#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_ACHILLES_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	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
CSF3R	1441	broad.mit.edu	37	1	36932904	36932904	+	Missense_Mutation	SNP	T	T	C			TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	T	T	-	-	T	T	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr1:36932904T>C	ENST00000373106.1	-	16	2514	c.1967A>G	c.(1966-1968)aAt>aGt	p.N656S	CSF3R_ENST00000338937.5_Missense_Mutation_p.I625V|CSF3R_ENST00000373104.1_Missense_Mutation_p.N656S|CSF3R_ENST00000361632.4_Missense_Mutation_p.N656S|CSF3R_ENST00000373103.1_Missense_Mutation_p.N656S|CSF3R_ENST00000418048.2_Missense_Mutation_p.N656S|CSF3R_ENST00000440588.2_Missense_Mutation_p.N656S|CSF3R_ENST00000331941.5_Missense_Mutation_p.N656S|CSF3R_ENST00000487540.2_5'UTR|MRPS15_ENST00000373116.5_5'Flank	NM_000760.3	NP_000751.1	Q99062	CSF3R_HUMAN	colony stimulating factor 3 receptor (granulocyte)	656					cell adhesion (GO:0007155)|defense response (GO:0006952)|neutrophil chemotaxis (GO:0030593)|odontogenesis of dentin-containing tooth (GO:0042475)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)	p.N656S(2)		central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)			Filgrastim(DB00099)|Pegfilgrastim(DB00019)	CCAGAGGGGATTCTTCCTGCT	0.592																																							uc001caw.1		NA																	2	Substitution - Missense(2)		lung(2)	central_nervous_system(2)|ovary(1)	3						c.(1966-1968)AAT>AGT		colony stimulating factor 3 receptor isoform a	Filgrastim(DB00099)|Pegfilgrastim(DB00019)						95.0	104.0	101.0					1																	36932904		2203	4300	6503	SO:0001583	missense	1441				cell adhesion|defense response	extracellular region|integral to plasma membrane	cytokine receptor activity	g.chr1:36932904T>C	M59820	CCDS412.1, CCDS413.1, CCDS414.1	1p35-p34.3	2014-09-17			ENSG00000119535	ENSG00000119535		"""CD molecules"", ""Fibronectin type III domain containing"""	2439	protein-coding gene	gene with protein product		138971		CD114		1371413	Standard	NM_000760		Approved	GCSFR	uc001cax.2	Q99062	OTTHUMG00000008010	ENST00000373106.1:c.1967A>G	1.37:g.36932904T>C	ENSP00000362198:p.Asn656Ser					MRPS15_uc001cas.2_5'Flank|CSF3R_uc001cat.1_Missense_Mutation_p.N218S|CSF3R_uc009vvc.1_Missense_Mutation_p.N185S|CSF3R_uc001cau.1_Missense_Mutation_p.N56S|CSF3R_uc001cav.1_Missense_Mutation_p.N656S|CSF3R_uc001cax.1_Missense_Mutation_p.N656S|CSF3R_uc001cay.1_Missense_Mutation_p.I625V	p.N656S	NM_000760	NP_000751	Q99062	CSF3R_HUMAN			16	2145	-		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)	656			Cytoplasmic (Potential).			Missense_Mutation	SNP	ENST00000373106.1	37	c.1967A>G	CCDS413.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.55|13.55	2.271451|2.271451	0.40194|0.40194	.|.	.|.	ENSG00000119535|ENSG00000119535	ENST00000464465;ENST00000338937|ENST00000373106;ENST00000373104;ENST00000373103;ENST00000361632;ENST00000331941;ENST00000418048;ENST00000440588	T|T;T;T;T;T;T;T	0.25579|0.48836	1.79|0.91;0.8;0.83;0.91;0.8;0.91;0.83	5.41|5.41	4.26|4.26	0.50523|0.50523	.|.	.|0.482256	.|0.23448	.|N	.|0.048063	T|T	0.35158|0.35158	0.0922|0.0922	L|L	0.46157|0.46157	1.445|1.445	0.19575|0.19575	N|N	0.999961|0.999961	B|P;P;P;B	0.27229|0.39282	0.172|0.666;0.617;0.666;0.274	B|B;B;B;B	0.25140|0.33960	0.058|0.162;0.173;0.162;0.122	T|T	0.12863|0.12863	-1.0531|-1.0531	9|10	0.52906|0.18276	T|T	0.07|0.48	-2.0062|-2.0062	10.3083|10.3083	0.43693|0.43693	0.0:0.0:0.1726:0.8274|0.0:0.0:0.1726:0.8274	.|.	625|656;656;656;656	E1B6W6|Q1ZYL6;Q99062-3;Q99062;Q99062-4	.|.;.;CSF3R_HUMAN;.	V|S	208;625|656	ENSP00000345013:I625V|ENSP00000362198:N656S;ENSP00000362196:N656S;ENSP00000362195:N656S;ENSP00000355406:N656S;ENSP00000332180:N656S;ENSP00000401588:N656S;ENSP00000397568:N656S	ENSP00000345013:I625V|ENSP00000332180:N656S	I|N	-|-	1|2	0|0	CSF3R|CSF3R	36705491|36705491	1.000000|1.000000	0.71417|0.71417	0.985000|0.985000	0.45067|0.45067	0.814000|0.814000	0.46013|0.46013	1.548000|1.548000	0.36201|0.36201	0.888000|0.888000	0.36160|0.36160	0.533000|0.533000	0.62120|0.62120	ATC|AAT		0.592	CSF3R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021997.2	NM_156039		54	67	0	0	0	0.048971	0	54	67				
CFH	3075	broad.mit.edu	37	1	196706690	196706690	+	Silent	SNP	G	G	C			TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr1:196706690G>C	ENST00000367429.4	+	17	2922	c.2682G>C	c.(2680-2682)ggG>ggC	p.G894G		NM_000186.3	NP_000177.2	P08603	CFAH_HUMAN	complement factor H	894	Sushi 15. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)	p.G894G(1)		NS(3)|breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(24)|lung(33)|ovary(1)|prostate(5)|skin(9)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	101						ATGCACATGGGACTAAATTGA	0.383																																							uc001gtj.3		NA																	1	Substitution - coding silent(1)		lung(1)	skin(4)|ovary(1)|breast(1)	6						c.(2680-2682)GGG>GGC		complement factor H isoform a precursor							83.0	78.0	80.0					1																	196706690		2203	4300	6503	SO:0001819	synonymous_variant	3075				complement activation, alternative pathway	extracellular space		g.chr1:196706690G>C	Y00716	CCDS1385.1	1q32	2014-09-17	2004-08-09	2004-08-12	ENSG00000000971	ENSG00000000971		"""Complement system"""	4883	protein-coding gene	gene with protein product	"""beta-1H"", ""H factor 2 (complement)"", ""age-related maculopathy susceptibility 1"""	134370	"""H factor 1 (complement)"""	HF, HF1, HF2		2889480, 2963625	Standard	NM_000186		Approved	HUS, FHL1, ARMS1, ARMD4	uc001gtj.4	P08603	OTTHUMG00000035607	ENST00000367429.4:c.2682G>C	1.37:g.196706690G>C							p.G894G	NM_000186	NP_000177	P08603	CFAH_HUMAN			17	2922	+			894			Sushi 15.		A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Silent	SNP	ENST00000367429.4	37	c.2682G>C	CCDS1385.1																																																																																				0.383	CFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086412.2	NM_000186		14	18	0	0	0	0.105934	0	14	18				
TRIM58	25893	broad.mit.edu	37	1	248039632	248039632	+	Nonsense_Mutation	SNP	C	C	G			TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr1:248039632C>G	ENST00000366481.3	+	6	1350	c.1302C>G	c.(1300-1302)taC>taG	p.Y434*	OR2W3_ENST00000537741.1_Intron	NM_015431.3	NP_056246.3	Q8NG06	TRI58_HUMAN	tripartite motif containing 58	434	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.Y434*(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(39)|ovary(4)|pancreas(1)|skin(7)|stomach(1)	63	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0286)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			CTTATATCTACACATTCAACC	0.433																																							uc001ido.2		NA																	1	Substitution - Nonsense(1)		lung(1)	skin(3)|ovary(1)|pancreas(1)|lung(1)|central_nervous_system(1)	7						c.(1300-1302)TAC>TAG		tripartite motif-containing 58							193.0	192.0	193.0					1																	248039632		2203	4300	6503	SO:0001587	stop_gained	25893					intracellular	zinc ion binding	g.chr1:248039632C>G	AF327057	CCDS1636.1	1q44	2013-01-09	2011-01-25		ENSG00000162722	ENSG00000162722		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	24150	protein-coding gene	gene with protein product			"""tripartite motif-containing 58"""				Standard	NM_015431		Approved	BIA2	uc001ido.3	Q8NG06	OTTHUMG00000040203	ENST00000366481.3:c.1302C>G	1.37:g.248039632C>G	ENSP00000355437:p.Tyr434*					OR2W3_uc001idp.1_Intron	p.Y434*	NM_015431	NP_056246	Q8NG06	TRI58_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.0319)		6	1350	+	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0286)	434			B30.2/SPRY.		Q6B0H9	Nonsense_Mutation	SNP	ENST00000366481.3	37	c.1302C>G	CCDS1636.1	.	.	.	.	.	.	.	.	.	.	C	18.42	3.620198	0.66787	.	.	ENSG00000162722	ENST00000366481	.	.	.	4.05	3.14	0.36123	.	0.000000	0.51477	D	0.000087	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.1353	0.42704	0.0:0.9011:0.0:0.0989	.	.	.	.	X	434	.	ENSP00000355437:Y434X	Y	+	3	2	TRIM58	246106255	1.000000	0.71417	0.966000	0.40874	0.160000	0.22226	2.092000	0.41700	1.313000	0.45069	0.650000	0.86243	TAC		0.433	TRIM58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096860.1	NM_015431		87	122	0	0	0	0.048971	0	87	122				
ANKRD30A	91074	broad.mit.edu	37	10	37430990	37430990	+	Nonsense_Mutation	SNP	G	G	T	rs552183541	byFrequency	TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr10:37430990G>T	ENST00000602533.1	+	7	1096	c.997G>T	c.(997-999)Gaa>Taa	p.E333*	ANKRD30A_ENST00000361713.1_Nonsense_Mutation_p.E333*|ANKRD30A_ENST00000374660.1_Nonsense_Mutation_p.E333*			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	389					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E333*(1)		NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						GGAGAAAAAAGAAGACACACC	0.428																																							uc001iza.1		NA																	1	Substitution - Nonsense(1)		lung(1)	ovary(7)|breast(1)|skin(1)	9						c.(997-999)GAA>TAA		ankyrin repeat domain 30A							113.0	112.0	112.0					10																	37430990		1838	4086	5924	SO:0001587	stop_gained	91074					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity	g.chr10:37430990G>T	AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"""Ankyrin repeat domain containing"""	17234	protein-coding gene	gene with protein product	"""breast cancer antigen NY-BR-1"""	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.997G>T	10.37:g.37430990G>T	ENSP00000473551:p.Glu333*						p.E333*	NM_052997	NP_443723	Q9BXX3	AN30A_HUMAN			7	1096	+			389					Q5W025	Nonsense_Mutation	SNP	ENST00000602533.1	37	c.997G>T		.	.	.	.	.	.	.	.	.	.	.	21.6	4.173189	0.78452	.	.	ENSG00000148513	ENST00000361713;ENST00000374660	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06494	T	0.89	.	.	.	.	.	.	.	.	X	333	.	ENSP00000354432:E333X	E	+	1	0	ANKRD30A	37470996	0.898000	0.30612	0.376000	0.26042	0.377000	0.30045	0.819000	0.27308	0.088000	0.17205	0.089000	0.15464	GAA		0.428	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997		14	33	1	0	1.52009e-12	0.024245	1.83678e-12	14	33				
GRID1	2894	broad.mit.edu	37	10	87487669	87487669	+	Silent	SNP	G	G	A	rs149876378		TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr10:87487669G>A	ENST00000327946.7	-	10	1561	c.1476C>T	c.(1474-1476)taC>taT	p.Y492Y	GRID1_ENST00000536331.1_Silent_p.Y63Y	NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	492					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|social behavior (GO:0035176)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|ionotropic glutamate receptor complex (GO:0008328)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)	p.Y492Y(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(46)|ovary(5)|prostate(4)|skin(5)|stomach(4)|upper_aerodigestive_tract(5)	106						GCTGGTGACCGTACCTGCCAT	0.557										Multiple Myeloma(13;0.14)																													uc001kdl.1		NA																	1	Substitution - coding silent(1)		lung(1)	ovary(5)|upper_aerodigestive_tract(2)|large_intestine(2)|central_nervous_system(1)	10						c.(1474-1476)TAC>TAT		glutamate receptor, ionotropic, delta 1	L-Glutamic Acid(DB00142)						140.0	131.0	134.0					10																	87487669		2203	4300	6503	SO:0001819	synonymous_variant	2894					cell junction|integral to membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity	g.chr10:87487669G>A	AB033046	CCDS31236.1	10q22	2012-08-29			ENSG00000182771	ENSG00000182771		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4575	protein-coding gene	gene with protein product		610659					Standard	NM_017551		Approved	GluD1, KIAA1220	uc001kdl.1	Q9ULK0	OTTHUMG00000018650	ENST00000327946.7:c.1476C>T	10.37:g.87487669G>A		Multiple Myeloma(13;0.14)				GRID1_uc009xsu.1_RNA|GRID1_uc010qmf.1_Silent_p.Y63Y	p.Y492Y	NM_017551	NP_060021	Q9ULK0	GRID1_HUMAN			10	1577	-			492			Extracellular (Potential).		B3KXD5|B7Z7L0|Q8IXT3	Silent	SNP	ENST00000327946.7	37	c.1476C>T	CCDS31236.1																																																																																				0.557	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049148.3	XM_043613		23	53	0	0	0	0.099896	0	23	53				
GRID1	2894	broad.mit.edu	37	10	87487760	87487760	+	Missense_Mutation	SNP	C	C	T	rs149107262		TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr10:87487760C>T	ENST00000327946.7	-	10	1470	c.1385G>A	c.(1384-1386)cGc>cAc	p.R462H	GRID1_ENST00000536331.1_Missense_Mutation_p.R33H	NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	462					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|social behavior (GO:0035176)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|ionotropic glutamate receptor complex (GO:0008328)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)	p.R462H(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(46)|ovary(5)|prostate(4)|skin(5)|stomach(4)|upper_aerodigestive_tract(5)	106						CCCTTTGTAGCGCTTGGGCTG	0.488										Multiple Myeloma(13;0.14)																													uc001kdl.1		NA																	1	Substitution - Missense(1)		lung(1)	ovary(5)|upper_aerodigestive_tract(2)|large_intestine(2)|central_nervous_system(1)	10						c.(1384-1386)CGC>CAC		glutamate receptor, ionotropic, delta 1	L-Glutamic Acid(DB00142)	C	HIS/ARG	0,4406		0,0,2203	176.0	169.0	172.0		1385	5.6	1.0	10	dbSNP_134	172	1,8599	1.2+/-3.3	0,1,4299	yes	missense	GRID1	NM_017551.2	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	462/1010	87487760	1,13005	2203	4300	6503	SO:0001583	missense	2894					cell junction|integral to membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity	g.chr10:87487760C>T	AB033046	CCDS31236.1	10q22	2012-08-29			ENSG00000182771	ENSG00000182771		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4575	protein-coding gene	gene with protein product		610659					Standard	NM_017551		Approved	GluD1, KIAA1220	uc001kdl.1	Q9ULK0	OTTHUMG00000018650	ENST00000327946.7:c.1385G>A	10.37:g.87487760C>T	ENSP00000330148:p.Arg462His	Multiple Myeloma(13;0.14)				GRID1_uc009xsu.1_RNA|GRID1_uc010qmf.1_Missense_Mutation_p.R33H	p.R462H	NM_017551	NP_060021	Q9ULK0	GRID1_HUMAN			10	1486	-			462			Extracellular (Potential).		B3KXD5|B7Z7L0|Q8IXT3	Missense_Mutation	SNP	ENST00000327946.7	37	c.1385G>A	CCDS31236.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.800071	0.90538	0.0	1.16E-4	ENSG00000182771	ENST00000327946;ENST00000536331	T;T	0.27890	1.64;1.64	5.62	5.62	0.85841	Extracellular solute-binding protein, family 3 (1);Glutamate receptor, L-glutamate/glycine-binding (1);Ionotropic glutamate receptor (1);	0.048861	0.85682	D	0.000000	T	0.38825	0.1055	M	0.70275	2.135	0.80722	D	1	P	0.42649	0.786	B	0.39465	0.3	T	0.42327	-0.9458	10	0.87932	D	0	.	18.6186	0.91313	0.0:1.0:0.0:0.0	.	462	Q9ULK0	GRID1_HUMAN	H	462;33	ENSP00000330148:R462H;ENSP00000444455:R33H	ENSP00000330148:R462H	R	-	2	0	GRID1	87477740	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.927000	0.63440	2.646000	0.89796	0.650000	0.86243	CGC		0.488	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049148.3	XM_043613		11	100	0	0	0	0.080935	0	11	100				
