WD repeat domain containing"""	13831	protein-coding gene	gene with protein product		606417	"""bromodomain and WD repeat domain containing 2"""	BRWD2		10718198, 11536051	Standard	NM_018117		Approved	KIAA1351, FLJ10506, WDR15, HH14, DR11	uc021pzt.1	Q9BZH6	OTTHUMG00000019171	ENST00000263461.6:c.585A>G	10.37:g.122622305A>G						WDR11_uc010qte.2_Intron|WDR11_uc001lfd.1_5'UTR	p.S195S	NM_018117	NP_060587	Q9BZH6	WDR11_HUMAN			4	831	+			195					A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000263461.6	37	c.585A>G	CCDS7619.1																																																																																				0.443	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2		
Unknown	0	broad.mit.edu	37	10	135491112	135491112	+	IGR	SNP	C	C	T	rs532291006	byFrequency	TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr10:135491112C>T								AL845259.1 (17933 upstream) : None (None downstream)																							GGGTCGCCTTCGCCCACACCG	0.776													.|||	1243	0.248203	0.2769	0.2795	5008	,	,		19918	0.2262		0.1789	False		,,,				2504	0.2812					uc021qbj.1																			0													Homo sapiens double homeobox 2 (DUX2), mRNA.							14.0	15.0	15.0					10																	135491112		1141	2189	3330	SO:0001628	intergenic_variant	653544					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chr10:135491112C>T																													10.37:g.135491112C>T						DUX4L3_uc010qvh.1_Silent_p.F241F|DUX4L3_uc021qbi.1_5'UTR		NM_012147	NP_036279	F5GZ66	F5GZ66_HUMAN					+									Silent	SNP		37																																																																																					0	0.776								
CDON	50937	broad.mit.edu	37	11	125853903	125853903	+	Frame_Shift_Del	DEL	C	C	-	rs139149075		TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr11:125853903delC	ENST00000392693.3	-	16	2986	c.2859delG	c.(2857-2859)gggfs	p.G953fs	CDON_ENST00000263577.7_Frame_Shift_Del_p.G953fs|CDON_ENST00000531738.1_Frame_Shift_Del_p.G330fs	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated	953					anterior/posterior pattern specification (GO:0009952)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cerebral cortex development (GO:0021987)|embryonic body morphogenesis (GO:0010172)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|lens development in camera-type eye (GO:0002088)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein heterodimerization activity (GO:0043497)|skeletal muscle satellite cell differentiation (GO:0014816)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(9)|ovary(3)|prostate(2)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	61	all_hematologic(175;0.177)	Breast(109;0.00157)|Lung NSC(97;0.0127)|all_lung(97;0.0133)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.51e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0604)		TGGTTGCAGGCCCCACATTTC	0.463																																						uc009zbw.3																			0				breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(9)|ovary(3)|prostate(2)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	61						c.(2857-2859)gggfs		Homo sapiens Cdon homolog (mouse) (CDON), transcript variant 1, mRNA.							68.0	62.0	64.0					11																	125853903		2201	4299	6500	SO:0001589	frameshift_variant	50937				cell adhesion|muscle cell differentiation|positive regulation of muscle cell differentiation	integral to membrane|plasma membrane	protein binding	g.chr11:125853903delC	AF004841	CCDS8468.1, CCDS58192.1	11q24.2	2013-02-11	2012-12-07		ENSG00000064309	ENSG00000064309		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	17104	protein-coding gene	gene with protein product	"""cell adhesion molecule-related/down-regulated by oncogenes"""	608707	"""Cdon homolog (mouse)"""			9214393	Standard	NM_016952		Approved	ORCAM, CDO, CDON1	uc009zbw.3	Q4KMG0	OTTHUMG00000165862	ENST00000392693.3:c.2859delG	11.37:g.125853903delC	ENSP00000376458:p.Gly953fs					CDON_uc001qdb.4_Frame_Shift_Del_p.G330fs|CDON_uc001qdc.4_Frame_Shift_Del_p.G953fs	p.G953fs	NM_001243597	NP_001230526	Q4KMG0	CDON_HUMAN		BRCA - Breast invasive adenocarcinoma(274;1.51e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0604)	15	2987	-	all_hematologic(175;0.177)	Breast(109;0.00157)|Lung NSC(97;0.0127)|all_lung(97;0.0133)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)	953					O14631	Frame_Shift_Del	DEL	ENST00000392693.3	37	c.2859delG	CCDS58192.1																																																																																				0.463	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952	
LRP1	4035	broad.mit.edu	37	12	57603612	57603612	+	Missense_Mutation	SNP	T	T	C			TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr12:57603612T>C	ENST00000243077.3	+	80	12866	c.12400T>C	c.(12400-12402)Tct>Cct	p.S4134P		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	4134					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	GAGCCACGCCTCTGACGTGGT	0.572																																						uc001snd.3																			0				NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184						c.(12400-12402)Tct>Cct		Homo sapiens low density lipoprotein receptor-related protein 1 (LRP1), mRNA.	Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)						63.0	60.0	61.0					12																	57603612		2203	4300	6503	SO:0001583	missense	4035				aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity	coated pit|integral to plasma membrane|nucleus	apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity	g.chr12:57603612T>C	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.12400T>C	12.37:g.57603612T>C	ENSP00000243077:p.Ser4134Pro						p.S4134P	NM_002332	NP_002323	Q07954	LRP1_HUMAN		BRCA - Breast invasive adenocarcinoma(357;0.0103)	79	12866	+			4134					Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	37	c.12400T>C	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	T	13.46	2.244925	0.39697	.	.	ENSG00000123384	ENST00000243077	D	0.91843	-2.92	4.45	4.45	0.53987	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.172475	0.37348	N	0.002127	D	0.84999	0.5597	L	0.33485	1.01	0.80722	D	1	P	0.36048	0.534	B	0.34138	0.176	T	0.82581	-0.0386	10	0.35671	T	0.21	.	7.4978	0.27500	0.301:0.0:0.0:0.699	.	4134	Q07954	LRP1_HUMAN	P	4134	ENSP00000243077:S4134P	ENSP00000243077:S4134P	S	+	1	0	LRP1	55889879	1.000000	0.71417	0.993000	0.49108	0.486000	0.33341	4.199000	0.58426	2.011000	0.59026	0.455000	0.32223	TCT		0.572	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
LUM	4060	broad.mit.edu	37	12	91498030	91498030	+	Missense_Mutation	SNP	C	C	T			TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr12:91498030C>T	ENST00000266718.4	-	3	1383	c.929G>A	c.(928-930)cGt>cAt	p.R310H	LUM_ENST00000548071.1_5'UTR	NM_002345.3	NP_002336.1	P51884	LUM_HUMAN	lumican	310					carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to growth factor (GO:0070848)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrillar collagen trimer (GO:0005583)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)	p.R310L(2)		central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	24						GCCATCCAAACGCAAATGCTT	0.373																																						uc001tbm.3																			2	Substitution - Missense(2)	p.R310L(4)	lung(2)	central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	24						c.(928-930)cGt>cAt		Homo sapiens lumican (LUM), mRNA.							105.0	100.0	102.0					12																	91498030		2203	4300	6503	SO:0001583	missense	4060				collagen fibril organization|visual perception	extracellular space|fibrillar collagen	collagen binding|extracellular matrix structural constituent	g.chr12:91498030C>T	BT006707	CCDS9038.1	12q21.33	2014-06-13			ENSG00000139329			"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	6724	protein-coding gene	gene with protein product	"""lumican proteoglycan"""	600616		LDC		7558030	Standard	NM_002345		Approved	SLRR2D	uc001tbm.3	P51884	OTTHUMG00000170074	ENST00000266718.4:c.929G>A	12.37:g.91498030C>T	ENSP00000266718:p.Arg310His						p.R310H	NM_002345	NP_002336	P51884	LUM_HUMAN			2	1318	-			310					B2R6R5|Q96QM7	Missense_Mutation	SNP	ENST00000266718.4	37	c.929G>A	CCDS9038.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.843078	0.91197	.	.	ENSG00000139329	ENST00000266718	T	0.18338	2.22	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	T	0.45915	0.1366	M	0.79123	2.44	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.49244	-0.8960	10	0.87932	D	0	-18.0187	18.3106	0.90199	0.0:1.0:0.0:0.0	.	310	P51884	LUM_HUMAN	H	310	ENSP00000266718:R310H	ENSP00000266718:R310H	R	-	2	0	LUM	90022161	1.000000	0.71417	0.980000	0.43619	0.790000	0.44656	7.146000	0.77373	2.398000	0.81561	0.591000	0.81541	CGT		0.373	LUM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407150.2	NM_002345	
SYNE2	23224	broad.mit.edu	37	14	64497733	64497733	+	Splice_Site	SNP	G	G	A			TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr14:64497733G>A	ENST00000344113.4	+	45	7091		c.e45-1		SYNE2_ENST00000357395.3_Splice_Site|SYNE2_ENST00000554584.1_Splice_Site|SYNE2_ENST00000358025.3_Splice_Site	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2						centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		TCCACTCGTAGGAACTAGAGA	0.353																																						uc001xgl.3																			0				NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224						c.e45-1		Homo sapiens spectrin repeat containing, nuclear envelope 2 (SYNE2), transcript variant 5, mRNA.							67.0	64.0	65.0					14																	64497733		1821	4078	5899	SO:0001630	splice_region_variant	23224				centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding	g.chr14:64497733G>A	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"""nuclear envelope spectrin repeat-2"", ""nucleus and actin connecting element"""	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.6880-1G>A	14.37:g.64497733G>A						SYNE2_uc001xgm.3_Splice_Site_p.E2294_splice|SYNE2_uc021ruh.1_Splice_Site_p.E2294_splice	p.E2294_splice	NM_182914	NP_878918	Q8WXH0	SYNE2_HUMAN		all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)	45	7110	+			2294					Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Splice_Site	SNP	ENST00000344113.4	37	c.6880_splice	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	G	14.47	2.543848	0.45280	.	.	ENSG00000054654	ENST00000358025;ENST00000344113;ENST00000554584;ENST00000261678	.	.	.	4.98	4.98	0.66077	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7628	0.78101	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SYNE2	63567486	1.000000	0.71417	0.987000	0.45799	0.588000	0.36517	5.769000	0.68865	2.456000	0.83038	0.313000	0.20887	.		0.353	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	Intron
GJD2	57369	broad.mit.edu	37	15	35045227	35045227	+	Nonsense_Mutation	SNP	G	G	A			TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr15:35045227G>A	ENST00000290374.4	-	2	894	c.418C>T	c.(418-420)Cga>Tga	p.R140*	RP11-814P5.1_ENST00000503496.1_RNA|RP11-814P5.1_ENST00000558707.1_RNA	NM_020660.2	NP_065711.1	Q9UKL4	CXD2_HUMAN	gap junction protein, delta 2, 36kDa	140					action potential (GO:0001508)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gap junction channel activity (GO:0005243)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|urinary_tract(1)	19		all_lung(180;9.67e-07)		all cancers(64;2.75e-18)|GBM - Glioblastoma multiforme(113;1.9e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0156)		TTATCTTCTCGTTTGCCCCCA	0.532																																						uc001zis.1																			0				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|urinary_tract(1)	19						c.(418-420)Cga>Tga		Homo sapiens gap junction protein, delta 2, 36kDa (GJD2), mRNA.							130.0	135.0	133.0					15																	35045227		2201	4298	6499	SO:0001587	stop_gained	57369				synaptic transmission	connexon complex|integral to membrane	gap junction channel activity	g.chr15:35045227G>A	AB037509	CCDS10040.1	15q13.1	2008-02-04	2007-11-06	2007-11-06	ENSG00000159248	ENSG00000159248		"""Ion channels / Gap junction proteins (connexins)"""	19154	protein-coding gene	gene with protein product	"""connexin 36"""	607058	"""gap junction protein, alpha 9, 36kDa"""	GJA9		10462698	Standard	NM_020660		Approved	CX36	uc001zis.2	Q9UKL4	OTTHUMG00000129674	ENST00000290374.4:c.418C>T	15.37:g.35045227G>A	ENSP00000290374:p.Arg140*					AK092087_uc001zit.1_5'Flank	p.R140*	NM_020660	NP_065711	Q9UKL4	CXD2_HUMAN		all cancers(64;2.75e-18)|GBM - Glioblastoma multiforme(113;1.9e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0156)	1	418	-		all_lung(180;9.67e-07)	140					Q2M241|Q9P2R0	Nonsense_Mutation	SNP	ENST00000290374.4	37	c.418C>T	CCDS10040.1	.	.	.	.	.	.	.	.	.	.	G	39	7.644941	0.98409	.	.	ENSG00000159248	ENST00000290374	.	.	.	5.44	3.48	0.39840	.	1.388510	0.04567	N	0.392577	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.10377	T	0.69	.	12.2373	0.54522	0.0:0.0:0.6906:0.3094	.	.	.	.	X	140	.	ENSP00000290374:R140X	R	-	1	2	GJD2	32832519	1.000000	0.71417	0.977000	0.42913	0.994000	0.84299	2.424000	0.44714	0.778000	0.33520	0.650000	0.86243	CGA		0.532	GJD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251875.2		
