#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
PRAMEF11	440560	broad.mit.edu	37	1	12885289	12885289	+	Silent	SNP	G	G	T	rs200907281	byFrequency	TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr1:12885289G>T	ENST00000535591.1	-	4	1017	c.822C>A	c.(820-822)ctC>ctA	p.L274L	RP5-845O24.8_ENST00000438401.1_lincRNA	NM_001146344.1	NP_001139816.1	O60813	PRA11_HUMAN	PRAME family member 11	274					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)			p.L274L(3)		NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|lung(7)|pancreas(2)|skin(4)|urinary_tract(1)	27						GGCACTGGGAGAGATGCTTCA	0.458													.|||	1958	0.390974	0.1899	0.3501	5008	,	,		13255	0.6895		0.4553	False		,,,				2504	0.318					uc001auk.2																			3	Substitution - coding silent(3)		kidney(2)|endometrium(1)		0						c.(820-822)CTC>CTA		PRAME family member 11							67.0	40.0	49.0					1																	12885289		582	1168	1750	SO:0001819	synonymous_variant	440560							g.chr1:12885289G>T	AL049680	CCDS53268.1	1p36.21	2013-01-17			ENSG00000204513	ENSG00000239810		"""-"""	14086	protein-coding gene	gene with protein product							Standard	XM_006710645		Approved		uc001auk.2	O60813	OTTHUMG00000001929	ENST00000535591.1:c.822C>A	1.37:g.12885289G>T							p.L274L	NM_001146344	NP_001139816	O60813	PRA11_HUMAN			4	1018	-			274			LRR 3.			Silent	SNP	ENST00000535591.1	37	c.822C>A	CCDS53268.1																																																																																				0.458	PRAMEF11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_496341	
KTI12	112970	broad.mit.edu	37	1	52498511	52498511	+	Missense_Mutation	SNP	C	C	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr1:52498511C>T	ENST00000371614.1	-	1	977	c.923G>A	c.(922-924)cGg>cAg	p.R308Q	RP11-91A18.4_ENST00000425802.1_RNA|TXNDC12_ENST00000371626.4_Intron	NM_138417.2	NP_612426.1	Q96EK9	KTI12_HUMAN	KTI12 homolog, chromatin associated (S. cerevisiae)	308							ATP binding (GO:0005524)			central_nervous_system(2)|endometrium(1)|kidney(1)|lung(4)|ovary(1)|stomach(2)|urinary_tract(1)	12						CCGGGTAAACCGCAAGTGCTC	0.552																																						uc001ctj.1																			0				central_nervous_system(2)	2						c.(922-924)CGG>CAG		KTI12 homolog, chromatin associated							86.0	86.0	86.0					1																	52498511		2203	4300	6503	SO:0001583	missense	112970						ATP binding	g.chr1:52498511C>T		CCDS562.1	1p32.3	2008-02-05			ENSG00000198841	ENSG00000198841			25160	protein-coding gene	gene with protein product						11929532	Standard	NM_138417		Approved	TOT4, MGC20419, SBBI81	uc001ctj.1	Q96EK9	OTTHUMG00000008630	ENST00000371614.1:c.923G>A	1.37:g.52498511C>T	ENSP00000360676:p.Arg308Gln					TXNDC12_uc001cti.2_Intron	p.R308Q	NM_138417	NP_612426	Q96EK9	KTI12_HUMAN			1	962	-			308						Missense_Mutation	SNP	ENST00000371614.1	37	c.923G>A	CCDS562.1	.	.	.	.	.	.	.	.	.	.	C	8.827	0.938874	0.18281	.	.	ENSG00000198841	ENST00000371614	T	0.30182	1.54	4.64	-4.94	0.03057	.	0.636054	0.14067	N	0.343689	T	0.11707	0.0285	N	0.12746	0.255	0.09310	N	1	B	0.17667	0.023	B	0.13407	0.009	T	0.20338	-1.0278	10	0.24483	T	0.36	.	5.3767	0.16170	0.5165:0.1715:0.0:0.312	.	308	Q96EK9	KTI12_HUMAN	Q	308	ENSP00000360676:R308Q	ENSP00000360676:R308Q	R	-	2	0	KTI12	52271099	0.000000	0.05858	0.041000	0.18516	0.702000	0.40608	-1.804000	0.01738	-0.683000	0.05190	0.557000	0.71058	CGG		0.552	KTI12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023821.1	NM_138417	
CACHD1	57685	broad.mit.edu	37	1	65141094	65141094	+	Missense_Mutation	SNP	C	C	T	rs182391558		TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr1:65141094C>T	ENST00000371073.2	+	20	2738	c.2738C>T	c.(2737-2739)aCg>aTg	p.T913M	CACHD1_ENST00000290039.5_Missense_Mutation_p.T862M|CACHD1_ENST00000495994.1_3'UTR			Q5VU97	CAHD1_HUMAN	cache domain containing 1	913					calcium ion transport (GO:0006816)	integral component of membrane (GO:0016021)				breast(4)|endometrium(3)|kidney(3)|large_intestine(20)|lung(14)|ovary(2)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						GGGGATTTGACGAACCTTGTG	0.463											OREG0013544	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1	0.000199681	0.0	0.0014	5008	,	,		17058	0.0		0.0	False		,,,				2504	0.0					uc001dbo.1																			0				ovary(2)	2						c.(2584-2586)ACG>ATG		cache domain containing 1							134.0	123.0	127.0					1																	65141094		2203	4300	6503	SO:0001583	missense	57685				calcium ion transport	integral to membrane		g.chr1:65141094C>T	AB046793	CCDS628.2	1p31.3	2008-02-05	2005-10-11	2005-10-11	ENSG00000158966	ENSG00000158966			29314	protein-coding gene	gene with protein product			"""von Willebrand factor type A and cache domain containing 1"""	VWCD1		10997877	Standard	NM_020925		Approved	KIAA1573	uc001dbo.1	Q5VU97	OTTHUMG00000009030	ENST00000371073.2:c.2738C>T	1.37:g.65141094C>T	ENSP00000360113:p.Thr913Met		OREG0013544	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1081	CACHD1_uc001dbp.1_Missense_Mutation_p.T617M|CACHD1_uc001dbq.1_Missense_Mutation_p.T617M|CACHD1_uc010opa.1_Missense_Mutation_p.T106M	p.T862M	NM_020925	NP_065976	Q5VU97	CAHD1_HUMAN			20	2690	+			913			Extracellular (Potential).		Q49AE9|Q658T4|Q7Z3P2|Q9H7W4|Q9H9W3|Q9HCJ9	Missense_Mutation	SNP	ENST00000371073.2	37	c.2585C>T		1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	20.7	4.031369	0.75504	.	.	ENSG00000158966	ENST00000371073;ENST00000290039	T;T	0.27720	1.65;1.66	5.85	5.85	0.93711	.	0.132555	0.64402	D	0.000002	T	0.25121	0.0610	M	0.67397	2.05	0.80722	D	1	P	0.51240	0.943	B	0.37304	0.246	T	0.26780	-1.0093	10	0.72032	D	0.01	-20.5642	20.1634	0.98142	0.0:1.0:0.0:0.0	.	913	Q5VU97	CAHD1_HUMAN	M	913;862	ENSP00000360113:T913M;ENSP00000290039:T862M	ENSP00000290039:T862M	T	+	2	0	CACHD1	64913682	1.000000	0.71417	0.984000	0.44739	0.798000	0.45092	7.304000	0.78882	2.773000	0.95371	0.655000	0.94253	ACG		0.463	CACHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_020925	
RPF1	80135	broad.mit.edu	37	1	84961638	84961638	+	Nonsense_Mutation	SNP	C	C	G			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr1:84961638C>G	ENST00000370654.5	+	7	788	c.773C>G	c.(772-774)tCa>tGa	p.S258*	GNG5_ENST00000487806.1_5'Flank	NM_025065.6	NP_079341.2	Q9H9Y2	RPF1_HUMAN	ribosome production factor 1 homolog (S. cerevisiae)	258	Brix. {ECO:0000255|PROSITE- ProRule:PRU00034}.				rRNA processing (GO:0006364)	nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)			breast(2)|endometrium(1)|kidney(3)|large_intestine(5)|lung(2)|prostate(1)	14						CTGGGTCATTCAATTGGACGT	0.373																																						uc001djv.3																			0					0						c.(772-774)TCA>TGA		RNA processing factor 1							107.0	99.0	101.0					1																	84961638		2203	4300	6503	SO:0001587	stop_gained	80135				rRNA processing|translation	nucleolus	aminoacyl-tRNA ligase activity|ATP binding|rRNA binding	g.chr1:84961638C>G	AF322053	CCDS695.1	1p22.3	2009-09-25	2009-09-25	2009-09-25	ENSG00000117133	ENSG00000117133			30350	protein-coding gene	gene with protein product	"""RNA processing factor 1"", ""ribosome production factor 1"""		"""brix domain containing 5"""	BXDC5		11864606	Standard	NM_025065		Approved		uc001djv.4	Q9H9Y2	OTTHUMG00000009857	ENST00000370654.5:c.773C>G	1.37:g.84961638C>G	ENSP00000359688:p.Ser258*						p.S258*	NM_025065	NP_079341	Q9H9Y2	RPF1_HUMAN			7	818	+			258			Brix.		Q5VSK7|Q6AHX1|Q8WXZ8	Nonsense_Mutation	SNP	ENST00000370654.5	37	c.773C>G	CCDS695.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.653061	0.88056	.	.	ENSG00000117133	ENST00000370654	.	.	.	5.96	5.03	0.67393	.	0.278882	0.40144	N	0.001175	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-15.6691	15.3433	0.74314	0.0:0.7356:0.2644:0.0	.	.	.	.	X	258	.	ENSP00000359688:S258X	S	+	2	0	RPF1	84734226	0.989000	0.36119	0.841000	0.33234	0.938000	0.57974	2.449000	0.44935	1.492000	0.48499	0.655000	0.94253	TCA		0.373	RPF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027238.1	NM_025065	
ODF2L	57489	broad.mit.edu	37	1	86851250	86851250	+	Missense_Mutation	SNP	T	T	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr1:86851250T>A	ENST00000359242.3	-	3	418	c.137A>T	c.(136-138)gAa>gTa	p.E46V	ODF2L_ENST00000370566.3_Missense_Mutation_p.E46V|ODF2L_ENST00000294678.2_Missense_Mutation_p.E46V|ODF2L_ENST00000317336.7_Missense_Mutation_p.E46V|ODF2L_ENST00000394731.1_Intron|ODF2L_ENST00000370567.1_Missense_Mutation_p.E46V	NM_001007022.2	NP_001007023.2	Q9ULJ1	ODF2L_HUMAN	outer dense fiber of sperm tails 2-like	46						centrosome (GO:0005813)				endometrium(2)|kidney(2)|large_intestine(10)|lung(6)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	24				all cancers(265;0.0313)|Epithelial(280;0.0611)		TTCAGTCTTTTCATTTAGAAT	0.343																																						uc001dll.1																			0				ovary(1)	1						c.(136-138)GAA>GTA		outer dense fiber of sperm tails 2-like isoform							83.0	79.0	80.0					1																	86851250		2202	4300	6502	SO:0001583	missense	57489					centrosome		g.chr1:86851250T>A		CCDS30763.1, CCDS41354.1, CCDS30763.2, CCDS41354.2, CCDS53339.1	1p22.3	2008-02-05			ENSG00000122417	ENSG00000122417			29225	protein-coding gene	gene with protein product						10574462	Standard	NM_020729		Approved	KIAA1229	uc001dll.2	Q9ULJ1	OTTHUMG00000010080	ENST00000359242.3:c.137A>T	1.37:g.86851250T>A	ENSP00000359600:p.Glu46Val					ODF2L_uc001dlm.1_Missense_Mutation_p.E46V|ODF2L_uc001dln.2_Missense_Mutation_p.E46V|ODF2L_uc001dlo.2_Intron|ODF2L_uc001dlp.2_Missense_Mutation_p.E46V|ODF2L_uc010osg.1_Missense_Mutation_p.E46V|ODF2L_uc001dlq.1_Intron|ODF2L_uc009wcr.1_Intron	p.E46V	NM_020729	NP_065780	Q9ULJ1	ODF2L_HUMAN		all cancers(265;0.0313)|Epithelial(280;0.0611)	3	477	-			46			Potential.		A8MU56|B4E037|Q05C40|Q5BJG5|Q5TBX3|Q5TBX4|Q86X31	Missense_Mutation	SNP	ENST00000359242.3	37	c.137A>T	CCDS41354.2	.	.	.	.	.	.	.	.	.	.	T	15.98	2.992723	0.54041	.	.	ENSG00000122417	ENST00000441121;ENST00000370566;ENST00000359242;ENST00000317336;ENST00000370567;ENST00000294678;ENST00000465959	T;T;T;T;T	0.29142	1.58;1.58;1.59;1.6;1.58	5.4	3.02	0.34903	.	1.148980	0.06127	N	0.669936	T	0.18087	0.0434	L	0.50333	1.59	0.09310	N	0.999999	B;P;P;P;P	0.48089	0.253;0.673;0.525;0.617;0.905	B;B;B;B;P	0.48189	0.17;0.242;0.165;0.173;0.57	T	0.17623	-1.0363	10	0.46703	T	0.11	-1.0E-4	5.7125	0.17943	0.0:0.0899:0.1777:0.7324	.	46;46;46;46;46	B4E037;Q9ULJ1-2;Q9ULJ1-4;Q9ULJ1-3;Q9ULJ1	.;.;.;.;ODF2L_HUMAN	V	46	ENSP00000359597:E46V;ENSP00000359600:E46V;ENSP00000320165:E46V;ENSP00000359598:E46V;ENSP00000294678:E46V	ENSP00000294678:E46V	E	-	2	0	ODF2L	86623838	0.125000	0.22332	0.001000	0.08648	0.872000	0.50106	1.185000	0.32065	0.422000	0.26005	0.529000	0.55759	GAA		0.343	ODF2L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027873.2		
S100A7L2	645922	broad.mit.edu	37	1	153409549	153409549	+	Silent	SNP	G	G	A	rs568882807		TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr1:153409549G>A	ENST00000368725.2	-	3	323	c.324C>T	c.(322-324)tcC>tcT	p.S108S		NM_001045479.1	NP_001038944.2	Q5SY68	S1A7B_HUMAN	S100 calcium binding protein A7-like 2	97							calcium ion binding (GO:0005509)			NS(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)	8	all_lung(78;2.4e-33)|Lung NSC(65;8.13e-32)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			GGCTTCCCCCGGAACAGGGTG	0.488													G|||	1	0.000199681	0.0	0.0	5008	,	,		17628	0.0		0.0	False		,,,				2504	0.001					uc010pdx.1																			0				ovary(1)	1						c.(322-324)TCC>TCT		S100 calcium binding protein A7-like 2							155.0	166.0	162.0					1																	153409549		2203	4300	6503	SO:0001819	synonymous_variant	645922							g.chr1:153409549G>A			1q21.3	2013-01-10			ENSG00000197364	ENSG00000197364		"""EF-hand domain containing"""	21655	protein-coding gene	gene with protein product							Standard	NM_001045479		Approved	s100a7b	uc010pdx.2	Q5SY68	OTTHUMG00000013129	ENST00000368725.2:c.324C>T	1.37:g.153409549G>A							p.S108S	NM_001045479	NP_001038944			LUSC - Lung squamous cell carcinoma(543;0.171)		3	402	-	all_lung(78;2.4e-33)|Lung NSC(65;8.13e-32)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)								Silent	SNP	ENST00000368725.2	37	c.324C>T																																																																																					0.488	S100A7L2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000036797.2	NM_001045479	