NAT10	55226	broad.mit.edu	37	11	34153690	34153690	+	Silent	SNP	T	T	C			TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	T	T	-	-	T	T	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr11:34153690T>C	ENST00000257829.3	+	15	1745	c.1539T>C	c.(1537-1539)gaT>gaC	p.D513D	NAT10_ENST00000531159.2_Silent_p.D441D|NAT10_ENST00000527971.1_Intron	NM_024662.2	NP_078938	Q9H0A0	NAT10_HUMAN	N-acetyltransferase 10 (GCN5-related)	513						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|N-acetyltransferase activity (GO:0008080)|poly(A) RNA binding (GO:0044822)	p.D513D(1)		endometrium(4)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	23		Acute lymphoblastic leukemia(5;0.0119)|all_hematologic(20;0.0231)				TTAATAGAGATACCCTCTTTT	0.458																																							uc001mvk.2		NA																	1	Substitution - coding silent(1)		lung(1)	ovary(1)|skin(1)	2						c.(1537-1539)GAT>GAC		N-acetyltransferase 10 isoform a							242.0	244.0	243.0					11																	34153690		2202	4298	6500	SO:0001819	synonymous_variant	55226					nucleolus	ATP binding|N-acetyltransferase activity|protein binding	g.chr11:34153690T>C	AF489535	CCDS7889.1, CCDS44568.1	11p13	2011-11-16	2008-09-24		ENSG00000135372	ENSG00000135372	2.3.1.-		29830	protein-coding gene	gene with protein product		609221	"""N-acetyltransferase 10"""			14592445, 21177859	Standard	NM_024662		Approved	hALP, FLJ10774, FLJ12179, NET43, KIAA1709	uc001mvk.3	Q9H0A0	OTTHUMG00000166249	ENST00000257829.3:c.1539T>C	11.37:g.34153690T>C						NAT10_uc010ren.1_Silent_p.D441D	p.D513D	NM_024662	NP_078938	Q9H0A0	NAT10_HUMAN			15	1783	+		Acute lymphoblastic leukemia(5;0.0119)|all_hematologic(20;0.0231)	513					B4DFD5|E7ESU4|E9PMN9|Q86WK5|Q9C0F4|Q9HA61|Q9NVF2	Silent	SNP	ENST00000257829.3	37	c.1539T>C	CCDS7889.1																																																																																				0.458	NAT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388693.1	NM_024662		52	298	0	0	0	0.048971	0	52	298				
EHF	26298	broad.mit.edu	37	11	34668230	34668230	+	Missense_Mutation	SNP	C	C	G			TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr11:34668230C>G	ENST00000527935.1	+	2	346	c.342C>G	c.(340-342)aaC>aaG	p.N114K	EHF_ENST00000257831.3_Splice_Site_p.N114K|EHF_ENST00000450654.2_Splice_Site_p.N114K|EHF_ENST00000533754.1_Splice_Site_p.N114K|EHF_ENST00000531794.1_Splice_Site_p.N136K|EHF_ENST00000530286.1_Splice_Site_p.N114K|EHF_ENST00000531728.1_Missense_Mutation_p.N114K					ets homologous factor									p.N114K(1)	NFIA/EHF(2)	autonomic_ganglia(1)|cervix(1)|endometrium(3)|kidney(3)|lung(8)|upper_aerodigestive_tract(1)	17		all_hematologic(20;0.117)	Epithelial(1;0.055)|all cancers(1;0.137)|STAD - Stomach adenocarcinoma(6;0.235)			TGAAGTGGAACGGTGACTCTC	0.557																																							uc001mvr.1		NA																	1	Substitution - Missense(1)		lung(1)		0						c.(340-342)AAC>AAG		ets homologous factor							101.0	101.0	101.0					11																	34668230		2202	4298	6500	SO:0001583	missense	26298				cell proliferation|epithelial cell differentiation|multicellular organismal development|positive regulation of transcription, DNA-dependent		protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chr11:34668230C>G	AF170583	CCDS7894.1, CCDS55752.1, CCDS55753.1	11p12	2008-07-18				ENSG00000135373			3246	protein-coding gene	gene with protein product	"""epithelium-specific ets factor 3"", ""ESE3 transcription factor"""	605439				10527851	Standard	NM_012153		Approved	ESE3, ESEJ	uc021qfu.1	Q9NZC4		ENST00000527935.1:c.342C>G	11.37:g.34668230C>G	ENSP00000436158:p.Asn114Lys					EHF_uc009yke.1_Missense_Mutation_p.N114K|EHF_uc009ykf.1_Missense_Mutation_p.N117K	p.N114K	NM_012153	NP_036285	Q9NZC4	EHF_HUMAN	Epithelial(1;0.055)|all cancers(1;0.137)|STAD - Stomach adenocarcinoma(6;0.235)		3	453	+		all_hematologic(20;0.117)	114			PNT.			Missense_Mutation	SNP	ENST00000527935.1	37	c.342C>G		.	.	.	.	.	.	.	.	.	.	C	18.25	3.582549	0.65992	.	.	ENSG00000135373	ENST00000257831;ENST00000450654;ENST00000530286;ENST00000533754;ENST00000529527;ENST00000531728;ENST00000525253;ENST00000531794;ENST00000532302;ENST00000527935	T;T;T;T;T;T;T;T;T;T	0.28454	1.61;1.61;1.61;1.61;1.61;1.61;1.61;1.61;1.61;1.61	5.24	-7.61	0.01299	Sterile alpha motif/pointed domain (2);Pointed domain (3);	0.316163	0.41500	N	0.000869	T	0.38026	0.1025	L	0.36672	1.1	0.47511	D	0.999441	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.91635	0.999;0.992;0.999	T	0.55186	-0.8180	9	.	.	.	.	18.0084	0.89216	0.0:0.2624:0.0:0.7376	.	136;114;114	E9PSB2;Q9NZC4-2;Q9NZC4	.;.;EHF_HUMAN	K	114;114;114;114;114;114;114;136;114;114	ENSP00000257831:N114K;ENSP00000399733:N114K;ENSP00000433508:N114K;ENSP00000435837:N114K;ENSP00000432905:N114K;ENSP00000436357:N114K;ENSP00000434395:N114K;ENSP00000435835:N136K;ENSP00000432460:N114K;ENSP00000436158:N114K	.	N	+	3	2	EHF	34624806	0.001000	0.12720	0.732000	0.30844	0.938000	0.57974	-1.366000	0.02585	-1.550000	0.01708	-0.263000	0.10527	AAC		0.557	EHF-012	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000389862.1	NM_012153		26	107	0	0	0	0.037714	0	26	107				
ALX4	60529	broad.mit.edu	37	11	44297153	44297153	+	Silent	SNP	C	C	A			TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr11:44297153C>A	ENST00000329255.3	-	2	625	c.522G>T	c.(520-522)ggG>ggT	p.G174G		NM_021926.3	NP_068745.2	Q9H161	ALX4_HUMAN	ALX homeobox 4	174					anterior/posterior pattern specification (GO:0009952)|digestive tract development (GO:0048565)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal system morphogenesis (GO:0048704)|hair follicle development (GO:0001942)|muscle organ development (GO:0007517)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of apoptotic process (GO:0042981)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G174G(1)		central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	16						TGCTGTCCATCCCCACAGTGT	0.587																																							uc001myb.2		NA																	1	Substitution - coding silent(1)		lung(1)		0						c.(520-522)GGG>GGT		aristaless-like homeobox 4							53.0	58.0	56.0					11																	44297153		2203	4299	6502	SO:0001819	synonymous_variant	60529				hair follicle development			g.chr11:44297153C>A	AF294629	CCDS31468.1	11p11.2	2011-06-20	2008-11-04		ENSG00000052850	ENSG00000052850		"""Homeoboxes / PRD class"""	450	protein-coding gene	gene with protein product		605420	"""parietal foramina 2"", ""aristaless-like homeobox 4"""	PFM2		11017806, 8644736	Standard	NM_021926		Approved	FPP, PFM, KIAA1788	uc001myb.3	Q9H161	OTTHUMG00000166557	ENST00000329255.3:c.522G>T	11.37:g.44297153C>A							p.G174G	NM_021926	NP_068745	Q9H161	ALX4_HUMAN			2	626	-			174					Q96JN7|Q9H198|Q9HAY9	Silent	SNP	ENST00000329255.3	37	c.522G>T	CCDS31468.1																																																																																				0.587	ALX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390399.1			34	52	1	0	1.22384e-17	0.054565	1.51027e-17	34	52				
TMX2	51075	broad.mit.edu	37	11	57480103	57480103	+	Missense_Mutation	SNP	G	G	C	rs375872090		TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr11:57480103G>C	ENST00000278422.4	+	1	25	c.13G>C	c.(13-15)Gca>Cca	p.A5P	MED19_ENST00000337672.2_5'Flank|MED19_ENST00000431606.2_5'Flank|TMX2-CTNND1_ENST00000528395.1_Missense_Mutation_p.A5P|TMX2_ENST00000378312.4_Missense_Mutation_p.A5P	NM_015959.3	NP_057043.1	Q9Y320	TMX2_HUMAN	thioredoxin-related transmembrane protein 2	5					cell redox homeostasis (GO:0045454)	integral component of membrane (GO:0016021)		p.A5P(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|urinary_tract(2)	12						GGCGGTCTTGGCACCTCTAAT	0.597																																							uc001nlc.1		NA																	1	Substitution - Missense(1)		lung(1)		0						c.(13-15)GCA>CCA		thioredoxin domain containing 14 isoform 1							67.0	54.0	58.0					11																	57480103		2201	4296	6497	SO:0001583	missense	51075				cell redox homeostasis	integral to membrane		g.chr11:57480103G>C	AF132965	CCDS7967.1, CCDS44601.1	11q12.1	2012-09-20	2009-02-23	2009-02-23	ENSG00000213593	ENSG00000213593		"""Protein disulfide isomerases"""	30739	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 12"""		"""thioredoxin domain containing 14"""	TXNDC14		12670024	Standard	NM_015959		Approved	PDIA12	uc001nlc.2	Q9Y320	OTTHUMG00000167200	ENST00000278422.4:c.13G>C	11.37:g.57480103G>C	ENSP00000278422:p.Ala5Pro					CTNND1_uc001nlf.1_5'UTR|MED19_uc001nla.1_5'Flank|MED19_uc001nlb.2_5'Flank|TMX2_uc001nld.1_5'UTR|TMX2_uc001nle.1_Missense_Mutation_p.A5P	p.A5P	NM_015959	NP_057043	Q9Y320	TMX2_HUMAN			1	62	+			5					B7Z4R4|Q53G73|Q561W0|Q5J7Q7|Q8NBP9|Q9H3L1	Missense_Mutation	SNP	ENST00000278422.4	37	c.13G>C	CCDS7967.1	.	.	.	.	.	.	.	.	.	.	G	19.75	3.885528	0.72410	.	.	ENSG00000213593	ENST00000378312;ENST00000278422	T	0.49432	0.78	5.98	5.98	0.97165	.	0.066052	0.64402	U	0.000010	T	0.42698	0.1214	N	0.22421	0.69	0.44719	D	0.997719	P;P	0.51351	0.867;0.944	B;B	0.44044	0.439;0.439	T	0.39099	-0.9630	10	0.59425	D	0.04	-6.166	20.0512	0.97629	0.0:0.0:1.0:0.0	.	5;5	Q9Y320-2;Q9Y320	.;TMX2_HUMAN	P	5	ENSP00000367562:A5P	ENSP00000436274:A5P	A	+	1	0	TMX2	57236679	1.000000	0.71417	0.292000	0.24919	0.290000	0.27261	5.385000	0.66231	2.847000	0.97988	0.591000	0.81541	GCA		0.597	TMX2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393708.1	NM_015959		5	15	0	0	0	0.021553	0	5	15				
CD163L1	283316	broad.mit.edu	37	12	7526177	7526177	+	Missense_Mutation	SNP	C	C	G			TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr12:7526177C>G	ENST00000313599.3	-	14	3526	c.3469G>C	c.(3469-3471)Gaa>Caa	p.E1157Q	CD163L1_ENST00000544331.1_5'Flank|CD163L1_ENST00000396630.1_Missense_Mutation_p.E1157Q|CD163L1_ENST00000416109.2_Missense_Mutation_p.E1167Q			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	1157	SRCR 11. {ECO:0000255|PROSITE- ProRule:PRU00196}.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)	p.E1157Q(1)		breast(5)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(18)|lung(37)|ovary(8)|prostate(3)|skin(6)|stomach(1)|urinary_tract(4)	96						TAGAAGACTTCCAATCTCCCA	0.488																																							uc001qsy.2		NA																	1	Substitution - Missense(1)		lung(1)	ovary(8)|skin(2)|central_nervous_system(1)	11						c.(3469-3471)GAA>CAA		scavenger receptor cysteine-rich type 1							141.0	149.0	146.0					12																	7526177		2203	4300	6503	SO:0001583	missense	283316					extracellular region|integral to membrane|plasma membrane	scavenger receptor activity	g.chr12:7526177C>G	AF264014	CCDS8577.1, CCDS73434.1	12p13.31	2006-03-28	2006-03-28			ENSG00000177675			30375	protein-coding gene	gene with protein product		606079	"""CD163 antigen-like 1"""			11124526, 11086079	Standard	XM_005253348		Approved	M160, CD163B	uc001qsy.3	Q9NR16		ENST00000313599.3:c.3469G>C	12.37:g.7526177C>G	ENSP00000315945:p.Glu1157Gln					CD163L1_uc010sge.1_Missense_Mutation_p.E1167Q	p.E1157Q	NM_174941	NP_777601	Q9NR16	C163B_HUMAN			14	3495	-			1157			SRCR 11.|Extracellular (Potential).		B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Missense_Mutation	SNP	ENST00000313599.3	37	c.3469G>C	CCDS8577.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.370957	0.82573	.	.	ENSG00000177675	ENST00000313599;ENST00000416109;ENST00000396630	T;T;T	0.44482	0.92;0.92;0.92	2.28	2.28	0.28536	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.000000	0.33199	U	0.005164	T	0.67344	0.2883	M	0.91140	3.18	0.30642	N	0.756353	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.69453	-0.5141	10	0.59425	D	0.04	.	10.6303	0.45532	0.0:1.0:0.0:0.0	.	1167;1157	E7EVK4;Q9NR16	.;C163B_HUMAN	Q	1157;1167;1157	ENSP00000315945:E1157Q;ENSP00000393474:E1167Q;ENSP00000379871:E1157Q	ENSP00000315945:E1157Q	E	-	1	0	CD163L1	7417444	1.000000	0.71417	0.029000	0.17559	0.816000	0.46133	5.173000	0.65010	1.583000	0.49898	0.557000	0.71058	GAA		0.488	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941		20	135	0	0	0	0.0918	0	20	135				
KRT7	3855	broad.mit.edu	37	12	52639248	52639248	+	Missense_Mutation	SNP	C	C	T	rs374918745		TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr12:52639248C>T	ENST00000331817.5	+	7	1220	c.1037C>T	c.(1036-1038)gCg>gTg	p.A346V	RP3-416H24.1_ENST00000546686.1_RNA|KRT7_ENST00000552322.1_3'UTR	NM_005556.3	NP_005547.3	P08729	K2C7_HUMAN	keratin 7	346	Coil 2.|Rod.				viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)	p.A346V(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(2)|stomach(1)|urinary_tract(1)	14				BRCA - Breast invasive adenocarcinoma(357;0.105)	Primaquine(DB01087)	GGGGAGCTGGCGCTCAAGGAT	0.647																																							uc001saa.1		NA																	1	Substitution - Missense(1)		lung(1)		0						c.(1036-1038)GCG>GTG		keratin 7		C	VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	35.0	36.0	36.0		1037	4.4	0.9	12		36	0,8600		0,0,4300	no	missense	KRT7	NM_005556.3	64	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	346/470	52639248	1,13005	2203	4300	6503	SO:0001583	missense	3855				cytoskeleton organization|DNA replication|interphase|interspecies interaction between organisms|regulation of translation	Golgi apparatus|keratin filament|nucleus	protein binding|structural molecule activity	g.chr12:52639248C>T		CCDS8822.1	12q13.13	2013-01-16			ENSG00000135480	ENSG00000135480		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6445	protein-coding gene	gene with protein product	"""keratin, type II cytoskeletal 7"", ""cytokeratin 7"", ""sarcolectin"", ""keratin, 55K type II cytoskeletal"""	148059				1713141, 16831889	Standard	XR_245927		Approved	K7, CK7, K2C7, SCL	uc001saa.1	P08729	OTTHUMG00000169580	ENST00000331817.5:c.1037C>T	12.37:g.52639248C>T	ENSP00000329243:p.Ala346Val					KRT7_uc009zmf.1_Intron	p.A346V	NM_005556	NP_005547	P08729	K2C7_HUMAN		BRCA - Breast invasive adenocarcinoma(357;0.105)	7	1164	+			346			Rod.|Coil 2.		Q92676|Q9BUD8|Q9Y3R7	Missense_Mutation	SNP	ENST00000331817.5	37	c.1037C>T	CCDS8822.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.640153	0.87760	2.27E-4	0.0	ENSG00000135480	ENST00000331817;ENST00000422319	D	0.88975	-2.45	4.4	4.4	0.53042	Filament (1);	0.000000	0.37577	N	0.002021	D	0.95017	0.8387	M	0.89785	3.06	0.80722	D	1	D	0.89917	1.0	D	0.63793	0.918	D	0.96089	0.9060	10	0.87932	D	0	.	17.5702	0.87933	0.0:1.0:0.0:0.0	.	346	P08729	K2C7_HUMAN	V	346;322	ENSP00000329243:A346V	ENSP00000329243:A346V	A	+	2	0	KRT7	50925515	1.000000	0.71417	0.947000	0.38551	0.925000	0.55904	4.563000	0.60823	2.455000	0.83008	0.561000	0.74099	GCG		0.647	KRT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404897.1	NM_005556		6	23	0	0	0	0.02938	0	6	23				