ADAMTSL3	57188	broad.mit.edu	37	15	84651232	84651232	+	Missense_Mutation	SNP	G	G	A	rs147113160		TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr15:84651232G>A	ENST00000286744.5	+	21	3076	c.2852G>A	c.(2851-2853)cGt>cAt	p.R951H	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.R951H	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	951	Ig-like C2-type 1.					proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			AAGGATGGCCGTTGCCTGCAG	0.532													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19321	0.0		0.0	False		,,,				2504	0.0					uc002bjz.4																			0				NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130						c.(2851-2853)cGt>cAt		Homo sapiens ADAMTS-like 3 (ADAMTSL3), mRNA.		G	HIS/ARG	0,4406		0,0,2203	107.0	106.0	106.0		2852	-3.9	0.4	15	dbSNP_134	106	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ADAMTSL3	NM_207517.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	951/1692	84651232	1,13005	2203	4300	6503	SO:0001583	missense	57188					proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding	g.chr15:84651232G>A	AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.2852G>A	15.37:g.84651232G>A	ENSP00000286744:p.Arg951His					ADAMTSL3_uc010bmt.1_Missense_Mutation_p.R951H	p.R951H	NM_207517	NP_997400	P82987	ATL3_HUMAN	BRCA - Breast invasive adenocarcinoma(143;0.211)		20	3076	+			951			Ig-like C2-type 1.		A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	37	c.2852G>A	CCDS10326.1	.	.	.	.	.	.	.	.	.	.	G	11.51	1.661534	0.29515	0.0	1.16E-4	ENSG00000156218	ENST00000286744	T	0.78003	-1.14	5.05	-3.93	0.04143	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.737426	0.11678	N	0.540087	T	0.69378	0.3104	L	0.53561	1.675	0.09310	N	0.999996	B;B	0.14012	0.006;0.009	B;B	0.12837	0.008;0.008	T	0.55315	-0.8160	10	0.29301	T	0.29	.	13.5384	0.61659	0.7761:0.0:0.2239:0.0	.	951;951	P82987-2;P82987	.;ATL3_HUMAN	H	951	ENSP00000286744:R951H	ENSP00000286744:R951H	R	+	2	0	ADAMTSL3	82442236	0.009000	0.17119	0.402000	0.26371	0.979000	0.70002	0.457000	0.21875	-0.595000	0.05828	0.563000	0.77884	CGT		0.532	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517	
MCTP2	55784	broad.mit.edu	37	15	94943189	94943189	+	Missense_Mutation	SNP	C	C	T	rs199555430		TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr15:94943189C>T	ENST00000357742.4	+	15	1930	c.1930C>T	c.(1930-1932)Cgc>Tgc	p.R644C	MCTP2_ENST00000557742.1_Missense_Mutation_p.R232C|MCTP2_ENST00000331706.4_Missense_Mutation_p.R232C|MCTP2_ENST00000451018.3_Missense_Mutation_p.R644C	NM_018349.3	NP_060819.3	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2	644					calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|liver(1)|lung(12)|ovary(1)|pancreas(1)|skin(9)|stomach(2)	49	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)			CCGGGAAAAGCGCTTTGTTGA	0.458													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18826	0.0		0.0	False		,,,				2504	0.0					uc002btj.3																			0				autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|liver(1)|lung(12)|ovary(1)|pancreas(1)|skin(9)|stomach(2)	49						c.(1930-1932)Cgc>Tgc		Homo sapiens multiple C2 domains, transmembrane 2 (MCTP2), transcript variant 1, mRNA.		C	CYS/ARG,CYS/ARG,CYS/ARG	4,4390	8.1+/-20.4	0,4,2193	93.0	93.0	93.0		1930,694,1930	4.3	1.0	15		93	1,8595	1.2+/-3.3	0,1,4297	no	missense,missense,missense	MCTP2	NM_001159643.1,NM_001159644.1,NM_018349.3	180,180,180	0,5,6490	TT,TC,CC		0.0116,0.091,0.0385	possibly-damaging,possibly-damaging,possibly-damaging	644/824,232/307,644/879	94943189	5,12985	2197	4298	6495	SO:0001583	missense	55784				calcium-mediated signaling	integral to membrane|membrane fraction	calcium ion binding	g.chr15:94943189C>T	AK002037	CCDS32338.1, CCDS53975.1, CCDS53976.1	15q26.2	2006-02-08				ENSG00000140563			25636	protein-coding gene	gene with protein product						15528213	Standard	NM_018349		Approved	FLJ11175, FLJ33303	uc002btj.3	Q6DN12		ENST00000357742.4:c.1930C>T	15.37:g.94943189C>T	ENSP00000350377:p.Arg644Cys					MCTP2_uc010boj.3_Missense_Mutation_p.R373C|MCTP2_uc010bok.3_Missense_Mutation_p.R644C|MCTP2_uc002btk.4_Missense_Mutation_p.R232C|MCTP2_uc002btl.3_Missense_Mutation_p.R232C	p.R644C	NM_018349	NP_060819	Q6DN12	MCTP2_HUMAN	BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)		14	1995	+	Lung NSC(78;0.0821)|all_lung(78;0.148)		644					A2RRC2|C6G483|C6G484|Q49AB0|Q8TAX2|Q9NUS2|Q9NUW7	Missense_Mutation	SNP	ENST00000357742.4	37	c.1930C>T	CCDS32338.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	19.89	3.910970	0.72983	9.1E-4	1.16E-4	ENSG00000140563	ENST00000451018;ENST00000331706;ENST00000357742	T;T;T	0.68331	-0.32;-0.07;-0.17	5.22	4.31	0.51392	C2 calcium/lipid-binding domain, CaLB (1);	0.150976	0.64402	D	0.000019	T	0.75989	0.3925	L	0.50333	1.59	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.69142	0.962;0.95;0.927	T	0.78375	-0.2228	10	0.87932	D	0	.	13.7373	0.62827	0.0:0.9252:0.0:0.0748	.	644;232;644	Q6DN12-2;Q6DN12-4;Q6DN12	.;.;MCTP2_HUMAN	C	644;232;644	ENSP00000395109:R644C;ENSP00000329646:R232C;ENSP00000350377:R644C	ENSP00000329646:R232C	R	+	1	0	MCTP2	92744193	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	3.698000	0.54771	1.196000	0.43129	-0.251000	0.11542	CGC		0.458	MCTP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415060.3	NM_018349	
ABCC6	368	broad.mit.edu	37	16	16272807	16272807	+	Missense_Mutation	SNP	C	C	T	rs72653787		TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr16:16272807C>T	ENST00000205557.7	-	18	2292	c.2263G>A	c.(2263-2265)Gga>Aga	p.G755R	ABCC6_ENST00000574094.1_5'Flank	NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	755	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.		G -> R (in PXE; dbSNP:rs72653787). {ECO:0000269|PubMed:17617515}.		response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|skin(6)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)	Cisplatin(DB00515)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Etoposide(DB00773)|Indomethacin(DB00328)|Probenecid(DB01032)|Sulfinpyrazone(DB01138)|Teniposide(DB00444)|Vinblastine(DB00570)	TTCTGGCCTCCGGAGAGATTC	0.627																																						uc002den.4																			0				NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|skin(6)|urinary_tract(1)	43	GRCh37	CM073961	ABCC6	M	rs72653787	c.(2263-2265)Gga>Aga		Homo sapiens ATP-binding cassette, sub-family C (CFTR/MRP), member 6 (ABCC6), transcript variant 1, mRNA.		C	ARG/GLY	0,4390		0,0,2195	30.0	26.0	27.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2263	4.0	0.9	16	dbSNP_130	27	1,8593		0,1,4296	no	missense	ABCC6	NM_001171.5	125	0,1,6491	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	755/1504	16272807	1,12983	2195	4297	6492	SO:0001583	missense	368				response to drug|visual perception	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances	g.chr16:16272807C>T	AF076622	CCDS10568.1, CCDS58430.1	16p13.11	2013-01-08			ENSG00000091262	ENSG00000091262		"""ATP binding cassette transporters / subfamily C"""	57	protein-coding gene	gene with protein product		603234	"""pseudoxanthoma elasticum"""	ARA, PXE		9721217, 11439001	Standard	NM_001079528		Approved	MRP6, EST349056, MLP1, URG7	uc002den.4	O95255	OTTHUMG00000129967	ENST00000205557.7:c.2263G>A	16.37:g.16272807C>T	ENSP00000205557:p.Gly755Arg					ABCC6_uc010bvo.3_Non-coding_Transcript	p.G755R	NM_001171	NP_001162	O95255	MRP6_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (3;0.123)	17	2300	-			755			ABC transporter 1.		A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Missense_Mutation	SNP	ENST00000205557.7	37	c.2263G>A	CCDS10568.1	.	.	.	.	.	.	.	.	.	.	C	16.65	3.183081	0.57800	0.0	1.16E-4	ENSG00000091262	ENST00000205557;ENST00000456970	D;D	0.95205	-2.92;-3.64	4.97	4.02	0.46733	ABC transporter, conserved site (1);ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.47093	U	0.000253	D	0.97589	0.9210	M	0.92604	3.325	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.97988	1.0353	10	0.87932	D	0	.	12.6183	0.56590	0.0:0.9187:0.0:0.0813	.	755	O95255	MRP6_HUMAN	R	755	ENSP00000205557:G755R;ENSP00000405002:G755R	ENSP00000205557:G755R	G	-	1	0	ABCC6	16180308	1.000000	0.71417	0.858000	0.33744	0.257000	0.26127	7.366000	0.79548	1.088000	0.41272	0.467000	0.42956	GGA		0.627	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2		
C16orf93	90835	broad.mit.edu	37	16	30770347	30770347	+	Missense_Mutation	SNP	G	G	C			TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr16:30770347G>C	ENST00000543610.1	-	8	1764	c.803C>G	c.(802-804)cCa>cGa	p.P268R	PHKG2_ENST00000424889.3_Intron|PHKG2_ENST00000563588.1_3'UTR|RNF40_ENST00000324685.6_5'Flank|C16orf93_ENST00000541260.1_Missense_Mutation_p.P333R	NM_001014979.2	NP_001014979.2	A1A4V9	CP093_HUMAN	chromosome 16 open reading frame 93	268										breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(6)	11						CTCTGGCTCTGGTGGGGCCAC	0.537																																						uc002dzm.3																			0				breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(6)	11						c.(802-804)cCa>cGa		Homo sapiens chromosome 16 open reading frame 93 (C16orf93), transcript variant 1, mRNA.							173.0	159.0	164.0					16																	30770347		2197	4300	6497	SO:0001583	missense	90835							g.chr16:30770347G>C	BC042548	CCDS32434.1, CCDS32434.2, CCDS55993.1	16p11.2	2012-10-10			ENSG00000196118	ENSG00000196118			28078	protein-coding gene	gene with protein product							Standard	NM_001195620		Approved	MGC104706	uc002dzm.3	A1A4V9	OTTHUMG00000167926	ENST00000543610.1:c.803C>G	16.37:g.30770347G>C	ENSP00000437532:p.Pro268Arg					PHKG2_uc021tgo.1_Intron|PHKG2_uc002dzk.2_3'UTR|C16orf93_uc002dzo.3_Missense_Mutation_p.P231R|C16orf93_uc021tgp.1_Silent_p.T154T|RNF40_uc010caa.3_5'Flank|RNF40_uc002dzq.3_5'Flank|RNF40_uc010cab.3_5'Flank|RNF40_uc010vfa.2_5'Flank	p.P268R	NM_001014979	NP_001014979	A1A4V9	CP093_HUMAN			7	1299	-			268					A1A4V8|F5GX13|Q569G2	Missense_Mutation	SNP	ENST00000543610.1	37	c.803C>G	CCDS32434.2	.	.	.	.	.	.	.	.	.	.	G	8.052	0.766152	0.15983	.	.	ENSG00000196118	ENST00000354963;ENST00000543610	.	.	.	4.76	3.8	0.43715	.	0.500851	0.19572	N	0.111061	T	0.33527	0.0866	N	0.19112	0.55	0.26651	N	0.972093	P;P;P	0.51351	0.815;0.944;0.815	B;P;P	0.56042	0.387;0.79;0.592	T	0.07635	-1.0762	9	0.24483	T	0.36	-0.3617	8.9043	0.35515	0.1015:0.0:0.8985:0.0	.	231;40;268	A1A4V9-2;A1A4V9-3;A1A4V9	.;.;CP093_HUMAN	R	231;268	.	ENSP00000347050:P231R	P	-	2	0	C16orf93	30677848	0.878000	0.30173	0.956000	0.39512	0.049000	0.14656	2.898000	0.48672	1.358000	0.45922	0.655000	0.94253	CCA		0.537	C16orf93-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397089.1	NM_001014979	