ZP4	57829	broad.mit.edu	37	1	238048511	238048511	+	Missense_Mutation	SNP	A	A	C			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr1:238048511A>C	ENST00000366570.4	-	9	1423	c.1265T>G	c.(1264-1266)tTc>tGc	p.F422C	RP11-193H5.1_ENST00000450451.1_RNA	NM_021186.3	NP_067009.1	Q12836	ZP4_HUMAN	zona pellucida glycoprotein 4	422	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				acrosomal vesicle exocytosis (GO:0060478)|binding of sperm to zona pellucida (GO:0007339)|intracellular signal transduction (GO:0035556)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of humoral immune response (GO:0002922)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of T cell proliferation (GO:0042102)|protein kinase A signaling (GO:0010737)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	acrosin binding (GO:0032190)|signal transducer activity (GO:0004871)			breast(6)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(42)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	73	Ovarian(103;0.103)	all_cancers(173;0.00175)|all_epithelial(177;0.162)|all_neural(198;0.164)|Melanoma(53;0.211)|Prostate(94;0.214)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			CACAAAGCTGAAGGTGAAGAT	0.537																																					NSCLC(166;160 2029 11600 18754 19936)	uc001hym.2																			0				ovary(2)|skin(1)	3						c.(1264-1266)TTC>TGC		zona pellucida glycoprotein 4 preproprotein							92.0	94.0	93.0					1																	238048511		2203	4300	6503	SO:0001583	missense	57829				acrosomal vesicle exocytosis|negative regulation of binding of sperm to zona pellucida|positive regulation of acrosome reaction|positive regulation of humoral immune response|positive regulation of protein kinase activity|positive regulation of T cell proliferation|protein kinase A signaling cascade|protein kinase C signaling cascade	integral to membrane|intracellular|plasma membrane|proteinaceous extracellular matrix	acrosin binding|receptor activity	g.chr1:238048511A>C	U05781	CCDS1615.1	1q43	2013-01-17			ENSG00000116996	ENSG00000116996		"""Zona pellucida glycoproteins"""	15770	protein-coding gene	gene with protein product		613514				7841460	Standard	NM_021186		Approved	ZPB	uc001hym.3	Q12836	OTTHUMG00000039586	ENST00000366570.4:c.1265T>G	1.37:g.238048511A>C	ENSP00000355529:p.Phe422Cys					LOC100130331_uc010pyc.1_Intron	p.F422C	NM_021186	NP_067009	Q12836	ZP4_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		9	1265	-	Ovarian(103;0.103)	all_cancers(173;0.00175)|all_epithelial(177;0.162)|all_neural(198;0.164)|Melanoma(53;0.211)|Prostate(94;0.214)	422			ZP.|Extracellular (Potential).		B2RAE1	Missense_Mutation	SNP	ENST00000366570.4	37	c.1265T>G	CCDS1615.1	.	.	.	.	.	.	.	.	.	.	A	15.74	2.922734	0.52653	.	.	ENSG00000116996	ENST00000366570	D	0.91068	-2.78	5.1	5.1	0.69264	Zona pellucida sperm-binding protein (3);	0.000000	0.85682	D	0.000000	D	0.96399	0.8825	H	0.94886	3.595	0.58432	D	0.999994	D	0.89917	1.0	D	0.97110	1.0	D	0.97241	0.9891	10	0.87932	D	0	-23.4067	12.8727	0.57975	1.0:0.0:0.0:0.0	.	422	Q12836	ZP4_HUMAN	C	422	ENSP00000355529:F422C	ENSP00000355529:F422C	F	-	2	0	ZP4	236115134	1.000000	0.71417	0.987000	0.45799	0.197000	0.23852	7.419000	0.80179	1.927000	0.55829	0.533000	0.62120	TTC		0.537	ZP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095476.1		
OR2G6	391211	broad.mit.edu	37	1	248685273	248685273	+	Missense_Mutation	SNP	C	C	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr1:248685273C>T	ENST00000343414.4	+	1	358	c.326C>T	c.(325-327)tCg>tTg	p.S109L		NM_001013355.1	NP_001013373.1	Q5TZ20	OR2G6_HUMAN	olfactory receptor, family 2, subfamily G, member 6	109						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S109L(1)		NS(1)|cervix(1)|endometrium(2)|large_intestine(7)|lung(40)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0156)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GGGTTGGGCTCGTCTGAGTGT	0.547																																						uc001ien.1																			1	Substitution - Missense(1)		lung(1)	ovary(2)|skin(1)	3						c.(325-327)TCG>TTG		olfactory receptor, family 2, subfamily G,							103.0	101.0	101.0					1																	248685273		2203	4300	6503	SO:0001583	missense	391211				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr1:248685273C>T		CCDS31119.1	1q44	2012-08-09			ENSG00000188558	ENSG00000188558		"""GPCR / Class A : Olfactory receptors"""	27019	protein-coding gene	gene with protein product							Standard	NM_001013355		Approved		uc001ien.1	Q5TZ20	OTTHUMG00000040462	ENST00000343414.4:c.326C>T	1.37:g.248685273C>T	ENSP00000341291:p.Ser109Leu						p.S109L	NM_001013355	NP_001013373	Q5TZ20	OR2G6_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.0265)		1	326	+	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0156)	109			Helical; Name=3; (Potential).		B2RP33	Missense_Mutation	SNP	ENST00000343414.4	37	c.326C>T	CCDS31119.1	.	.	.	.	.	.	.	.	.	.	N	10.94	1.492442	0.26774	.	.	ENSG00000188558	ENST00000343414	T	0.03094	4.05	3.68	3.68	0.42216	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42964	U	0.000624	T	0.11793	0.0287	M	0.67625	2.065	0.09310	N	1	D	0.89917	1.0	P	0.60949	0.881	T	0.01675	-1.1298	10	0.72032	D	0.01	.	9.8654	0.41140	0.0:0.6416:0.3584:0.0	.	109	Q5TZ20	OR2G6_HUMAN	L	109	ENSP00000341291:S109L	ENSP00000341291:S109L	S	+	2	0	OR2G6	246751896	0.000000	0.05858	0.013000	0.15412	0.011000	0.07611	-4.456000	0.00231	1.869000	0.54173	0.400000	0.26472	TCG		0.547	OR2G6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097358.1	XM_372842	
ZNF37A	7587	broad.mit.edu	37	10	38407548	38407548	+	Missense_Mutation	SNP	T	T	C	rs201777153		TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr10:38407548T>C	ENST00000361085.5	+	7	1814	c.1469T>C	c.(1468-1470)aTa>aCa	p.I490T	ZNF37A_ENST00000351773.3_Missense_Mutation_p.I490T	NM_001178101.1|NM_003421.2	NP_001171572.1|NP_003412.1	P17032	ZN37A_HUMAN	zinc finger protein 37A	490					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(13)|prostate(1)	28						AGAACTCATATAAGACAGAAA	0.413																																						uc001izk.2																			0				breast(1)	1						c.(1468-1470)ATA>ACA		zinc finger protein 37a							59.0	59.0	59.0					10																	38407548		2203	4300	6503	SO:0001583	missense	7587					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr10:38407548T>C	X69115	CCDS31183.1	10p11.2	2013-01-08	2006-05-11		ENSG00000075407	ENSG00000075407		"""Zinc fingers, C2H2-type"", ""-"""	13102	protein-coding gene	gene with protein product			"""zinc finger protein 37a (KOX 21)"""			2014798, 8464732	Standard	NM_001178101		Approved	KOX21, ZNF37	uc001izl.3	P17032	OTTHUMG00000017990	ENST00000361085.5:c.1469T>C	10.37:g.38407548T>C	ENSP00000354377:p.Ile490Thr					ZNF37A_uc001izl.2_Missense_Mutation_p.I490T|ZNF37A_uc001izm.2_Missense_Mutation_p.I490T	p.I490T	NM_001007094	NP_001007095	P17032	ZN37A_HUMAN			8	2288	+			490					B3KRQ3|D3DRZ3|Q96B88	Missense_Mutation	SNP	ENST00000361085.5	37	c.1469T>C	CCDS31183.1	.	.	.	.	.	.	.	.	.	.	T	0.001	-2.944340	0.00052	.	.	ENSG00000075407	ENST00000351773;ENST00000361085	T;T	0.00995	5.46;5.46	2.34	-3.36	0.04913	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00271	0.0008	N	0.00205	-1.85	0.22581	N	0.998965	B	0.02656	0.0	B	0.04013	0.001	T	0.42816	-0.9429	9	0.02654	T	1	.	4.59	0.12302	0.0:0.3785:0.3937:0.2278	.	490	P17032	ZN37A_HUMAN	T	490	ENSP00000329141:I490T;ENSP00000354377:I490T	ENSP00000329141:I490T	I	+	2	0	ZNF37A	38447554	0.005000	0.15991	0.226000	0.23910	0.154000	0.21943	0.399000	0.20916	-0.691000	0.05135	-1.272000	0.01410	ATA		0.413	ZNF37A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047624.2	NM_003421	
PGR	5241	broad.mit.edu	37	11	100999671	100999671	+	Missense_Mutation	SNP	G	G	T	rs141862537		TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr11:100999671G>T	ENST00000325455.5	-	1	1584	c.131C>A	c.(130-132)aCc>aAc	p.T44N	PGR_ENST00000263463.5_Missense_Mutation_p.T44N|PGR_ENST00000534013.1_Intron	NM_000926.4|NM_001202474.1|NM_001271162.1	NP_000917.3|NP_001189403.1|NP_001258091.1	P06401	PRGR_HUMAN	progesterone receptor	44	Modulating, Pro-Rich.				cell-cell signaling (GO:0007267)|epithelial cell maturation (GO:0002070)|gene expression (GO:0010467)|negative regulation of gene expression (GO:0010629)|ovulation from ovarian follicle (GO:0001542)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone receptor signaling pathway (GO:0050847)|regulation of epithelial cell proliferation (GO:0050678)|signal transduction (GO:0007165)|tertiary branching involved in mammary gland duct morphogenesis (GO:0060748)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mitochondrial outer membrane (GO:0005741)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|liver(1)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	36		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	Allylestrenol(DB01431)|Danazol(DB01406)|Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluticasone Propionate(DB00588)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Megestrol acetate(DB00351)|Mifepristone(DB00834)|Norelgestromin(DB06713)|Norethindrone(DB00717)|Norgestimate(DB00957)|Progesterone(DB00396)|Spironolactone(DB00421)	TTCAGGCAAGGTGTCCGAGGT	0.692																																					Pancreas(124;2271 2354 21954 22882)	uc001pgh.2																			0				lung(1)|liver(1)|central_nervous_system(1)|pancreas(1)	4						c.(130-132)ACC>AAC		progesterone receptor	Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol Diacetate(DB00823)|Etonogestrel(DB00294)|Levonorgestrel(DB00367)|Medroxyprogesterone(DB00603)|Megestrol(DB00351)|Mifepristone(DB00834)|Norethindrone(DB00717)|Norgestimate(DB00957)|Norgestrel(DB00506)|Progesterone(DB00396)						37.0	29.0	31.0					11																	100999671		2203	4300	6503	SO:0001583	missense	5241				cell-cell signaling|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	enzyme binding|receptor binding|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding	g.chr11:100999671G>T	M15716	CCDS8310.1, CCDS59229.1	11q22-q23	2013-01-16			ENSG00000082175	ENSG00000082175		"""Nuclear hormone receptors"""	8910	protein-coding gene	gene with protein product		607311					Standard	NM_000926		Approved	PR, NR3C3	uc001pgh.2	P06401	OTTHUMG00000167531	ENST00000325455.5:c.131C>A	11.37:g.100999671G>T	ENSP00000325120:p.Thr44Asn					PGR_uc001pgi.2_Missense_Mutation_p.T44N|PGR_uc009yww.1_RNA|PGR_uc001pgj.2_RNA|PGR_uc009ywx.1_RNA|uc010rum.1_5'Flank	p.T44N	NM_000926	NP_000917	P06401	PRGR_HUMAN		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	1	874	-		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)	44			Modulating, Pro-Rich.		A7LQ08|A7X8B0|B4E3T0|Q8TDS3|Q9UPF7	Missense_Mutation	SNP	ENST00000325455.5	37	c.131C>A	CCDS8310.1	.	.	.	.	.	.	.	.	.	.	G	4.728	0.135385	0.09032	.	.	ENSG00000082175	ENST00000325455;ENST00000263463;ENST00000537623	T;T	0.07688	3.17;3.17	4.53	-0.233	0.13078	.	1.340710	0.05130	N	0.492346	T	0.04724	0.0128	N	0.14661	0.345	0.09310	N	1	B;B	0.23990	0.095;0.095	B;B	0.17433	0.018;0.018	T	0.41305	-0.9516	10	0.54805	T	0.06	.	1.0784	0.01638	0.2074:0.159:0.4336:0.2001	.	44;44	Q8TDS3;P06401	.;PRGR_HUMAN	N	44	ENSP00000325120:T44N;ENSP00000263463:T44N	ENSP00000263463:T44N	T	-	2	0	PGR	100504881	0.000000	0.05858	0.000000	0.03702	0.054000	0.15201	0.594000	0.24014	-0.009000	0.14296	0.561000	0.74099	ACC		0.692	PGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394934.1		