PARPBP	55010	broad.mit.edu	37	12	102569349	102569349	+	Missense_Mutation	SNP	G	G	A			TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr12:102569349G>A	ENST00000358383.5	+	7	955	c.910G>A	c.(910-912)Gaa>Aaa	p.E304K	PARPBP_ENST00000543784.1_Intron|PARPBP_ENST00000327680.2_Missense_Mutation_p.E223K|PARPBP_ENST00000541394.1_Missense_Mutation_p.E381K|PARPBP_ENST00000392911.2_Missense_Mutation_p.E223K|PARPBP_ENST00000378128.3_Intron|PARPBP_ENST00000535811.1_Intron			Q9NWS1	PARI_HUMAN	PARP1 binding protein	304					DNA repair (GO:0006281)|negative regulation of double-strand break repair via homologous recombination (GO:2000042)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E304K(1)|p.E223K(1)		endometrium(1)|lung(8)|urinary_tract(2)	11						AGCAATAGAGGAAGTTGCTCA	0.398																																							uc001tjf.2		NA																	2	Substitution - Missense(2)		lung(2)		0						c.(910-912)GAA>AAA		hypothetical protein LOC55010							101.0	104.0	103.0					12																	102569349		2203	4300	6503	SO:0001583	missense	55010				response to DNA damage stimulus	cytoplasm|nucleus	DNA binding	g.chr12:102569349G>A	AK000648	CCDS9090.1, CCDS9090.2	12q23.2	2013-03-14	2012-01-24	2012-01-24		ENSG00000185480			26074	protein-coding gene	gene with protein product	"""PARP-1 binding protein"""	613687	"""chromosome 12 open reading frame 48"""	C12orf48		20931645	Standard	NM_017915		Approved	FLJ20641, PARI	uc001tjf.3	Q9NWS1		ENST00000358383.5:c.910G>A	12.37:g.102569349G>A	ENSP00000351153:p.Glu304Lys					C12orf48_uc001tjg.2_Missense_Mutation_p.E223K|C12orf48_uc010swa.1_Missense_Mutation_p.E381K|C12orf48_uc001tjh.2_Missense_Mutation_p.E223K|C12orf48_uc010swb.1_Intron|C12orf48_uc009zuc.2_Intron|C12orf48_uc001tjj.2_Missense_Mutation_p.E19K|C12orf48_uc001tjk.2_Intron|C12orf48_uc009zud.2_Intron	p.E304K	NM_017915	NP_060385	Q9NWS1	PR1BP_HUMAN			7	1022	+			304					B4E0Y0|Q05C00|Q499L8|Q4FZA0|Q4KMW7|Q6NSC6|Q6PJA1|Q86W36	Missense_Mutation	SNP	ENST00000358383.5	37	c.910G>A	CCDS9090.2	.	.	.	.	.	.	.	.	.	.	G	18.17	3.564194	0.65651	.	.	ENSG00000185480	ENST00000327680;ENST00000541394;ENST00000358383;ENST00000392911	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	6.03	4.19	0.49359	.	0.226336	0.52532	N	0.000074	T	0.29945	0.0749	L	0.27053	0.805	0.40313	D	0.978734	B;B	0.19583	0.037;0.011	B;B	0.22386	0.039;0.027	T	0.08146	-1.0736	10	0.46703	T	0.11	-18.2779	9.7702	0.40585	0.1287:0.1169:0.7544:0.0	.	381;304	B4DZ31;Q9NWS1	.;PR1BP_HUMAN	K	223;381;304;223	ENSP00000332915:E223K;ENSP00000440850:E381K;ENSP00000351153:E304K;ENSP00000376643:E223K	ENSP00000332915:E223K	E	+	1	0	C12orf48	101093479	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	3.774000	0.55341	0.856000	0.35383	0.655000	0.94253	GAA		0.398	PARPBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397030.2	NM_017915		23	37	0	0	0	0.083992	0	23	37				
NCOR2	9612	broad.mit.edu	37	12	124840077	124840077	+	Silent	SNP	G	G	A	rs564573781	byFrequency	TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr12:124840077G>A	ENST00000405201.1	-	24	3282	c.3282C>T	c.(3280-3282)ccC>ccT	p.P1094P	NCOR2_ENST00000397355.1_Silent_p.P1085P|NCOR2_ENST00000404621.1_Silent_p.P1084P|NCOR2_ENST00000429285.2_Silent_p.P1084P|NCOR2_ENST00000356219.3_Silent_p.P1101P|NCOR2_ENST00000404121.2_Silent_p.P655P			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	1102					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)	p.P1094P(1)|p.P1101P(1)		breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		GCGGCAGGACGGGCCGGGCAG	0.667													G|||	2	0.000399361	0.0	0.0	5008	,	,		15397	0.0		0.0	False		,,,				2504	0.002						uc010tba.1		NA																	2	Substitution - coding silent(2)		lung(2)	skin(3)|ovary(1)	4						c.(3304-3306)CCC>CCT		nuclear receptor co-repressor 2 isoform 2							46.0	68.0	60.0					12																	124840077		2129	4208	6337	SO:0001819	synonymous_variant	9612				cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity	g.chr12:124840077G>A	U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"""nuclear receptor co-repressor 2"""			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.3282C>T	12.37:g.124840077G>A						NCOR2_uc010tay.1_Silent_p.P1101P|NCOR2_uc010taz.1_Silent_p.P1085P|NCOR2_uc010tbb.1_Silent_p.P1094P|NCOR2_uc010tbc.1_Silent_p.P1084P|NCOR2_uc001ugj.1_Silent_p.P1102P	p.P1102P	NM_001077261	NP_001070729	Q9Y618	NCOR2_HUMAN		Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)	24	3423	-	all_neural(191;0.0804)|Medulloblastoma(191;0.163)		1102					O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Silent	SNP	ENST00000405201.1	37	c.3306C>T	CCDS41858.2																																																																																				0.667	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312		12	19	0	0	0	0.080935	0	12	19				
SYNE3	161176	broad.mit.edu	37	14	95932465	95932465	+	Silent	SNP	G	G	A			TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr14:95932465G>A	ENST00000334258.5	-	3	444	c.430C>T	c.(430-432)Ctg>Ttg	p.L144L	SYNE3_ENST00000557275.1_Silent_p.L144L|SYNE3_ENST00000553340.1_Silent_p.L144L	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	144					cytoskeletal anchoring at nuclear membrane (GO:0090286)|cytoskeleton organization (GO:0007010)|establishment of protein localization to membrane (GO:0090150)|regulation of cell shape (GO:0008360)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear outer membrane (GO:0005640)|SUN-KASH complex (GO:0034993)	actin filament binding (GO:0051015)	p.L144L(3)		breast(1)|endometrium(2)|lung(25)	28						TTCAGGCCCAGCTGGAGCTCG	0.637																																							uc001yei.3		NA																	3	Substitution - coding silent(3)		lung(3)	central_nervous_system(1)	1						c.(430-432)CTG>TTG		nesprin-3							61.0	61.0	61.0					14																	95932465		2203	4300	6503	SO:0001819	synonymous_variant	161176				cytoskeletal anchoring at nuclear membrane	integral to membrane|nuclear outer membrane|SUN-KASH complex	actin binding	g.chr14:95932465G>A	AK098471	CCDS9935.1	14q32.13	2012-05-31	2012-05-31	2012-05-31	ENSG00000176438	ENSG00000176438			19861	protein-coding gene	gene with protein product		610861	"""chromosome 14 open reading frame 49"""	C14orf49			Standard	NM_152592		Approved	FLJ25605, NET53, Nesprin-3, Nesp3	uc001yei.4	Q6ZMZ3	OTTHUMG00000171632	ENST00000334258.5:c.430C>T	14.37:g.95932465G>A						C14orf49_uc010avi.2_Silent_p.L144L|C14orf49_uc001yej.1_Silent_p.L144L	p.L144L	NM_152592	NP_689805	Q6ZMZ3	SYNE3_HUMAN		COAD - Colon adenocarcinoma(157;0.245)	3	445	-		all_cancers(154;0.0937)	144			Cytoplasmic (Potential).		A6H8H3|Q86SX5|Q8N7G8	Silent	SNP	ENST00000334258.5	37	c.430C>T	CCDS9935.1																																																																																				0.637	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592		32	41	0	0	0	0.045705	0	32	41				
PHKB	5257	broad.mit.edu	37	16	47549445	47549445	+	Missense_Mutation	SNP	C	C	T			TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr16:47549445C>T	ENST00000323584.5	+	6	551	c.527C>T	c.(526-528)tCa>tTa	p.S176L	PHKB_ENST00000299167.8_Missense_Mutation_p.S176L|PHKB_ENST00000566044.1_Missense_Mutation_p.S169L|PHKB_ENST00000567402.1_3'UTR|PHKB_ENST00000455779.1_Missense_Mutation_p.S169L	NM_000293.2	NP_000284.1	Q93100	KPBB_HUMAN	phosphorylase kinase, beta	176					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)	p.S176L(2)|p.S169L(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|liver(1)|lung(18)|ovary(1)|skin(1)	41		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)				AATGCAGTGTCACTTTATCTC	0.313																																							uc002eev.3		NA																	3	Substitution - Missense(3)		lung(3)	ovary(1)|large_intestine(1)|breast(1)	3						c.(526-528)TCA>TTA		phosphorylase kinase, beta isoform a							141.0	131.0	134.0					16																	47549445		2201	4299	6500	SO:0001583	missense	5257				glucose metabolic process|glycogen catabolic process	cytosol|plasma membrane	calmodulin binding|glucan 1,4-alpha-glucosidase activity	g.chr16:47549445C>T		CCDS10729.1, CCDS42161.1	16q12-q13	2009-07-10			ENSG00000102893	ENSG00000102893	2.7.11.19		8927	protein-coding gene	gene with protein product		172490					Standard	NM_000293		Approved		uc002eev.4	Q93100	OTTHUMG00000133102	ENST00000323584.5:c.527C>T	16.37:g.47549445C>T	ENSP00000313504:p.Ser176Leu					PHKB_uc010vgi.1_Missense_Mutation_p.S169L|PHKB_uc002eeu.3_Missense_Mutation_p.S169L	p.S176L	NM_000293	NP_000284	Q93100	KPBB_HUMAN			6	579	+		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)	176					Q8N4T5	Missense_Mutation	SNP	ENST00000323584.5	37	c.527C>T	CCDS10729.1	.	.	.	.	.	.	.	.	.	.	C	31	5.081350	0.94050	.	.	ENSG00000102893	ENST00000299167;ENST00000455779;ENST00000323584	D;D	0.93811	-3.29;-3.29	5.73	5.73	0.89815	Six-hairpin glycosidase-like (1);Glycoside hydrolase 15-related (1);	0.062767	0.64402	D	0.000003	D	0.97632	0.9224	M	0.92219	3.285	0.80722	D	1	D;D;D	0.89917	0.994;0.996;1.0	D;D;D	0.87578	0.927;0.983;0.998	D	0.98061	1.0393	10	0.87932	D	0	-10.2045	19.0305	0.92955	0.0:1.0:0.0:0.0	.	169;176;169	B4DQ16;Q93100;Q93100-4	.;KPBB_HUMAN;.	L	169;169;176	ENSP00000414345:S169L;ENSP00000313504:S176L	ENSP00000299167:S169L	S	+	2	0	PHKB	46106946	1.000000	0.71417	0.983000	0.44433	0.988000	0.76386	6.163000	0.71880	2.861000	0.98227	0.655000	0.94253	TCA		0.313	PHKB-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000430413.1			9	26	0	0	0	0.058154	0	9	26				
MGAT5B	146664	broad.mit.edu	37	17	74921106	74921106	+	Missense_Mutation	SNP	G	G	A	rs537970370		TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr17:74921106G>A	ENST00000569840.2	+	9	1658	c.1084G>A	c.(1084-1086)Gac>Aac	p.D362N	MGAT5B_ENST00000301618.4_Missense_Mutation_p.D362N|MGAT5B_ENST00000428789.2_Missense_Mutation_p.D373N	NM_001199172.1	NP_001186101.1	Q3V5L5	MGT5B_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B	362					protein N-linked glycosylation (GO:0006487)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity (GO:0030144)|metal ion binding (GO:0046872)	p.D362N(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(15)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CCTGCCCTTCGACCTCATCTA	0.617													G|||	1	0.000199681	0.0	0.0	5008	,	,		10463	0.0		0.0	False		,,,				2504	0.001						uc002jti.2		NA																	1	Substitution - Missense(1)		lung(1)	ovary(2)|skin(1)	3						c.(1117-1119)GAC>AAC		N-acetylglucosaminyltranferase VB isoform 2							93.0	89.0	90.0					17																	74921106		2203	4300	6503	SO:0001583	missense	146664					Golgi membrane|integral to membrane	alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase activity|metal ion binding	g.chr17:74921106G>A	AB109185	CCDS11751.1, CCDS45788.1, CCDS59299.1	17q25.3	2013-02-25	2005-11-16		ENSG00000167889	ENSG00000167889		"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	24140	protein-coding gene	gene with protein product		612441	"""mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isoenzyme B"""			14617637, 14623122	Standard	NM_001199172		Approved	GnT-IX, FLJ25132, GnT-VB	uc002jth.3	Q3V5L5	OTTHUMG00000177278	ENST00000569840.2:c.1084G>A	17.37:g.74921106G>A	ENSP00000456037:p.Asp362Asn					MGAT5B_uc002jth.2_Missense_Mutation_p.D362N	p.D373N	NM_198955	NP_945193	Q3V5L5	MGT5B_HUMAN			8	1220	+			362			Lumenal (Potential).		Q6P3S8|Q6P6B3|Q766X5|Q76D04|Q96LS2	Missense_Mutation	SNP	ENST00000569840.2	37	c.1117G>A	CCDS59299.1	.	.	.	.	.	.	.	.	.	.	G	36	5.955962	0.97145	.	.	ENSG00000167889	ENST00000301618;ENST00000428789	T;T	0.59083	0.3;0.29	5.25	5.25	0.73442	.	0.111999	0.64402	D	0.000015	T	0.76772	0.4034	M	0.75615	2.305	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.79729	-0.1681	10	0.87932	D	0	-34.1486	17.8384	0.88707	0.0:0.0:1.0:0.0	.	373;362	Q3V5L5-2;Q3V5L5-5	.;.	N	362;373	ENSP00000301618:D362N;ENSP00000391227:D373N	ENSP00000301618:D362N	D	+	1	0	MGAT5B	72432701	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	9.681000	0.98653	2.453000	0.82957	0.561000	0.74099	GAC		0.617	MGAT5B-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460624.2	NM_144677		15	62	0	0	0	0.028581	0	15	62				
SLC25A10	1468	broad.mit.edu	37	17	79687107	79687107	+	Nonstop_Mutation	SNP	A	A	C			TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	A	A	-	-	A	A	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr17:79687107A>C	ENST00000350690.5	+	11	950	c.864A>C	c.(862-864)tgA>tgC	p.*288C	SLC25A10_ENST00000541223.1_Nonstop_Mutation_p.*443C|SLC25A10_ENST00000331531.5_Nonstop_Mutation_p.*297C|SLC25A10_ENST00000545862.1_Nonstop_Mutation_p.*245C|SLC25A10_ENST00000571730.1_Nonstop_Mutation_p.*443C	NM_001270953.1|NM_012140.4	NP_001257882.1|NP_036272.2	Q9UBX3	DIC_HUMAN	solute carrier family 25 (mitochondrial carrier; dicarboxylate transporter), member 10	0					carbohydrate metabolic process (GO:0005975)|cellular nitrogen compound metabolic process (GO:0034641)|dicarboxylic acid transport (GO:0006835)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|ion transport (GO:0006811)|mitochondrial transport (GO:0006839)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	dicarboxylic acid transmembrane transporter activity (GO:0005310)	p.*288C(1)		endometrium(1)|lung(9)|ovary(1)|prostate(1)|skin(2)	14	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0117)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)		Succinic acid(DB00139)	TGCCATCCTGACCAGCCGTGG	0.607																																							uc002kbi.2		NA																	1	Nonstop extension(1)		lung(1)		0						c.(862-864)TGA>TGC		solute carrier family 25 (mitochondrial carrier;	Succinic acid(DB00139)						39.0	38.0	38.0					17																	79687107		2202	4300	6502	SO:0001578	stop_lost	1468				gluconeogenesis|mitochondrial transport	integral to membrane|mitochondrial inner membrane|nucleus	protein binding	g.chr17:79687107A>C		CCDS11786.1, CCDS59301.1, CCDS74176.1	17q25.3	2013-07-15			ENSG00000183048	ENSG00000183048		"""Solute carriers"""	10980	protein-coding gene	gene with protein product		606794		DIC		9733776, 10072589	Standard	NM_001270953		Approved		uc031rew.1	Q9UBX3	OTTHUMG00000178173	ENST00000350690.5:c.864A>C	17.37:g.79687107A>C	ENSP00000345580:p.*288Cysext*14					SLC25A10_uc010wut.1_Nonstop_Mutation_p.*443C|SLC25A10_uc010dif.2_Nonstop_Mutation_p.*297C|SLC25A10_uc010wuu.1_Nonstop_Mutation_p.*242C	p.*288C	NM_012140	NP_036272	Q9UBX3	DIC_HUMAN	BRCA - Breast invasive adenocarcinoma(99;0.0117)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)		11	950	+	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.23)		288					Q542Z3|Q96BA1|Q96IP1	Nonstop_Mutation	SNP	ENST00000350690.5	37	c.864A>C	CCDS11786.1	.	.	.	.	.	.	.	.	.	.	A	16.85	3.235774	0.58886	.	.	ENSG00000183048	ENST00000541223;ENST00000331531;ENST00000350690;ENST00000545862	.	.	.	4.35	3.25	0.37280	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.9301	0.41517	0.9158:0.0:0.0842:0.0	.	.	.	.	C	443;297;288;245	.	.	X	+	3	0	SLC25A10	77297512	1.000000	0.71417	0.903000	0.35520	0.516000	0.34256	4.848000	0.62874	1.600000	0.50102	0.528000	0.53228	TGA		0.607	SLC25A10-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000440816.1			7	27	0	0	0	0.105934	0	7	27				