MYH10	4628	broad.mit.edu	37	17	8390908	8390908	+	Missense_Mutation	SNP	C	C	A			TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr17:8390908C>A	ENST00000269243.4	-	34	4934	c.4796G>T	c.(4795-4797)cGg>cTg	p.R1599L	MYH10_ENST00000360416.3_Missense_Mutation_p.R1630L|MYH10_ENST00000379980.4_Missense_Mutation_p.R1615L|MYH10_ENST00000396239.1_Missense_Mutation_p.R1620L	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	1599					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cardiac myofibril assembly (GO:0055003)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cerebellar Purkinje cell layer development (GO:0021680)|exocytosis (GO:0006887)|fourth ventricle development (GO:0021592)|in utero embryonic development (GO:0001701)|lateral ventricle development (GO:0021670)|mitotic cytokinesis (GO:0000281)|neuromuscular process controlling balance (GO:0050885)|neuron migration (GO:0001764)|nuclear migration (GO:0007097)|plasma membrane repair (GO:0001778)|regulation of cell shape (GO:0008360)|retina development in camera-type eye (GO:0060041)|substrate-dependent cell migration, cell extension (GO:0006930)|third ventricle development (GO:0021678)|ventricular cardiac muscle cell development (GO:0055015)	actomyosin (GO:0042641)|axon (GO:0030424)|cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|midbody (GO:0030496)|myosin complex (GO:0016459)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						CTCGAGCTCCCGCACCTAATG	0.542																																						uc002glm.3																			0		p.E1630K(1)		breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						c.(4888-4890)cGg>cTg		Homo sapiens myosin, heavy chain 10, non-muscle (MYH10), transcript variant 2, mRNA.							155.0	159.0	158.0					17																	8390908		2203	4300	6503	SO:0001583	missense	4628				actin filament-based movement|axon guidance|cytokinesis after mitosis|regulation of cell shape	cell cortex|cleavage furrow|midbody|myosin complex|stress fiber	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity	g.chr17:8390908C>A	M69181	CCDS11144.1, CCDS58515.1, CCDS73984.1	17p13	2011-09-27	2006-09-29		ENSG00000133026	ENSG00000133026		"""Myosins / Myosin superfamily : Class II"""	7568	protein-coding gene	gene with protein product		160776	"""myosin, heavy polypeptide 10, non-muscle"""			1860190	Standard	NM_001256012		Approved	NMMHCB	uc002glm.4	P35580	OTTHUMG00000108195	ENST00000269243.4:c.4796G>T	17.37:g.8390908C>A	ENSP00000269243:p.Arg1599Leu					MYH10_uc002gll.3_Missense_Mutation_p.R1599L|MYH10_uc010cnx.3_Missense_Mutation_p.R1608L	p.R1630L	NM_005964	NP_005955	P35580	MYH10_HUMAN			35	4985	-			1599					B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Missense_Mutation	SNP	ENST00000269243.4	37	c.4889G>T	CCDS11144.1	.	.	.	.	.	.	.	.	.	.	C	35	5.538511	0.96474	.	.	ENSG00000133026	ENST00000269243;ENST00000360416;ENST00000396239;ENST00000379980	T;T;T;T	0.79033	-1.23;-1.23;-1.23;-1.23	4.99	4.99	0.66335	Myosin tail (1);	0.000000	0.85682	D	0.000000	D	0.89908	0.6851	M	0.90082	3.085	0.80722	D	1	D;P;D	0.58620	0.983;0.956;0.983	D;P;D	0.64776	0.929;0.884;0.929	D	0.91689	0.5364	10	0.87932	D	0	.	18.8124	0.92063	0.0:1.0:0.0:0.0	.	1608;1630;1599	B2RWP9;F8VTL3;P35580	.;.;MYH10_HUMAN	L	1599;1630;1620;1615	ENSP00000269243:R1599L;ENSP00000353590:R1630L;ENSP00000379539:R1620L;ENSP00000369315:R1615L	ENSP00000269243:R1599L	R	-	2	0	MYH10	8331633	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	7.572000	0.82409	2.754000	0.94517	0.655000	0.94253	CGG		0.542	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2		
GLP2R	9340	broad.mit.edu	37	17	9792806	9792806	+	Silent	SNP	G	G	A	rs184873596		TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr17:9792806G>A	ENST00000262441.5	+	13	1959	c.1446G>A	c.(1444-1446)tcG>tcA	p.S482S	GLP2R_ENST00000574745.1_Silent_p.S302S	NM_004246.1	NP_004237.1	O95838	GLP2R_HUMAN	glucagon-like peptide 2 receptor	482					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|positive regulation of cell proliferation (GO:0008284)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|glucagon receptor activity (GO:0004967)			endometrium(4)|large_intestine(7)|lung(22)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	44					Glucagon recombinant(DB00040)|Teduglutide(DB08900)	AGAAGCTCTCGGAAGGAGATG	0.597													G|||	1	0.000199681	0.0	0.0	5008	,	,		19622	0.0		0.001	False		,,,				2504	0.0					uc002gmd.1																			0		p.L481L(1)		endometrium(4)|large_intestine(7)|lung(22)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	44						c.(1444-1446)tcG>tcA		Homo sapiens glucagon-like peptide 2 receptor (GLP2R), mRNA.	Glucagon recombinant(DB00040)	G		0,4406		0,0,2203	58.0	58.0	58.0		1446	-11.1	0.0	17		58	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	GLP2R	NM_004246.1		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		482/554	9792806	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9340				G-protein signaling, coupled to cAMP nucleotide second messenger|positive regulation of cell proliferation	integral to membrane|plasma membrane		g.chr17:9792806G>A	AF105367	CCDS11150.1	17p13.3	2012-08-10			ENSG00000065325	ENSG00000065325		"""GPCR / Class B : Glucagon receptors"""	4325	protein-coding gene	gene with protein product		603659				9990065	Standard	NM_004246		Approved		uc002gmd.1	O95838	OTTHUMG00000130269	ENST00000262441.5:c.1446G>A	17.37:g.9792806G>A							p.S482S	NM_004246	NP_004237	O95838	GLP2R_HUMAN			12	1446	+			482					Q4VAT3	Silent	SNP	ENST00000262441.5	37	c.1446G>A	CCDS11150.1																																																																																				0.597	GLP2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252601.4		
KRT35	3886	broad.mit.edu	37	17	39633981	39633981	+	Silent	SNP	A	A	G			TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr17:39633981A>G	ENST00000393989.1	-	6	1051	c.1009T>C	c.(1009-1011)Ttg>Ctg	p.L337L	KRT35_ENST00000246639.2_Silent_p.L307L	NM_002280.4	NP_002271.3	Q92764	KRT35_HUMAN	keratin 35	337	Coil 2.|Rod.				anatomical structure morphogenesis (GO:0009653)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	29		Breast(137;0.000286)				GTGGATTCCAAAGCATCTCTC	0.577																																						uc002hws.3																			0				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	29						c.(1009-1011)Ttg>Ctg		Homo sapiens keratin 35 (KRT35), mRNA.							32.0	35.0	34.0					17																	39633981		2203	4300	6503	SO:0001819	synonymous_variant	3886				anatomical structure morphogenesis	intermediate filament	protein binding|structural molecule activity	g.chr17:39633981A>G	X90762	CCDS11394.2	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000197079	ENSG00000197079		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6453	protein-coding gene	gene with protein product	"""hard keratin type I 5"""	602764	"""keratin, hair, acidic, 5"""	KRTHA5		8823373, 16831889	Standard	NM_002280		Approved	Ha-5	uc002hws.3	Q92764	OTTHUMG00000133425	ENST00000393989.1:c.1009T>C	17.37:g.39633981A>G							p.L337L	NM_002280	NP_002271	Q92764	KRT35_HUMAN			5	1052	-		Breast(137;0.000286)	337			Coil 2.|Rod.		O76012|Q92651	Silent	SNP	ENST00000393989.1	37	c.1009T>C	CCDS11394.2																																																																																				0.577	KRT35-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_002280	
TBC1D3P2	440452	broad.mit.edu	37	17	60345574	60345574	+	RNA	SNP	C	C	T	rs74660978	byFrequency	TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr17:60345574C>T	ENST00000581291.1	-	0	777									TBC1 domain family, member 3 pseudogene 2											breast(2)|kidney(1)|lung(2)	5						AGCCCCTGGACGGTCCCGCCA	0.567													.|||	471	0.0940495	0.2057	0.1009	5008	,	,		16255	0.005		0.0815	False		,,,				2504	0.0429					uc002izq.2																			0				breast(2)|kidney(1)|lung(2)	5						c.(694-696)Gtc>Atc		Homo sapiens TBC1 domain family, member 3 pseudogene 2 (TBC1D3P2), non-coding RNA.																																						440452							g.chr17:60345574C>T			17q23.2	2009-05-14				ENSG00000188755			27783	pseudogene	pseudogene							Standard	NR_027486		Approved		uc002izq.2				17.37:g.60345574C>T						TBC1D3P2_uc010woz.2_Non-coding_Transcript|DQ574804_uc010wpb.2_5'Flank|DQ573965_uc021ube.1_5'Flank|DQ581615_uc021ubf.1_5'Flank	p.V232I							9	806	-									Missense_Mutation	SNP	ENST00000581291.1	37	c.694G>A																																																																																					0.567	TBC1D3P2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000445021.1	NR_027486	
ENGASE	64772	broad.mit.edu	37	17	77073856	77073856	+	Missense_Mutation	SNP	A	A	G			TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr17:77073856A>G	ENST00000579016.1	+	3	326	c.326A>G	c.(325-327)gAg>gGg	p.E109G	ENGASE_ENST00000539857.2_5'UTR	NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	109						cytoplasm (GO:0005737)	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity (GO:0033925)			breast(2)|endometrium(4)|large_intestine(1)|lung(15)|prostate(2)|skin(1)	25						GTGGCCCTGGAGCCCCTGGCG	0.592																																						uc002jwv.3																			0				breast(2)|endometrium(4)|large_intestine(1)|lung(15)|prostate(2)|skin(1)	25						c.(325-327)gAg>gGg		Homo sapiens endo-beta-N-acetylglucosaminidase (ENGASE), mRNA.							59.0	62.0	61.0					17																	77073856		1936	4138	6074	SO:0001583	missense	64772					cytosol	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity	g.chr17:77073856A>G	AF512564	CCDS42394.1	17q25.3	2009-03-03			ENSG00000167280	ENSG00000167280	3.2.1.96		24622	protein-coding gene	gene with protein product	"""Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase"", ""Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase"""	611898				12114544, 18586680	Standard	NM_001042573		Approved	FLJ21865	uc002jwv.4	Q8NFI3	OTTHUMG00000167714	ENST00000579016.1:c.326A>G	17.37:g.77073856A>G	ENSP00000462333:p.Glu109Gly					ENGASE_uc002jwu.1_Missense_Mutation_p.E109G|ENGASE_uc010wtz.1_5'UTR|ENGASE_uc002jww.3_5'Flank	p.E109G	NM_001042573	NP_001036038	Q8NFI3	ENASE_HUMAN			2	334	+			109					Q659F0|Q8TB86|Q9H6U4	Missense_Mutation	SNP	ENST00000579016.1	37	c.326A>G	CCDS42394.1	.	.	.	.	.	.	.	.	.	.	A	8.523	0.869192	0.17322	.	.	ENSG00000167280	ENST00000311595;ENST00000545583	.	.	.	4.92	-0.441	0.12257	.	0.336644	0.30365	N	0.009785	T	0.17492	0.0420	L	0.27053	0.805	0.20563	N	0.99989	B;B	0.15141	0.002;0.012	B;B	0.15052	0.002;0.012	T	0.08106	-1.0738	9	0.37606	T	0.19	-6.138	0.5499	0.00661	0.2855:0.1136:0.222:0.3788	.	109;109	Q8NFI3;Q8NFI3-3	ENASE_HUMAN;.	G	109	.	ENSP00000308158:E109G	E	+	2	0	ENGASE	74585451	0.992000	0.36948	0.818000	0.32626	0.335000	0.28730	1.035000	0.30216	-0.040000	0.13580	0.460000	0.39030	GAG		0.592	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759	