COL2A1	1280	broad.mit.edu	37	12	48371798	48371798	+	Nonsense_Mutation	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr12:48371798G>A	ENST00000380518.3	-	44	3270	c.3106C>T	c.(3106-3108)Cga>Tga	p.R1036*	COL2A1_ENST00000493991.1_5'UTR|COL2A1_ENST00000337299.6_Nonsense_Mutation_p.R967*	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN	collagen, type II, alpha 1	1036	Triple-helical region.				axon guidance (GO:0007411)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to BMP stimulus (GO:0071773)|central nervous system development (GO:0007417)|chondrocyte differentiation (GO:0002062)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal joint morphogenesis (GO:0060272)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|limb bud formation (GO:0060174)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|notochord development (GO:0030903)|otic vesicle development (GO:0071599)|palate development (GO:0060021)|proteoglycan metabolic process (GO:0006029)|regulation of gene expression (GO:0010468)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|tissue homeostasis (GO:0001894)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen type II trimer (GO:0005585)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(3)	64		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)	CTCACCTCTCGTCCAGGTTCA	0.662																																						uc001rqu.2																			0				ovary(1)|skin(1)	2	GRCh37	CM062563	COL2A1	M	rs145684327	c.(3106-3108)CGA>TGA		collagen, type II, alpha 1 isoform 1 precursor	Collagenase(DB00048)						34.0	36.0	35.0					12																	48371798		2203	4300	6503	SO:0001587	stop_gained	1280				axon guidance|collagen fibril organization|embryonic skeletal joint morphogenesis|sensory perception of sound|visual perception	collagen type II	identical protein binding|platelet-derived growth factor binding	g.chr12:48371798G>A	X16468	CCDS8759.1, CCDS41778.1	12q12-q13.2	2013-11-14	2008-02-04		ENSG00000139219	ENSG00000139219		"""Collagens"""	2200	protein-coding gene	gene with protein product		120140	"""collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital)"", ""arthroophthalmopathy, progressive (Stickler syndrome)"""	SEDC, AOM		1677770	Standard	NM_033150		Approved	STL1	uc001rqu.3	P02458	OTTHUMG00000149896	ENST00000380518.3:c.3106C>T	12.37:g.48371798G>A	ENSP00000369889:p.Arg1036*					COL2A1_uc001rqt.2_5'Flank|COL2A1_uc009zkw.2_RNA|COL2A1_uc001rqv.2_Nonsense_Mutation_p.R967*	p.R1036*	NM_001844	NP_001835	P02458	CO2A1_HUMAN			44	3287	-		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)	1036			Triple-helical region.		A6NGA0|Q12985|Q14009|Q14044|Q14045|Q14046|Q14047|Q14056|Q14058|Q16672|Q1JQ82|Q2V4X7|Q6LBY1|Q6LBY2|Q6LBY3|Q96IT5|Q99227|Q9UE38|Q9UE39|Q9UE40|Q9UE41|Q9UE42|Q9UE43	Nonsense_Mutation	SNP	ENST00000380518.3	37	c.3106C>T	CCDS41778.1	.	.	.	.	.	.	.	.	.	.	G	43	10.452940	0.99408	.	.	ENSG00000139219	ENST00000380518;ENST00000395281;ENST00000337299	.	.	.	5.39	4.48	0.54585	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.2554	0.66048	0.0:0.0:0.8496:0.1504	.	.	.	.	X	1036;967;967	.	ENSP00000338213:R967X	R	-	1	2	COL2A1	46658065	0.993000	0.37304	1.000000	0.80357	0.996000	0.88848	2.461000	0.45040	1.223000	0.43536	0.563000	0.77884	CGA		0.662	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313810.2	NM_001844	
GLT8D2	83468	broad.mit.edu	37	12	104390580	104390580	+	Missense_Mutation	SNP	G	G	A	rs373952967		TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr12:104390580G>A	ENST00000360814.4	-	8	938	c.533C>T	c.(532-534)gCg>gTg	p.A178V	GLT8D2_ENST00000548660.1_Missense_Mutation_p.A178V|GLT8D2_ENST00000546436.1_Missense_Mutation_p.A178V	NM_031302.3	NP_112592.1	Q9H1C3	GL8D2_HUMAN	glycosyltransferase 8 domain containing 2	178						integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			kidney(3)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)	16						GAAAGCCGCCGCGTGGCCCAG	0.483																																						uc001tkh.1																			0				ovary(1)|skin(1)	2						c.(532-534)GCG>GTG		glycosyltransferase 8 domain containing 2		G	VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	100.0	103.0	102.0		533	5.1	0.4	12		102	0,8600		0,0,4300	no	missense	GLT8D2	NM_031302.3	64	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging	178/350	104390580	1,13005	2203	4300	6503	SO:0001583	missense	83468					integral to membrane	transferase activity, transferring glycosyl groups	g.chr12:104390580G>A	BC022343	CCDS9096.1	12q23.3	2013-02-22			ENSG00000120820	ENSG00000120820		"""Glycosyltransferase family 8 domain containing"""	24890	protein-coding gene	gene with protein product							Standard	NM_031302		Approved	FLJ31494	uc001tkh.1	Q9H1C3	OTTHUMG00000170120	ENST00000360814.4:c.533C>T	12.37:g.104390580G>A	ENSP00000354053:p.Ala178Val					GLT8D2_uc001tki.1_Missense_Mutation_p.A178V	p.A178V	NM_031302	NP_112592	Q9H1C3	GL8D2_HUMAN			8	939	-			178			Lumenal (Potential).		Q96KA2	Missense_Mutation	SNP	ENST00000360814.4	37	c.533C>T	CCDS9096.1	.	.	.	.	.	.	.	.	.	.	G	13.89	2.371150	0.42003	2.27E-4	0.0	ENSG00000120820	ENST00000360814;ENST00000546436;ENST00000548660	T;T;T	0.36699	1.24;1.24;1.24	5.13	5.13	0.70059	.	0.052669	0.85682	D	0.000000	T	0.18045	0.0433	N	0.20483	0.58	0.80722	D	1	P	0.52692	0.955	B	0.38327	0.271	T	0.13980	-1.0489	10	0.02654	T	1	.	12.0178	0.53324	0.0791:0.0:0.9209:0.0	.	178	Q9H1C3	GL8D2_HUMAN	V	178	ENSP00000354053:A178V;ENSP00000449750:A178V;ENSP00000447450:A178V	ENSP00000354053:A178V	A	-	2	0	GLT8D2	102914710	1.000000	0.71417	0.428000	0.26697	0.778000	0.44026	7.962000	0.87912	2.385000	0.81259	0.563000	0.77884	GCG		0.483	GLT8D2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407371.1	NM_031302	
CUX2	23316	broad.mit.edu	37	12	111772341	111772341	+	Missense_Mutation	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr12:111772341G>A	ENST00000261726.6	+	19	3177	c.3023G>A	c.(3022-3024)aGc>aAc	p.S1008N		NM_015267.3	NP_056082.2	O14529	CUX2_HUMAN	cut-like homeobox 2	1008					cellular response to organic substance (GO:0071310)|cognition (GO:0050890)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of synapse assembly (GO:0051965)|short-term memory (GO:0007614)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(24)|ovary(5)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	55						TCCCTGGAGAGCAGCAAGGAG	0.647																																						uc001tsa.1																			0				ovary(3)|skin(2)|breast(1)	6						c.(3022-3024)AGC>AAC		cut-like 2							33.0	40.0	38.0					12																	111772341		2012	4173	6185	SO:0001583	missense	23316					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chr12:111772341G>A	AB006631	CCDS41837.1	12q24.12	2011-06-20	2007-11-07	2007-11-07	ENSG00000111249	ENSG00000111249		"""Homeoboxes / CUT class"""	19347	protein-coding gene	gene with protein product		610648	"""cut-like 2 (Drosophila)"""	CUTL2			Standard	NM_015267		Approved	KIAA0293, CDP2	uc001tsa.2	O14529	OTTHUMG00000169546	ENST00000261726.6:c.3023G>A	12.37:g.111772341G>A	ENSP00000261726:p.Ser1008Asn						p.S1008N	NM_015267	NP_056082	O14529	CUX2_HUMAN			19	3176	+			1008					A7E2Y4	Missense_Mutation	SNP	ENST00000261726.6	37	c.3023G>A	CCDS41837.1	.	.	.	.	.	.	.	.	.	.	G	18.29	3.590712	0.66219	.	.	ENSG00000111249	ENST00000261726	T	0.48201	0.82	5.09	4.19	0.49359	.	0.079792	0.85682	D	0.000000	T	0.37919	0.1021	L	0.32530	0.975	0.54753	D	0.999988	B	0.31383	0.321	B	0.29663	0.105	T	0.18587	-1.0332	10	0.37606	T	0.19	-14.6805	15.5784	0.76410	0.0:0.1386:0.8614:0.0	.	1008	O14529	CUX2_HUMAN	N	1008	ENSP00000261726:S1008N	ENSP00000261726:S1008N	S	+	2	0	CUX2	110256724	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.886000	0.87288	1.260000	0.44134	0.655000	0.94253	AGC		0.647	CUX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404765.1	NM_015267	
ABCC4	10257	broad.mit.edu	37	13	95705392	95705392	+	Missense_Mutation	SNP	A	A	C			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr13:95705392A>C	ENST00000376887.4	-	27	3527	c.3413T>G	c.(3412-3414)tTt>tGt	p.F1138C	ABCC4_ENST00000412704.1_Missense_Mutation_p.F1091C	NM_005845.3	NP_005836.2	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	1138	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				blood coagulation (GO:0007596)|oxidation-reduction process (GO:0055114)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of smooth muscle cell proliferation (GO:0048661)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|response to organonitrogen compound (GO:0010243)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense granule membrane (GO:0031088)	15-hydroxyprostaglandin dehydrogenase (NAD+) activity (GO:0016404)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(1)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cefazolin(DB01327)|Celecoxib(DB00482)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Flurbiprofen(DB00712)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Lamivudine(DB00709)|Leucovorin(DB00650)|Meloxicam(DB00814)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Probenecid(DB01032)|Rosuvastatin(DB01098)|Sildenafil(DB00203)|Sorafenib(DB00398)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tenofovir(DB00300)|Tioguanine(DB00352)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Zidovudine(DB00495)	GTGCTCATTAAAGGGATCCAG	0.373																																						uc001vmd.3																			0				central_nervous_system(3)|skin(1)	4						c.(3412-3414)TTT>TGT		ATP-binding cassette, sub-family C, member 4	Cefazolin(DB01327)						156.0	138.0	144.0					13																	95705392		2203	4300	6503	SO:0001583	missense	10257				platelet activation|platelet degranulation	integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity	g.chr13:95705392A>C	U66682	CCDS9474.1	13q31	2012-03-14			ENSG00000125257	ENSG00000125257		"""ATP binding cassette transporters / subfamily C"""	55	protein-coding gene	gene with protein product	"""canalicular multispecific organic anion transporter (ABC superfamily)"", ""bA464I2.1 (ATP-binding cassette, sub-family C (CFTR/MRP), member 4)"", ""multidrug resistance-associated protein 4"", ""multispecific organic anion transporter B"""	605250				8894702, 9661885	Standard	NM_005845		Approved	MRP4, EST170205, MOAT-B, MOATB	uc001vmd.4	O15439	OTTHUMG00000017216	ENST00000376887.4:c.3413T>G	13.37:g.95705392A>C	ENSP00000366084:p.Phe1138Cys					ABCC4_uc010afj.2_Missense_Mutation_p.F22C|ABCC4_uc010afk.2_Missense_Mutation_p.F1091C	p.F1138C	NM_005845	NP_005836	O15439	MRP4_HUMAN			27	3532	-	all_neural(89;0.0878)|Medulloblastoma(90;0.163)		1138			ABC transporter 2.		A9Z1Z7|Q8IVZ4|Q8IZN6|Q8NEW8|Q9Y6J2	Missense_Mutation	SNP	ENST00000376887.4	37	c.3413T>G	CCDS9474.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.239882	0.79912	.	.	ENSG00000125257	ENST00000412704;ENST00000376887	D;D	0.90620	-2.7;-2.7	5.81	5.81	0.92471	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.85682	D	0.000000	D	0.94673	0.8282	M	0.67625	2.065	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.986;0.997;0.999	D	0.95136	0.8259	10	0.87932	D	0	.	16.1713	0.81820	1.0:0.0:0.0:0.0	.	1091;728;1138	O15439-2;O75555;O15439	.;.;MRP4_HUMAN	C	1091;1138	ENSP00000388657:F1091C;ENSP00000366084:F1138C	ENSP00000366084:F1138C	F	-	2	0	ABCC4	94503393	1.000000	0.71417	0.995000	0.50966	0.803000	0.45373	8.957000	0.93082	2.221000	0.72209	0.528000	0.53228	TTT		0.373	ABCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045478.2	NM_005845	