SMAD4	4089	broad.mit.edu	37	18	48604655	48604655	+	Missense_Mutation	SNP	G	G	A	rs121912578		TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr18:48604655G>A	ENST00000342988.3	+	12	2015	c.1477G>A	c.(1477-1479)Gat>Aat	p.D493N	SMAD4_ENST00000398417.2_Missense_Mutation_p.D493N|SMAD4_ENST00000588745.1_Missense_Mutation_p.D397N|SMAD4_ENST00000586253.1_3'UTR	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	493	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.		D -> H (in pancreatic carcinoma; dbSNP:rs28936392). {ECO:0000269|PubMed:8553070}.		atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(2)|p.D493N(2)|p.D493H(1)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		AATTGGTGTTGATGACCTTCG	0.463																																							uc010xdp.1		NA																	41	Whole gene deletion(36)|Substitution - Missense(3)|Unknown(2)	p.0?(35)|p.?(2)|p.D493A(1)|p.D493H(1)|p.D493N(1)	pancreas(28)|large_intestine(3)|lung(3)|breast(3)|stomach(2)|upper_aerodigestive_tract(1)|oesophagus(1)	pancreas(170)|large_intestine(108)|thyroid(19)|lung(11)|small_intestine(9)|upper_aerodigestive_tract(8)|biliary_tract(8)|ovary(7)|breast(6)|stomach(5)|oesophagus(3)|testis(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|kidney(1)|urinary_tract(1)|vulva(1)|skin(1)|NS(1)	369						c.(1477-1479)GAT>AAT		mothers against decapentaplegic homolog 4							121.0	102.0	109.0					18																	48604655		2203	4300	6503	SO:0001583	missense	4089	Juvenile_Polyposis|Hereditary_Hemorrhagic_Telangiectasia			BMP signaling pathway|negative regulation of cell growth|negative regulation of protein catabolic process|negative regulation of transcription, DNA-dependent|palate development|positive regulation of epithelial to mesenchymal transition|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of transforming growth factor-beta2 production|response to hypoxia|response to transforming growth factor beta stimulus|SMAD protein complex assembly|SMAD protein signal transduction|transforming growth factor beta receptor signaling pathway	activin responsive factor complex|centrosome|cytosol	I-SMAD binding|protein homodimerization activity|R-SMAD binding|transcription regulatory region DNA binding|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity	g.chr18:48604655G>A	U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"""SMADs"""	6770	protein-coding gene	gene with protein product		600993	"""MAD, mothers against decapentaplegic homolog 4 (Drosophila)"", ""SMAD, mothers against DPP homolog 4 (Drosophila)"""	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.1477G>A	18.37:g.48604655G>A	ENSP00000341551:p.Asp493Asn					SMAD4_uc002lfb.3_Missense_Mutation_p.D338N	p.D493N	NM_005359	NP_005350	Q13485	SMAD4_HUMAN		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)	12	2015	+		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)	493			MH2.		A8K405	Missense_Mutation	SNP	ENST00000342988.3	37	c.1477G>A	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.601198	0.87055	.	.	ENSG00000141646	ENST00000342988;ENST00000398417	D;D	0.98862	-5.19;-5.19	5.99	5.99	0.97316	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.044013	0.85682	D	0.000000	D	0.98985	0.9654	M	0.81682	2.555	0.80722	D	1	P	0.48911	0.917	P	0.57846	0.828	D	0.99679	1.0998	10	0.66056	D	0.02	.	19.2202	0.93793	0.0:0.0:1.0:0.0	.	493	Q13485	SMAD4_HUMAN	N	493	ENSP00000341551:D493N;ENSP00000381452:D493N	ENSP00000341551:D493N	D	+	1	0	SMAD4	46858653	1.000000	0.71417	0.997000	0.53966	0.994000	0.84299	9.544000	0.98092	2.843000	0.97960	0.655000	0.94253	GAT		0.463	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359		11	19	0	0	0	0.105934	0	11	19				
CIRBP	1153	broad.mit.edu	37	19	1270962	1270962	+	Silent	SNP	T	T	G			TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	T	T	-	-	T	T	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr19:1270962T>G	ENST00000588030.1	+	2	290	c.30T>G	c.(28-30)gtT>gtG	p.V10V	CIRBP-AS1_ENST00000585832.1_RNA|CIRBP_ENST00000444172.2_5'UTR|CIRBP_ENST00000587323.1_Silent_p.V10V|CIRBP_ENST00000588090.1_Silent_p.V10V|CIRBP_ENST00000586773.1_Silent_p.V10V|CIRBP_ENST00000586472.1_Silent_p.V10V|CIRBP_ENST00000589235.1_Silent_p.V10V|CIRBP_ENST00000585630.1_Silent_p.V10V|CIRBP_ENST00000587896.1_Silent_p.V10V|CIRBP_ENST00000588230.1_Silent_p.V10V|CIRBP_ENST00000589686.1_Silent_p.V10V|CIRBP_ENST00000413636.2_Silent_p.V10V|CIRBP_ENST00000589660.1_Silent_p.V10V|CIRBP-AS1_ENST00000600215.1_RNA|CIRBP_ENST00000591935.1_Silent_p.V10V|CIRBP_ENST00000320936.5_Silent_p.V10V|CIRBP_ENST00000589710.1_Silent_p.V10V			Q14011	CIRBP_HUMAN	cold inducible RNA binding protein	10	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA stabilization (GO:0048255)|positive regulation of translation (GO:0045727)|response to cold (GO:0009409)|response to UV (GO:0009411)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|small ribosomal subunit rRNA binding (GO:0070181)|translation repressor activity (GO:0030371)	p.V10V(1)		endometrium(1)|large_intestine(1)|lung(3)	5		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000332)|all_lung(49;0.000498)|Breast(49;0.0014)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		aactttttgttggagggctga	0.557																																							uc002lrr.3		NA																	1	Substitution - coding silent(1)		lung(1)		0						c.(28-30)GTT>GTG		cold inducible RNA binding protein							187.0	194.0	191.0					19																	1270962		2203	4300	6503	SO:0001819	synonymous_variant	1153				mRNA stabilization|positive regulation of translation|response to cold|response to UV|stress granule assembly	nucleoplasm|stress granule	mRNA 3'-UTR binding|nucleotide binding|protein binding|SSU rRNA binding|translation repressor activity	g.chr19:1270962T>G	D78134	CCDS12059.1, CCDS74244.1, CCDS74245.1	19p13.3	2013-02-12	2001-11-28		ENSG00000099622	ENSG00000099622		"""RNA binding motif (RRM) containing"""	1982	protein-coding gene	gene with protein product	"""Cold-inducible RNA-binding protein"", ""glycine-rich RNA binding protein"""	602649	"""cold inducible RNA-binding protein"""			9434172, 9151692	Standard	NM_001280		Approved	CIRP	uc002lrr.4	Q14011		ENST00000588030.1:c.30T>G	19.37:g.1270962T>G						C19orf23_uc010xgk.1_5'Flank|CIRBP_uc010dsg.1_5'UTR|CIRBP_uc002lrt.2_Silent_p.V10V|CIRBP_uc010xgl.1_Silent_p.V10V|CIRBP_uc002lrv.3_Silent_p.V10V|CIRBP_uc002lru.2_RNA	p.V10V	NM_001280	NP_001271	Q14011	CIRBP_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	2	179	+		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000332)|all_lung(49;0.000498)|Breast(49;0.0014)	10			RRM.		B3KT17|B4E2X2	Silent	SNP	ENST00000588030.1	37	c.30T>G	CCDS12059.1																																																																																				0.557	CIRBP-011	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449969.1	NM_001280		13	140	0	0	0	0.105934	0	13	140				
RYR1	6261	broad.mit.edu	37	19	38951104	38951104	+	Missense_Mutation	SNP	G	G	A			TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr19:38951104G>A	ENST00000359596.3	+	20	2450	c.2450G>A	c.(2449-2451)cGa>cAa	p.R817Q	RYR1_ENST00000360985.3_Missense_Mutation_p.R817Q|RYR1_ENST00000355481.4_Missense_Mutation_p.R817Q			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	817					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.R817Q(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GTGCTCCCTCGAGAGCGACTC	0.632																																							uc002oit.2		NA																	1	Substitution - Missense(1)		lung(1)	ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12						c.(2449-2451)CGA>CAA		skeletal muscle ryanodine receptor isoform 1	Dantrolene(DB01219)						110.0	106.0	108.0					19																	38951104		2203	4300	6503	SO:0001583	missense	6261				muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity	g.chr19:38951104G>A	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.2450G>A	19.37:g.38951104G>A	ENSP00000352608:p.Arg817Gln					RYR1_uc002oiu.2_Missense_Mutation_p.R817Q	p.R817Q	NM_000540	NP_000531	P21817	RYR1_HUMAN	Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		20	2580	+	all_cancers(60;7.91e-06)		817			Cytoplasmic.		Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	c.2450G>A	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	g	15.61	2.884122	0.51908	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.96716	-4.09;-4.1;-4.09	4.13	4.13	0.48395	.	0.077525	0.47455	U	0.000238	D	0.95579	0.8563	N	0.25647	0.755	0.30487	N	0.771726	D;P	0.89917	1.0;0.617	D;B	0.71870	0.975;0.233	D	0.92301	0.5849	10	0.37606	T	0.19	.	11.6131	0.51072	0.0911:0.0:0.9089:0.0	.	817;817	P21817-2;P21817	.;RYR1_HUMAN	Q	817	ENSP00000352608:R817Q;ENSP00000347667:R817Q;ENSP00000354254:R817Q	ENSP00000347667:R817Q	R	+	2	0	RYR1	43642944	0.997000	0.39634	0.900000	0.35374	0.979000	0.70002	2.909000	0.48758	2.301000	0.77427	0.299000	0.19835	CGA		0.632	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			22	69	0	0	0	0.099896	0	22	69				
FPR1	2357	broad.mit.edu	37	19	52249869	52249869	+	Missense_Mutation	SNP	C	C	T	rs186613919	byFrequency	TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr19:52249869C>T	ENST00000595042.1	-	3	520	c.379G>A	c.(379-381)Gtc>Atc	p.V127I	FPR1_ENST00000304748.4_Missense_Mutation_p.V127I	NM_001193306.1	NP_001180235.1	P21462	FPR1_HUMAN	formyl peptide receptor 1	127					activation of MAPK activity (GO:0000187)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|nitric oxide mediated signal transduction (GO:0007263)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|signal transduction (GO:0007165)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	N-formyl peptide receptor activity (GO:0004982)|receptor activity (GO:0004872)	p.V127I(1)		endometrium(2)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(3)	20		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00106)|OV - Ovarian serous cystadenocarcinoma(262;0.018)	Nedocromil(DB00716)	GGATGCAGGACGCAAACACAG	0.557													C|||	5	0.000998403	0.0038	0.0	5008	,	,		21762	0.0		0.0	False		,,,				2504	0.0						uc002pxq.2		NA																	1	Substitution - Missense(1)		lung(1)	ovary(1)|lung(1)|skin(1)	3						c.(379-381)GTC>ATC		formyl peptide receptor 1	Nedocromil(DB00716)	C	ILE/VAL,ILE/VAL	2,4404		0,2,2201	98.0	78.0	85.0		379,379	3.7	0.9	19		85	0,8600		0,0,4300	no	missense,missense	FPR1	NM_001193306.1,NM_002029.3	29,29	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging,probably-damaging	127/351,127/351	52249869	2,13004	2203	4300	6503	SO:0001583	missense	2357				activation of MAPK activity|cellular component movement|chemotaxis|G-protein signaling, coupled to cAMP nucleotide second messenger|nitric oxide mediated signal transduction	endosome|integral to membrane|plasma membrane	N-formyl peptide receptor activity	g.chr19:52249869C>T	M60627	CCDS12839.1	19q13.41	2014-09-17				ENSG00000171051		"""GPCR / Class A : Formyl peptide receptors"""	3826	protein-coding gene	gene with protein product		136537				2161213, 12595898	Standard	NM_001193306		Approved	FPR, FMLP	uc002pxq.3	P21462		ENST00000595042.1:c.379G>A	19.37:g.52249869C>T	ENSP00000471493:p.Val127Ile						p.V127I	NM_002029	NP_002020	P21462	FPR1_HUMAN		GBM - Glioblastoma multiforme(134;0.00106)|OV - Ovarian serous cystadenocarcinoma(262;0.018)	2	474	-		all_neural(266;0.0189)|Medulloblastoma(540;0.146)	127			Cytoplasmic (Potential).		Q14939|Q7Z6A4|Q86U52|Q9NS48	Missense_Mutation	SNP	ENST00000595042.1	37	c.379G>A	CCDS12839.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	.	14.73	2.623574	0.46840	4.54E-4	0.0	ENSG00000171051	ENST00000304748	T	0.65364	-0.15	3.66	3.66	0.41972	GPCR, rhodopsin-like superfamily (1);	0.271283	0.29300	N	0.012550	T	0.70029	0.3177	L	0.46947	1.48	0.34989	D	0.75482	D	0.76494	0.999	D	0.67900	0.954	T	0.76105	-0.3081	10	0.36615	T	0.2	.	13.6424	0.62260	0.0:1.0:0.0:0.0	.	127	P21462	FPR1_HUMAN	I	127	ENSP00000302707:V127I	ENSP00000302707:V127I	V	-	1	0	FPR1	56941681	0.998000	0.40836	0.924000	0.36721	0.032000	0.12392	2.666000	0.46799	1.960000	0.56953	0.655000	0.94253	GTC		0.557	FPR1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466905.1	NM_002029		15	35	0	0	0	0.049695	0	15	35				
PXDN	7837	broad.mit.edu	37	2	1653369	1653369	+	Missense_Mutation	SNP	C	C	T			TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr2:1653369C>T	ENST00000252804.4	-	17	2233	c.2183G>A	c.(2182-2184)cGc>cAc	p.R728H		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	728					extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.R728H(1)		breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		GTTGTTCACGCGCCGGTGGGC	0.602																																							uc002qxa.2		NA																	1	Substitution - Missense(1)		lung(1)	pancreas(6)|ovary(2)	8						c.(2182-2184)CGC>CAC		peroxidasin precursor							84.0	91.0	89.0					2																	1653369		2089	4207	6296	SO:0001583	missense	7837				extracellular matrix organization|hydrogen peroxide catabolic process|immune response	endoplasmic reticulum|extracellular space|proteinaceous extracellular matrix	extracellular matrix structural constituent|heme binding|interleukin-1 receptor antagonist activity|peroxidase activity	g.chr2:1653369C>T	AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"""Immunoglobulin superfamily / I-set domain containing"""	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.2183G>A	2.37:g.1653369C>T	ENSP00000252804:p.Arg728His						p.R728H	NM_012293	NP_036425	Q92626	PXDN_HUMAN		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)	17	2247	-	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)	728					A8QM65|D6W4Y0|Q4KMG2	Missense_Mutation	SNP	ENST00000252804.4	37	c.2183G>A	CCDS46221.1	.	.	.	.	.	.	.	.	.	.	C	17.13	3.310209	0.60414	.	.	ENSG00000130508	ENST00000252804	T	0.61510	0.1	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.50582	0.1624	L	0.34521	1.04	0.80722	D	1	B	0.26775	0.159	B	0.24701	0.055	T	0.41698	-0.9494	10	0.36615	T	0.2	-42.8173	19.7328	0.96190	0.0:1.0:0.0:0.0	.	728	Q92626	PXDN_HUMAN	H	728	ENSP00000252804:R728H	ENSP00000252804:R728H	R	-	2	0	PXDN	1632376	1.000000	0.71417	0.982000	0.44146	0.843000	0.47879	7.702000	0.84576	2.661000	0.90470	0.558000	0.71614	CGC		0.602	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455		4	61	0	0	0	0.009096	0	4	61				
GKN2	200504	broad.mit.edu	37	2	69173459	69173459	+	Missense_Mutation	SNP	T	T	G			TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	T	T	-	-	T	T	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr2:69173459T>G	ENST00000328895.4	-	5	557	c.449A>C	c.(448-450)aAg>aCg	p.K150T	GKN2_ENST00000481498.1_Missense_Mutation_p.K150T	NM_182536.2	NP_872342.2	Q86XP6	GKN2_HUMAN	gastrokine 2	150	BRICHOS. {ECO:0000255|PROSITE- ProRule:PRU00255}.					extracellular region (GO:0005576)		p.K150T(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|urinary_tract(1)	15						CACTTCCCCCTTATACAAAGG	0.453																																							uc002sfa.2		NA																	1	Substitution - Missense(1)		lung(1)		0						c.(448-450)AAG>ACG		trefoil factor interactions(z) 1 precursor							156.0	155.0	155.0					2																	69173459		2203	4300	6503	SO:0001583	missense	200504					extracellular region		g.chr2:69173459T>G	AF494509	CCDS33215.1	2p14	2012-10-10			ENSG00000183607	ENSG00000183607		"""BRICHOS domain containing"""	24588	protein-coding gene	gene with protein product	"""down regulated in gastric cancer GDDR"", ""BRICHOS domain containing 1B"""					15774165, 15924415, 16888721	Standard	NM_182536		Approved	TFIZ1, PRO813, VLTI465, blottin, GDDR, BRICD1B	uc002sfa.3	Q86XP6	OTTHUMG00000152655	ENST00000328895.4:c.449A>C	2.37:g.69173459T>G	ENSP00000329292:p.Lys150Thr					GKN2_uc002sfb.3_Missense_Mutation_p.K150T	p.K150T	NM_182536	NP_872342	Q86XP6	GKN2_HUMAN			5	558	-			150			BRICHOS.		Q6UWS6	Missense_Mutation	SNP	ENST00000328895.4	37	c.449A>C	CCDS33215.1	.	.	.	.	.	.	.	.	.	.	T	15.35	2.808054	0.50421	.	.	ENSG00000183607	ENST00000328895;ENST00000481498	T;T	0.79749	-1.3;-1.3	4.65	4.65	0.58169	BRICHOS (2);	0.284575	0.29830	N	0.011095	D	0.84800	0.5552	M	0.65975	2.015	0.25356	N	0.988825	D;D	0.58268	0.968;0.982	P;P	0.59825	0.773;0.864	T	0.76399	-0.2973	10	0.34782	T	0.22	-32.0339	10.402	0.44235	0.0:0.0:0.0:1.0	.	150;150	E5RHQ8;Q86XP6	.;GKN2_HUMAN	T	150	ENSP00000329292:K150T;ENSP00000428538:K150T	ENSP00000329292:K150T	K	-	2	0	GKN2	69026963	0.100000	0.21855	0.496000	0.27539	0.673000	0.39480	1.629000	0.37071	1.947000	0.56498	0.454000	0.30748	AAG		0.453	GKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327191.1	NM_182536		27	63	0	0	0	0.108266	0	27	63				