SLC1A6	6511	broad.mit.edu	37	19	15067457	15067457	+	Missense_Mutation	SNP	C	C	T			TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr19:15067457C>T	ENST00000221742.3	-	6	1007	c.1000G>A	c.(1000-1002)Gtc>Atc	p.V334I	SLC1A6_ENST00000600144.1_Intron|SLC1A6_ENST00000430939.2_Missense_Mutation_p.V270I	NM_005071.1	NP_005062.1	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6	334					aspartate transport (GO:0015810)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)	p.V334I(1)		breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(8)|liver(1)|lung(12)|ovary(3)|pancreas(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42						CCCCCCAGGACGGCCATGTCT	0.582																																						uc002naa.1																			1	Substitution - Missense(1)	p.V334I(2)	pancreas(1)	breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(8)|liver(1)|lung(12)|ovary(3)|pancreas(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42						c.(1000-1002)Gtc>Atc		Homo sapiens solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6 (SLC1A6), mRNA.	L-Glutamic Acid(DB00142)						130.0	114.0	120.0					19																	15067457		2203	4300	6503	SO:0001583	missense	6511				synaptic transmission	integral to plasma membrane|membrane fraction	high-affinity glutamate transmembrane transporter activity|L-aspartate transmembrane transporter activity|sodium:dicarboxylate symporter activity	g.chr19:15067457C>T		CCDS12321.1, CCDS62578.1	19p13.12	2013-07-15			ENSG00000105143	ENSG00000105143		"""Solute carriers"""	10944	protein-coding gene	gene with protein product		600637				7791878	Standard	NM_005071		Approved	EAAT4	uc002naa.2	P48664	OTTHUMG00000183351	ENST00000221742.3:c.1000G>A	19.37:g.15067457C>T	ENSP00000221742:p.Val334Ile					SLC1A6_uc010dzu.1_Intron|SLC1A6_uc010xod.1_Missense_Mutation_p.V270I	p.V334I	NM_005071	NP_005062	P48664	EAA4_HUMAN			5	1007	-			334					Q8N753	Missense_Mutation	SNP	ENST00000221742.3	37	c.1000G>A	CCDS12321.1	.	.	.	.	.	.	.	.	.	.	c	10.37	1.332150	0.24167	.	.	ENSG00000105143	ENST00000430939;ENST00000221742	T;T	0.58940	0.3;0.34	3.99	3.99	0.46301	.	0.353602	0.29159	N	0.012978	T	0.52773	0.1755	L	0.39020	1.185	0.34985	D	0.754498	P;B	0.45957	0.869;0.041	P;B	0.45913	0.497;0.028	T	0.67051	-0.5768	10	0.51188	T	0.08	-23.2893	13.9426	0.64064	0.0:1.0:0.0:0.0	.	270;334	E7EV13;P48664	.;EAA4_HUMAN	I	270;334	ENSP00000409386:V270I;ENSP00000221742:V334I	ENSP00000221742:V334I	V	-	1	0	SLC1A6	14928457	0.934000	0.31675	0.408000	0.26446	0.839000	0.47603	1.813000	0.38962	2.238000	0.73509	0.609000	0.83330	GTC		0.582	SLC1A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466283.1	NM_005071	
PTPRH	5794	broad.mit.edu	37	19	55698964	55698964	+	Missense_Mutation	SNP	G	G	A			TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr19:55698964G>A	ENST00000376350.3	-	14	2505	c.2483C>T	c.(2482-2484)tCc>tTc	p.S828F	PTPRH_ENST00000263434.5_Missense_Mutation_p.S650F	NM_002842.3	NP_002833.3	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	828	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				apoptotic process (GO:0006915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	67		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		GCCCACCAGGGAGAGTTGCTG	0.587																																						uc002qjq.3																			0				breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	67						c.(2482-2484)tCc>tTc		Homo sapiens protein tyrosine phosphatase, receptor type, H (PTPRH), transcript variant 1, mRNA.							78.0	66.0	70.0					19																	55698964		2203	4300	6503	SO:0001583	missense	5794				apoptosis	cytoplasm|integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity	g.chr19:55698964G>A		CCDS33110.1, CCDS54321.1	19q13.4	2013-02-11				ENSG00000080031		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9672	protein-coding gene	gene with protein product		602510				8294459	Standard	XM_006723312		Approved	SAP-1	uc002qjq.3	Q9HD43		ENST00000376350.3:c.2483C>T	19.37:g.55698964G>A	ENSP00000365528:p.Ser828Phe					PTPRH_uc010esv.3_Missense_Mutation_p.S650F|BC034929_uc002qjr.3_5'Flank	p.S828F	NM_002842	NP_002833	Q9HD43	PTPRH_HUMAN	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)	13	2556	-		Renal(1328;0.245)	828			Tyrosine-protein phosphatase.		C9JCH2|Q15426|Q2NKN9|Q2NKP0	Missense_Mutation	SNP	ENST00000376350.3	37	c.2483C>T	CCDS33110.1	.	.	.	.	.	.	.	.	.	.	G	12.01	1.810166	0.32053	.	.	ENSG00000080031	ENST00000376350;ENST00000263434	T;T	0.11169	2.8;2.8	5.11	-1.68	0.08212	Protein-tyrosine phosphatase, receptor/non-receptor type (2);	1.252950	0.05986	N	0.645225	T	0.10035	0.0246	L	0.52126	1.63	0.09310	N	1	B;P	0.36199	0.087;0.543	B;B	0.27887	0.034;0.084	T	0.36359	-0.9751	10	0.66056	D	0.02	.	8.9578	0.35829	0.0:0.3667:0.2589:0.3744	.	650;828	C9JCH2;Q9HD43	.;PTPRH_HUMAN	F	828;650	ENSP00000365528:S828F;ENSP00000263434:S650F	ENSP00000263434:S650F	S	-	2	0	PTPRH	60390776	0.000000	0.05858	0.000000	0.03702	0.408000	0.30992	-0.945000	0.03909	-0.318000	0.08665	0.655000	0.94253	TCC		0.587	PTPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452649.1		
DYSF	8291	broad.mit.edu	37	2	71886153	71886153	+	Missense_Mutation	SNP	C	C	G			TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr2:71886153C>G	ENST00000258104.3	+	43	5061	c.4784C>G	c.(4783-4785)cCc>cGc	p.P1595R	DYSF_ENST00000410020.3_Missense_Mutation_p.P1634R|DYSF_ENST00000429174.2_Missense_Mutation_p.P1616R|DYSF_ENST00000409366.1_Missense_Mutation_p.P1617R|DYSF_ENST00000394120.2_Missense_Mutation_p.P1596R|DYSF_ENST00000409651.1_Missense_Mutation_p.P1627R|DYSF_ENST00000410041.1_Missense_Mutation_p.P1613R|DYSF_ENST00000413539.2_Missense_Mutation_p.P1626R|DYSF_ENST00000409744.1_Missense_Mutation_p.P1603R|DYSF_ENST00000409582.3_Missense_Mutation_p.P1633R|DYSF_ENST00000409762.1_Missense_Mutation_p.P1612R|DYSF_ENST00000479049.2_3'UTR	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	1595	C2 6. {ECO:0000255|PROSITE- ProRule:PRU00041}.				plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						CCCAAGGACCCCAATGGAAAG	0.577																																						uc010fen.3																			0				autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						c.(4900-4902)cCc>cGc		Homo sapiens dysferlin, limb girdle muscular dystrophy 2B (autosomal recessive) (DYSF), transcript variant 1, mRNA.							69.0	69.0	69.0					2																	71886153		2203	4300	6503	SO:0001583	missense	8291					cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding	g.chr2:71886153C>G	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.4784C>G	2.37:g.71886153C>G	ENSP00000258104:p.Pro1595Arg					DYSF_uc010fei.3_Missense_Mutation_p.P1612R|DYSF_uc010feh.3_Missense_Mutation_p.P1602R|DYSF_uc002sig.4_Missense_Mutation_p.P1581R|DYSF_uc010yqx.2_Non-coding_Transcript|DYSF_uc010feg.3_Missense_Mutation_p.P1626R|DYSF_uc010fee.3_Missense_Mutation_p.P1616R|DYSF_uc010fef.3_Missense_Mutation_p.P1633R|DYSF_uc002sie.3_Missense_Mutation_p.P1595R|DYSF_uc010feo.3_Missense_Mutation_p.P1627R|DYSF_uc010fej.3_Missense_Mutation_p.P1603R|DYSF_uc010fel.3_Missense_Mutation_p.P1582R|DYSF_uc010fem.3_Missense_Mutation_p.P1617R|DYSF_uc002sif.3_Missense_Mutation_p.P1596R|DYSF_uc010fek.3_Missense_Mutation_p.P1613R|DYSF_uc010yqy.2_Missense_Mutation_p.P476R|DYSF_uc010yqz.2_Missense_Mutation_p.P356R	p.P1634R	NM_001130987	NP_001124459	O75923	DYSF_HUMAN			43	5042	+			1595			C2 5.		A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Missense_Mutation	SNP	ENST00000258104.3	37	c.4901C>G	CCDS1918.1	.	.	.	.	.	.	.	.	.	.	C	14.66	2.601512	0.46423	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	T;T;T;T;T;T;T;T;T;T;T	0.69175	-0.38;-0.38;-0.38;-0.38;-0.38;-0.38;-0.38;-0.38;-0.38;-0.38;-0.38	5.63	5.63	0.86233	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.443641	0.25708	N	0.028826	T	0.60209	0.2251	L	0.35854	1.095	0.35923	D	0.831938	B;B;P;P;P;P;P;P;B;P;B;P;B;P;P	0.48911	0.001;0.02;0.868;0.696;0.696;0.523;0.523;0.758;0.012;0.868;0.004;0.917;0.016;0.696;0.741	B;B;P;P;P;B;B;B;B;P;B;P;B;P;P	0.48770	0.021;0.029;0.454;0.454;0.454;0.283;0.355;0.196;0.061;0.454;0.021;0.476;0.029;0.454;0.589	T	0.60326	-0.7285	10	0.10111	T	0.7	-17.1896	12.1787	0.54199	0.1706:0.8294:0.0:0.0	.	359;1627;1634;1617;1582;1613;1603;1612;1602;1626;1633;1616;1581;1596;1595	B7Z8G4;O75923-8;O75923-13;O75923-10;O75923-9;O75923-11;O75923-12;O75923-5;O75923-6;O75923-2;O75923-7;O75923-4;O75923-3;O75923-14;O75923	.;.;.;.;.;.;.;.;.;.;.;.;.;.;DYSF_HUMAN	R	1626;1612;1633;1616;1595;1627;1596;1603;1617;1634;1613	ENSP00000407046:P1626R;ENSP00000387137:P1612R;ENSP00000386547:P1633R;ENSP00000398305:P1616R;ENSP00000258104:P1595R;ENSP00000386683:P1627R;ENSP00000377678:P1596R;ENSP00000386285:P1603R;ENSP00000386512:P1617R;ENSP00000386881:P1634R;ENSP00000386617:P1613R	ENSP00000258104:P1595R	P	+	2	0	DYSF	71739661	0.996000	0.38824	1.000000	0.80357	0.995000	0.86356	3.110000	0.50352	2.649000	0.89929	0.650000	0.86243	CCC		0.577	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494	
EVA1A	84141	broad.mit.edu	37	2	75720533	75720533	+	Silent	SNP	G	G	A			TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr2:75720533G>A	ENST00000233712.1	-	4	725	c.288C>T	c.(286-288)tcC>tcT	p.S96S	EVA1A_ENST00000410010.1_Silent_p.S84S|EVA1A_ENST00000410071.1_Silent_p.S96S|EVA1A_ENST00000490746.1_Intron|EVA1A_ENST00000393913.3_Silent_p.S96S|EVA1A_ENST00000410113.1_Silent_p.S96S	NM_032181.2	NP_115557.1	Q9H8M9	EVA1A_HUMAN	eva-1 homolog A (C. elegans)	96					apoptotic process (GO:0006915)|autophagy (GO:0006914)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|plasma membrane (GO:0005886)											GTCTCCGCACGGAGAGATCGG	0.647																																						uc002sni.2																			0		p.S96F(1)		endometrium(1)|large_intestine(4)|lung(1)|skin(2)	8						c.(286-288)tcC>tcT		Homo sapiens family with sequence similarity 176, member A (FAM176A), transcript variant 1, mRNA.							58.0	53.0	55.0					2																	75720533		2203	4300	6503	SO:0001819	synonymous_variant	84141				apoptosis|autophagy	endoplasmic reticulum membrane|integral to membrane|lysosomal membrane|plasma membrane		g.chr2:75720533G>A	BC016157	CCDS1959.1	2p12	2012-11-05	2012-11-05	2012-11-05	ENSG00000115363	ENSG00000115363			25816	protein-coding gene	gene with protein product			"""transmembrane protein 166"", ""family with sequence similarity 176, member A"""	TMEM166, FAM176A		12477932	Standard	NM_001135032		Approved	FLJ13391	uc002sni.2	Q9H8M9	OTTHUMG00000129991	ENST00000233712.1:c.288C>T	2.37:g.75720533G>A						FAM176A_uc002snj.1_Silent_p.S83S|FAM176A_uc002snk.1_Silent_p.S96S	p.S96S	NM_001135032	NP_115557	Q9H8M9	F176A_HUMAN			3	766	-			96					D6W5J3|Q9HC41	Silent	SNP	ENST00000233712.1	37	c.288C>T	CCDS1959.1																																																																																				0.647	EVA1A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328707.1	NM_032181	
NEB	4703	broad.mit.edu	37	2	152363440	152363440	+	Missense_Mutation	SNP	G	G	T			TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr2:152363440G>T	ENST00000172853.10	-	135	18583	c.18436C>A	c.(18436-18438)Cag>Aag	p.Q6146K	NEB_ENST00000427231.2_Missense_Mutation_p.Q7847K|NEB_ENST00000397345.3_Missense_Mutation_p.Q7847K|NEB_ENST00000409198.1_Missense_Mutation_p.Q6146K|NEB_ENST00000509223.2_5'UTR|NEB_ENST00000498015.2_5'UTR|NEB_ENST00000603639.1_Missense_Mutation_p.Q7847K|NEB_ENST00000604864.1_Missense_Mutation_p.Q7847K			P20929	NEBU_HUMAN	nebulin	6146					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		AAATTCTTCTGATTTTCTTTT	0.318																																						uc021vrb.1																			0				NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301						c.(18436-18438)Cag>Aag		Homo sapiens nebulin (NEB), transcript variant 3, mRNA.							113.0	109.0	110.0					2																	152363440		1804	4068	5872	SO:0001583	missense	4703				muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle	g.chr2:152363440G>T	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"""nemaline myopathy type 2"""	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.18436C>A	2.37:g.152363440G>T	ENSP00000172853:p.Gln6146Lys					NEB_uc002txr.3_Missense_Mutation_p.Q2612K|NEB_uc002txu.3_Missense_Mutation_p.Q7847K|NEB_uc021vrc.1_Missense_Mutation_p.Q7847K|NEB_uc010fnx.3_Missense_Mutation_p.Q6134K|NEB_uc021vrd.1_Missense_Mutation_p.Q6146K|RIF1_uc002txp.3_Intron|NEB_uc010zca.2_5'Flank|NEB_uc010zcb.2_5'UTR|NEB_uc002txt.4_Missense_Mutation_p.Q651K	p.Q6146K	NM_004543	NP_004534	P20929	NEBU_HUMAN		BRCA - Breast invasive adenocarcinoma(221;0.219)	133	18465	-			6146					F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37	c.18436C>A		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.2|20.2	3.948069|3.948069	0.73787|0.73787	.|.	.|.	ENSG00000183091|ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000397342;ENST00000413693;ENST00000172853;ENST00000424585|ENST00000421461	T;T;T;T;T;T|.	0.49432|.	0.78;0.78;0.78;0.78;0.78;0.78|.	6.06|6.06	6.06|6.06	0.98353|0.98353	.|.	0.214410|.	0.47455|.	D|.	0.000226|.	D|.	0.84220|.	0.5424|.	M|M	0.86740|0.86740	2.835|2.835	0.80722|0.80722	D|D	1|1	D;D;P|.	0.54964|.	0.969;0.961;0.726|.	P;P;P|.	0.60012|.	0.867;0.839;0.665|.	D|.	0.84812|.	0.0791|.	10|.	0.32370|.	T|.	0.25|.	.|.	19.609|19.609	0.95594|0.95594	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	6146;7847;2577|.	P20929;F8WCP0;Q14215|.	NEBU_HUMAN;.;.|.	K|X	6146;7847;7847;2195;2577;6146;74|23	ENSP00000386259:Q6146K;ENSP00000380505:Q7847K;ENSP00000416578:Q7847K;ENSP00000410961:Q2577K;ENSP00000172853:Q6146K;ENSP00000404876:Q74K|.	ENSP00000172853:Q6146K|.	Q|S	-|-	1|2	0|0	NEB|NEB	152071686|152071686	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	5.905000|5.905000	0.69893|0.69893	2.882000|2.882000	0.98803|0.98803	0.655000|0.655000	0.94253|0.94253	CAG|TCA		0.318	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