TEP1	7011	broad.mit.edu	37	14	20846241	20846241	+	Missense_Mutation	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr14:20846241G>A	ENST00000262715.5	-	39	5703	c.5663C>T	c.(5662-5664)gCt>gTt	p.A1888V	TEP1_ENST00000545983.1_Missense_Mutation_p.A226V|TEP1_ENST00000556935.1_Missense_Mutation_p.A1780V	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1888					RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		AAGCGCAGCAGCAACAAAGCC	0.632																																						uc001vxe.2																			0				ovary(5)	5						c.(5662-5664)GCT>GTT		telomerase-associated protein 1							88.0	86.0	87.0					14																	20846241		2203	4300	6503	SO:0001583	missense	7011				telomere maintenance via recombination	chromosome, telomeric region|cytoplasm|nuclear matrix|soluble fraction|telomerase holoenzyme complex	ATP binding|RNA binding	g.chr14:20846241G>A		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"""WD repeat domain containing"""	11726	protein-coding gene	gene with protein product	"""TROVE domain family, member 1"""	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.5663C>T	14.37:g.20846241G>A	ENSP00000262715:p.Ala1888Val					TEP1_uc010ahk.2_Missense_Mutation_p.A1231V|TEP1_uc010tlf.1_RNA|TEP1_uc010tlg.1_Missense_Mutation_p.A1780V|TEP1_uc010tlh.1_Missense_Mutation_p.A226V	p.A1888V	NM_007110	NP_009041	Q99973	TEP1_HUMAN	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)	39	5703	-	all_cancers(95;0.00123)	all_lung(585;0.235)	1888			WD 7.		A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	37	c.5663C>T	CCDS9548.1	.	.	.	.	.	.	.	.	.	.	G	7.138	0.581172	0.13686	.	.	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935;ENST00000545983	T;T;T	0.59772	0.24;0.24;0.24	5.48	3.66	0.41972	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.693990	0.14988	N	0.286855	T	0.33206	0.0855	N	0.08118	0	0.09310	N	1	B;B;B;B	0.14438	0.003;0.004;0.01;0.005	B;B;B;B	0.15052	0.008;0.005;0.01;0.012	T	0.18178	-1.0345	10	0.12430	T	0.62	-0.0093	9.7615	0.40534	0.1634:0.0:0.8366:0.0	.	226;1780;1231;1888	B4E0B6;G3V5X7;G3V2A4;Q99973	.;.;.;TEP1_HUMAN	V	1888;1888;1780;226	ENSP00000262715:A1888V;ENSP00000452574:A1780V;ENSP00000438849:A226V	ENSP00000262715:A1888V	A	-	2	0	TEP1	19916081	0.012000	0.17670	0.001000	0.08648	0.242000	0.25591	1.877000	0.39598	0.688000	0.31529	0.557000	0.71058	GCT		0.632	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
MGAT2	4247	broad.mit.edu	37	14	50089072	50089072	+	Nonsense_Mutation	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr14:50089072G>A	ENST00000305386.2	+	1	1584	c.1086G>A	c.(1084-1086)tgG>tgA	p.W362*	RP11-649E7.5_ENST00000555043.1_RNA|RPL36AL_ENST00000298289.6_5'Flank	NM_002408.3	NP_002399.1	Q10469	MGAT2_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,2-N-acetylglucosaminyltransferase	362					cellular protein metabolic process (GO:0044267)|oligosaccharide biosynthetic process (GO:0009312)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	alpha-1,6-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity (GO:0008455)|carbohydrate binding (GO:0030246)			cervix(1)|endometrium(3)|large_intestine(1)|lung(6)	11	all_epithelial(31;0.0021)|Breast(41;0.0124)					CAAAATTCTGGAAAGTGCTGG	0.423																																						uc001wwr.2																			0					0						c.(1084-1086)TGG>TGA		mannosyl (alpha-1,6-)-glycoprotein							125.0	122.0	123.0					14																	50089072		2203	4300	6503	SO:0001587	stop_gained	4247				oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|Golgi stack|integral to membrane|membrane fraction	alpha-1,6-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity	g.chr14:50089072G>A	U15128	CCDS9690.1	14q21	2013-02-25			ENSG00000168282	ENSG00000168282	2.4.1.143	"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	7045	protein-coding gene	gene with protein product		602616				7635144	Standard	NM_002408		Approved	GNT-II	uc001wwr.3	Q10469	OTTHUMG00000140271	ENST00000305386.2:c.1086G>A	14.37:g.50089072G>A	ENSP00000307423:p.Trp362*					SDCCAG1_uc010anj.1_Intron|RPL36AL_uc001wwq.1_5'Flank	p.W362*	NM_002408	NP_002399	Q10469	MGAT2_HUMAN			1	1584	+	all_epithelial(31;0.0021)|Breast(41;0.0124)		362			Lumenal (Potential).		B3KPC5|B3KQM0	Nonsense_Mutation	SNP	ENST00000305386.2	37	c.1086G>A	CCDS9690.1	.	.	.	.	.	.	.	.	.	.	G	39	7.424078	0.98275	.	.	ENSG00000168282	ENST00000305386;ENST00000504161	.	.	.	5.61	4.71	0.59529	.	0.160850	0.44688	D	0.000428	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.10111	T	0.7	-8.3904	15.942	0.79763	0.0:0.0:0.8639:0.1361	.	.	.	.	X	362;368	.	ENSP00000307423:W362X	W	+	3	0	MGAT2	49158822	1.000000	0.71417	1.000000	0.80357	0.861000	0.49209	6.412000	0.73303	1.363000	0.46019	-0.324000	0.08512	TGG		0.423	MGAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276807.1	NM_002408	
SRSF5	6430	broad.mit.edu	37	14	70237710	70237710	+	Splice_Site	SNP	A	A	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr14:70237710A>T	ENST00000553521.1	+	8	1893		c.e8-1		SRSF5_ENST00000553635.1_Splice_Site|SRSF5_ENST00000557154.1_Splice_Site|SRSF5_ENST00000394366.2_Splice_Site|SRSF5_ENST00000556587.1_Splice_Site			Q13243	SRSF5_HUMAN	serine/arginine-rich splicing factor 5						gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|regulation of cell cycle (GO:0051726)|response to wounding (GO:0009611)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			large_intestine(1)|liver(1)	2						TTTCCATTTTAGGGTGGTTGA	0.348																																						uc001xll.2																			0					0						c.e8-2		splicing factor, arginine/serine-rich 5							115.0	111.0	112.0					14																	70237710		2203	4300	6503	SO:0001630	splice_region_variant	6430				mRNA 3'-end processing|mRNA export from nucleus|mRNA splice site selection|termination of RNA polymerase II transcription	nuclear speck	nucleotide binding|protein binding|RNA binding	g.chr14:70237710A>T	AF020307	CCDS32109.1	14q24	2013-02-12	2010-06-22	2010-06-22	ENSG00000100650	ENSG00000100650		"""Serine/arginine-rich splicing factors"", ""RNA binding motif (RRM) containing"""	10787	protein-coding gene	gene with protein product	"""SR splicing factor 5"""	600914	"""splicing factor, arginine/serine-rich 5"""	SFRS5		7686911, 20516191	Standard	XM_005267998		Approved	SRP40, HRS	uc001xlp.3	Q13243		ENST00000553521.1:c.441-1A>T	14.37:g.70237710A>T						SFRS5_uc001xlm.2_Splice_Site|SFRS5_uc001xlo.2_Splice_Site_p.G147_splice|SFRS5_uc001xlp.2_Splice_Site_p.G147_splice|SFRS5_uc001xlq.2_Splice_Site_p.G144_splice	p.G147_splice	NM_006925	NP_008856	Q13243	SRSF5_HUMAN		all cancers(60;0.00144)|BRCA - Breast invasive adenocarcinoma(234;0.0132)|OV - Ovarian serous cystadenocarcinoma(108;0.0154)	8	1892	+								O14797|Q16662|Q49AD6|Q6FGE0	Splice_Site	SNP	ENST00000553521.1	37	c.441_splice	CCDS32109.1	.	.	.	.	.	.	.	.	.	.	A	15.07	2.724070	0.48728	.	.	ENSG00000100650	ENST00000553521;ENST00000394366;ENST00000557154;ENST00000553635	.	.	.	5.78	5.78	0.91487	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.1021	0.81178	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SRSF5	69307463	1.000000	0.71417	0.957000	0.39632	0.665000	0.39181	9.310000	0.96267	2.210000	0.71456	0.533000	0.62120	.		0.348	SRSF5-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412456.1	NM_001039465	Intron
UBR1	197131	broad.mit.edu	37	15	43269028	43269028	+	Missense_Mutation	SNP	T	T	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr15:43269028T>A	ENST00000290650.4	-	39	4334	c.4256A>T	c.(4255-4257)gAt>gTt	p.D1419V	UBR1_ENST00000382177.2_3'UTR	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1	1419					cellular response to leucine (GO:0071233)|negative regulation of TOR signaling (GO:0032007)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|proteasome complex (GO:0000502)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(7)|large_intestine(12)|lung(25)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	58		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		AACAGGGTCATCCCAATACAA	0.388																																						uc001zqq.2																			0				lung(1)	1						c.(4255-4257)GAT>GTT		ubiquitin protein ligase E3 component n-recognin							130.0	108.0	115.0					15																	43269028		2203	4299	6502	SO:0001583	missense	197131				cellular response to leucine|negative regulation of TOR signaling cascade	cytosol	leucine binding|zinc ion binding	g.chr15:43269028T>A		CCDS10091.1	15q13	2008-06-23			ENSG00000159459	ENSG00000159459		"""Ubiquitin protein ligase E3 component n-recognins"""	16808	protein-coding gene	gene with protein product		605981				9653112	Standard	NM_174916		Approved		uc001zqq.3	Q8IWV7	OTTHUMG00000130702	ENST00000290650.4:c.4256A>T	15.37:g.43269028T>A	ENSP00000290650:p.Asp1419Val						p.D1419V	NM_174916	NP_777576	Q8IWV7	UBR1_HUMAN		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)	39	4322	-		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)	1419					O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Missense_Mutation	SNP	ENST00000290650.4	37	c.4256A>T	CCDS10091.1	.	.	.	.	.	.	.	.	.	.	T	18.00	3.525582	0.64860	.	.	ENSG00000159459	ENST00000290650	T	0.46819	0.86	5.2	5.2	0.72013	.	0.049879	0.85682	D	0.000000	T	0.39655	0.1086	L	0.47716	1.5	0.80722	D	1	P	0.49961	0.93	B	0.38428	0.273	T	0.29181	-1.0020	10	0.29301	T	0.29	-12.4925	15.0106	0.71547	0.0:0.0:0.0:1.0	.	1419	Q8IWV7	UBR1_HUMAN	V	1419	ENSP00000290650:D1419V	ENSP00000290650:D1419V	D	-	2	0	UBR1	41056320	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.085000	0.76875	2.082000	0.62665	0.477000	0.44152	GAT		0.388	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1	NM_174916	
EDC3	80153	broad.mit.edu	37	15	74925078	74925078	+	Missense_Mutation	SNP	C	C	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr15:74925078C>A	ENST00000315127.4	-	7	1583	c.1402G>T	c.(1402-1404)Ggg>Tgg	p.G468W	EDC3_ENST00000426797.3_Missense_Mutation_p.G468W|EDC3_ENST00000568176.1_Missense_Mutation_p.G468W	NM_001142444.1|NM_025083.3	NP_001135916.1|NP_079359.2	Q96F86	EDC3_HUMAN	enhancer of mRNA decapping 3	468	YjeF N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00719}.				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)|membrane (GO:0016020)	identical protein binding (GO:0042802)|RNA binding (GO:0003723)			breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	16						GCGTGCTCCCCCAGTGGCAGA	0.577											OREG0023286	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										uc002ayn.2																			0				ovary(1)	1						c.(1402-1404)GGG>TGG		enhancer of mRNA decapping 3							77.0	67.0	71.0					15																	74925078		2197	4296	6493	SO:0001583	missense	80153				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay	cytoplasmic mRNA processing body|cytosol	protein binding|RNA binding	g.chr15:74925078C>A	BC011534	CCDS10267.1	15q24.1	2013-05-02	2013-05-02	2006-07-07	ENSG00000179151	ENSG00000179151			26114	protein-coding gene	gene with protein product		609842	"""yjeF domain containing (E.coli)"", ""LSM16 homolog (EDC3, S. cerevisiae)"", ""enhancer of mRNA decapping 3 homolog (S. cerevisiae)"""	YJDC, LSM16		15225602, 17533573, 22483619	Standard	NM_025083		Approved	FLJ21128, hYjeF_N2-15q23, YJEFN2	uc002aym.3	Q96F86	OTTHUMG00000142815	ENST00000315127.4:c.1402G>T	15.37:g.74925078C>A	ENSP00000320503:p.Gly468Trp		OREG0023286	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1156	EDC3_uc002ayo.2_Missense_Mutation_p.G468W|EDC3_uc002aym.2_Missense_Mutation_p.G468W	p.G468W	NM_001142443	NP_001135915	Q96F86	EDC3_HUMAN			10	1890	-			468			YjeF N-terminal.		B3KPH0|D3DW61|Q9H797	Missense_Mutation	SNP	ENST00000315127.4	37	c.1402G>T	CCDS10267.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.234251	0.79688	.	.	ENSG00000179151	ENST00000315127;ENST00000426797	T;T	0.42513	0.97;0.97	5.52	5.52	0.82312	YjeF-related protein, N-terminal (3);	0.150703	0.64402	D	0.000014	T	0.50837	0.1639	L	0.40543	1.245	0.54753	D	0.999985	D	0.67145	0.996	P	0.55303	0.773	T	0.40440	-0.9563	10	0.37606	T	0.19	-3.8245	19.4249	0.94737	0.0:1.0:0.0:0.0	.	468	Q96F86	EDC3_HUMAN	W	468	ENSP00000320503:G468W;ENSP00000401343:G468W	ENSP00000320503:G468W	G	-	1	0	EDC3	72712131	1.000000	0.71417	0.972000	0.41901	0.905000	0.53344	4.804000	0.62554	2.589000	0.87451	0.561000	0.74099	GGG		0.577	EDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286399.1	NM_025083	