MARCO	8685	broad.mit.edu	37	2	119752091	119752091	+	Missense_Mutation	SNP	G	G	A	rs200590124	byFrequency	TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr2:119752091G>A	ENST00000327097.4	+	17	1693	c.1558G>A	c.(1558-1560)Gtc>Atc	p.V520I	MARCO_ENST00000541757.1_Missense_Mutation_p.V442I	NM_006770.3	NP_006761.1	Q9UEW3	MARCO_HUMAN	macrophage receptor with collagenous structure	520					apoptotic cell clearance (GO:0043277)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)	collagen trimer (GO:0005581)|endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|transmembrane signaling receptor activity (GO:0004888)	p.V520I(3)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(12)|lung(37)|ovary(4)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	70						GGAGTGCAGCGTCTGACCCGG	0.602													G|||	2	0.000399361	0.0	0.0	5008	,	,		19902	0.001		0.001	False		,,,				2504	0.0				GBM(8;18 374 7467 11269 32796)	GBM(8;18 374 7467 11269 32796)	uc002tln.1		NA																	3	Substitution - Missense(3)		large_intestine(1)|lung(1)|breast(1)	ovary(3)|skin(2)|central_nervous_system(1)	6						c.(1558-1560)GTC>ATC		macrophage receptor with collagenous structure		G	ILE/VAL	0,4406		0,0,2203	113.0	88.0	96.0		1558	-1.5	0.0	2		96	1,8599	1.2+/-3.3	0,1,4299	yes	missense	MARCO	NM_006770.3	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	520/521	119752091	1,13005	2203	4300	6503	SO:0001583	missense	8685				cell surface receptor linked signaling pathway|innate immune response	collagen|integral to plasma membrane	pattern recognition receptor activity|scavenger receptor activity	g.chr2:119752091G>A	AF035819	CCDS2124.1	2q14.2	2011-10-11			ENSG00000019169	ENSG00000019169			6895	protein-coding gene	gene with protein product	"""scavenger receptor class A, member 2"""	604870				9468508, 7867067, 10331948	Standard	NM_006770		Approved	SCARA2	uc002tln.1	Q9UEW3	OTTHUMG00000131400	ENST00000327097.4:c.1558G>A	2.37:g.119752091G>A	ENSP00000318916:p.Val520Ile					MARCO_uc010yyf.1_Missense_Mutation_p.V442I	p.V520I	NM_006770	NP_006761	Q9UEW3	MARCO_HUMAN			17	1690	+			520			Extracellular (Potential).		B4DW79|Q9Y5S3	Missense_Mutation	SNP	ENST00000327097.4	37	c.1558G>A	CCDS2124.1	2	9.157509157509158E-4	0	0.0	0	0.0	1	0.0017482517482517483	1	0.0013192612137203166	G	0.017	-1.509622	0.00984	0.0	1.16E-4	ENSG00000019169	ENST00000327097;ENST00000410021;ENST00000541757	D;D	0.90788	-2.73;-2.69	0.758	-1.52	0.08637	.	.	.	.	.	D	0.85427	0.5694	M	0.65677	2.01	0.09310	N	1	P	0.42692	0.787	B	0.35240	0.198	T	0.71583	-0.4549	8	.	.	.	.	6.6215	0.22806	0.3734:0.0:0.6266:0.0	.	520	Q9UEW3	MARCO_HUMAN	I	520;466;442	ENSP00000318916:V520I;ENSP00000441769:V442I	.	V	+	1	0	MARCO	119468561	0.003000	0.15002	0.007000	0.13788	0.002000	0.02628	-0.355000	0.07671	-2.165000	0.00781	-2.299000	0.00261	GTC		0.602	MARCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254190.2	NM_006770		13	44	0	0	0	0.038395	0	13	44				
STAT1	6772	broad.mit.edu	37	2	191873763	191873763	+	Nonsense_Mutation	SNP	G	G	A			TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr2:191873763G>A	ENST00000361099.3	-	4	586	c.199C>T	c.(199-201)Caa>Taa	p.Q67*	STAT1_ENST00000392322.3_Nonsense_Mutation_p.Q67*|STAT1_ENST00000540176.1_Nonsense_Mutation_p.Q67*|STAT1_ENST00000409465.1_Nonsense_Mutation_p.Q67*|STAT1_ENST00000392323.2_Nonsense_Mutation_p.Q69*	NM_007315.3	NP_009330.1	P42224	STAT1_HUMAN	signal transducer and activator of transcription 1, 91kDa	67					apoptotic process (GO:0006915)|blood circulation (GO:0008015)|cellular response to insulin stimulus (GO:0032869)|cellular response to interferon-beta (GO:0035458)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchymal cell proliferation involved in metanephros development (GO:0072136)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of macrophage fusion (GO:0034240)|negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003340)|negative regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072308)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|renal tubule development (GO:0061326)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to exogenous dsRNA (GO:0043330)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|transcription from RNA polymerase II promoter (GO:0006366)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|tumor necrosis factor receptor binding (GO:0005164)	p.Q67*(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			OV - Ovarian serous cystadenocarcinoma(117;0.00434)|Epithelial(96;0.0555)|all cancers(119;0.141)			CGACTATATTGATCATCCAGC	0.388																																							uc002usj.2		NA																	1	Substitution - Nonsense(1)		lung(1)	lung(3)|breast(3)|central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)	10						c.(199-201)CAA>TAA		signal transducer and activator of transcription	Fludarabine(DB01073)						107.0	101.0	103.0					2																	191873763		2203	4300	6503	SO:0001587	stop_gained	6772				activation of caspase activity|I-kappaB kinase/NF-kappaB cascade|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway|tyrosine phosphorylation of STAT protein	cytosol|nucleolus|nucleoplasm	calcium ion binding|protein binding|RNA polymerase II core promoter sequence-specific DNA binding|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity|signal transducer activity	g.chr2:191873763G>A		CCDS2309.1, CCDS42793.1	2q32.2-q32.3	2014-09-17	2002-08-29		ENSG00000115415	ENSG00000115415		"""SH2 domain containing"""	11362	protein-coding gene	gene with protein product	"""transcription factor ISGF-3 components p91/p84"""	600555	"""signal transducer and activator of transcription 1, 91kD"""			7885841	Standard	NM_139266		Approved	STAT91, ISGF-3	uc002usj.2	P42224	OTTHUMG00000132699	ENST00000361099.3:c.199C>T	2.37:g.191873763G>A	ENSP00000354394:p.Gln67*					STAT1_uc010fse.1_Nonsense_Mutation_p.Q67*|STAT1_uc002usk.2_Nonsense_Mutation_p.Q67*|STAT1_uc002usl.2_Nonsense_Mutation_p.Q69*|STAT1_uc010fsf.1_5'UTR	p.Q67*	NM_007315	NP_009330	P42224	STAT1_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.00434)|Epithelial(96;0.0555)|all cancers(119;0.141)		4	587	-			67					A8K989|B2RCA0|D2KFR8|D3DPI7|Q53S88|Q53XW4|Q68D00|Q9UDL5	Nonsense_Mutation	SNP	ENST00000361099.3	37	c.199C>T	CCDS2309.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.703700	0.88924	.	.	ENSG00000115415	ENST00000361099;ENST00000409465;ENST00000540176;ENST00000392322;ENST00000392323;ENST00000424722;ENST00000454414;ENST00000432058	.	.	.	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.16420	T	0.52	-28.5849	18.7673	0.91878	0.0:0.0:1.0:0.0	.	.	.	.	X	67;67;67;67;69;67;67;67	.	ENSP00000354394:Q67X	Q	-	1	0	STAT1	191582008	1.000000	0.71417	0.927000	0.36925	0.956000	0.61745	9.869000	0.99810	2.683000	0.91414	0.557000	0.71058	CAA		0.388	STAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255997.3	NM_007315		8	20	0	0	0	0.047766	0	8	20				
COL6A3	1293	broad.mit.edu	37	2	238280738	238280738	+	Missense_Mutation	SNP	G	G	A	rs140330124	byFrequency	TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr2:238280738G>A	ENST00000295550.4	-	9	4374	c.3922C>T	c.(3922-3924)Cgg>Tgg	p.R1308W	COL6A3_ENST00000347401.3_Missense_Mutation_p.R1107W|COL6A3_ENST00000409809.1_Missense_Mutation_p.R1102W|COL6A3_ENST00000346358.4_Missense_Mutation_p.R1108W|COL6A3_ENST00000392003.2_Missense_Mutation_p.R901W|COL6A3_ENST00000353578.4_Missense_Mutation_p.R1102W|COL6A3_ENST00000392004.3_Missense_Mutation_p.R1102W|COL6A3_ENST00000472056.1_Missense_Mutation_p.R701W	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	1308	Nonhelical region.|VWFA 7. {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)	p.R1102W(1)|p.R1308W(1)		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)		TTGATCTGCCGCCCTCCCTTG	0.617																																							uc002vwl.2		NA																	2	Substitution - Missense(2)		lung(2)	ovary(8)|central_nervous_system(6)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	18						c.(3922-3924)CGG>TGG		alpha 3 type VI collagen isoform 1 precursor		G	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	62.0	55.0	57.0		3922,2701,3304,2101,3304	-11.7	0.0	2	dbSNP_134	57	0,8600		0,0,4300	no	missense,missense,missense,missense,missense	COL6A3	NM_004369.3,NM_057164.4,NM_057165.4,NM_057166.4,NM_057167.3	101,101,101,101,101	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	1308/3178,901/1037,1102/1238,701/2571,1102/2972	238280738	1,13005	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.chr2:238280738G>A	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.3922C>T	2.37:g.238280738G>A	ENSP00000295550:p.Arg1308Trp					COL6A3_uc002vwo.2_Missense_Mutation_p.R1102W|COL6A3_uc010znj.1_Missense_Mutation_p.R701W|COL6A3_uc002vwq.2_Missense_Mutation_p.R1102W|COL6A3_uc002vwr.2_Missense_Mutation_p.R901W	p.R1308W	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)	9	4207	-		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)	1308			VWFA 7.|Nonhelical region.		A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	c.3922C>T	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	G	14.40	2.525430	0.44969	2.27E-4	0.0	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358;ENST00000392004;ENST00000392003	D;D;D;D;D;D;D;D	0.83591	-1.74;-1.74;-1.74;-1.74;-1.74;-1.74;-1.74;-1.74	5.84	-11.7	0.00046	von Willebrand factor, type A (3);	0.249631	0.26983	N	0.021507	D	0.87912	0.6297	L	0.60957	1.885	0.09310	N	1	D;D;D;D;D	0.89917	1.0;0.997;0.999;1.0;0.996	D;D;D;D;P	0.79784	0.993;0.932;0.932;0.988;0.828	T	0.82137	-0.0606	10	0.72032	D	0.01	.	28.1915	0.99998	0.0:0.0:0.7715:0.2285	.	701;901;1102;1102;1308	E9PFQ6;A8MT30;E9PGQ9;P12111-2;P12111	.;.;.;.;CO6A3_HUMAN	W	1308;1107;1102;701;1102;1108;1102;901	ENSP00000295550:R1308W;ENSP00000315609:R1107W;ENSP00000315873:R1102W;ENSP00000418285:R701W;ENSP00000386844:R1102W;ENSP00000295546:R1108W;ENSP00000375861:R1102W;ENSP00000375860:R901W	ENSP00000295550:R1308W	R	-	1	2	COL6A3	237945477	0.000000	0.05858	0.004000	0.12327	0.342000	0.28953	-0.192000	0.09587	-1.909000	0.01085	-1.014000	0.02459	CGG		0.617	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		4	42	0	0	0	0.014758	0	4	42				
PROKR2	128674	broad.mit.edu	37	20	5283319	5283319	+	Silent	SNP	G	G	A			TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr20:5283319G>A	ENST00000217270.3	-	2	521	c.522C>T	c.(520-522)atC>atT	p.I174I	PROKR2_ENST00000546004.1_Silent_p.I174I	NM_144773.2	NP_658986.1	Q8NFJ6	PKR2_HUMAN	prokineticin receptor 2	174					circadian rhythm (GO:0007623)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)	p.I174I(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(3)|lung(22)|ovary(5)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	53						AGACCAAGGCGATCAGGAAGG	0.488										HNSCC(71;0.22)																													uc010zqw.1		NA																	1	Substitution - coding silent(1)		lung(1)	ovary(3)|central_nervous_system(1)|pancreas(1)	5						c.(520-522)ATC>ATT		prokineticin receptor 2							135.0	142.0	140.0					20																	5283319		2203	4300	6503	SO:0001819	synonymous_variant	128674					integral to membrane|plasma membrane	neuropeptide Y receptor activity	g.chr20:5283319G>A	AL121755	CCDS13089.1	20p12.3	2012-08-08	2006-02-15	2006-02-15	ENSG00000101292	ENSG00000101292		"""GPCR / Class A : Prokineticin receptors"""	15836	protein-coding gene	gene with protein product		607123	"""G protein-coupled receptor 73-like 1"", ""Kallmann syndrome 3 (autosomal dominant)"""	GPR73L1, KAL3		11886876, 17054399	Standard	NM_144773		Approved	GPR73b, PKR2, GPRg2, dJ680N4.3	uc010zqw.2	Q8NFJ6	OTTHUMG00000031800	ENST00000217270.3:c.522C>T	20.37:g.5283319G>A		HNSCC(71;0.22)				PROKR2_uc010zqx.1_Silent_p.I174I|PROKR2_uc010zqy.1_Silent_p.I174I	p.I174I	NM_144773	NP_658986	Q8NFJ6	PKR2_HUMAN			2	522	-			174			Helical; Name=4; (Potential).		A5JUU1|Q2M3C0|Q5TDY1|Q9NTT0	Silent	SNP	ENST00000217270.3	37	c.522C>T	CCDS13089.1																																																																																				0.488	PROKR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077854.1	NM_144773		5	76	0	0	0	0.014758	0	5	76				
TTLL9	164395	broad.mit.edu	37	20	30522516	30522516	+	Missense_Mutation	SNP	C	C	T	rs369485862		TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr20:30522516C>T	ENST00000375938.4	+	12	1082	c.829C>T	c.(829-831)Cgc>Tgc	p.R277C	TTLL9_ENST00000375921.2_Intron|TTLL9_ENST00000375922.4_Missense_Mutation_p.R219C|TTLL9_ENST00000375934.4_Silent_p.S244S|TTLL9_ENST00000535842.1_Missense_Mutation_p.R277C|TTLL9_ENST00000310998.4_Missense_Mutation_p.R242C			Q3SXZ7	TTLL9_HUMAN	tubulin tyrosine ligase-like family, member 9	277	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)	cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)	ligase activity (GO:0016874)	p.R277C(1)|p.R266C(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	26			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			GACGCTGCAGCGCTTCCGGCA	0.607																																							uc010gdx.1		NA																	2	Substitution - Missense(2)		lung(2)	ovary(2)	2						c.(829-831)CGC>TGC		tubulin tyrosine ligase-like family, member 9		C	CYS/ARG	0,3982		0,0,1991	27.0	28.0	28.0		829	4.2	1.0	20		28	2,8324		0,2,4161	no	missense	TTLL9	NM_001008409.2	180	0,2,6152	TT,TC,CC		0.024,0.0,0.0162	benign	277/440	30522516	2,12306	1991	4163	6154	SO:0001583	missense	164395				protein modification process	cilium|microtubule|microtubule basal body	ATP binding|tubulin-tyrosine ligase activity	g.chr20:30522516C>T	AL031658	CCDS42863.1	20q11	2013-02-14	2005-07-28	2005-07-28		ENSG00000131044		"""Tubulin tyrosine ligase-like family"""	16118	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 125"""	C20orf125		15890843	Standard	NM_001008409		Approved	dJ310O13.1	uc010gdx.1	Q3SXZ7		ENST00000375938.4:c.829C>T	20.37:g.30522516C>T	ENSP00000365105:p.Arg277Cys					TTLL9_uc002wwy.1_RNA|TTLL9_uc002wwz.1_Intron|TTLL9_uc002wxa.1_RNA|TTLL9_uc002wxb.1_RNA|TTLL9_uc010zto.1_RNA|TTLL9_uc002wxc.2_Missense_Mutation_p.R179C|TTLL9_uc010ztp.1_RNA|TTLL9_uc010ztq.1_RNA	p.R277C	NM_001008409	NP_001008409	Q3SXZ7	TTLL9_HUMAN	Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)		12	1082	+			277			TTL.		A6NH06|A6NIS5|B3KSG8|Q3SXZ8|Q5JYS3|Q5JYS4	Missense_Mutation	SNP	ENST00000375938.4	37	c.829C>T	CCDS42863.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.672569	0.88348	0.0	2.4E-4	ENSG00000131044	ENST00000375938;ENST00000535842;ENST00000310998;ENST00000375935;ENST00000375922	T;T;T;T	0.05855	3.38;3.38;3.38;3.38	5.09	4.15	0.48705	.	0.197212	0.46145	D	0.000316	T	0.16727	0.0402	L	0.46157	1.445	0.80722	D	1	D;D	0.67145	0.992;0.996	P;D	0.65443	0.809;0.935	T	0.00501	-1.1702	10	0.72032	D	0.01	.	12.8253	0.57716	0.0:0.9199:0.0:0.0801	.	277;179	Q3SXZ7;B1ANK8	TTLL9_HUMAN;.	C	277;277;242;266;219	ENSP00000365105:R277C;ENSP00000442515:R277C;ENSP00000308980:R242C;ENSP00000365088:R219C	ENSP00000308980:R242C	R	+	1	0	TTLL9	29986177	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	4.034000	0.57289	1.279000	0.44446	-0.254000	0.11334	CGC		0.607	TTLL9-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001008409		4	15	0	0	0	0.021553	0	4	15				