COL6A3	1293	broad.mit.edu	37	2	238275426	238275426	+	Missense_Mutation	SNP	C	C	T			TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr2:238275426C>T	ENST00000295550.4	-	11	5856	c.5404G>A	c.(5404-5406)Gtc>Atc	p.V1802I	COL6A3_ENST00000347401.3_Missense_Mutation_p.V1601I|COL6A3_ENST00000346358.4_Missense_Mutation_p.V1602I|COL6A3_ENST00000409809.1_Missense_Mutation_p.V1596I|COL6A3_ENST00000353578.4_Missense_Mutation_p.V1596I|COL6A3_ENST00000472056.1_Missense_Mutation_p.V1195I	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	1802	Nonhelical region.|VWFA 9. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		AGCTCCTGGACGTTGCCCACG	0.532																																						uc002vwl.2																			0				breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217						c.(5404-5406)Gtc>Atc		Homo sapiens collagen, type VI, alpha 3 (COL6A3), transcript variant 1, mRNA.							100.0	92.0	95.0					2																	238275426		2203	4300	6503	SO:0001583	missense	1293				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity	g.chr2:238275426C>T	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"""Collagens"""	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.5404G>A	2.37:g.238275426C>T	ENSP00000295550:p.Val1802Ile					COL6A3_uc002vwo.2_Missense_Mutation_p.V1596I|COL6A3_uc010znj.1_Missense_Mutation_p.V1195I	p.V1802I	NM_004369	NP_004360	P12111	CO6A3_HUMAN		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)	10	5689	-		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)	1802			Nonhelical region.|VWFA 9.		A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	c.5404G>A	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	16.16	3.045872	0.55110	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	T;T;T;T;T;T	0.78126	-1.15;-1.15;-1.15;-1.15;-1.15;-1.15	5.52	4.58	0.56647	von Willebrand factor, type A (3);	0.266592	0.26255	N	0.025422	T	0.75042	0.3796	L	0.42245	1.32	0.31698	N	0.641073	P;P;B	0.51449	0.945;0.827;0.037	P;P;B	0.46940	0.532;0.465;0.013	T	0.79555	-0.1755	10	0.62326	D	0.03	.	13.1225	0.59336	0.0:0.9164:0.0:0.0836	.	1195;1596;1802	E9PFQ6;P12111-2;P12111	.;.;CO6A3_HUMAN	I	1802;1601;1596;1195;1596;1602	ENSP00000295550:V1802I;ENSP00000315609:V1601I;ENSP00000315873:V1596I;ENSP00000418285:V1195I;ENSP00000386844:V1596I;ENSP00000295546:V1602I	ENSP00000295550:V1802I	V	-	1	0	COL6A3	237940165	0.990000	0.36364	0.327000	0.25402	0.958000	0.62258	2.991000	0.49409	1.193000	0.43086	0.655000	0.94253	GTC		0.532	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
TRAIP	10293	broad.mit.edu	37	3	49869443	49869443	+	Missense_Mutation	SNP	C	C	A	rs557403443		TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr3:49869443C>A	ENST00000331456.2	-	11	1056	c.943G>T	c.(943-945)Gat>Tat	p.D315Y	TRAIP_ENST00000469027.1_Missense_Mutation_p.D160Y	NM_005879.2	NP_005870.2	Q9BWF2	TRAIP_HUMAN	TRAF interacting protein	315	Interaction with CYLD.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|receptor signaling protein activity (GO:0005057)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(9)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		GCATTGAGATCAATATCATCA	0.542																																						uc003cxs.1																			0				breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(9)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24						c.(943-945)Gat>Tat		Homo sapiens TRAF interacting protein (TRAIP), mRNA.							94.0	97.0	96.0					3																	49869443		2203	4300	6503	SO:0001583	missense	10293				cell proliferation|induction of apoptosis	perinuclear region of cytoplasm	protein binding|zinc ion binding	g.chr3:49869443C>A	BC019283	CCDS2806.1	3p21.31	2013-01-09			ENSG00000183763	ENSG00000183763		"""RING-type (C3HC4) zinc fingers"""	30764	protein-coding gene	gene with protein product	"""ring finger protein 206"""	605958				9104814	Standard	NM_005879		Approved	TRIP, RNF206	uc003cxs.1	Q9BWF2	OTTHUMG00000158269	ENST00000331456.2:c.943G>T	3.37:g.49869443C>A	ENSP00000328203:p.Asp315Tyr					TRAIP_uc010hla.1_Missense_Mutation_p.D216Y	p.D315Y	NM_005879	NP_005870	Q9BWF2	TRAIP_HUMAN		BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)	10	1049	-			315			Interaction with CYLD.		B5BU84|B5BUL3|O00467	Missense_Mutation	SNP	ENST00000331456.2	37	c.943G>T	CCDS2806.1	.	.	.	.	.	.	.	.	.	.	C	18.90	3.721420	0.68959	.	.	ENSG00000183763	ENST00000331456;ENST00000469027	T	0.58506	0.33	5.83	4.95	0.65309	.	0.125034	0.64402	D	0.000001	T	0.70561	0.3238	M	0.65498	2.005	0.33858	D	0.633455	D;D	0.89917	0.999;1.0	D;D	0.75020	0.915;0.985	T	0.79600	-0.1736	10	0.66056	D	0.02	-9.4284	8.8903	0.35429	0.0:0.7664:0.0:0.2336	.	315;315	A8K807;Q9BWF2	.;TRAIP_HUMAN	Y	315;160	ENSP00000420085:D160Y	ENSP00000328203:D315Y	D	-	1	0	TRAIP	49844447	1.000000	0.71417	0.999000	0.59377	0.918000	0.54935	1.360000	0.34125	1.472000	0.48140	0.655000	0.94253	GAT		0.542	TRAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350518.1	NM_005879	
MUC4	4585	broad.mit.edu	37	3	195505836	195505836	+	Missense_Mutation	SNP	G	G	C	rs369326402	byFrequency	TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr3:195505836G>C	ENST00000463781.3	-	2	13074	c.12615C>G	c.(12613-12615)caC>caG	p.H4205Q	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H4205Q|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.H4205Q(10)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGGGTGGCGTGACCTGTGG	0.597																																						uc021xjp.1																			10	Substitution - Missense(10)	p.H4205Q(10)	kidney(4)|prostate(3)|urinary_tract(2)|endometrium(1)	NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						c.(12613-12615)caC>caG		Homo sapiens mucin 4, cell surface associated (MUC4), transcript variant 1, mRNA.							15.0	14.0	14.0					3																	195505836		687	1573	2260	SO:0001583	missense	4585				cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity	g.chr3:195505836G>C	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12615C>G	3.37:g.195505836G>C	ENSP00000417498:p.His4205Gln					MUC4_uc003fva.3_5'Flank|MUC4_uc003fvb.3_5'Flank|MUC4_uc003fvc.3_5'Flank|MUC4_uc003fvd.3_5'Flank|MUC4_uc003fve.3_5'Flank|MUC4_uc010hzr.3_5'Flank|MUC4_uc021xjm.1_Intron|MUC4_uc021xjn.1_Intron|MUC4_uc021xjo.1_Intron|MUC4_uc021xjg.1_Intron|MUC4_uc021xjh.1_Intron|MUC4_uc021xji.1_Intron|MUC4_uc021xjj.1_Intron|MUC4_uc021xjk.1_Intron|MUC4_uc021xjl.1_Intron|MUC4_uc003fvo.3_Intron|MUC4_uc003fvp.3_Intron	p.H4205Q	NM_018406	NP_060876	Q99102	MUC4_HUMAN	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)	1	12771	-	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	968					O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	c.12615C>G	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	0.099	-1.155501	0.01686	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30448	1.55;1.53	.	.	.	.	.	.	.	.	T	0.17619	0.0423	N	0.19112	0.55	0.21950	N	0.999454	P	0.35208	0.49	B	0.40038	0.317	T	0.24368	-1.0162	6	.	.	.	.	.	.	.	.	4077	E7ESK3	.	Q	4205	ENSP00000417498:H4205Q;ENSP00000420243:H4205Q	.	H	-	3	2	MUC4	196990615	.	.	0.016000	0.15963	0.046000	0.14306	.	.	-0.849000	0.04158	0.074000	0.15403	CAC		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TLR6	10333	broad.mit.edu	37	4	38830190	38830190	+	Missense_Mutation	SNP	G	G	A	rs374845111		TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr4:38830190G>A	ENST00000381950.1	-	1	970	c.905C>T	c.(904-906)aCg>aTg	p.T302M	TLR6_ENST00000436693.2_Missense_Mutation_p.T302M			Q9Y2C9	TLR6_HUMAN	toll-like receptor 6	302					activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to diacyl bacterial lipopeptide (GO:0071726)|defense response to bacterium (GO:0042742)|detection of diacyl bacterial lipopeptide (GO:0042496)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|nitric oxide metabolic process (GO:0046209)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of JUN kinase activity (GO:0043507)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 6 signaling pathway (GO:0034150)|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)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Toll-like receptor 2-Toll-like receptor 6 protein complex (GO:0035355)	diacyl lipopeptide binding (GO:0042498)|lipopeptide binding (GO:0071723)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TTTCAATGTCGTTTTAGAATA	0.323																																						uc010ifg.2																			0				breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						c.(904-906)aCg>aTg		Homo sapiens toll-like receptor 6 (TLR6), mRNA.		G	MET/THR	0,4404		0,0,2202	60.0	63.0	62.0		905	5.5	0.1	4		62	1,8597	1.2+/-3.3	0,1,4298	no	missense	TLR6	NM_006068.4	81	0,1,6500	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	302/797	38830190	1,13001	2202	4299	6501	SO:0001583	missense	10333				activation of NF-kappaB-inducing kinase activity|cellular response to diacyl bacterial lipopeptide|defense response to bacterium|detection of diacyl bacterial lipopeptide|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-6 biosynthetic process|positive regulation of JUN kinase activity|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	integral to plasma membrane|phagocytic vesicle membrane	lipopeptide binding|transmembrane receptor activity	g.chr4:38830190G>A		CCDS3446.1	4p16.1	2009-11-23			ENSG00000174130	ENSG00000174130		"""CD molecules"""	16711	protein-coding gene	gene with protein product		605403				10231569	Standard	NM_006068		Approved	CD286	uc010ifg.2	Q9Y2C9	OTTHUMG00000128579	ENST00000381950.1:c.905C>T	4.37:g.38830190G>A	ENSP00000371376:p.Thr302Met					TLR6_uc003gtm.3_Missense_Mutation_p.T302M	p.T302M	NM_006068	NP_006059	Q9Y2C9	TLR6_HUMAN			1	1026	-			302					B3Y640|B6CH35|B6RFS4|B6RFS5|Q2NKL3	Missense_Mutation	SNP	ENST00000381950.1	37	c.905C>T	CCDS3446.1	.	.	.	.	.	.	.	.	.	.	G	15.37	2.813939	0.50527	0.0	1.16E-4	ENSG00000174130	ENST00000436693;ENST00000381950;ENST00000508542	T;T	0.09350	2.99;2.99	5.5	5.5	0.81552	.	0.097074	0.45361	D	0.000368	T	0.37404	0.1002	M	0.86178	2.8	0.40044	D	0.975696	D	0.89917	1.0	D	0.69142	0.962	T	0.33163	-0.9879	10	0.87932	D	0	.	16.1107	0.81261	0.0:0.0:1.0:0.0	.	302	Q9Y2C9	TLR6_HUMAN	M	302	ENSP00000389600:T302M;ENSP00000371376:T302M	ENSP00000371376:T302M	T	-	2	0	TLR6	38506585	0.100000	0.21855	0.082000	0.20525	0.480000	0.33159	1.269000	0.33074	2.584000	0.87258	0.491000	0.48974	ACG		0.323	TLR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250431.1		