CSPG4	1464	broad.mit.edu	37	15	75980829	75980829	+	Nonsense_Mutation	SNP	A	A	C			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr15:75980829A>C	ENST00000308508.5	-	3	2669	c.2577T>G	c.(2575-2577)taT>taG	p.Y859*		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	859	Gly/Ser-rich (glycosaminoglycan attachment domain).|Interaction with COL5A1. {ECO:0000250}.|Interaction with COL6A2. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						CTGTGGCCCCATAGGTCACCC	0.577																																						uc002baw.2																			0				ovary(2)|pancreas(1)	3						c.(2575-2577)TAT>TAG		chondroitin sulfate proteoglycan 4 precursor							48.0	49.0	49.0					15																	75980829		2197	4292	6489	SO:0001587	stop_gained	1464				angiogenesis|cell differentiation|intracellular signal transduction|positive regulation of peptidyl-tyrosine phosphorylation|tissue remodeling	apical plasma membrane|cell surface|integral to plasma membrane|intracellular|lamellipodium membrane	protein kinase binding|signal transducer activity	g.chr15:75980829A>C	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.2577T>G	15.37:g.75980829A>C	ENSP00000312506:p.Tyr859*						p.Y859*	NM_001897	NP_001888	Q6UVK1	CSPG4_HUMAN			3	2670	-			859			CSPG 4.|Extracellular (Potential).|Gly/Ser-rich (glycosaminoglycan attachment domain).|Interaction with COL5A1 (By similarity).|Interaction with COL6A2 (By similarity).		D3DW77|Q92675	Nonsense_Mutation	SNP	ENST00000308508.5	37	c.2577T>G	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	.	36	5.920070	0.97105	.	.	ENSG00000173546	ENST00000308508	.	.	.	5.3	-3.65	0.04502	.	0.000000	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.3139	0.74059	0.256:0.0:0.744:0.0	.	.	.	.	X	859	.	ENSP00000312506:Y859X	Y	-	3	2	CSPG4	73767884	0.030000	0.19436	0.190000	0.23270	0.630000	0.37929	0.042000	0.13949	-0.581000	0.05937	-0.256000	0.11100	TAT		0.577	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
TICRR	90381	broad.mit.edu	37	15	90142688	90142688	+	Silent	SNP	A	A	G			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr15:90142688A>G	ENST00000268138.7	+	8	2139	c.2034A>G	c.(2032-2034)aaA>aaG	p.K678K	TICRR_ENST00000560985.1_Silent_p.K677K			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	678					cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|formation of translation preinitiation complex (GO:0001731)|mitotic DNA replication checkpoint (GO:0033314)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)	chromatin binding (GO:0003682)										TAAAATCAAAAGGCACCAAGG	0.408																																						uc002boe.2																			0				ovary(4)|central_nervous_system(2)|skin(1)	7						c.(2032-2034)AAA>AAG		leucine-rich repeat kinase 1							92.0	85.0	87.0					15																	90142688		1878	4117	5995	SO:0001819	synonymous_variant	90381				cell cycle|DNA repair|DNA replication|formation of translation preinitiation complex|G2/M transition checkpoint|mitotic cell cycle DNA replication checkpoint|regulation of DNA-dependent DNA replication initiation|response to ionizing radiation	nucleus	chromatin binding|protein binding	g.chr15:90142688A>G	AK123612	CCDS10352.2	15q26.1	2012-07-11	2012-07-11	2012-07-11	ENSG00000140534	ENSG00000140534			28704	protein-coding gene	gene with protein product	"""TOPBP1-interacting replication-stimulating protein"", ""SLD3 homolog (S. cerevisiae)"""	613298	"""chromosome 15 open reading frame 42"""	C15orf42		20116089, 20080954	Standard	NM_152259		Approved	MGC45866, FLJ41618, Treslin, SLD3	uc002boe.3	Q7Z2Z1	OTTHUMG00000149648	ENST00000268138.7:c.2034A>G	15.37:g.90142688A>G							p.K678K	NM_152259	NP_689472	Q7Z2Z1	TICRR_HUMAN	BRCA - Breast invasive adenocarcinoma(143;0.128)		8	2034	+	Lung NSC(78;0.0237)|all_lung(78;0.0478)		678					B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Silent	SNP	ENST00000268138.7	37	c.2034A>G	CCDS10352.2																																																																																				0.408	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259	
SPG7	6687	broad.mit.edu	37	16	89598461	89598461	+	Silent	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr16:89598461G>A	ENST00000268704.2	+	8	1152	c.1137G>A	c.(1135-1137)gtG>gtA	p.V379V	RNU7-117P_ENST00000516770.1_RNA|SPG7_ENST00000341316.2_Silent_p.V379V	NM_003119.2	NP_003110.1	Q9UQ90	SPG7_HUMAN	spastic paraplegia 7 (pure and complicated autosomal recessive)	379					anterograde axon cargo transport (GO:0008089)|cell death (GO:0008219)|mitochondrion organization (GO:0007005)|nervous system development (GO:0007399)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metalloendopeptidase activity (GO:0004222)|peptidase activity (GO:0008233)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|urinary_tract(1)	20		all_hematologic(23;0.00824)|Colorectal(91;0.102)		all cancers(4;1.39e-07)|OV - Ovarian serous cystadenocarcinoma(4;5.64e-06)|BRCA - Breast invasive adenocarcinoma(80;0.015)		CAGAGTTCGTGGAGGTCATTG	0.647																																						uc002fnj.2																			0					0						c.(1135-1137)GTG>GTA		spastic paraplegia 7 isoform 1							56.0	52.0	53.0					16																	89598461		2198	4300	6498	SO:0001819	synonymous_variant	6687				cell death|nervous system development|protein catabolic process|proteolysis	integral to membrane|mitochondrial membrane	ATP binding|metalloendopeptidase activity|nucleoside-triphosphatase activity|unfolded protein binding|zinc ion binding	g.chr16:89598461G>A	Y16610	CCDS10977.1, CCDS10978.1	16q24.3	2010-04-21	2007-04-23		ENSG00000197912	ENSG00000197912		"""ATPases / AAA-type"""	11237	protein-coding gene	gene with protein product	"""paraplegin"""	602783	"""cell matrix adhesion regulator"""	CMAR		9635427, 9634528	Standard	XM_006721264		Approved	CAR, SPG5C	uc002fnj.3	Q9UQ90	OTTHUMG00000138046	ENST00000268704.2:c.1137G>A	16.37:g.89598461G>A						SPG7_uc002fni.2_Silent_p.V379V	p.V379V	NM_003119	NP_003110	Q9UQ90	SPG7_HUMAN		all cancers(4;1.39e-07)|OV - Ovarian serous cystadenocarcinoma(4;5.64e-06)|BRCA - Breast invasive adenocarcinoma(80;0.015)	8	1158	+		all_hematologic(23;0.00824)|Colorectal(91;0.102)	379			Mitochondrial matrix (Potential).		O75756|Q2TB70|Q58F00|Q96IB0	Silent	SNP	ENST00000268704.2	37	c.1137G>A	CCDS10977.1																																																																																				0.647	SPG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269921.2	NM_003119	
CCL2	6347	broad.mit.edu	37	17	32583358	32583358	+	Splice_Site	SNP	T	T	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr17:32583358T>A	ENST00000225831.4	+	2	259	c.194T>A	c.(193-195)aTc>aAc	p.I65N	AC005549.3_ENST00000601918.1_5'Flank|CCL2_ENST00000580907.1_Missense_Mutation_p.M65K	NM_002982.3	NP_002973.1	P13500	CCL2_HUMAN	chemokine (C-C motif) ligand 2	65					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|aging (GO:0007568)|angiogenesis (GO:0001525)|astrocyte cell migration (GO:0043615)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cellular calcium ion homeostasis (GO:0006874)|cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to interferon-gamma (GO:0071346)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to organic cyclic compound (GO:0071407)|cellular response to tumor necrosis factor (GO:0071356)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeleton organization (GO:0007010)|endoplasmic reticulum unfolded protein response (GO:0030968)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|helper T cell extravasation (GO:0035684)|humoral immune response (GO:0006959)|inflammatory response (GO:0006954)|JAK-STAT cascade (GO:0007259)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|lymphocyte chemotaxis (GO:0048247)|macrophage chemotaxis (GO:0048246)|MAPK cascade (GO:0000165)|maternal process involved in parturition (GO:0060137)|monocyte chemotaxis (GO:0002548)|negative regulation of angiogenesis (GO:0016525)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of natural killer cell chemotaxis (GO:2000502)|negative regulation of neuron apoptotic process (GO:0043524)|neutrophil chemotaxis (GO:0030593)|organ morphogenesis (GO:0009887)|organ regeneration (GO:0031100)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of calcium ion import (GO:0090280)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of immune complex clearance by monocytes and macrophages (GO:0090265)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of synaptic transmission (GO:0050806)|positive regulation of T cell activation (GO:0050870)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|regulation of vascular endothelial growth factor production (GO:0010574)|response to activity (GO:0014823)|response to amino acid (GO:0043200)|response to antibiotic (GO:0046677)|response to bacterium (GO:0009617)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to gamma radiation (GO:0010332)|response to glucocorticoid (GO:0051384)|response to heat (GO:0009408)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to vitamin B3 (GO:0033552)|response to wounding (GO:0009611)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|viral genome replication (GO:0019079)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)	CCR2 chemokine receptor binding (GO:0031727)|chemokine activity (GO:0008009)|heparin binding (GO:0008201)|protein kinase activity (GO:0004672)|receptor binding (GO:0005102)			kidney(1)|lung(3)|pancreas(1)|upper_aerodigestive_tract(1)	6	Breast(3;0.00224)	Ovarian(249;0.0694)|Breast(31;0.151)|Lung NSC(157;0.153)		UCEC - Uterine corpus endometrioid carcinoma (308;0.000241)|BRCA - Breast invasive adenocarcinoma(366;0.0103)	Danazol(DB01406)|Mimosine(DB01055)	GAAGCTGTGATGTGAGTTCAG	0.478																																						uc002hhy.2																			0				pancreas(1)	1						c.