LAMA5	3911	broad.mit.edu	37	20	60889674	60889674	+	Silent	SNP	G	G	A			TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr20:60889674G>A	ENST00000252999.3	-	61	8370	c.8304C>T	c.(8302-8304)ggC>ggT	p.G2768G		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	2768	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)	p.G2768G(1)		breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			CAGGCTCTGGGCCCTGCAGGT	0.647																																							uc002ycq.2		NA																	1	Substitution - coding silent(1)		lung(1)	ovary(1)|pancreas(1)|skin(1)	3						c.(8302-8304)GGC>GGT		laminin alpha 5 precursor	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)						61.0	66.0	65.0					20																	60889674		2201	4300	6501	SO:0001819	synonymous_variant	3911				angiogenesis|cell proliferation|cell recognition|cytoskeleton organization|endothelial cell differentiation|focal adhesion assembly|integrin-mediated signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	integrin binding	g.chr20:60889674G>A	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.8304C>T	20.37:g.60889674G>A							p.G2768G	NM_005560	NP_005551	O15230	LAMA5_HUMAN	BRCA - Breast invasive adenocarcinoma(19;4.36e-06)		61	8371	-	Breast(26;1.57e-08)		2768			Laminin G-like 1.		Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	c.8304C>T	CCDS33502.1																																																																																				0.647	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		10	47	0	0	0	0.069234	0	10	47				
ARHGEF3	50650	broad.mit.edu	37	3	56807778	56807778	+	Missense_Mutation	SNP	C	C	T			TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr3:56807778C>T	ENST00000296315.3	-	2	331	c.163G>A	c.(163-165)Gtg>Atg	p.V55M	ARHGEF3_ENST00000413728.2_Missense_Mutation_p.V61M|ARHGEF3_ENST00000338458.4_Missense_Mutation_p.V87M|ARHGEF3_ENST00000497267.1_Missense_Mutation_p.V26M|ARHGEF3_ENST00000496106.1_Missense_Mutation_p.V61M|ARHGEF3_ENST00000498517.1_5'UTR|ARHGEF3_ENST00000495373.1_Missense_Mutation_p.V55M	NM_019555.2	NP_062455.1	Q9NR81	ARHG3_HUMAN	Rho guanine nucleotide exchange factor (GEF) 3	55					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|intracellular (GO:0005622)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.V55M(2)|p.V87M(1)		cervix(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(1)	25				KIRC - Kidney renal clear cell carcinoma(284;0.0161)|Kidney(284;0.019)|OV - Ovarian serous cystadenocarcinoma(275;0.193)		GTGGCCTTCACGGGCGGGATG	0.478																																							uc003dig.2		NA																	3	Substitution - Missense(3)		lung(3)	ovary(1)	1						c.(163-165)GTG>ATG		Rho guanine nucleotide exchange factor 3 isoform							114.0	108.0	110.0					3																	56807778		2203	4300	6503	SO:0001583	missense	50650				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|Rho protein signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity	g.chr3:56807778C>T	AB209661	CCDS2878.1, CCDS46854.1, CCDS46855.1, CCDS74948.1	3p14.3	2012-09-20			ENSG00000163947	ENSG00000163947		"""Rho guanine nucleotide exchange factors"""	683	protein-coding gene	gene with protein product	"""exchange factor found in platelets and leukemic and neuronal tissues, XPLN"", ""RhoGEF protein"""	612115				10873612	Standard	NM_019555		Approved	STA3, XPLN, GEF3, DKFZP434F2429	uc003dih.2	Q9NR81	OTTHUMG00000158857	ENST00000296315.3:c.163G>A	3.37:g.56807778C>T	ENSP00000296315:p.Val55Met					ARHGEF3_uc011bew.1_Missense_Mutation_p.V55M|ARHGEF3_uc003dih.2_Missense_Mutation_p.V87M|ARHGEF3_uc011bev.1_Missense_Mutation_p.V26M|ARHGEF3_uc003dif.2_Missense_Mutation_p.V61M|ARHGEF3_uc010hmy.1_Translation_Start_Site|ARHGEF3_uc003dii.2_Missense_Mutation_p.V55M	p.V55M	NM_019555	NP_062455	Q9NR81	ARHG3_HUMAN		KIRC - Kidney renal clear cell carcinoma(284;0.0161)|Kidney(284;0.019)|OV - Ovarian serous cystadenocarcinoma(275;0.193)	2	332	-			55					A8K5U7|Q4FZB6|Q4QQI5|Q4QQQ0|Q59F00|Q6NUN3|Q7Z4U2|Q7Z5T2|Q9H7T4	Missense_Mutation	SNP	ENST00000296315.3	37	c.163G>A	CCDS2878.1	.	.	.	.	.	.	.	.	.	.	C	29.7	5.024752	0.93518	.	.	ENSG00000163947	ENST00000296315;ENST00000338458;ENST00000413728;ENST00000496106;ENST00000497267;ENST00000495373;ENST00000468727;ENST00000473779;ENST00000468466	T;T;T;T;T;T	0.26957	1.81;1.7;1.7;1.73;1.72;1.88	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.52980	0.1768	M	0.73962	2.25	0.80722	D	1	D;D;D;D;D;D	0.89917	0.999;0.999;0.999;1.0;1.0;1.0	D;P;P;D;P;D	0.68943	0.915;0.88;0.88;0.961;0.88;0.961	T	0.55679	-0.8103	10	0.72032	D	0.01	-9.238	19.3092	0.94179	0.0:1.0:0.0:0.0	.	61;26;55;87;55;61	E9PG37;E7EU49;C9J586;Q9NR81-2;Q9NR81;Q9NR81-3	.;.;.;.;ARHG3_HUMAN;.	M	55;87;61;61;26;55;56;73;87	ENSP00000296315:V55M;ENSP00000341071:V87M;ENSP00000410922:V61M;ENSP00000420420:V61M;ENSP00000418826:V26M;ENSP00000417986:V55M	ENSP00000296315:V55M	V	-	1	0	ARHGEF3	56782818	1.000000	0.71417	0.967000	0.41034	0.902000	0.53008	7.306000	0.78905	2.655000	0.90218	0.650000	0.86243	GTG		0.478	ARHGEF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352431.2	NM_019555		3	12	0	0	0	0.014758	0	3	12				
EGF	1950	broad.mit.edu	37	4	110914495	110914495	+	Missense_Mutation	SNP	C	C	T	rs144527372		TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr4:110914495C>T	ENST00000265171.5	+	19	3272	c.2827C>T	c.(2827-2829)Cgc>Tgc	p.R943C	EGF_ENST00000503392.1_Intron|RNU6-35P_ENST00000384530.1_RNA|EGF_ENST00000509793.1_Missense_Mutation_p.R901C	NM_001178130.1|NM_001963.4	NP_001171601.1|NP_001954.2	P01133	EGF_HUMAN	epidermal growth factor	943	EGF-like 8; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				activation of MAPKK activity (GO:0000186)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|branching morphogenesis of an epithelial tube (GO:0048754)|DNA replication (GO:0006260)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mammary gland alveolus development (GO:0060749)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of secretion (GO:0051048)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cerebellar granule cell precursor proliferation (GO:0021940)|positive regulation of DNA binding (GO:0043388)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of calcium ion import (GO:0090279)|regulation of protein localization to cell surface (GO:2000008)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)	p.R943C(2)		breast(1)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Hepatocellular(203;0.0893)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	Sucralfate(DB00364)	GTGTGCTGGACGCCTGTCTGA	0.527													C|||	1	0.000199681	0.0008	0.0	5008	,	,		13715	0.0		0.0	False		,,,				2504	0.0						uc003hzy.3		NA																	2	Substitution - Missense(2)		lung(1)|endometrium(1)	ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4						c.(2827-2829)CGC>TGC		epidermal growth factor precursor	Sulindac(DB00605)	C	,CYS/ARG,CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	206.0	182.0	191.0		,2701,2827	-8.3	0.0	4	dbSNP_134	191	0,8600		0,0,4300	yes	intron,missense,missense	EGF	NM_001178130.1,NM_001178131.1,NM_001963.4	,180,180	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	,benign,benign	,901/1166,943/1208	110914495	2,13004	2203	4300	6503	SO:0001583	missense	1950				angiogenesis|DNA replication|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of secretion|platelet activation|platelet degranulation|positive regulation of catenin import into nucleus|positive regulation of epidermal growth factor receptor activity|positive regulation of MAP kinase activity|positive regulation of mitosis|regulation of calcium ion import|regulation of protein localization at cell surface	integral to membrane|plasma membrane|platelet alpha granule lumen	calcium ion binding|epidermal growth factor receptor binding|growth factor activity|transmembrane receptor protein tyrosine kinase activator activity	g.chr4:110914495C>T	X04571	CCDS3689.1, CCDS54794.1, CCDS54795.1	4q25	2012-10-02	2010-05-11		ENSG00000138798	ENSG00000138798			3229	protein-coding gene	gene with protein product		131530	"""epidermal growth factor (beta-urogastrone)"""				Standard	NM_001963		Approved		uc003hzy.4	P01133	OTTHUMG00000132044	ENST00000265171.5:c.2827C>T	4.37:g.110914495C>T	ENSP00000265171:p.Arg943Cys					EGF_uc011cfu.1_Missense_Mutation_p.R901C|EGF_uc011cfv.1_Intron|EGF_uc010imk.2_Missense_Mutation_p.R91C	p.R943C	NM_001963	NP_001954	P01133	EGF_HUMAN		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	19	3279	+		Hepatocellular(203;0.0893)	943			EGF-like 8; calcium-binding (Potential).|Extracellular (Potential).		B4DRK7|E7EVD2|E9PBF0|Q52LZ6	Missense_Mutation	SNP	ENST00000265171.5	37	c.2827C>T	CCDS3689.1	.	.	.	.	.	.	.	.	.	.	C	11.78	1.739752	0.30865	4.54E-4	0.0	ENSG00000138798	ENST00000509793;ENST00000265171	T;T	0.19105	2.17;2.17	4.75	-8.32	0.00996	Epidermal growth factor-like, type 3 (1);	0.673689	0.15418	N	0.263368	T	0.08626	0.0214	N	0.19112	0.55	0.09310	N	1	B;B	0.12013	0.004;0.005	B;B	0.12156	0.004;0.007	T	0.10451	-1.0629	10	0.44086	T	0.13	.	5.4013	0.16297	0.1394:0.3142:0.4491:0.0973	.	901;943	P01133-2;P01133	.;EGF_HUMAN	C	901;943	ENSP00000424316:R901C;ENSP00000265171:R943C	ENSP00000265171:R943C	R	+	1	0	EGF	111133944	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.503000	0.06383	-1.650000	0.01506	0.650000	0.86243	CGC		0.527	EGF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255065.1			17	64	0	0	0	0.0333	0	17	64				
SLC4A9	83697	broad.mit.edu	37	5	139751848	139751848	+	Nonsense_Mutation	SNP	C	C	T			TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr5:139751848C>T	ENST00000230993.6	+	20	2799	c.2764C>T	c.(2764-2766)Cga>Tga	p.R922*	SLC4A9_ENST00000507527.1_Nonsense_Mutation_p.R922*|SLC4A9_ENST00000506757.2_Nonsense_Mutation_p.R898*|SLC4A9_ENST00000506545.1_Nonsense_Mutation_p.R835*|SLC4A9_ENST00000432095.2_Nonsense_Mutation_p.R884*|CTC-329D1.2_ENST00000507521.1_RNA	NM_001258428.1	NP_001245357.1	Q96Q91	B3A4_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 9	922	Membrane (anion exchange).				bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)	p.R922*(2)|p.R896*(1)		endometrium(4)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGTGGGGGTCCGAAAGGCCCT	0.542																																							uc003lfm.2		NA																	3	Substitution - Nonsense(3)		lung(3)	large_intestine(1)	1						c.(2764-2766)CGA>TGA		solute carrier family 4, sodium bicarbonate							27.0	28.0	28.0					5																	139751848		1882	4108	5990	SO:0001587	stop_gained	83697					integral to membrane|plasma membrane	inorganic anion exchanger activity|sodium:bicarbonate symporter activity	g.chr5:139751848C>T	AF313465	CCDS47278.1, CCDS58973.1, CCDS58974.1, CCDS58975.1	5q31.3	2013-05-22			ENSG00000113073	ENSG00000113073		"""Solute carriers"""	11035	protein-coding gene	gene with protein product		610207				11305939	Standard	NM_031467		Approved	AE4	uc003lfk.2	Q96Q91	OTTHUMG00000163352	ENST00000230993.6:c.2764C>T	5.37:g.139751848C>T	ENSP00000230993:p.Arg922*					SLC4A9_uc003lfj.2_Nonsense_Mutation_p.R898*|SLC4A9_uc011czg.1_Nonsense_Mutation_p.R835*|SLC4A9_uc003lfl.2_Nonsense_Mutation_p.R898*|SLC4A9_uc003lfk.2_Nonsense_Mutation_p.R884*	p.R922*	NM_031467	NP_113655	Q96Q91	B3A4_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		20	2799	+			922			Membrane (anion exchange).		B7ZL63|D3DQD4|D3DQD5|D3DQD6|E9PDK1|Q96RM5|Q9BXF2|Q9BXN3	Nonsense_Mutation	SNP	ENST00000230993.6	37	c.2764C>T	CCDS58973.1	.	.	.	.	.	.	.	.	.	.	C	39	7.568913	0.98365	.	.	ENSG00000113073	ENST00000230993;ENST00000506757;ENST00000432095;ENST00000506545;ENST00000507527	.	.	.	4.99	4.09	0.47781	.	0.000000	0.52532	D	0.000069	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.2128	0.65776	0.1506:0.8494:0.0:0.0	.	.	.	.	X	922;898;884;835;922	.	ENSP00000230993:R922X	R	+	1	2	SLC4A9	139732032	0.487000	0.25988	1.000000	0.80357	0.997000	0.91878	0.310000	0.19356	1.275000	0.44379	0.557000	0.71058	CGA		0.542	SLC4A9-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000372823.1	NM_031467		6	9	0	0	0	0.021553	0	6	9				
PCDHB4	56131	broad.mit.edu	37	5	140503027	140503027	+	Missense_Mutation	SNP	G	G	A			TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr5:140503027G>A	ENST00000194152.1	+	1	1447	c.1447G>A	c.(1447-1449)Gcc>Acc	p.A483T	AC005754.8_ENST00000606030.1_lincRNA	NM_018938.2	NP_061761.1	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4	483	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A483T(1)		autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|lung(35)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	67			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGGCACCAACGCCCAGGTCAC	0.657																																							uc003lip.1		NA																	1	Substitution - Missense(1)		lung(1)	upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3						c.(1447-1449)GCC>ACC		protocadherin beta 4 precursor							39.0	45.0	43.0					5																	140503027		2199	4290	6489	SO:0001583	missense	56131				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	cytoplasm|integral to plasma membrane|intermediate filament cytoskeleton	calcium ion binding	g.chr5:140503027G>A	AF152497	CCDS4246.1	5q31	2010-01-26			ENSG00000081818	ENSG00000081818		"""Cadherins / Protocadherins : Clustered"""	8689	other	protocadherin		606330				10380929	Standard	NM_018938		Approved	PCDH-BETA4	uc003lip.1	Q9Y5E5	OTTHUMG00000129617	ENST00000194152.1:c.1447G>A	5.37:g.140503027G>A	ENSP00000194152:p.Ala483Thr						p.A483T	NM_018938	NP_061761	Q9Y5E5	PCDB4_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)		1	1447	+			483			Cadherin 5.|Extracellular (Potential).		Q4V761	Missense_Mutation	SNP	ENST00000194152.1	37	c.1447G>A	CCDS4246.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.979987	0.74360	.	.	ENSG00000081818	ENST00000194152	T	0.52295	0.67	4.1	4.1	0.47936	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.74974	0.3787	M	0.92691	3.335	0.51233	D	0.999911	D	0.76494	0.999	D	0.71656	0.974	T	0.83099	-0.0129	9	0.87932	D	0	.	16.5721	0.84615	0.0:0.0:1.0:0.0	.	483	Q9Y5E5	PCDB4_HUMAN	T	483	ENSP00000194152:A483T	ENSP00000194152:A483T	A	+	1	0	PCDHB4	140483211	0.327000	0.24678	0.992000	0.48379	0.501000	0.33797	2.316000	0.43761	2.307000	0.77673	0.650000	0.86243	GCC		0.657	PCDHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251812.2	NM_018938		16	61	0	0	0	0.049695	0	16	61				
PCDHGA3	56112	broad.mit.edu	37	5	140723793	140723793	+	Missense_Mutation	SNP	C	C	T			TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr5:140723793C>T	ENST00000253812.6	+	1	193	c.193C>T	c.(193-195)Cgc>Tgc	p.R65C	PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018916.3|NM_032011.1	NP_061739.2|NP_114400.1	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3	65	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R65C(1)		breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGCGGAGTCCGCATCGTCTC	0.617											OREG0016855	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																											uc003ljm.1		NA																	1	Substitution - Missense(1)		lung(1)	breast(1)	1						c.(193-195)CGC>TGC		protocadherin gamma subfamily A, 3 isoform 1							77.0	91.0	86.0					5																	140723793		2178	4288	6466	SO:0001583	missense	56112				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	g.chr5:140723793C>T	AF152510	CCDS47290.1, CCDS75329.1	5q31	2010-01-26			ENSG00000254245	ENSG00000254245		"""Cadherins / Protocadherins : Clustered"""	8701	other	protocadherin		606290				10380929	Standard	NM_032011		Approved	PCDH-GAMMA-A3		Q9Y5H0	OTTHUMG00000163680	ENST00000253812.6:c.193C>T	5.37:g.140723793C>T	ENSP00000253812:p.Arg65Cys		OREG0016855	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1658	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc010jfx.1_5'UTR|PCDHGA3_uc011dap.1_Missense_Mutation_p.R65C	p.R65C	NM_018916	NP_061739	Q9Y5H0	PCDG3_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		1	193	+			65			Cadherin 1.|Extracellular (Potential).		Q9Y5D4	Missense_Mutation	SNP	ENST00000253812.6	37	c.193C>T	CCDS47290.1	.	.	.	.	.	.	.	.	.	.	.	18.21	3.573221	0.65765	.	.	ENSG00000254245	ENST00000253812	T	0.38887	1.11	5.65	5.65	0.86999	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	0.000000	0.34025	U	0.004321	D	0.82586	0.5069	H	0.99800	4.79	0.51233	D	0.999914	D;D	0.89917	1.0;1.0	D;D	0.85130	0.995;0.997	D	0.90474	0.4455	10	0.87932	D	0	.	19.7068	0.96076	0.0:1.0:0.0:0.0	.	65;65	Q9Y5H0-2;Q9Y5H0	.;PCDG3_HUMAN	C	65	ENSP00000253812:R65C	ENSP00000253812:R65C	R	+	1	0	PCDHGA3	140703977	0.998000	0.40836	1.000000	0.80357	0.473000	0.32948	3.834000	0.55798	2.824000	0.97209	0.655000	0.94253	CGC		0.617	PCDHGA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377017.1	NM_018916		7	113	0	0	0	0.038147	0	7	113				