TNIP3	79931	broad.mit.edu	37	4	122085228	122085228	+	Missense_Mutation	SNP	G	G	A	rs144762502	byFrequency	TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr4:122085228G>A	ENST00000509841.1	-	4	362	c.284C>T	c.(283-285)aCg>aTg	p.T95M	TNIP3_ENST00000507879.1_Missense_Mutation_p.T88M|TNIP3_ENST00000057513.3_Missense_Mutation_p.T18M|TNIP3_ENST00000454328.1_Missense_Mutation_p.T18M	NM_001244764.1	NP_001231693.1			TNFAIP3 interacting protein 3									p.T18M(1)		NS(1)|endometrium(4)|large_intestine(4)|lung(9)|ovary(1)|prostate(3)|skin(2)	24						TTTATGCTCCGTAGAACTTTC	0.398													G|||	2	0.000399361	0.0015	0.0	5008	,	,		16364	0.0		0.0	False		,,,				2504	0.0					uc021xrj.1																			1	Substitution - Missense(1)	p.T18M(1)	prostate(1)	NS(1)|endometrium(4)|large_intestine(4)|lung(9)|ovary(1)|prostate(3)|skin(2)	24						c.(283-285)aCg>aTg		Homo sapiens TNFAIP3 interacting protein 3 (TNIP3), transcript variant 3, mRNA.		G	MET/THR,MET/THR	4,4402	8.1+/-20.4	0,4,2199	127.0	114.0	119.0		53,53	1.1	0.0	4	dbSNP_134	119	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	TNIP3	NM_001128843.2,NM_024873.5	81,81	0,5,6498	AA,AG,GG		0.0116,0.0908,0.0384	benign,benign	18/326,18/326	122085228	5,13001	2203	4300	6503	SO:0001583	missense	79931							g.chr4:122085228G>A	AJ320534	CCDS3718.1, CCDS58925.1, CCDS58926.1	4q27	2008-02-05			ENSG00000050730	ENSG00000050730			19315	protein-coding gene	gene with protein product		608019				11345586	Standard	NM_024873		Approved	LIND, FLJ21162, ABIN-3	uc021xrj.1	Q96KP6	OTTHUMG00000132969	ENST00000509841.1:c.284C>T	4.37:g.122085228G>A	ENSP00000426613:p.Thr95Met					TNIP3_uc010ing.3_Missense_Mutation_p.T18M|TNIP3_uc011cgj.2_Missense_Mutation_p.T88M|TNIP3_uc010ini.3_Missense_Mutation_p.T18M	p.T95M	NM_001244764	NP_001231693	Q96KP6	TNIP3_HUMAN			3	363	-			18						Missense_Mutation	SNP	ENST00000509841.1	37	c.284C>T	CCDS58926.1	.	.	.	.	.	.	.	.	.	.	G	7.418	0.636144	0.14386	9.08E-4	1.16E-4	ENSG00000050730	ENST00000057513;ENST00000454328;ENST00000507879;ENST00000509841	T;T;T;T	0.48201	0.92;0.92;0.82;0.82	5.44	1.14	0.20703	.	1.071200	0.07204	N	0.858040	T	0.27205	0.0667	N	0.21448	0.665	0.09310	N	1	P;B;P	0.42357	0.777;0.414;0.777	B;B;B	0.29267	0.1;0.031;0.1	T	0.11324	-1.0592	10	0.33141	T	0.24	-2.4328	7.7995	0.29166	0.4206:0.0:0.5794:0.0	.	88;18;18	B4DVF5;A5HU65;Q96KP6	.;.;TNIP3_HUMAN	M	18;18;88;95	ENSP00000057513:T18M;ENSP00000411817:T18M;ENSP00000427106:T88M;ENSP00000426613:T95M	ENSP00000057513:T18M	T	-	2	0	TNIP3	122304678	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.669000	0.25142	0.043000	0.15746	-0.157000	0.13467	ACG		0.398	TNIP3-003	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364000.4	NM_024873	
HCN1	348980	broad.mit.edu	37	5	45695952	45695952	+	Missense_Mutation	SNP	C	C	T			TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr5:45695952C>T	ENST00000303230.4	-	1	301	c.244G>A	c.(244-246)Gaa>Aaa	p.E82K		NM_021072.3	NP_066550.2	O60741	HCN1_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 1	82					apical protein localization (GO:0045176)|cellular response to cAMP (GO:0071320)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|retinal cone cell development (GO:0046549)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|intracellular cAMP activated cation channel activity (GO:0005222)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(3)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(21)|liver(1)|lung(98)|ovary(1)|prostate(7)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(5)	156						TCGGCGTCTTCGAAGCCCCCC	0.711																																						uc003jok.3																			0		p.F81I(1)		NS(3)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(21)|liver(1)|lung(98)|ovary(1)|prostate(7)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(5)	156						c.(244-246)Gaa>Aaa		Homo sapiens hyperpolarization activated cyclic nucleotide-gated potassium channel 1 (HCN1), mRNA.							10.0	13.0	12.0					5																	45695952		2109	4172	6281	SO:0001583	missense	348980					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity	g.chr5:45695952C>T	AF064876	CCDS3952.1	5p12	2011-07-05			ENSG00000164588	ENSG00000164588		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	4845	protein-coding gene	gene with protein product		602780		BCNG1		9405696, 9630217, 16382102	Standard	NM_021072		Approved	BCNG-1, HAC-2	uc003jok.3	O60741	OTTHUMG00000131155	ENST00000303230.4:c.244G>A	5.37:g.45695952C>T	ENSP00000307342:p.Glu82Lys						p.E82K	NM_021072	NP_066550	O60741	HCN1_HUMAN			0	269	-			82						Missense_Mutation	SNP	ENST00000303230.4	37	c.244G>A	CCDS3952.1	.	.	.	.	.	.	.	.	.	.	C	10.44	1.351120	0.24512	.	.	ENSG00000164588	ENST00000303230	D	0.97455	-4.39	4.18	4.18	0.49190	.	0.123300	0.32593	N	0.005897	D	0.92877	0.7734	L	0.27053	0.805	0.41016	D	0.985041	B	0.12013	0.005	B	0.06405	0.002	D	0.90052	0.4150	10	0.15499	T	0.54	.	15.2177	0.73281	0.0:1.0:0.0:0.0	.	82	O60741	HCN1_HUMAN	K	82	ENSP00000307342:E82K	ENSP00000307342:E82K	E	-	1	0	HCN1	45731709	0.998000	0.40836	0.836000	0.33094	0.180000	0.23129	4.004000	0.57068	2.132000	0.65825	0.462000	0.41574	GAA		0.711	HCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253847.1	NM_021072	
ZNF366	167465	broad.mit.edu	37	5	71757119	71757120	+	Missense_Mutation	DNP	CG	CG	AT			TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr5:71757119_71757120CG>AT	ENST00000318442.5	-	2	694_695	c.204_205CG>AT	c.(202-207)ccCGgg>ccATgg	p.G69W		NM_152625.1	NP_689838.1	Q8N895	ZN366_HUMAN	zinc finger protein 366	69					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|estrogen receptor binding (GO:0030331)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	35		Lung NSC(167;0.0247)|Ovarian(174;0.0908)|Prostate(461;0.155)		OV - Ovarian serous cystadenocarcinoma(47;2.51e-53)		TCGAAGACCCCGGGGAACCCAT	0.584																																						uc003kce.1																			0				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	35						c.(202-207)cccggg>ccATgg		Homo sapiens zinc finger protein 366 (ZNF366), mRNA.																																				SO:0001583	missense	167465				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr5:71757119_71757120CG>AT	AK097115	CCDS4015.1	5q13.1	2013-01-08			ENSG00000178175	ENSG00000178175		"""Zinc fingers, C2H2-type"""	18316	protein-coding gene	gene with protein product		610159					Standard	NM_152625		Approved	FLJ39796	uc003kce.1	Q8N895	OTTHUMG00000100965	ENST00000318442.5:c.204_205delinsAT	5.37:g.71757119_71757120delinsAT	ENSP00000313158:p.Gly69Trp						p.G69W	NM_152625	NP_689838	Q8N895	ZN366_HUMAN		OV - Ovarian serous cystadenocarcinoma(47;2.51e-53)	1	390_391	-		Lung NSC(167;0.0247)|Ovarian(174;0.0908)|Prostate(461;0.155)	69					Q5HYI9|Q7RTV4	Missense_Mutation	DNP	ENST00000318442.5	37	c.204_205CG>AT	CCDS4015.1																																																																																				0.584	ZNF366-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218574.3		
E2F3	1871	broad.mit.edu	37	6	20402625	20402625	+	Silent	SNP	G	G	C			TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr6:20402625G>C	ENST00000346618.3	+	1	228	c.162G>C	c.(160-162)ccG>ccC	p.P54P	E2F3_ENST00000535432.1_5'Flank	NM_001949.4	NP_001940.1	O00716	E2F3_HUMAN	E2F transcription factor 3	54					mitotic cell cycle (GO:0000278)|Notch signaling pathway (GO:0007219)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(3)	7	all_cancers(95;0.154)|all_epithelial(95;0.0585)|Breast(50;0.146)|Ovarian(93;0.148)		OV - Ovarian serous cystadenocarcinoma(7;0.0068)|all cancers(50;0.0148)|Epithelial(50;0.0562)			ccgccgccCCGGGCGCGTACA	0.731																																						uc003nda.2																			0				central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(3)	7						c.(160-162)ccG>ccC		Homo sapiens E2F transcription factor 3 (E2F3), transcript variant 1, mRNA.							18.0	25.0	23.0					6																	20402625		2169	4234	6403	SO:0001819	synonymous_variant	1871				G1 phase of mitotic cell cycle|G2 phase of mitotic cell cycle|transcription initiation from RNA polymerase II promoter	transcription factor complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity	g.chr6:20402625G>C	Y10479	CCDS4545.1, CCDS58999.1	6p22	2008-08-29			ENSG00000112242	ENSG00000112242			3115	protein-coding gene	gene with protein product		600427				8246996	Standard	NM_001949		Approved		uc003nda.2	O00716	OTTHUMG00000016389	ENST00000346618.3:c.162G>C	6.37:g.20402625G>C						E2F3_uc003ncz.2_Silent_p.P54P|E2F3_uc021ymj.1_5'Flank	p.P54P	NM_001949	NP_001940	O00716	E2F3_HUMAN	OV - Ovarian serous cystadenocarcinoma(7;0.0068)|all cancers(50;0.0148)|Epithelial(50;0.0562)		0	489	+	all_cancers(95;0.154)|all_epithelial(95;0.0585)|Breast(50;0.146)|Ovarian(93;0.148)		54					Q15000|Q68DT0|Q9BZ44	Silent	SNP	ENST00000346618.3	37	c.162G>C	CCDS4545.1																																																																																				0.731	E2F3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043828.1		
PRRC2A	7916	broad.mit.edu	37	6	31599728	31599728	+	Missense_Mutation	SNP	A	A	G			TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr6:31599728A>G	ENST00000376033.2	+	16	3512	c.3278A>G	c.(3277-3279)gAg>gGg	p.E1093G	PRRC2A_ENST00000376007.4_Missense_Mutation_p.E1093G	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1093	4 X 57 AA type A repeats.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						GAGGGTTCAGAGTATGAGGAA	0.632																																						uc003nvb.4																			0				breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						c.(3277-3279)gAg>gGg		Homo sapiens proline-rich coiled-coil 2A (PRRC2A), transcript variant 1, mRNA.							33.0	41.0	38.0					6																	31599728		1507	2707	4214	SO:0001583	missense	7916					cytoplasm|nucleus	protein binding	g.chr6:31599728A>G	M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"""HLA-B associated transcript 2"""	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.3278A>G	6.37:g.31599728A>G	ENSP00000365201:p.Glu1093Gly					PRRC2A_uc011dnv.1_Intron|PRRC2A_uc003nvc.4_Missense_Mutation_p.E1093G	p.E1093G	NM_080686	NP_542417	P48634	PRC2A_HUMAN			15	3527	+			1093			4 X 57 AA type A repeats.		B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Missense_Mutation	SNP	ENST00000376033.2	37	c.3278A>G	CCDS4708.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.51|12.51	1.960159|1.960159	0.34565|0.34565	.|.	.|.	ENSG00000204469|ENSG00000204469	ENST00000376007;ENST00000376033;ENST00000376010|ENST00000424184;ENST00000435052	T;T|.	0.02103|.	4.45;4.45|.	4.88|4.88	4.88|4.88	0.63580|0.63580	.|.	0.000000|.	0.53938|.	D|.	0.000058|.	T|T	0.51363|0.51363	0.1670|0.1670	L|L	0.49778|0.49778	1.585|1.585	0.53688|0.53688	D|D	0.99997|0.99997	D|.	0.89917|.	1.0|.	D|.	0.69307|.	0.963|.	T|T	0.51601|0.51601	-0.8685|-0.8685	10|5	0.87932|.	D|.	0|.	-17.3987|-17.3987	13.6117|13.6117	0.62083|0.62083	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	1093|.	P48634|.	PRC2A_HUMAN|.	G|G	1093;1093;318|1092;1081	ENSP00000365175:E1093G;ENSP00000365201:E1093G|.	ENSP00000365175:E1093G|.	E|S	+|+	2|1	0|0	PRRC2A|PRRC2A	31707707|31707707	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.910000|0.910000	0.53928|0.53928	8.754000|8.754000	0.91642|0.91642	2.071000|2.071000	0.62044|0.62044	0.533000|0.533000	0.62120|0.62120	GAG|AGT		0.632	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686	
LAMA2	3908	broad.mit.edu	37	6	129802525	129802525	+	Missense_Mutation	SNP	C	C	G			TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr6:129802525C>G	ENST00000421865.2	+	55	7739	c.7690C>G	c.(7690-7692)Ctt>Gtt	p.L2564V	RP1-69D17.3_ENST00000442449.1_RNA	NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	2564	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.		L -> P (in MDC1A). {ECO:0000269|PubMed:11591858}.		axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		CGGCATCATTCTTTTGGGAAG	0.488																																						uc021zfb.1																			0				NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194						c.(7690-7692)Ctt>Gtt		Homo sapiens laminin, alpha 2 (LAMA2), transcript variant 1, mRNA.							151.0	144.0	146.0					6																	129802525		2203	4300	6503	SO:0001583	missense	3908				cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity	g.chr6:129802525C>G	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"""Laminins"""	6482	protein-coding gene	gene with protein product	"""merosin"", ""congenital muscular dystrophy"""	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.7690C>G	6.37:g.129802525C>G	ENSP00000400365:p.Leu2564Val					LAMA2_uc003qbn.3_Missense_Mutation_p.L2562V|LAMA2_uc003qbo.3_Missense_Mutation_p.L2558V|BC035400_uc003qbq.3_Non-coding_Transcript	p.L2564V	NM_000426	NP_000417	P24043	LAMA2_HUMAN		OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)	54	7795	+			2564		L -> P (in MDC1A).	Laminin G-like 3.		Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	37	c.7690C>G	CCDS5138.1	.	.	.	.	.	.	.	.	.	.	C	13.91	2.378614	0.42207	.	.	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865;ENST00000443169	D	0.85955	-2.05	5.22	5.22	0.72569	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 1 (1);	0.062441	0.64402	D	0.000004	D	0.88190	0.6370	M	0.75615	2.305	0.50313	D	0.999866	D;D	0.69078	0.997;0.997	D;D	0.66196	0.942;0.942	D	0.88342	0.2975	9	.	.	.	.	9.5561	0.39339	0.0:0.837:0.0:0.163	.	2565;2564	A6NF00;P24043	.;LAMA2_HUMAN	V	2564;2563;2564;582	ENSP00000400365:L2564V	.	L	+	1	0	LAMA2	129844218	0.999000	0.42202	0.894000	0.35097	0.372000	0.29890	2.291000	0.43540	2.599000	0.87857	0.563000	0.77884	CTT		0.488	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1		