(193-195)ATC>AAC		small inducible cytokine A2 precursor	Atorvastatin(DB01076)|Danazol(DB01406)|Mimosine(DB01055)|Simvastatin(DB00641)						92.0	87.0	89.0					17																	32583358		2203	4300	6503	SO:0001630	splice_region_variant	6347				angiogenesis|anti-apoptosis|apoptotic cell clearance|astrocyte cell migration|cell adhesion|cellular response to interferon-gamma|cellular response to interleukin-1|cellular response to lipopolysaccharide|cellular response to tumor necrosis factor|G-protein signaling, coupled to cyclic nucleotide second messenger|helper T cell extravasation|humoral immune response|inflammatory response|JAK-STAT cascade|macrophage chemotaxis|monocyte chemotaxis|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of T cell activation|viral genome replication	extracellular space	CCR2 chemokine receptor binding|chemokine activity|protein kinase activity|signal transducer activity	g.chr17:32583358T>A	BC009716	CCDS11277.1	17q11.2-q21.1	2013-02-25	2002-08-22	2002-08-23	ENSG00000108691	ENSG00000108691		"""Chemokine ligands"", ""Endogenous ligands"""	10618	protein-coding gene	gene with protein product	"""monocyte chemotactic protein 1, homologous to mouse Sig-je"", ""monocyte chemoattractant protein-1"", ""monocyte chemotactic and activating factor"", ""monocyte secretory protein JE"", ""small inducible cytokine subfamily A (Cys-Cys), member 2"""	158105	"""small inducible cytokine A2 (monocyte chemotactic protein 1, homologous to mouse Sig-je)"""	SCYA2		2004761	Standard	NM_002982		Approved	MCP1, MCP-1, MCAF, SMC-CF, GDCF-2, HC11, MGC9434	uc002hhy.3	P13500	OTTHUMG00000132887	ENST00000225831.4:c.194+1T>A	17.37:g.32583358T>A							p.I65N	NM_002982	NP_002973	P13500	CCL2_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (308;0.000241)|BRCA - Breast invasive adenocarcinoma(366;0.0103)	2	267	+	Breast(3;0.00224)	Ovarian(249;0.0694)|Breast(31;0.151)|Lung NSC(157;0.153)	65	Missing: 90% reduction in activity.|Missing: 83% reduction in activity.				B2R4V3|Q9UDF3	Missense_Mutation	SNP	ENST00000225831.4	37	c.194T>A	CCDS11277.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.975561	0.74360	.	.	ENSG00000108691	ENST00000225831	T	0.14144	2.53	4.61	4.61	0.57282	CC chemokine, conserved site (1);Chemokine interleukin-8-like domain (3);	0.384087	0.22239	N	0.062712	T	0.35307	0.0927	.	.	.	0.44587	D	0.99755	D	0.89917	1.0	D	0.85130	0.997	T	0.09796	-1.0658	9	0.87932	D	0	.	10.5563	0.45118	0.0:0.0:0.0:1.0	.	65	P13500	CCL2_HUMAN	N	65	ENSP00000225831:I65N	ENSP00000225831:I65N	I	+	2	0	CCL2	29607471	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	3.383000	0.52471	2.062000	0.61559	0.402000	0.26972	ATC		0.478	CCL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256384.2	NM_002982	Missense_Mutation
TNS4	84951	broad.mit.edu	37	17	38641225	38641225	+	Silent	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr17:38641225G>A	ENST00000254051.6	-	5	1481	c.1323C>T	c.(1321-1323)ttC>ttT	p.F441F		NM_032865.5	NP_116254.4	Q8IZW8	TENS4_HUMAN	tensin 4	441					apoptotic process (GO:0006915)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	30		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(5;5.91e-05)			TGTCCATCACGAACTTCATGG	0.547																																						uc010cxb.2																			0				large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4						c.(1321-1323)TTC>TTT		tensin 4 precursor							115.0	100.0	105.0					17																	38641225		2203	4300	6503	SO:0001819	synonymous_variant	84951				apoptosis|protein localization	cytoplasm|cytoskeleton|focal adhesion	actin binding	g.chr17:38641225G>A	AF417488	CCDS11368.1	17q21.2	2013-02-14			ENSG00000131746	ENSG00000131746		"""SH2 domain containing"""	24352	protein-coding gene	gene with protein product	"""C terminal tensin like"""	608385				12154022, 12711115	Standard	NM_032865		Approved	CTEN	uc010cxb.3	Q8IZW8	OTTHUMG00000133330	ENST00000254051.6:c.1323C>T	17.37:g.38641225G>A							p.F441F	NM_032865	NP_116254	Q8IZW8	TENS4_HUMAN	STAD - Stomach adenocarcinoma(5;5.91e-05)		5	1487	-		Breast(137;0.000496)	441					A6NMJ7|Q71RB7|Q8WV64|Q96JV4	Silent	SNP	ENST00000254051.6	37	c.1323C>T	CCDS11368.1																																																																																				0.547	TNS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257154.3	NM_032865	
KRT39	390792	broad.mit.edu	37	17	39116597	39116597	+	Missense_Mutation	SNP	C	C	T	rs200663246		TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr17:39116597C>T	ENST00000355612.2	-	6	1188	c.1153G>A	c.(1153-1155)Gtc>Atc	p.V385I	AC004231.2_ENST00000418393.1_RNA	NM_213656.3	NP_998821.3	Q6A163	K1C39_HUMAN	keratin 39	385	Coil 2.|Rod.					intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)	p.V385F(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	17		Breast(137;0.00043)|Ovarian(249;0.15)				CGGGACTTGACGTCCAGCAGG	0.493													C|||	1	0.000199681	0.0	0.0	5008	,	,		19964	0.0		0.001	False		,,,				2504	0.0					uc002hvo.1																			1	Substitution - Missense(1)		NS(1)		0						c.(1153-1155)GTC>ATC		type I hair keratin KA35		C	ILE/VAL	0,4406		0,0,2203	152.0	130.0	137.0		1153	-5.1	0.0	17		137	1,8591	1.2+/-3.3	0,1,4295	yes	missense	KRT39	NM_213656.3	29	0,1,6498	TT,TC,CC		0.0116,0.0,0.0077	benign	385/492	39116597	1,12997	2203	4296	6499	SO:0001583	missense	390792					intermediate filament	structural molecule activity	g.chr17:39116597C>T	AJ786657	CCDS11382.1	17q21.2	2013-01-16			ENSG00000196859	ENSG00000196859		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	32971	protein-coding gene	gene with protein product						16831889	Standard	NM_213656		Approved	KA35	uc002hvo.1	Q6A163	OTTHUMG00000133424	ENST00000355612.2:c.1153G>A	17.37:g.39116597C>T	ENSP00000347823:p.Val385Ile					KRT39_uc010wfm.1_Missense_Mutation_p.V118I	p.V385I	NM_213656	NP_998821	Q6A163	K1C39_HUMAN			6	1189	-		Breast(137;0.00043)|Ovarian(249;0.15)	385			Coil 2.|Rod.		B2RXK6|Q6IFU6	Missense_Mutation	SNP	ENST00000355612.2	37	c.1153G>A	CCDS11382.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	8.520	0.868562	0.17322	0.0	1.16E-4	ENSG00000196859	ENST00000355612	D	0.90620	-2.7	5.7	-5.1	0.02911	Filament (1);	0.391181	0.18823	N	0.130198	T	0.79375	0.4435	N	0.20357	0.565	0.09310	N	1	P	0.35328	0.495	B	0.34180	0.177	T	0.67848	-0.5564	10	0.23302	T	0.38	.	13.2836	0.60230	0.0:0.349:0.0:0.651	.	385	Q6A163	K1C39_HUMAN	I	385	ENSP00000347823:V385I	ENSP00000347823:V385I	V	-	1	0	KRT39	36370123	0.000000	0.05858	0.001000	0.08648	0.162000	0.22319	-0.385000	0.07379	-1.340000	0.02227	-1.596000	0.00833	GTC		0.493	KRT39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257287.1	NM_213656	
KRTAP4-11	653240	broad.mit.edu	37	17	39274291	39274291	+	Missense_Mutation	SNP	T	T	C	rs200214744|rs565505867	byFrequency	TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr17:39274291T>C	ENST00000391413.2	-	1	315	c.277A>G	c.(277-279)Atg>Gtg	p.M93V		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	93	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament (GO:0045095)		p.M93V(4)		endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			TGGCAGCACATAGACTGGCAG	0.662																																						uc002hvz.2																			4	Substitution - Missense(4)		endometrium(3)|kidney(1)		0						c.(277-279)ATG>GTG		keratin associated protein 4-11							6.0	10.0	8.0					17																	39274291		651	1556	2207	SO:0001583	missense	653240					keratin filament		g.chr17:39274291T>C	AC025904	CCDS45675.1	17q21.2	2013-06-25			ENSG00000212721	ENSG00000212721		"""Keratin associated proteins"""	18911	protein-coding gene	gene with protein product			"""keratin associated protein 4-14"""	KRTAP4-14			Standard	NM_033059		Approved	KAP4.11, KAP4.14	uc002hvz.3	Q9BYQ6	OTTHUMG00000133586	ENST00000391413.2:c.277A>G	17.37:g.39274291T>C	ENSP00000375232:p.Met93Val						p.M93V	NM_033059	NP_149048	Q9BYQ6	KR411_HUMAN	STAD - Stomach adenocarcinoma(17;0.000371)		1	316	-		Breast(137;0.000496)	93			14.|27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].		A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	37	c.277A>G	CCDS45675.1	.	.	.	.	.	.	.	.	.	.	.	0.073	-1.199029	0.01581	.	.	ENSG00000212721	ENST00000391413	T	0.00580	6.43	4.25	-4.9	0.03094	.	.	.	.	.	T	0.00109	0.0003	N	0.00040	-2.49	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43097	-0.9412	9	0.02654	T	1	.	0.4739	0.00536	0.3479:0.2455:0.1203:0.2863	.	93	Q9BYQ6	KR411_HUMAN	V	93	ENSP00000375232:M93V	ENSP00000375232:M93V	M	-	1	0	KRTAP4-11	36527817	.	.	0.012000	0.15200	0.010000	0.07245	.	.	-1.319000	0.02286	-1.132000	0.01976	ATG		0.662	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1		
SGCA	6442	broad.mit.edu	37	17	48246591	48246591	+	Silent	SNP	C	C	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr17:48246591C>T	ENST00000262018.3	+	6	759	c.723C>T	c.(721-723)cgC>cgT	p.R241R	SGCA_ENST00000543315.1_Intron|SGCA_ENST00000344627.6_Intron|HILS1_ENST00000504307.1_RNA|SGCA_ENST00000513942.1_Intron|SGCA_ENST00000451235.2_Silent_p.R139R	NM_000023.2	NP_000014.1	Q16586	SGCA_HUMAN	sarcoglycan, alpha (50kDa dystrophin-associated glycoprotein)	241					muscle contraction (GO:0006936)|muscle organ development (GO:0007517)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(7)|ovary(2)|skin(1)	14						CCCACTTCCGCGTTGACTGGT	0.662											OREG0024558	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										uc002iqi.2																			0				ovary(2)	2						c.(721-723)CGC>CGT		sarcoglycan, alpha isoform 1 precursor							79.0	67.0	71.0					17																	48246591		2203	4300	6503	SO:0001819	synonymous_variant	6442				muscle contraction|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma	calcium ion binding	g.chr17:48246591C>T	L34355	CCDS32679.1, CCDS45729.1	17q21	2014-09-17	2002-08-29		ENSG00000108823	ENSG00000108823			10805	protein-coding gene	gene with protein product	"""50kD DAG"", ""Sarcoglycan, alpha (50kD dystrophin-associated glycoprotein; adhalin)"", ""adhalin (limb girdle muscular dystrophy 2D)"""	600119	"""sarcoglycan, alpha (50kD dystrophin-associated glycoprotein)"""	ADL		7937874	Standard	NM_000023		Approved	SCARMD1, LGMD2D, adhalin, DMDA2, A2	uc002iqi.3	Q16586	OTTHUMG00000162024	ENST00000262018.3:c.723C>T	17.37:g.48246591C>T			OREG0024558	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	953	SGCA_uc010wmh.1_Silent_p.R139R|SGCA_uc002iqj.2_Intron|SGCA_uc010wmi.1_RNA|uc010dbn.1_5'Flank	p.R241R	NM_000023	NP_000014	Q16586	SGCA_HUMAN			6	759	+			241			Extracellular (Potential).		A6NEB8|A8K3K7|Q13710|Q13712	Silent	SNP	ENST00000262018.3	37	c.723C>T	CCDS32679.1																																																																																				0.662	SGCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366841.1	NM_000023	
EPX	8288	broad.mit.edu	37	17	56277732	56277732	+	Nonsense_Mutation	SNP	C	C	T	rs376157164		TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr17:56277732C>T	ENST00000225371.5	+	10	1794	c.1684C>T	c.(1684-1686)Cga>Tga	p.R562*		NM_000502.4	NP_000493.1	P11678	PERE_HUMAN	eosinophil peroxidase	562					defense response to nematode (GO:0002215)|eosinophil migration (GO:0072677)|hydrogen peroxide catabolic process (GO:0042744)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-5 production (GO:0032714)|positive regulation of interleukin-4 production (GO:0032753)	extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(2)|endometrium(9)|kidney(1)|large_intestine(9)|liver(2)|lung(20)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	48					Melatonin(DB01065)	CAACATGCAACGAAGCCGGGA	0.617											OREG0024608	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										uc002ivq.2																			0				ovary(2)	2						c.(1684-1686)CGA>TGA		eosinophil peroxidase preproprotein		C	stop/ARG	0,4406		0,0,2203	60.0	58.0	59.0		1684	5.7	1.0	17		59	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained	EPX	NM_000502.4		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		562/716	56277732	1,13005	2203	4300	6503	SO:0001587	stop_gained	8288				hydrogen peroxide catabolic process		heme binding|peroxidase activity|protein binding	g.chr17:56277732C>T	M26515	CCDS11602.1	17q23.1	2006-09-25				ENSG00000121053	1.11.1.7		3423	protein-coding gene	gene with protein product		131399				2550461, 2541222	Standard	NM_000502		Approved	EPO, EPP, EPX-PEN	uc002ivq.3	P11678		ENST00000225371.5:c.1684C>T	17.37:g.56277732C>T	ENSP00000225371:p.Arg562*		OREG0024608	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1014		p.R562*	NM_000502	NP_000493	P11678	PERE_HUMAN			10	1770	+			562					Q4TVP3	Nonsense_Mutation	SNP	ENST00000225371.5	37	c.1684C>T	CCDS11602.1	.	.	.	.	.	.	.	.	.	.	C	39	7.469497	0.98302	0.0	1.16E-4	ENSG00000121053	ENST00000225371	.	.	.	5.66	5.66	0.87406	.	0.090906	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.2861	12.5507	0.56225	0.1662:0.8338:0.0:0.0	.	.	.	.	X	562	.	ENSP00000225371:R562X	R	+	1	2	EPX	53632731	0.997000	0.39634	0.995000	0.50966	0.984000	0.73092	3.997000	0.57016	2.832000	0.97577	0.655000	0.94253	CGA		0.617	EPX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443367.1	NM_000502	