TENM2	57451	broad.mit.edu	37	5	167671581	167671581	+	Missense_Mutation	SNP	G	G	A			TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr5:167671581G>A	ENST00000518659.1	+	26	5716	c.5677G>A	c.(5677-5679)Gtg>Atg	p.V1893M	TENM2_ENST00000519204.1_Missense_Mutation_p.V1772M|TENM2_ENST00000520394.1_Missense_Mutation_p.V1654M|TENM2_ENST00000403607.2_Missense_Mutation_p.V1717M|TENM2_ENST00000545108.1_Missense_Mutation_p.V1892M	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	1893					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.V1893M(1)|p.V1772M(1)|p.V1726M(1)									AGCTGTCAACGTGTCATACTT	0.597																																							uc010jjd.2		NA																	3	Substitution - Missense(3)		lung(3)	ovary(6)|central_nervous_system(4)	10						c.(5650-5652)GTG>ATG		odz, odd Oz/ten-m homolog 2							60.0	67.0	65.0					5																	167671581		2006	4178	6184	SO:0001583	missense	57451							g.chr5:167671581G>A	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"""odz, odd Oz/ten-m homolog 2 (Drosophila)"""	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.5677G>A	5.37:g.167671581G>A	ENSP00000429430:p.Val1893Met					ODZ2_uc003lzr.3_Missense_Mutation_p.V1654M|ODZ2_uc003lzt.3_Missense_Mutation_p.V1257M|ODZ2_uc010jje.2_Missense_Mutation_p.V1148M	p.V1884M	NM_001122679	NP_001116151			Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)	26	5650	+	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)						Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	37	c.5650G>A		.	.	.	.	.	.	.	.	.	.	G	19.93	3.917278	0.73098	.	.	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	D;D;D;D;D	0.90676	-2.24;-2.23;-2.34;-2.68;-2.71	4.79	4.79	0.61399	.	0.000000	0.85682	D	0.000000	D	0.94860	0.8339	M	0.71581	2.175	0.58432	D	0.999999	D;D;D	0.89917	0.999;0.998;1.0	D;D;D	0.80764	0.967;0.928;0.994	D	0.95535	0.8607	10	0.87932	D	0	.	17.8465	0.88731	0.0:0.0:1.0:0.0	.	1892;1893;1654	F5H2D1;Q9NT68;F8VNQ3	.;TEN2_HUMAN;.	M	1893;1892;1772;1654;1717	ENSP00000429430:V1893M;ENSP00000438635:V1892M;ENSP00000428964:V1772M;ENSP00000427874:V1654M;ENSP00000384905:V1717M	ENSP00000384905:V1717M	V	+	1	0	ODZ2	167604159	1.000000	0.71417	0.975000	0.42487	0.424000	0.31475	7.965000	0.87945	2.214000	0.71695	0.561000	0.74099	GTG		0.597	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679		3	51	0	0	0	0.004672	0	3	51				
FOXP2	93986	broad.mit.edu	37	7	114282647	114282647	+	Missense_Mutation	SNP	C	C	A			TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr7:114282647C>A	ENST00000393494.2	+	7	1237	c.958C>A	c.(958-960)Cag>Aag	p.Q320K	FOXP2_ENST00000390668.3_Missense_Mutation_p.Q344K|FOXP2_ENST00000403559.4_Missense_Mutation_p.Q337K|FOXP2_ENST00000408937.3_Missense_Mutation_p.Q345K|FOXP2_ENST00000393491.3_Missense_Mutation_p.Q228K|FOXP2_ENST00000393500.3_Missense_Mutation_p.Q245K|FOXP2_ENST00000360232.4_Missense_Mutation_p.Q320K|FOXP2_ENST00000378237.3_Missense_Mutation_p.Q320K|FOXP2_ENST00000350908.4_Missense_Mutation_p.Q320K|FOXP2_ENST00000393498.2_Missense_Mutation_p.Q299K|FOXP2_ENST00000393489.3_Missense_Mutation_p.Q228K			O15409	FOXP2_HUMAN	forkhead box P2	320					camera-type eye development (GO:0043010)|caudate nucleus development (GO:0021757)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|growth (GO:0040007)|lung alveolus development (GO:0048286)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of mesenchymal cell proliferation (GO:0002053)|post-embryonic development (GO:0009791)|putamen development (GO:0021758)|righting reflex (GO:0060013)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|vocal learning (GO:0042297)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q345K(1)		breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	52						AGTGAATGGACAGTCTTCAGT	0.388																																							uc003vhb.2		NA																	1	Substitution - Missense(1)		lung(1)	ovary(4)|pancreas(1)|lung(1)|breast(1)|skin(1)	8						c.(958-960)CAG>AAG		forkhead box P2 isoform I							187.0	159.0	168.0					7																	114282647		2203	4300	6503	SO:0001583	missense	93986				camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of transcription, DNA-dependent|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding	g.chr7:114282647C>A	U80741	CCDS5760.1, CCDS5761.1, CCDS43635.1, CCDS5761.2, CCDS55154.1	7q31	2008-07-18			ENSG00000128573	ENSG00000128573		"""Forkhead boxes"""	13875	protein-coding gene	gene with protein product	"""trinucleotide repeat containing 10"", ""forkhead/winged-helix transcription factor"", ""speech and language disorder 1"", ""CAG repeat protein 44"""	605317		TNRC10, SPCH1		11586359, 9225980	Standard	NM_014491		Approved	CAGH44	uc003vgz.3	O15409	OTTHUMG00000023131	ENST00000393494.2:c.958C>A	7.37:g.114282647C>A	ENSP00000377132:p.Gln320Lys					FOXP2_uc003vgu.2_RNA|FOXP2_uc003vgz.2_Missense_Mutation_p.Q345K|FOXP2_uc003vha.2_Missense_Mutation_p.Q228K|FOXP2_uc011kmu.1_Missense_Mutation_p.Q337K|FOXP2_uc011kmv.1_Missense_Mutation_p.Q319K|FOXP2_uc010ljz.1_Missense_Mutation_p.Q228K|FOXP2_uc003vgx.2_Missense_Mutation_p.Q320K|FOXP2_uc003vhd.2_Missense_Mutation_p.Q320K|FOXP2_uc003vhc.2_Missense_Mutation_p.Q345K	p.Q320K	NM_014491	NP_055306	O15409	FOXP2_HUMAN			7	1332	+			320					A0AUV6|A4D0U8|A6NNW4|B4DLD9|Q6ZND1|Q75MJ3|Q8IZE0|Q8N0W2|Q8N6B7|Q8N6B8|Q8NFQ1|Q8NFQ2|Q8NFQ3|Q8NFQ4|Q8TD74	Missense_Mutation	SNP	ENST00000393494.2	37	c.958C>A	CCDS5760.1	.	.	.	.	.	.	.	.	.	.	C	16.09	3.023365	0.54683	.	.	ENSG00000128573	ENST00000393500;ENST00000393494;ENST00000408937;ENST00000403559;ENST00000350908;ENST00000393498;ENST00000378237;ENST00000393489;ENST00000360232;ENST00000390668;ENST00000393491	T;T;T;T;T;T;T;T;T;T	0.19806	2.16;2.16;2.16;2.16;2.16;2.12;2.16;2.16;2.16;2.16	5.02	4.14	0.48551	.	0.108672	0.64402	D	0.000003	T	0.42040	0.1185	M	0.72118	2.19	0.58432	D	0.999996	P;P;P;P;P;P;P	0.43578	0.713;0.713;0.458;0.593;0.811;0.713;0.811	P;P;P;P;P;P;P	0.57846	0.678;0.678;0.678;0.828;0.828;0.678;0.828	T	0.36065	-0.9763	10	0.66056	D	0.02	.	13.6889	0.62533	0.0:0.9249:0.0:0.0751	.	319;337;228;320;344;320;345	B7ZLK5;B4DLD9;Q0PRL4;O15409-6;Q8N6B5;O15409;O15409-4	.;.;.;.;.;FOXP2_HUMAN;.	K	245;320;345;337;320;297;320;228;320;344;228	ENSP00000377137:Q245K;ENSP00000377132:Q320K;ENSP00000386200:Q345K;ENSP00000385069:Q337K;ENSP00000265436:Q320K;ENSP00000367482:Q320K;ENSP00000377129:Q228K;ENSP00000353367:Q320K;ENSP00000375084:Q344K;ENSP00000377130:Q228K	ENSP00000265436:Q320K	Q	+	1	0	FOXP2	114069883	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.442000	0.80503	1.248000	0.43934	-0.384000	0.06662	CAG		0.388	FOXP2-014	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317366.1	NM_014491		8	74	1	0	0.00448238	0.047766	0.00499958	8	74				
PTPRZ1	5803	broad.mit.edu	37	7	121651781	121651781	+	Missense_Mutation	SNP	G	G	A	rs200882556	byFrequency	TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr7:121651781G>A	ENST00000393386.2	+	12	3092	c.2681G>A	c.(2680-2682)aGt>aAt	p.S894N	PTPRZ1_ENST00000449182.1_Intron|PTPRZ1_ENST00000483028.1_Intron	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	894					axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.S894N(2)		NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						GAATTTGGTAGTGAATCTGGT	0.478													G|||	13	0.00259585	0.0	0.0	5008	,	,		20973	0.0		0.0	False		,,,				2504	0.0133						uc003vjy.2		NA																	2	Substitution - Missense(2)		lung(2)	ovary(3)|large_intestine(2)|lung(2)|central_nervous_system(1)|kidney(1)	9						c.(2680-2682)AGT>AAT		protein tyrosine phosphatase, receptor-type,							100.0	88.0	92.0					7																	121651781		2203	4300	6503	SO:0001583	missense	5803				central nervous system development	integral to plasma membrane	protein binding|protein tyrosine/threonine phosphatase activity|transmembrane receptor protein tyrosine phosphatase activity	g.chr7:121651781G>A	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.2681G>A	7.37:g.121651781G>A	ENSP00000377047:p.Ser894Asn					PTPRZ1_uc003vjz.2_Intron|PTPRZ1_uc011knt.1_Intron	p.S894N	NM_002851	NP_002842	P23471	PTPRZ_HUMAN			12	3076	+			894			Extracellular (Potential).		A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	37	c.2681G>A	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	G	8.425	0.847369	0.17034	.	.	ENSG00000106278	ENST00000393386	T	0.42513	0.97	5.86	4.88	0.63580	.	0.201850	0.44097	D	0.000485	T	0.22126	0.0533	N	0.25647	0.755	0.80722	D	1	B	0.10296	0.003	B	0.08055	0.003	T	0.19844	-1.0293	10	0.08179	T	0.78	.	3.8921	0.09123	0.3231:0.0:0.6769:0.0	.	894	P23471	PTPRZ_HUMAN	N	894	ENSP00000377047:S894N	ENSP00000377047:S894N	S	+	2	0	PTPRZ1	121439017	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.706000	0.47135	2.774000	0.95407	0.650000	0.86243	AGT		0.478	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		16	30	0	0	0	0.028581	0	16	30				
SPAM1	6677	broad.mit.edu	37	7	123594255	123594255	+	Missense_Mutation	SNP	C	C	T	rs377689190		TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr7:123594255C>T	ENST00000439500.1	+	4	1244	c.631C>T	c.(631-633)Cgg>Tgg	p.R211W	SPAM1_ENST00000402183.2_Missense_Mutation_p.R211W|SPAM1_ENST00000223028.7_Missense_Mutation_p.R211W|SPAM1_ENST00000460182.1_Missense_Mutation_p.R211W|SPAM1_ENST00000340011.5_Missense_Mutation_p.R211W	NM_001174045.1|NM_001174046.1	NP_001167516.1|NP_001167517.1	P38567	HYALP_HUMAN	sperm adhesion molecule 1 (PH-20 hyaluronidase, zona pellucida binding)	211					binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	hyalurononglucosaminidase activity (GO:0004415)	p.R211W(2)		breast(1)|cervix(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(23)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						AAAATTACTTCGGCCAAATCA	0.378																																							uc003vld.2		NA																	2	Substitution - Missense(2)		lung(2)	ovary(3)|kidney(1)	4						c.(631-633)CGG>TGG		sperm adhesion molecule 1 isoform 2	Hyaluronidase(DB00070)	C	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	77.0	83.0	81.0		631,631,631,631,631	-1.0	0.0	7		81	1,8597	1.2+/-3.3	0,1,4298	no	missense,missense,missense,missense,missense	SPAM1	NM_001174044.1,NM_001174045.1,NM_001174046.1,NM_003117.4,NM_153189.2	101,101,101,101,101	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	211/510,211/510,211/510,211/512,211/510	123594255	1,13003	2203	4299	6502	SO:0001583	missense	6677				binding of sperm to zona pellucida|carbohydrate metabolic process|cell adhesion|fusion of sperm to egg plasma membrane	anchored to membrane|plasma membrane	hyalurononglucosaminidase activity	g.chr7:123594255C>T	L13781	CCDS5790.1, CCDS5791.1	7q31	2008-05-02			ENSG00000106304	ENSG00000106304			11217	protein-coding gene	gene with protein product		600930				8282124, 8575780	Standard	NM_153189		Approved	HYAL5, PH-20, SPAG15	uc003vle.3	P38567	OTTHUMG00000157284	ENST00000439500.1:c.631C>T	7.37:g.123594255C>T	ENSP00000402123:p.Arg211Trp					SPAM1_uc003vle.2_Missense_Mutation_p.R211W|SPAM1_uc011koa.1_5'Flank|SPAM1_uc003vlf.3_Missense_Mutation_p.R211W|SPAM1_uc010lku.2_Missense_Mutation_p.R211W	p.R211W	NM_153189	NP_694859	P38567	HYALP_HUMAN			4	1033	+			211	R->G: Reduces activity by over 90%.				Q8TC30	Missense_Mutation	SNP	ENST00000439500.1	37	c.631C>T	CCDS5791.1	.	.	.	.	.	.	.	.	.	.	C	18.35	3.605065	0.66445	0.0	1.16E-4	ENSG00000106304	ENST00000402183;ENST00000460182;ENST00000340011;ENST00000439500;ENST00000223028	T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93	6.17	-0.96	0.10340	Aldolase-type TIM barrel (1);Glycoside hydrolase, superfamily (1);	0.204215	0.42548	D	0.000688	T	0.74861	0.3772	H	0.96547	3.84	0.21290	N	0.999731	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.77038	-0.2736	9	.	.	.	-26.04	20.5191	0.99215	0.8136:0.1864:0.0:0.0	.	211;211	Q8TC30;P38567	.;HYALP_HUMAN	W	211	ENSP00000386028:R211W;ENSP00000417934:R211W;ENSP00000345849:R211W;ENSP00000402123:R211W;ENSP00000223028:R211W	.	R	+	1	2	SPAM1	123381491	0.007000	0.16637	0.022000	0.16811	0.934000	0.57294	0.147000	0.16202	-0.161000	0.10983	0.655000	0.94253	CGG		0.378	SPAM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000348309.1			8	69	0	0	0	0.038147	0	8	69				
PTGER4P2	5736	broad.mit.edu	37	9	66499770	66499770	+	IGR	SNP	G	G	T	rs75046133	byFrequency	TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr9:66499770G>T								RP11-262H14.1 (30460 upstream) : RP11-262H14.7 (17435 downstream)																							CAACCTGGTGGCCATCGTGGT	0.582													g|||	500	0.0998403	0.0983	0.1614	5008	,	,		41958	0.0585		0.1342	False		,,,				2504	0.0654						uc004aee.1		NA																	0					0						c.(580-582)GCC>TCC		Homo sapiens hypothetical LOC442421, mRNA (cDNA clone IMAGE:40031134).																																				SO:0001628	intergenic_variant	442421							g.chr9:66499770G>T																													9.37:g.66499770G>T						LOC442421_uc004aed.1_RNA	p.A194S							1	580	+									Missense_Mutation	SNP		37	c.580G>T																																																																																				0	0.582									7	69	1	0	0.000673444	0.069234	0.000765878	7	69				
CBWD6	644019	broad.mit.edu	37	9	69247529	69247529	+	Silent	SNP	G	G	A			TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr9:69247529G>A	ENST00000377457.5	-	5	588	c.483C>T	c.(481-483)taC>taT	p.Y161Y	CBWD6_ENST00000377449.1_Silent_p.Y125Y|CBWD6_ENST00000382399.4_Intron	NM_001085457.1	NP_001078926.1	Q4V339	CBWD6_HUMAN	COBW domain containing 6	161							ATP binding (GO:0005524)	p.Y161Y(1)		lung(4)	4						TACCATCAAGGTAAATATCAC	0.299																																							uc004afj.3		NA																	1	Substitution - coding silent(1)		lung(1)		0						c.(481-483)TAC>TAT		COBW domain containing 6																																				SO:0001819	synonymous_variant	644019						ATP binding	g.chr9:69247529G>A		CCDS43827.1	9q13	2006-06-30			ENSG00000204790	ENSG00000204790			31978	protein-coding gene	gene with protein product							Standard	NM_001085457		Approved	OTTHUMG00000066820	uc004afj.4	Q4V339	OTTHUMG00000066820	ENST00000377457.5:c.483C>T	9.37:g.69247529G>A						CBWD6_uc004afk.3_Intron|CBWD6_uc011lrf.1_Intron	p.Y161Y	NM_001085457	NP_001078926	Q4V339	CBWD6_HUMAN			5	589	-			161						Silent	SNP	ENST00000377457.5	37	c.483C>T	CCDS43827.1																																																																																				0.299	CBWD6-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143172.2	XM_928822		3	18	0	0	0	0.004672	0	3	18				