SYNE1	23345	broad.mit.edu	37	6	152861113	152861113	+	Missense_Mutation	SNP	G	G	C			TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr6:152861113G>C	ENST00000367255.5	-	4	712	c.111C>G	c.(109-111)atC>atG	p.I37M	SYNE1_ENST00000448038.1_Missense_Mutation_p.I37M|SYNE1_ENST00000423061.1_Missense_Mutation_p.I37M|SYNE1_ENST00000413186.2_Missense_Mutation_p.I37M|SYNE1_ENST00000466159.2_Missense_Mutation_p.I37M|SYNE1_ENST00000367248.3_Missense_Mutation_p.I37M|SYNE1_ENST00000341594.5_Missense_Mutation_p.I37M|SYNE1_ENST00000367253.4_Missense_Mutation_p.I37M|SYNE1_ENST00000265368.4_Missense_Mutation_p.I37M	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	37	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GATGAGAGTTGATCCATTTTG	0.338										HNSCC(10;0.0054)																												uc021zhb.1																			0				NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524						c.(109-111)atC>atG		Homo sapiens spectrin repeat containing, nuclear envelope 1 (SYNE1), transcript variant 1, mRNA.							259.0	249.0	252.0					6																	152861113		2203	4300	6503	SO:0001583	missense	23345				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding	g.chr6:152861113G>C	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.111C>G	6.37:g.152861113G>C	ENSP00000356224:p.Ile37Met	HNSCC(10;0.0054)				SYNE1_uc003qot.4_Missense_Mutation_p.I37M|SYNE1_uc003qou.4_Missense_Mutation_p.I37M|SYNE1_uc010kjb.1_Missense_Mutation_p.I37M|SYNE1_uc003qpa.1_Missense_Mutation_p.I37M	p.I37M	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)	1	334	-		Ovarian(120;0.0955)	37			Actin-binding.|CH 1.		E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	c.111C>G	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	G	17.01	3.278968	0.59758	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000367253;ENST00000367248;ENST00000413186;ENST00000466159;ENST00000537750	D;D;D;D;D;D;D;D;D;D	0.96365	-3.99;-3.99;-3.99;-3.99;-3.99;-3.99;-3.99;-3.99;-3.99;-3.99	5.36	5.36	0.76844	Actinin-type, actin-binding, conserved site (1);Calponin homology domain (5);	0.000000	0.45126	D	0.000384	D	0.96470	0.8848	M	0.64080	1.96	0.80722	D	1	P;P;P;P;P	0.51240	0.627;0.89;0.943;0.89;0.867	P;P;P;P;P	0.59487	0.603;0.858;0.777;0.858;0.777	D	0.96550	0.9407	10	0.72032	D	0.01	.	11.9615	0.53011	0.0:0.0:0.8267:0.1733	.	37;37;37;37;37	B3W695;Q8NF91;F5H4Q0;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.;.	M	37	ENSP00000356224:I37M;ENSP00000396024:I37M;ENSP00000265368:I37M;ENSP00000390975:I37M;ENSP00000341887:I37M;ENSP00000356222:I37M;ENSP00000356217:I37M;ENSP00000414510:I37M;ENSP00000446021:I37M;ENSP00000441264:I37M	ENSP00000265368:I37M	I	-	3	3	SYNE1	152902806	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.375000	0.66173	2.669000	0.90835	0.655000	0.94253	ATC		0.338	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
GRB10	2887	broad.mit.edu	37	7	50674041	50674041	+	Missense_Mutation	SNP	G	G	A			TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr7:50674041G>A	ENST00000401949.1	-	14	1734	c.1265C>T	c.(1264-1266)aCg>aTg	p.T422M	GRB10_ENST00000403097.1_Missense_Mutation_p.T416M|GRB10_ENST00000439599.1_Missense_Mutation_p.T416M|GRB10_ENST00000398812.2_Missense_Mutation_p.T422M|GRB10_ENST00000406641.1_Missense_Mutation_p.T364M|GRB10_ENST00000398810.2_Missense_Mutation_p.T364M|GRB10_ENST00000357271.5_Missense_Mutation_p.T376M|GRB10_ENST00000335866.3_Missense_Mutation_p.T364M|GRB10_ENST00000402578.1_Missense_Mutation_p.T364M|GRB10_ENST00000407526.1_Missense_Mutation_p.T364M|GRB10_ENST00000402497.1_Missense_Mutation_p.T364M			Q13322	GRB10_HUMAN	growth factor receptor-bound protein 10	422					insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of glucose import (GO:0046325)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of phosphorylation (GO:0042326)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of phosphorylation (GO:0042327)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|response to insulin (GO:0032868)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	insulin receptor binding (GO:0005158)|SH3/SH2 adaptor activity (GO:0005070)	p.T422M(1)|p.T416M(1)		NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(19)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	41	Glioma(55;0.08)|all_neural(89;0.245)					TACCACTGGCGTCGAGAACGG	0.517									Russell-Silver syndrome																													uc003tpi.2																			2	Substitution - Missense(2)	p.T422M(2)|p.T416M(1)	endometrium(2)	NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(19)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	41						c.(1264-1266)aCg>aTg		Homo sapiens growth factor receptor-bound protein 10 (GRB10), transcript variant 1, mRNA.							106.0	110.0	109.0					7																	50674041		1975	4150	6125	SO:0001583	missense	2887	Russell-Silver syndrome	Familial Cancer Database	Silver-Russell Dwarfism, Silver-Russell syndrome, SRS, Russel-Silver Dwarfism	insulin receptor signaling pathway|negative regulation of glucose import|negative regulation of glycogen biosynthetic process|negative regulation of insulin receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of phosphorylation|positive regulation of vascular endothelial growth factor receptor signaling pathway	cytosol|plasma membrane	insulin receptor binding|SH3/SH2 adaptor activity	g.chr7:50674041G>A		CCDS43582.1, CCDS43583.1, CCDS47586.1	7p12.2	2013-02-14			ENSG00000106070	ENSG00000106070		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	4564	protein-coding gene	gene with protein product		601523					Standard	NM_005311		Approved		uc003tpi.2	Q13322	OTTHUMG00000150622	ENST00000401949.1:c.1265C>T	7.37:g.50674041G>A	ENSP00000385770:p.Thr422Met					GRB10_uc003tph.3_Missense_Mutation_p.T364M|GRB10_uc003tpj.2_Missense_Mutation_p.T376M|GRB10_uc003tpk.2_Missense_Mutation_p.T422M|GRB10_uc010kzb.2_Missense_Mutation_p.T364M|GRB10_uc003tpl.2_Missense_Mutation_p.T416M|GRB10_uc003tpm.2_Missense_Mutation_p.T364M	p.T422M	NM_005311	NP_005302	Q13322	GRB10_HUMAN			10	1311	-	Glioma(55;0.08)|all_neural(89;0.245)		422					A4D258|A7VJ95|A8K0E6|D3DVM9|O00427|O00701|O75222|Q92606|Q92907|Q92948	Missense_Mutation	SNP	ENST00000401949.1	37	c.1265C>T	CCDS43582.1	.	.	.	.	.	.	.	.	.	.	G	11.38	1.620564	0.28801	.	.	ENSG00000106070	ENST00000398812;ENST00000439599;ENST00000335866;ENST00000398810;ENST00000402578;ENST00000403097;ENST00000406641;ENST00000357271;ENST00000407526;ENST00000401949;ENST00000402497	D;D;D;D;D;D;D;D;D;D;D	0.83075	-1.54;-1.54;-1.68;-1.68;-1.68;-1.54;-1.68;-1.53;-1.68;-1.54;-1.68	5.34	5.34	0.76211	.	0.201005	0.52532	D	0.000063	T	0.78259	0.4255	L	0.31926	0.97	0.31484	N	0.666761	B;B;B	0.29270	0.24;0.24;0.049	B;B;B	0.29440	0.063;0.102;0.018	T	0.79266	-0.1874	10	0.56958	D	0.05	-6.8663	19.0286	0.92946	0.0:0.0:1.0:0.0	.	416;376;422	Q13322-4;Q13322-2;Q13322	.;.;GRB10_HUMAN	M	422;416;364;364;364;416;364;376;364;422;364	ENSP00000381793:T422M;ENSP00000406716:T416M;ENSP00000338543:T364M;ENSP00000381790:T364M;ENSP00000385189:T364M;ENSP00000385544:T416M;ENSP00000385366:T364M;ENSP00000349818:T376M;ENSP00000385046:T364M;ENSP00000385770:T422M;ENSP00000385748:T364M	ENSP00000338543:T364M	T	-	2	0	GRB10	50641535	0.991000	0.36638	0.009000	0.14445	0.042000	0.13812	6.235000	0.72332	2.463000	0.83235	0.655000	0.94253	ACG		0.517	GRB10-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319157.1		
DLC1	10395	broad.mit.edu	37	8	12957581	12957581	+	Silent	SNP	C	C	T	rs138749997	byFrequency	TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr8:12957581C>T	ENST00000276297.4	-	9	2674	c.2265G>A	c.(2263-2265)acG>acA	p.T755T	DLC1_ENST00000358919.2_Silent_p.T318T|DLC1_ENST00000520226.1_Silent_p.T244T|DLC1_ENST00000512044.2_Silent_p.T352T	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	755	Focal adhesion-targeting (FAT).				actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						CAGGGCTGGGCGTGCTGACCG	0.582																																						uc003wwm.2																			0				NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						c.(2263-2265)acG>acA		Homo sapiens deleted in liver cancer 1 (DLC1), transcript variant 1, mRNA.							55.0	49.0	51.0					8																	12957581		2203	4300	6503	SO:0001819	synonymous_variant	10395				actin cytoskeleton organization|activation of caspase activity|focal adhesion assembly|forebrain development|heart morphogenesis|hindbrain morphogenesis|induction of apoptosis|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of stress fiber assembly|neural tube closure|positive regulation of protein dephosphorylation|regulation of cell shape|small GTPase mediated signal transduction	caveola|cytosol|focal adhesion|nucleus	Rho GTPase activator activity|SH2 domain binding	g.chr8:12957581C>T	AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	2897	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 12"""	604258	"""deleted in liver cancer 1"""			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.2265G>A	8.37:g.12957581C>T						DLC1_uc003wwk.1_Silent_p.T318T|DLC1_uc003wwl.1_Silent_p.T352T|DLC1_uc011kxx.1_Silent_p.T244T	p.T755T	NM_182643	NP_872584	Q96QB1	RHG07_HUMAN			8	2709	-			755					B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Silent	SNP	ENST00000276297.4	37	c.2265G>A	CCDS5989.1																																																																																				0.582	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094	