ENPP7	339221	broad.mit.edu	37	17	77711814	77711814	+	Missense_Mutation	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr17:77711814G>A	ENST00000328313.5	+	5	1567	c.1346G>A	c.(1345-1347)gGg>gAg	p.G449E		NM_178543.3	NP_848638.3			ectonucleotide pyrophosphatase/phosphodiesterase 7											breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(6)|skin(3)	34			OV - Ovarian serous cystadenocarcinoma(97;0.016)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			GGACTGCTGGGGACCGTGATT	0.632																																						uc002jxa.2																			0				central_nervous_system(2)|ovary(1)	3						c.(1345-1347)GGG>GAG		ectonucleotide pyrophosphatase/phosphodiesterase							90.0	82.0	85.0					17																	77711814		2203	4300	6503	SO:0001583	missense	339221				negative regulation of cell proliferation|negative regulation of DNA replication|sphingomyelin metabolic process	Golgi apparatus|integral to membrane|microvillus	sphingomyelin phosphodiesterase activity	g.chr17:77711814G>A	AY230663	CCDS11763.1	17q25.3	2014-04-09			ENSG00000182156	ENSG00000182156			23764	protein-coding gene	gene with protein product	"""alkaline sphingomyelinase"""					12885774	Standard	NM_178543		Approved	alk-SMase, NPP7	uc002jxa.3	Q6UWV6	OTTHUMG00000177462	ENST00000328313.5:c.1346G>A	17.37:g.77711814G>A	ENSP00000332656:p.Gly449Glu						p.G449E	NM_178543	NP_848638	Q6UWV6	ENPP7_HUMAN	OV - Ovarian serous cystadenocarcinoma(97;0.016)|BRCA - Breast invasive adenocarcinoma(99;0.0224)		5	1366	+			449			Helical; (Potential).			Missense_Mutation	SNP	ENST00000328313.5	37	c.1346G>A	CCDS11763.1	.	.	.	.	.	.	.	.	.	.	G	12.78	2.039323	0.35989	.	.	ENSG00000182156	ENST00000328313	T	0.73897	-0.79	2.65	1.61	0.23674	.	5.269940	0.01269	U	0.009411	T	0.70988	0.3287	L	0.32530	0.975	0.20196	N	0.999924	P	0.51933	0.949	P	0.49799	0.622	T	0.57785	-0.7751	10	0.28530	T	0.3	.	6.0892	0.19985	0.0:0.0:0.564:0.436	.	449	Q6UWV6	ENPP7_HUMAN	E	449	ENSP00000332656:G449E	ENSP00000332656:G449E	G	+	2	0	ENPP7	75326409	0.002000	0.14202	0.367000	0.25926	0.112000	0.19704	-0.041000	0.12084	0.577000	0.29470	0.462000	0.41574	GGG		0.632	ENPP7-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437038.1	NM_178543	
LAMA1	284217	broad.mit.edu	37	18	6977852	6977852	+	Silent	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr18:6977852G>A	ENST00000389658.3	-	44	6312	c.6219C>T	c.(6217-6219)gaC>gaT	p.D2073D		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2073	Domain II and I.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				GAATTTCCACGTCTTTGACTT	0.398																																						uc002knm.2																			0				ovary(8)|large_intestine(4)|upper_aerodigestive_tract(2)|breast(2)|skin(2)|pancreas(2)|central_nervous_system(1)	21						c.(6217-6219)GAC>GAT		laminin, alpha 1 precursor	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)						56.0	54.0	54.0					18																	6977852		2203	4300	6503	SO:0001819	synonymous_variant	284217				axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding	g.chr18:6977852G>A	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.6219C>T	18.37:g.6977852G>A						LAMA1_uc010wzj.1_Silent_p.D1549D	p.D2073D	NM_005559	NP_005550	P25391	LAMA1_HUMAN			44	6313	-		Colorectal(10;0.172)	2073			Domain II and I.			Silent	SNP	ENST00000389658.3	37	c.6219C>T	CCDS32787.1																																																																																				0.398	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
POTEC	388468	broad.mit.edu	37	18	14542921	14542921	+	Silent	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr18:14542921G>A	ENST00000358970.5	-	1	224	c.225C>T	c.(223-225)agC>agT	p.S75S	POTEC_ENST00000389891.4_5'UTR	NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	75								p.S75S(1)|p.S75R(1)		NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						TGCTCGTGCCGCTCCCCCTGC	0.567																																						uc010dln.2																			2	Substitution - Missense(1)|Substitution - coding silent(1)		lung(1)|kidney(1)	skin(3)	3						c.(223-225)AGC>AGT		ANKRD26-like family B, member 2							43.0	53.0	50.0					18																	14542921		692	1591	2283	SO:0001819	synonymous_variant	388468							g.chr18:14542921G>A	BX649118	CCDS45835.1	18p11.21	2013-01-10	2008-11-26	2008-11-26	ENSG00000183206	ENSG00000183206		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33894	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 6"""		"""ANKRD26-like family B, member 2"""	A26B2			Standard	NM_001137671		Approved	POTE18, POTE-18, DKFZp686J0529, CT104.6	uc010dln.3	B2RU33	OTTHUMG00000162963	ENST00000358970.5:c.225C>T	18.37:g.14542921G>A						POTEC_uc010xaj.1_RNA	p.S75S	NM_001137671	NP_001131143	B2RU33	POTEC_HUMAN			1	679	-			75						Silent	SNP	ENST00000358970.5	37	c.225C>T	CCDS45835.1																																																																																				0.567	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371179.1	XM_496269	
SERPINB11	89778	broad.mit.edu	37	18	61387390	61387390	+	RNA	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr18:61387390G>A	ENST00000382749.5	+	0	863				SERPINB11_ENST00000544088.1_RNA|SERPINB11_ENST00000489748.1_RNA|SERPINB11_ENST00000536691.1_RNA|SERPINB11_ENST00000538847.1_RNA			Q96P15	SPB11_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 11 (gene/pseudogene)						negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|cervix(1)|kidney(1)|lung(3)	6		Esophageal squamous(42;0.129)				GCTAAGTGAGGTAAGTATTTT	0.313																																					Ovarian(27;496 784 5942 8975 23930)	uc002ljk.3																			0				breast(1)	1						c.e7+1		serpin peptidase inhibitor, clade B, member 11							42.0	43.0	43.0					18																	61387390		1825	4077	5902			89778				regulation of proteolysis	cytoplasm	serine-type endopeptidase inhibitor activity	g.chr18:61387390G>A			18q21.33	2014-02-18	2009-01-22		ENSG00000206072	ENSG00000206072		"""Serine (or cysteine) peptidase inhibitors"""	14221	protein-coding gene	gene with protein product		615682	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 11"", ""serpin peptidase inhibitor, clade B (ovalbumin), member 11"""			17562709, 24172014	Standard	XM_006722569		Approved	EPIPIN	uc002ljk.4	Q96P15	OTTHUMG00000060404		18.37:g.61387390G>A						SERPINB11_uc010xes.1_Splice_Site_p.E31_splice|SERPINB11_uc010dqd.2_Splice_Site_p.E92_splice|SERPINB11_uc002ljj.3_Splice_Site_p.E92_splice|SERPINB11_uc010dqe.2_Intron|SERPINB11_uc010dqf.2_Intron	p.E206_splice	NM_080475	NP_536723	Q96P15	SPB11_HUMAN			7	680	+		Esophageal squamous(42;0.129)						A8K9R0|Q5Q120|Q5Q121|Q5Q122|Q5Q123|Q6ISD3|Q96P13|Q96P14	Splice_Site	SNP	ENST00000382749.5	37	c.618_splice		.	.	.	.	.	.	.	.	.	.	G	21.4	4.146532	0.77888	.	.	ENSG00000206072	ENST00000544088;ENST00000536691	.	.	.	5.62	5.62	0.85841	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.0236	0.92923	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SERPINB11	59538370	1.000000	0.71417	0.983000	0.44433	0.806000	0.45545	8.590000	0.90821	2.805000	0.96524	0.655000	0.94253	.		0.313	SERPINB11-002	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000207392.3	NM_080475	
PTPRS	5802	broad.mit.edu	37	19	5273496	5273496	+	Silent	SNP	C	C	T	rs528468686	byFrequency	TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr19:5273496C>T	ENST00000587303.1	-	3	435	c.336G>A	c.(334-336)tcG>tcA	p.S112S	PTPRS_ENST00000348075.2_Silent_p.S112S|PTPRS_ENST00000353284.2_Silent_p.S112S|PTPRS_ENST00000590509.1_Silent_p.S112S|PTPRS_ENST00000588552.1_5'UTR|PTPRS_ENST00000372412.4_Silent_p.S112S|PTPRS_ENST00000262963.6_Silent_p.S112S|PTPRS_ENST00000357368.4_Silent_p.S112S|PTPRS_ENST00000588012.1_Silent_p.S112S|PTPRS_ENST00000592099.1_Silent_p.S112S			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	112	Ig-like C2-type 1.				cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|corpus callosum development (GO:0022038)|extracellular matrix organization (GO:0030198)|hippocampus development (GO:0021766)|peptidyl-tyrosine dephosphorylation (GO:0035335)|spinal cord development (GO:0021510)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(9)|ovary(4)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)	61				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)	Alendronate(DB00630)|Etidronic acid(DB01077)	TCTCCCCAACCGAGTTCTGGG	0.587													C|||	3	0.000599042	0.0	0.0	5008	,	,		19646	0.0		0.0	False		,,,				2504	0.0031					uc002mbv.2																			0				large_intestine(2)|ovary(1)|central_nervous_system(1)	4						c.(334-336)TCG>TCA		protein tyrosine phosphatase, receptor type,							135.0	113.0	120.0					19																	5273496		2203	4300	6503	SO:0001819	synonymous_variant	5802				cell adhesion	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity	g.chr19:5273496C>T	U35234	CCDS12139.1, CCDS12140.1, CCDS45930.1, CCDS74265.1	19p13.3	2013-02-11				ENSG00000105426		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9681	protein-coding gene	gene with protein product		601576				8954782, 8524829	Standard	NM_002850		Approved		uc002mbv.3	Q13332		ENST00000587303.1:c.336G>A	19.37:g.5273496C>T						PTPRS_uc002mbu.1_Silent_p.S112S|PTPRS_uc010xin.1_Silent_p.S112S|PTPRS_uc002mbw.2_Silent_p.S112S|PTPRS_uc002mbx.2_Silent_p.S112S|PTPRS_uc002mby.2_Silent_p.S112S|PTPRS_uc002mbz.1_Silent_p.S112S	p.S112S	NM_002850	NP_002841	Q13332	PTPRS_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)	4	570	-			112			Ig-like C2-type 1.|Extracellular (Potential).		O75255|O75870|Q15718|Q16341|Q2M3R7	Silent	SNP	ENST00000587303.1	37	c.336G>A	CCDS45930.1																																																																																				0.587	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2		
KRTDAP	388533	broad.mit.edu	37	19	35979579	35979579	+	Silent	SNP	G	G	A	rs376125312		TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr19:35979579G>A	ENST00000338897.3	-	3	241	c.153C>T	c.(151-153)atC>atT	p.I51I	KRTDAP_ENST00000484218.2_Intron|KRTDAP_ENST00000479340.1_5'UTR	NM_207392.2	NP_997275.1	P60985	KTDAP_HUMAN	keratinocyte differentiation-associated protein	51					cell differentiation (GO:0030154)	extracellular region (GO:0005576)				breast(1)|lung(4)|prostate(1)	6	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			GCAATTTGTCGATGTTCAGGA	0.512																																						uc002nzh.2																			0					0						c.(151-153)ATC>ATT		keratinocyte differentiation-associated protein		G		1,4405	2.1+/-5.4	0,1,2202	141.0	129.0	133.0		153	-6.9	0.0	19		133	0,8600		0,0,4300	no	coding-synonymous	KRTDAP	NM_207392.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		51/100	35979579	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	388533				cell differentiation	extracellular region		g.chr19:35979579G>A	AA297512	CCDS12462.1, CCDS59377.1	19q13.12	2013-06-20			ENSG00000188508	ENSG00000188508			16313	protein-coding gene	gene with protein product						11054531	Standard	NM_207392		Approved	KDAP, UNQ467	uc002nzh.3	P60985	OTTHUMG00000155449	ENST00000338897.3:c.153C>T	19.37:g.35979579G>A							p.I51I	NM_207392	NP_997275	P60985	KTDAP_HUMAN	LUSC - Lung squamous cell carcinoma(66;0.0724)		3	165	-	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		51					A1L4D7	Silent	SNP	ENST00000338897.3	37	c.153C>T	CCDS12462.1																																																																																				0.512	KRTDAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340164.1		