GARNL3	84253	broad.mit.edu	37	9	130027251	130027251	+	Missense_Mutation	SNP	G	G	A			TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	G	G	-	-	G	G	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr9:130027251G>A	ENST00000373387.4	+	1	447	c.95G>A	c.(94-96)gGc>gAc	p.G32D	GARNL3_ENST00000314904.5_Missense_Mutation_p.G32D|GARNL3_ENST00000435213.2_Missense_Mutation_p.G10D	NM_032293.4	NP_115669.3	Q5VVW2	GARL3_HUMAN	GTPase activating Rap/RanGAP domain-like 3	32					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)|small GTPase regulator activity (GO:0005083)	p.G14D(1)		NS(1)|central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(24)|ovary(1)|skin(1)|urinary_tract(2)	41						GAAGACCTAGGCTGTAGACGT	0.408																																							uc011mae.1		NA																	1	Substitution - Missense(1)		lung(1)	ovary(1)|central_nervous_system(1)|skin(1)	3						c.(94-96)GGC>GAC		GTPase activating Rap/RanGAP domain-like 3							256.0	243.0	248.0					9																	130027251		2203	4300	6503	SO:0001583	missense	84253				regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity|small GTPase regulator activity	g.chr9:130027251G>A	BC034983	CCDS6869.2, CCDS69663.1	9q34.13	2009-09-14	2004-08-09		ENSG00000136895	ENSG00000136895			25425	protein-coding gene	gene with protein product			"""GTPase activating RANGAP domain-like 3"""			11230166	Standard	NM_032293		Approved	DKFZp761J1523, bA356B19.1	uc011mae.2	Q5VVW2	OTTHUMG00000020700	ENST00000373387.4:c.95G>A	9.37:g.130027251G>A	ENSP00000362485:p.Gly32Asp					GARNL3_uc011mad.1_Missense_Mutation_p.G10D	p.G32D	NM_032293	NP_115669	Q5VVW2	GARL3_HUMAN			1	496	+			32					B4DEP7|B7Z3Q6|Q8IYU1|Q8N951|Q8ND89|Q9BQH6	Missense_Mutation	SNP	ENST00000373387.4	37	c.95G>A	CCDS6869.2	.	.	.	.	.	.	.	.	.	.	G	19.23	3.787923	0.70337	.	.	ENSG00000136895	ENST00000439286;ENST00000444677;ENST00000446764;ENST00000373399;ENST00000425970;ENST00000435213;ENST00000314904;ENST00000373387	T;T;T;D;D;D	0.87966	1.85;0.81;0.91;-2.32;-2.27;-2.32	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	D	0.87083	0.6089	N	0.24115	0.695	0.48236	D	0.999614	D;D	0.71674	0.998;0.998	P;P	0.59115	0.852;0.852	D	0.86011	0.1501	9	.	.	.	.	17.5847	0.87978	0.0:0.0:1.0:0.0	.	32;10	Q5VVW2;B7Z3Q6	GARL3_HUMAN;.	D	55;55;55;55;10;10;32;32	ENSP00000400579:G55D;ENSP00000411160:G55D;ENSP00000411329:G10D;ENSP00000396205:G10D;ENSP00000313970:G32D;ENSP00000362485:G32D	.	G	+	2	0	GARNL3	129067072	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.000000	0.88501	2.553000	0.86117	0.650000	0.86243	GGC		0.408	GARNL3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054151.3	NM_032293		20	122	0	0	0	0.076483	0	20	122				
BMP15	9210	broad.mit.edu	37	X	50659038	50659038	+	Nonsense_Mutation	SNP	C	C	T			TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	C	C	-	-	C	C	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chrX:50659038C>T	ENST00000252677.3	+	2	610	c.610C>T	c.(610-612)Cga>Tga	p.R204*		NM_005448.2	NP_005439.2	O95972	BMP15_HUMAN	bone morphogenetic protein 15	204					female gamete generation (GO:0007292)|granulosa cell development (GO:0060016)|ovarian follicle development (GO:0001541)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)		p.R204*(2)		NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|skin(1)	26	Ovarian(276;0.236)					CAGGATCCTACGACTCCGTTT	0.438																																							uc011mnw.1		NA																	2	Substitution - Nonsense(2)		large_intestine(1)|lung(1)	ovary(2)	2						c.(610-612)CGA>TGA		bone morphogenetic protein 15 precursor							143.0	114.0	124.0					X																	50659038		2203	4299	6502	SO:0001587	stop_gained	9210				female gamete generation|granulosa cell development|ovarian follicle development	extracellular space	cytokine activity|growth factor activity	g.chrX:50659038C>T	AF082349	CCDS14334.1	Xp11.2	2013-02-06			ENSG00000130385	ENSG00000130385		"""Bone morphogenetic proteins"""	1068	protein-coding gene	gene with protein product		300247				9849956	Standard	NM_005448		Approved	GDF9B	uc011mnw.2	O95972	OTTHUMG00000021525	ENST00000252677.3:c.610C>T	X.37:g.50659038C>T	ENSP00000252677:p.Arg204*						p.R204*	NM_005448	NP_005439	O95972	BMP15_HUMAN			2	610	+	Ovarian(276;0.236)		204					Q17RM6|Q5JST1|Q9UMS1	Nonsense_Mutation	SNP	ENST00000252677.3	37	c.610C>T	CCDS14334.1	.	.	.	.	.	.	.	.	.	.	c	10.74	1.435110	0.25813	.	.	ENSG00000130385	ENST00000252677	.	.	.	5.52	3.72	0.42706	.	0.992853	0.08201	N	0.982285	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07644	T	0.81	.	3.8331	0.08882	0.2037:0.6096:0.0:0.1867	.	.	.	.	X	204	.	ENSP00000252677:R204X	R	+	1	2	BMP15	50675778	0.000000	0.05858	0.029000	0.17559	0.009000	0.06853	0.433000	0.21477	1.082000	0.41137	0.556000	0.70494	CGA		0.438	BMP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056572.1	NM_005448		16	25	0	0	0	0.0333	0	16	25				
KLHL21	9903	broad.mit.edu	37	1	6655560	6655561	+	Frame_Shift_Ins	INS	-	-	A			TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr1:6655560_6655561insA	ENST00000377658.4	-	3	1535_1536	c.1484_1485insT	c.(1483-1485)atcfs	p.I495fs	KLHL21_ENST00000377663.3_Frame_Shift_Ins_p.I495fs|KLHL21_ENST00000467612.1_Frame_Shift_Ins_p.I128fs|KLHL21_ENST00000463043.1_Frame_Shift_Ins_p.I128fs	NM_014851.2	NP_055666.2	Q9UJP4	KLH21_HUMAN	kelch-like family member 21	495					chromosome passenger complex localization to spindle midzone (GO:0035853)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)|regulation of cytokinesis (GO:0032465)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|polar microtubule (GO:0005827)				central_nervous_system(1)|endometrium(1)|kidney(1)|lung(3)|prostate(2)	8	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;7.39e-28)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;1.36e-07)|COAD - Colon adenocarcinoma(227;1.4e-05)|Kidney(185;4.95e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000528)|KIRC - Kidney renal clear cell carcinoma(229;0.000927)|STAD - Stomach adenocarcinoma(132;0.0172)|READ - Rectum adenocarcinoma(331;0.0644)		TCATGGACGGGATCTTGTCCCA	0.554																																							uc001aoa.2		NA																	0				central_nervous_system(1)	1						c.(1483-1485)ATCfs		kelch-like 21																																				SO:0001589	frameshift_variant	9903				anaphase|cytokinesis|mitosis|protein ubiquitination	Cul3-RING ubiquitin ligase complex|cytoplasm|polar microtubule		g.chr1:6655560_6655561insA	AK090472	CCDS30575.1	1p36	2013-01-30	2013-01-30		ENSG00000162413	ENSG00000162413		"""Kelch-like"", ""BTB/POZ domain containing"""	29041	protein-coding gene	gene with protein product			"""kelch-like 21 (Drosophila)"""				Standard	XM_005263542		Approved	KIAA0469	uc001aoa.3	Q9UJP4	OTTHUMG00000001437	ENST00000377658.4:c.1485dupT	1.37:g.6655561_6655561dupA	ENSP00000366886:p.Ile495fs					KLHL21_uc001anz.1_Frame_Shift_Ins_p.I495fs|KLHL21_uc009vme.2_Frame_Shift_Ins_p.I128fs	p.I495fs	NM_014851	NP_055666	Q9UJP4	KLH21_HUMAN		Colorectal(212;1.36e-07)|COAD - Colon adenocarcinoma(227;1.4e-05)|Kidney(185;4.95e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000528)|KIRC - Kidney renal clear cell carcinoma(229;0.000927)|STAD - Stomach adenocarcinoma(132;0.0172)|READ - Rectum adenocarcinoma(331;0.0644)	3	1536_1537	-	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;7.39e-28)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)	495			Kelch 5.		B3KQP2|O75057|Q5SY26|Q5SY28|Q8N4I6|Q8NF10	Frame_Shift_Ins	INS	ENST00000377658.4	37	c.1484_1485insT	CCDS30575.1																																																																																				0.554	KLHL21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004188.1	NM_014851		9	23	NA	NA	NA	NA	NA	9	23	---	---	---	---
RNF43	54894	broad.mit.edu	37	17	56440903	56440904	+	Frame_Shift_Ins	INS	-	-	AT	rs151209912		TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	-	-	-	-	-	-	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr17:56440903_56440904insAT	ENST00000584437.1	-	3	2388_2389	c.433_434insAT	c.(433-435)cgafs	p.R145fs	RNF43_ENST00000581868.1_Frame_Shift_Ins_p.R18fs|RNF43_ENST00000577625.1_Frame_Shift_Ins_p.R18fs|BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000577716.1_Frame_Shift_Ins_p.R145fs|RNF43_ENST00000500597.2_Frame_Shift_Ins_p.R104fs|RNF43_ENST00000407977.2_Frame_Shift_Ins_p.R145fs|RNF43_ENST00000583753.1_Frame_Shift_Ins_p.R104fs			Q68DV7	RNF43_HUMAN	ring finger protein 43	145					negative regulation of Wnt signaling pathway (GO:0030178)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|stem cell proliferation (GO:0072089)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R145*(1)		NS(1)|biliary_tract(5)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(14)|lung(9)|ovary(2)|pancreas(10)|prostate(1)|skin(4)	60	Medulloblastoma(34;0.127)|all_neural(34;0.237)					AGCAGCAGCTCGATCCTCAGTG	0.594																																							uc002iwf.2		NA																	1	Substitution - Nonsense(1)		pancreas(1)	ovary(1)	1						c.(433-435)CGAfs		ring finger protein 43 precursor																																				SO:0001589	frameshift_variant	54894					endoplasmic reticulum membrane|integral to membrane|nuclear envelope	ligase activity|protein binding|zinc ion binding	g.chr17:56440903_56440904insAT		CCDS11607.1	17q23.2	2013-01-09						"""RING-type (C3HC4) zinc fingers"""	18505	protein-coding gene	gene with protein product		612482					Standard	NM_017763		Approved	FLJ20315, DKFZp781H0392, URCC	uc002iwh.4	Q68DV7		ENST00000584437.1:c.433_434insAT	17.37:g.56440903_56440904insAT	ENSP00000463069:p.Arg145fs					RNF43_uc010wnv.1_Frame_Shift_Ins_p.R104fs|RNF43_uc002iwh.3_Frame_Shift_Ins_p.R145fs|RNF43_uc002iwg.3_Frame_Shift_Ins_p.R145fs|RNF43_uc010dcw.2_Frame_Shift_Ins_p.R18fs	p.R145fs	NM_017763	NP_060233	Q68DV7	RNF43_HUMAN			3	2389_2390	-	Medulloblastoma(34;0.127)|all_neural(34;0.237)		145			Extracellular (Potential).		A8K4R2|B7Z443|B7Z5D5|B7Z5J5|Q65ZA4|Q6AI04|Q9NXD0	Frame_Shift_Ins	INS	ENST00000584437.1	37	c.433_434insAT	CCDS11607.1																																																																																				0.594	RNF43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444713.1	NM_017763		16	153	NA	NA	NA	NA	NA	16	153	---	---	---	---
DNAJC13	23317	broad.mit.edu	37	3	132182659	132182662	+	Splice_Site	DEL	TAGG	TAGG	-			TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	TAGG	TAGG	-	-	TAGG	TAGG	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr3:132182659_132182662delTAGG	ENST00000260818.6	+	17	2138_2140	c.1890_1892delTAGG	c.(1888-1893)aatagg>aag	p.NR630fs	DNAJC13_ENST00000486798.1_3'UTR	NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	630					osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						TGCTTACAAATAGGTAGGTGATTT	0.353																																							uc003eor.2		NA																	0				ovary(1)|breast(1)	2						c.e17+1		DnaJ (Hsp40) homolog, subfamily C, member 13																																				SO:0001630	splice_region_variant	23317						heat shock protein binding	g.chr3:132182659_132182662delTAGG	AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246		"""Heat shock proteins / DNAJ (HSP40)"""	30343	protein-coding gene	gene with protein product		614334				12438707	Standard	NM_015268		Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.1892+1TAGG>-	3.37:g.132182663_132182666delTAGG						DNAJC13_uc010htq.1_Splice_Site_p.R631_splice	p.R631_splice	NM_015268	NP_056083	O75165	DJC13_HUMAN			17	1957	+								Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Splice_Site	DEL	ENST00000260818.6	37	c.1892_splice	CCDS33857.1																																																																																				0.353	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268	Frame_Shift_Del	10	77	NA	NA	NA	NA	NA	10	77	---	---	---	---
SLC35G2	80723	broad.mit.edu	37	3	136573486	136573486	+	Frame_Shift_Del	DEL	A	A	-			TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	A	A	-	-	A	A	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr3:136573486delA	ENST00000446465.2	+	2	812	c.184delA	c.(184-186)aaafs	p.K64fs	SLC35G2_ENST00000393079.3_Frame_Shift_Del_p.K64fs|RP11-85F14.5_ENST00000470236.1_RNA|RP11-85F14.5_ENST00000461864.1_RNA|RP11-85F14.5_ENST00000474250.1_RNA	NM_025246.2	NP_079522.2			solute carrier family 35, member G2																		GAGTGAAATGAAAAAAAAAGG	0.413																																							uc003erf.3		NA																	0				ovary(1)	1						c.(184-186)AAAfs		transmembrane protein 22							88.0	99.0	95.0					3																	136573486		2203	4300	6503	SO:0001589	frameshift_variant	80723					Golgi apparatus|integral to membrane		g.chr3:136573486delA	BC022557	CCDS3091.1	3q22.3	2013-05-22	2012-03-09	2012-03-09	ENSG00000168917	ENSG00000168917		"""Solute carriers"""	28480	protein-coding gene	gene with protein product			"""transmembrane protein 22"""	TMEM22		11230166	Standard	NM_001097600		Approved	MGC3295, DKFZp564K2464	uc003erf.4	Q8TBE7	OTTHUMG00000159787	ENST00000446465.2:c.184delA	3.37:g.136573486delA	ENSP00000400839:p.Lys64fs					TMEM22_uc003erg.3_Frame_Shift_Del_p.K62fs|TMEM22_uc010hub.2_Frame_Shift_Del_p.K62fs	p.K62fs	NM_001097600	NP_001091069	Q8TBE7	TMM22_HUMAN			2	398	+			62						Frame_Shift_Del	DEL	ENST00000446465.2	37	c.184delA	CCDS3091.1																																																																																				0.413	SLC35G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357317.1	NM_025246		8	141	NA	NA	NA	NA	NA	8	141	---	---	---	---
ZDHHC14	79683	broad.mit.edu	37	6	157803062	157803064	+	In_Frame_Del	DEL	CGG	CGG	-			TCGA-05-5429-01A-01D-1625-08	TCGA-05-5429-10A-01D-1625-08	CGG	CGG	-	-	CGG	CGG	Unknown	Untested	Somatic	Unspecified	WXS	none	NA	NA	Illumina HiSeq	37d0cf1b-1743-4852-8073-372b16b5c17d	feaed996-83e7-46af-9e74-3d70b303ea6a	g.chr6:157803062_157803064delCGG	ENST00000359775.5	+	1	898_900	c.9_11delCGG	c.(7-12)cccggc>ccc	p.G7del	ZDHHC14_ENST00000414563.2_In_Frame_Del_p.G7del			Q8IZN3	ZDH14_HUMAN	zinc finger, DHHC-type containing 14	7					protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|skin(1)	17		Breast(66;0.00586)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.9e-17)|BRCA - Breast invasive adenocarcinoma(81;5.8e-05)		GGATGCCTCCCGGCGGCGGCGGG	0.754																																							uc003qqt.2		NA																	0				ovary(1)|skin(1)	2						c.(7-12)CCCGGC>CCC		zinc finger, DHHC-type containing 14 isoform 1			,	28,4004		2,24,1990					,	4.2	1.0			9	81,7879		3,75,3902	no	coding,coding	ZDHHC14	NM_153746.1,NM_024630.2	,	5,99,5892	A1A1,A1R,RR		1.0176,0.6944,0.9089	,	,		109,11883				SO:0001651	inframe_deletion	79683					integral to membrane	acyltransferase activity|zinc ion binding	g.chr6:157803062_157803064delCGG	AF542388	CCDS5252.1, CCDS47510.1	6q25.3	2008-05-02			ENSG00000175048	ENSG00000175048		"""Zinc fingers, DHHC-type"""	20341	protein-coding gene	gene with protein product							Standard	NM_024630		Approved	FLJ20984, NEW1CP	uc003qqt.3	Q8IZN3	OTTHUMG00000015896	ENST00000359775.5:c.9_11delCGG	6.37:g.157803071_157803073delCGG	ENSP00000352821:p.Gly7del					ZDHHC14_uc003qqs.2_In_Frame_Del_p.G7del	p.G7del	NM_024630	NP_078906	Q8IZN3	ZDH14_HUMAN		OV - Ovarian serous cystadenocarcinoma(65;2.9e-17)|BRCA - Breast invasive adenocarcinoma(81;5.8e-05)	1	506_508	+		Breast(66;0.00586)|Ovarian(120;0.123)	7					A6NDB7|Q5JS07|Q5JS08|Q6PHS4|Q8IZN2|Q9H7F1	In_Frame_Del	DEL	ENST00000359775.5	37	c.9_11delCGG	CCDS5252.1																																																																																				0.754	ZDHHC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042841.2	NM_153746		2	4	NA	NA	NA	NA	NA	2	4	---	---	---	---