SEMA4D	10507	broad.mit.edu	37	9	92003832	92003832	+	Missense_Mutation	SNP	G	G	T	rs201242261		TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr9:92003832G>T	ENST00000450295.1	-	10	1681	c.905C>A	c.(904-906)cCg>cAg	p.P302Q	SEMA4D_ENST00000356444.2_Missense_Mutation_p.P302Q|SEMA4D_ENST00000343780.4_Missense_Mutation_p.P302Q|SEMA4D_ENST00000420987.1_Missense_Mutation_p.P302Q|SEMA4D_ENST00000339861.4_Missense_Mutation_p.P302Q|SEMA4D_ENST00000438547.2_Missense_Mutation_p.P302Q|SEMA4D_ENST00000455551.2_Missense_Mutation_p.P302Q|SEMA4D_ENST00000422704.2_Missense_Mutation_p.P302Q			Q92854	SEM4D_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	302	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|immune response (GO:0006955)|leukocyte aggregation (GO:0070486)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|ossification involved in bone maturation (GO:0043931)|positive regulation of cell migration (GO:0030335)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell projection organization (GO:0031344)|regulation of cell shape (GO:0008360)|regulation of dendrite morphogenesis (GO:0048814)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(8)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	34						CTTCAGGCCCGGGGACCTGAG	0.602																																						uc004aqo.1																			0				NS(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(8)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	34						c.(904-906)cCg>cAg		Homo sapiens sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D (SEMA4D), transcript variant 1, mRNA.							112.0	114.0	113.0					9																	92003832		2203	4300	6503	SO:0001583	missense	10507				anti-apoptosis|axon guidance|cell adhesion|immune response	integral to membrane|plasma membrane	receptor activity|receptor binding	g.chr9:92003832G>T	U60800	CCDS6685.1, CCDS47991.1	9q22-q31	2013-01-11			ENSG00000187764	ENSG00000187764		"""Semaphorins"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10732	protein-coding gene	gene with protein product	"""M-sema G"""	601866	"""chromosome 9 open reading frame 164"""	SEMAJ, C9orf164		8876214, 8969198	Standard	NM_006378		Approved	CD100, coll-4, FLJ39737	uc004aqo.1	Q92854	OTTHUMG00000020185	ENST00000450295.1:c.905C>A	9.37:g.92003832G>T	ENSP00000416523:p.Pro302Gln					SEMA4D_uc011ltm.1_Missense_Mutation_p.P302Q|SEMA4D_uc011ltn.1_Non-coding_Transcript|SEMA4D_uc011lto.1_Non-coding_Transcript|SEMA4D_uc004aqp.1_Missense_Mutation_p.P302Q	p.P302Q	NM_006378	NP_006369	Q92854	SEM4D_HUMAN			11	1477	-			302			Sema.		B2RPM6|Q7Z5S4|Q8N8B0	Missense_Mutation	SNP	ENST00000450295.1	37	c.905C>A	CCDS6685.1	.	.	.	.	.	.	.	.	.	.	G	9.345	1.064019	0.20067	.	.	ENSG00000187764	ENST00000339861;ENST00000420987;ENST00000455551;ENST00000343780;ENST00000450295;ENST00000438547;ENST00000356444;ENST00000422704	T;T;T;T;T;T;T;T	0.10005	2.92;2.92;2.92;2.92;2.92;2.92;2.92;2.92	4.96	4.03	0.46877	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.746260	0.13589	N	0.376774	T	0.10078	0.0247	L	0.31476	0.935	0.18873	N	0.999986	B;B	0.21753	0.005;0.06	B;B	0.23419	0.011;0.046	T	0.27739	-1.0065	10	0.21540	T	0.41	.	15.1351	0.72558	0.0:0.142:0.858:0.0	.	302;302	Q92854-2;Q92854	.;SEM4D_HUMAN	Q	302	ENSP00000344923:P302Q;ENSP00000391733:P302Q;ENSP00000411981:P302Q;ENSP00000343418:P302Q;ENSP00000416523:P302Q;ENSP00000405102:P302Q;ENSP00000348822:P302Q;ENSP00000388768:P302Q	ENSP00000344923:P302Q	P	-	2	0	SEMA4D	91193652	0.614000	0.27017	0.011000	0.14972	0.323000	0.28346	2.237000	0.43061	1.254000	0.44035	0.561000	0.74099	CCG		0.602	SEMA4D-018	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342411.1	NM_006378	
ST6GALNAC4	27090	broad.mit.edu	37	9	130670779	130670779	+	Silent	SNP	C	C	T			TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr9:130670779C>T	ENST00000335791.5	-	6	1076	c.801G>A	c.(799-801)gaG>gaA	p.E267E	ST6GALNAC4_ENST00000495983.1_5'UTR|ST6GALNAC4_ENST00000343609.2_Silent_p.E183E	NM_175039.3	NP_778204.1	Q9H4F1	SIA7D_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 4	267					cellular protein metabolic process (GO:0044267)|glycolipid metabolic process (GO:0006664)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	(alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl-galactosaminide 6-alpha-sialyltransferase activity (GO:0047290)|sialyltransferase activity (GO:0008373)			endometrium(1)|large_intestine(2)|lung(2)|prostate(2)	7						GGGGCGCCTGCTCGTGTGCCA	0.627																																						uc004bss.3																			0				endometrium(1)|large_intestine(2)|lung(2)|prostate(2)	7						c.(799-801)gaG>gaA		Homo sapiens ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1, 3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 4 (ST6GALNAC4), transcript variant 1, mRNA.							70.0	72.0	71.0					9																	130670779		2203	4300	6503	SO:0001819	synonymous_variant	27090				glycolipid metabolic process|protein glycosylation	integral to Golgi membrane|nucleus|soluble fraction	(alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl-galactosaminide 6-alpha-sialyltransferase activity	g.chr9:130670779C>T	AB035172	CCDS6883.1	9q34	2013-03-01	2005-02-07	2005-02-07	ENSG00000136840	ENSG00000136840	2.4.99.7	"""Sialyltransferases"""	17846	protein-coding gene	gene with protein product		606378	"""sialyltransferase 7D ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase)"""	SIAT7D		10207017, 11062056	Standard	XM_005251922		Approved	ST6GALNACIV, SIAT3C	uc004bss.3	Q9H4F1	OTTHUMG00000020724	ENST00000335791.5:c.801G>A	9.37:g.130670779C>T						ST6GALNAC4_uc004bst.3_Silent_p.E183E	p.E267E	NM_175039	NP_778205	Q9H4F1	SIA7D_HUMAN			5	1077	-			267					Q5T9D0|Q9NWU6|Q9UKU1|Q9ULB9|Q9Y3G3|Q9Y3G4	Silent	SNP	ENST00000335791.5	37	c.801G>A	CCDS6883.1																																																																																				0.627	ST6GALNAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054317.2	NM_175040	
PKN3	29941	broad.mit.edu	37	9	131476566	131476566	+	Missense_Mutation	SNP	C	C	T	rs370634438		TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chr9:131476566C>T	ENST00000291906.4	+	11	1796	c.1403C>T	c.(1402-1404)cCg>cTg	p.P468L		NM_013355.3	NP_037487.2	Q6P5Z2	PKN3_HUMAN	protein kinase N3	468	Pro-rich.				epithelial cell migration (GO:0010631)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24						TGCAGCTCCCCGAGCACAATC	0.652													C|||	1	0.000199681	0.0	0.0	5008	,	,		13514	0.001		0.0	False		,,,				2504	0.0					uc004bvw.3																			0				breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24						c.(1402-1404)cCg>cTg		Homo sapiens protein kinase N3 (PKN3), mRNA.		C	LEU/PRO	0,4406		0,0,2203	62.0	70.0	67.0		1403	4.1	0.9	9		67	1,8599	1.2+/-3.3	0,1,4299	no	missense	PKN3	NM_013355.3	98	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	468/890	131476566	1,13005	2203	4300	6503	SO:0001583	missense	29941				signal transduction	Golgi apparatus|nucleus|perinuclear region of cytoplasm	ATP binding|protein binding|protein kinase C activity	g.chr9:131476566C>T	AB019692	CCDS6908.1	9q34.13	2008-02-05			ENSG00000160447	ENSG00000160447			17999	protein-coding gene	gene with protein product		610714				10441506	Standard	NM_013355		Approved	PKNbeta	uc004bvw.3	Q6P5Z2	OTTHUMG00000020757	ENST00000291906.4:c.1403C>T	9.37:g.131476566C>T	ENSP00000291906:p.Pro468Leu					PKN3_uc010myh.3_Missense_Mutation_p.P468L|PKN3_uc022bom.1_Non-coding_Transcript	p.P468L	NM_013355	NP_037487	Q6P5Z2	PKN3_HUMAN			10	1796	+			468			Pro-rich.		Q9UM03	Missense_Mutation	SNP	ENST00000291906.4	37	c.1403C>T	CCDS6908.1	.	.	.	.	.	.	.	.	.	.	C	11.66	1.703689	0.30232	0.0	1.16E-4	ENSG00000160447	ENST00000291906	T	0.28666	1.6	4.97	4.05	0.47172	.	.	.	.	.	T	0.22936	0.0554	L	0.41236	1.265	0.38784	D	0.954828	B	0.15719	0.014	B	0.11329	0.006	T	0.07673	-1.0760	9	0.29301	T	0.29	.	8.2305	0.31595	0.0:0.819:0.0:0.181	.	468	Q6P5Z2	PKN3_HUMAN	L	468	ENSP00000291906:P468L	ENSP00000291906:P468L	P	+	2	0	PKN3	130516387	0.041000	0.20044	0.928000	0.36995	0.480000	0.33159	1.216000	0.32443	2.478000	0.83669	0.563000	0.77884	CCG		0.652	PKN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054487.1	NM_013355	
ARHGAP6	395	broad.mit.edu	37	X	11682473	11682473	+	Missense_Mutation	SNP	G	G	A			TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chrX:11682473G>A	ENST00000337414.4	-	1	1348	c.476C>T	c.(475-477)tCc>tTc	p.S159F	ARHGAP6_ENST00000380732.3_Missense_Mutation_p.S159F|ARHGAP6_ENST00000380718.1_Missense_Mutation_p.S159F	NM_013427.2	NP_038286.2	O43182	RHG06_HUMAN	Rho GTPase activating protein 6	159					actin filament polymerization (GO:0030041)|activation of phospholipase C activity (GO:0007202)|focal adhesion assembly (GO:0048041)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of signal transduction (GO:0009967)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|Rho GTPase activator activity (GO:0005100)|SH3/SH2 adaptor activity (GO:0005070)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						GCCTCCCCCGGATGAACAGAG	0.657																																						uc004cup.1																			0				cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						c.(475-477)tCc>tTc		Homo sapiens Rho GTPase activating protein 6 (ARHGAP6), transcript variant 1, mRNA.							25.0	27.0	26.0					X																	11682473		2202	4300	6502	SO:0001583	missense	395				actin filament polymerization|activation of phospholipase C activity|negative regulation of focal adhesion assembly|negative regulation of stress fiber assembly|Rho protein signal transduction	actin filament|cytosol	phospholipase activator activity|phospholipase binding|Rho GTPase activator activity|SH3 domain binding|SH3/SH2 adaptor activity	g.chrX:11682473G>A	AF012272	CCDS14140.1, CCDS14141.1, CCDS14142.1	Xp22.3	2008-02-05			ENSG00000047648	ENSG00000047648		"""Rho GTPase activating proteins"""	676	protein-coding gene	gene with protein product		300118				9417914	Standard	XM_005274507		Approved	rhoGAPX-1	uc004cup.1	O43182	OTTHUMG00000021134	ENST00000337414.4:c.476C>T	X.37:g.11682473G>A	ENSP00000338967:p.Ser159Phe					ARHGAP6_uc004cuo.1_Non-coding_Transcript|ARHGAP6_uc004cur.1_Missense_Mutation_p.S159F	p.S159F	NM_013427	NP_038286	O43182	RHG06_HUMAN			0	1349	-			159					B2RWQ0|O43437|Q9P1B3|Q9UK81|Q9UK82	Missense_Mutation	SNP	ENST00000337414.4	37	c.476C>T	CCDS14140.1	.	.	.	.	.	.	.	.	.	.	G	13.07	2.128040	0.37533	.	.	ENSG00000047648	ENST00000337414;ENST00000380718;ENST00000380732	T;T;T	0.25912	1.97;1.89;1.77	4.44	4.44	0.53790	.	.	.	.	.	T	0.18676	0.0448	N	0.14661	0.345	0.80722	D	1	P;P	0.37864	0.514;0.61	B;B	0.41236	0.351;0.28	T	0.06972	-1.0797	9	0.66056	D	0.02	.	11.3794	0.49748	0.0:0.0:1.0:0.0	.	159;159	O43182-2;O43182	.;RHG06_HUMAN	F	159	ENSP00000338967:S159F;ENSP00000370094:S159F;ENSP00000370108:S159F	ENSP00000338967:S159F	S	-	2	0	ARHGAP6	11592394	0.424000	0.25490	0.852000	0.33557	0.399000	0.30720	2.946000	0.49050	2.062000	0.61559	0.600000	0.82982	TCC		0.657	ARHGAP6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055760.2	NM_013427	
MAGEC2	51438	broad.mit.edu	37	X	141291609	141291609	+	Missense_Mutation	SNP	G	G	T			TCGA-28-5211-01C-11D-1845-08	TCGA-28-5211-10B-01D-1845-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f8dc846b-1b17-4699-9dc5-3f79e21eee94	fb345933-459e-4ab9-b876-7b07b709d6fe	g.chrX:141291609G>T	ENST00000247452.3	-	3	512	c.165C>A	c.(163-165)ttC>ttA	p.F55L		NM_016249.3	NP_057333.1	Q9UBF1	MAGC2_HUMAN	melanoma antigen family C, 2	55	Ser-rich.				cellular protein catabolic process (GO:0044257)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin protein ligase binding (GO:0031625)			NS(2)|breast(3)|endometrium(3)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)	47	Acute lymphoblastic leukemia(192;6.56e-05)					AGGATGTGGAGAAAGAAGAGG	0.512										HNSCC(46;0.14)																												uc022cfj.1																			0				NS(2)|breast(3)|endometrium(3)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)	47						c.(163-165)ttC>ttA		Homo sapiens melanoma antigen family C, 2 (MAGEC2), mRNA.							87.0	89.0	89.0					X																	141291609		2203	4300	6503	SO:0001583	missense	51438					cytoplasm|nucleus		g.chrX:141291609G>T	AF116195	CCDS14678.1	Xq27	2009-03-25	2004-06-08	2004-06-09	ENSG00000046774	ENSG00000046774			13574	protein-coding gene	gene with protein product	"""cancer/testis antigen 10"""	300468	"""melanoma antigen, family E, 1, cancer/testis specific"""	MAGEE1		10699956	Standard	NM_016249		Approved	CT10, MAGE-C2	uc004fbu.2	Q9UBF1	OTTHUMG00000022574	ENST00000247452.3:c.165C>A	X.37:g.141291609G>T	ENSP00000354660:p.Phe55Leu	HNSCC(46;0.14)				MAGEC2_uc004fbu.2_Missense_Mutation_p.F55L	p.F55L	NM_016249	NP_057333	Q9UBF1	MAGC2_HUMAN			0	165	-	Acute lymphoblastic leukemia(192;6.56e-05)		55			Ser-rich.		Q5JZ00|Q96D45|Q9P1M6|Q9P1M7	Missense_Mutation	SNP	ENST00000247452.3	37	c.165C>A	CCDS14678.1	.	.	.	.	.	.	.	.	.	.	-	0.013	-1.646379	0.00792	.	.	ENSG00000046774	ENST00000247452	T	0.02121	4.44	0.897	-1.79	0.07932	.	.	.	.	.	T	0.01092	0.0036	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.48293	-0.9048	9	0.11485	T	0.65	.	4.6481	0.12582	0.0:0.0:0.4728:0.5271	.	55	Q9UBF1	MAGC2_HUMAN	L	55	ENSP00000354660:F55L	ENSP00000354660:F55L	F	-	3	2	MAGEC2	141119275	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.145000	0.01295	-1.105000	0.03011	-0.769000	0.03391	TTC		0.512	MAGEC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058611.1	NM_016249	