SIPA1L3	23094	broad.mit.edu	37	19	38621245	38621245	+	Silent	SNP	C	C	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr19:38621245C>T	ENST00000222345.6	+	10	3485	c.2976C>T	c.(2974-2976)gaC>gaT	p.D992D		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	992	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			AGGTTGAGGACTATGGGTTCG	0.662																																						uc002ohk.2																			0				ovary(1)|central_nervous_system(1)	2						c.(2974-2976)GAC>GAT		signal-induced proliferation-associated 1 like							74.0	67.0	69.0					19																	38621245		2203	4300	6503	SO:0001819	synonymous_variant	23094				regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity	g.chr19:38621245C>T	AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738			23801	protein-coding gene	gene with protein product							Standard	XM_005258671		Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.2976C>T	19.37:g.38621245C>T							p.D992D	NM_015073	NP_055888	O60292	SI1L3_HUMAN	Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)		10	3485	+			992			PDZ.		Q2TV87	Silent	SNP	ENST00000222345.6	37	c.2976C>T	CCDS33007.1																																																																																				0.662	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278	
LTBP4	8425	broad.mit.edu	37	19	41133127	41133127	+	Silent	SNP	C	C	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr19:41133127C>T	ENST00000308370.7	+	32	4431	c.4431C>T	c.(4429-4431)gaC>gaT	p.D1477D	LTBP4_ENST00000396819.3_Silent_p.D1410D|LTBP4_ENST00000545697.1_Silent_p.D845D|LTBP4_ENST00000602240.1_3'UTR|LTBP4_ENST00000204005.9_Silent_p.D1440D|LTBP4_ENST00000243562.9_3'UTR	NM_001042544.1	NP_001036009.1	Q8N2S1	LTBP4_HUMAN	latent transforming growth factor beta binding protein 4	1478	Pro-rich.				extracellular matrix organization (GO:0030198)|growth hormone secretion (GO:0030252)|multicellular organismal development (GO:0007275)|protein folding (GO:0006457)|regulation of cell differentiation (GO:0045595)|regulation of cell growth (GO:0001558)|regulation of proteolysis (GO:0030162)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|glycosaminoglycan binding (GO:0005539)|integrin binding (GO:0005178)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			central_nervous_system(1)	1			Lung(22;0.000158)|LUSC - Lung squamous cell carcinoma(20;0.000384)			ACTTTGAGGACGATGGTGGCC	0.701																																						uc002ooh.1																			0				central_nervous_system(1)	1						c.(4432-4434)GAC>GAT		latent transforming growth factor beta binding							19.0	23.0	22.0					19																	41133127		1966	4151	6117	SO:0001819	synonymous_variant	8425				growth hormone secretion|multicellular organismal development|protein folding|regulation of cell differentiation|regulation of cell growth|regulation of proteolysis|regulation of transforming growth factor beta receptor signaling pathway	extracellular space|proteinaceous extracellular matrix	calcium ion binding|glycosaminoglycan binding|integrin binding|transforming growth factor beta binding|transforming growth factor beta receptor activity	g.chr19:41133127C>T	Y13622	CCDS74368.1, CCDS74369.1, CCDS74370.1	19q13.1-q13.2	2011-10-20				ENSG00000090006		"""Latent transforming growth factor, beta binding proteins"""	6717	protein-coding gene	gene with protein product		604710				9660815, 9271198	Standard	NM_003573		Approved	LTBP-4, LTBP-4L, FLJ46318, FLJ90018	uc002ooh.1	Q8N2S1		ENST00000308370.7:c.4431C>T	19.37:g.41133127C>T						LTBP4_uc002oog.1_Silent_p.D1441D|LTBP4_uc002ooi.1_Silent_p.D1411D|LTBP4_uc002ooj.1_Silent_p.D351D|LTBP4_uc002ook.1_Silent_p.D612D|LTBP4_uc002ool.1_Silent_p.D490D|LTBP4_uc010xvp.1_Silent_p.D238D	p.D1478D	NM_001042544	NP_001036009	Q8N2S1	LTBP4_HUMAN	Lung(22;0.000158)|LUSC - Lung squamous cell carcinoma(20;0.000384)		32	4434	+			1478			Pro-rich.		O00508|O75412|O75413	Silent	SNP	ENST00000308370.7	37	c.4434C>T																																																																																					0.701	LTBP4-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_003573	
CEACAM3	1084	broad.mit.edu	37	19	42301582	42301582	+	Silent	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr19:42301582G>A	ENST00000357396.3	+	2	367	c.126G>A	c.(124-126)ccG>ccA	p.P42P	CEACAM3_ENST00000344550.4_Silent_p.P42P|CEACAM3_ENST00000595255.1_3'UTR|CEACAM3_ENST00000221999.4_Silent_p.P42P	NM_001815.2	NP_001806.2	P40198	CEAM3_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 3	42	Ig-like V-type.					integral component of membrane (GO:0016021)		p.P42P(1)		endometrium(2)|kidney(4)|large_intestine(1)|lung(4)|prostate(3)|skin(4)|stomach(1)	19						AATCCATGCCGCTCAGTGTCG	0.522																																						uc002orn.1																			1	Substitution - coding silent(1)		prostate(1)	skin(1)	1						c.(124-126)CCG>CCA		carcinoembryonic antigen-related cell adhesion							157.0	146.0	150.0					19																	42301582		2203	4300	6503	SO:0001819	synonymous_variant	1084					integral to membrane		g.chr19:42301582G>A	E03349	CCDS12586.2, CCDS62685.1	19q13.2	2013-01-11			ENSG00000170956	ENSG00000170956		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1815	protein-coding gene	gene with protein product		609142		CGM1			Standard	NM_001815		Approved	CD66d	uc002orn.2	P40198	OTTHUMG00000150142	ENST00000357396.3:c.126G>A	19.37:g.42301582G>A						CEACAM3_uc010eia.1_Silent_p.P42P|CEACAM3_uc002oro.1_RNA	p.P42P	NM_001815	NP_001806	P40198	CEAM3_HUMAN			2	202	+			42			Ig-like V-type.|Extracellular (Potential).		G5E978|Q3KPH9	Silent	SNP	ENST00000357396.3	37	c.126G>A	CCDS12586.2																																																																																				0.522	CEACAM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316509.2	NM_001815	
PSG1	5669	broad.mit.edu	37	19	43383725	43383725	+	Silent	SNP	G	G	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr19:43383725G>T	ENST00000436291.2	-	1	125	c.9C>A	c.(7-9)acC>acA	p.T3T	PSG1_ENST00000244296.2_Silent_p.T3T|PSG1_ENST00000595356.1_Silent_p.T3T|PSG1_ENST00000403380.3_Silent_p.T3T|PSG1_ENST00000595124.1_Silent_p.T3T|PSG1_ENST00000312439.6_Silent_p.T3T|PSG1_ENST00000601073.1_5'UTR	NM_001184825.1|NM_001184826.1	NP_001171754.1|NP_001171755.1	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	3					female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30		Prostate(69;0.00682)				GGGCTGAGAGGGTTCCCATGG	0.572																																						uc002ovb.2																			0				ovary(2)	2						c.(7-9)ACC>ACA		pregnancy specific beta-1-glycoprotein 1							185.0	154.0	165.0					19																	43383725		1510	2707	4217	SO:0001819	synonymous_variant	5669				female pregnancy	extracellular region		g.chr19:43383725G>T		CCDS12612.1, CCDS54275.1, CCDS59392.1, CCDS74380.1	19q13.2	2013-01-29			ENSG00000231924	ENSG00000231924		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9514	protein-coding gene	gene with protein product		176390		PSBG1			Standard	NM_006905		Approved	PSGGA, CD66f, PBG1		P11464	OTTHUMG00000151123	ENST00000436291.2:c.9C>A	19.37:g.43383725G>T						PSG3_uc002ouf.2_Intron|PSG1_uc002oug.1_Silent_p.T3T|PSG11_uc002ouw.2_Intron|PSG7_uc002ous.1_Intron|PSG7_uc002out.1_Intron|PSG10_uc002ouv.1_Intron|PSG1_uc002oun.2_RNA|PSG1_uc002our.1_Silent_p.T3T|PSG1_uc010eio.1_Silent_p.T3T|PSG1_uc002oux.1_5'Flank|PSG1_uc002ouy.1_Silent_p.T3T|PSG1_uc002ouz.1_Silent_p.T3T|PSG1_uc002ova.1_Silent_p.T3T|PSG1_uc002ovc.2_Silent_p.T3T|PSG1_uc002ovd.1_Silent_p.T3T	p.T3T	NM_006905	NP_008836	P11464	PSG1_HUMAN			1	147	-		Prostate(69;0.00682)	3					O75236|P11462|P11463|Q15231|Q15241|Q15243|Q16660|Q6ICR4|Q9P1W5|Q9UQ79	Silent	SNP	ENST00000436291.2	37	c.9C>A	CCDS54275.1																																																																																				0.572	PSG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321426.1		
TRAPPC12	51112	broad.mit.edu	37	2	3392072	3392072	+	Silent	SNP	C	C	T	rs189855582		TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr2:3392072C>T	ENST00000324266.5	+	2	873	c.678C>T	c.(676-678)tcC>tcT	p.S226S	TRAPPC12_ENST00000382110.2_Silent_p.S226S	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	226					vesicle-mediated transport (GO:0016192)												TCTTCGACTCCTTTACTACCT	0.711																																						uc002qxm.1																			0				ovary(2)|breast(1)|pancreas(1)	4						c.(676-678)TCC>TCT		tetratricopeptide repeat domain 15							44.0	50.0	48.0					2																	3392072		2203	4300	6503	SO:0001819	synonymous_variant	51112						binding	g.chr2:3392072C>T	BC017475	CCDS1652.1	2p25.3	2013-01-10	2011-12-12	2011-12-12	ENSG00000171853	ENSG00000171853		"""Trafficking protein particle complex"", ""Tetratricopeptide (TTC) repeat domain containing"""	24284	protein-coding gene	gene with protein product		614139	"""tetratricopeptide repeat domain 15"""	TTC15		10810093, 21525244, 20562859	Standard	NM_016030		Approved	CGI-87, TTC-15	uc002qxm.1	Q8WVT3	OTTHUMG00000090328	ENST00000324266.5:c.678C>T	2.37:g.3392072C>T						TTC15_uc002qxn.1_Silent_p.S226S|TTC15_uc010ewm.1_Silent_p.S226S|TTC15_uc002qxl.1_Silent_p.S226S	p.S226S	NM_016030	NP_057114	Q8WVT3	TTC15_HUMAN		OV - Ovarian serous cystadenocarcinoma(76;0.0402)|Epithelial(75;0.0986)|all cancers(51;0.149)	2	884	+	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)	all_cancers(51;0.214)	226					B3KV01|D6W4Y2|Q8WVW1|Q9Y395	Silent	SNP	ENST00000324266.5	37	c.678C>T	CCDS1652.1																																																																																				0.711	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206693.2	NM_016030	
MAP4K4	9448	broad.mit.edu	37	2	102440436	102440436	+	Missense_Mutation	SNP	A	A	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr2:102440436A>T	ENST00000347699.4	+	4	227	c.227A>T	c.(226-228)tAc>tTc	p.Y76F	MAP4K4_ENST00000413150.2_Missense_Mutation_p.Y76F|MAP4K4_ENST00000456652.1_Missense_Mutation_p.Y76F|MAP4K4_ENST00000324219.4_Missense_Mutation_p.Y76F|MAP4K4_ENST00000350198.4_Missense_Mutation_p.Y76F|MAP4K4_ENST00000350878.4_Missense_Mutation_p.Y56F|MAP4K4_ENST00000302217.5_Missense_Mutation_p.Y76F|MAP4K4_ENST00000425019.1_Missense_Mutation_p.Y76F	NM_001242559.1|NM_145687.3	NP_001229488.1|NP_663720.1	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase kinase 4	76	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of JNK cascade (GO:0046328)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						CTAAAGAAATACTCTCATCAC	0.368																																						uc002tbg.2																			0				stomach(1)|lung(1)|central_nervous_system(1)|skin(1)	4						c.(226-228)TAC>TTC		mitogen-activated protein kinase kinase kinase							84.0	81.0	82.0					2																	102440436		1860	4099	5959	SO:0001583	missense	9448				intracellular protein kinase cascade|regulation of JNK cascade|response to stress	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity	g.chr2:102440436A>T	AF096300	CCDS56130.1, CCDS74546.1	2q11.2-q12	2011-06-09			ENSG00000071054	ENSG00000071054		"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6866	protein-coding gene	gene with protein product	"""HPK/GCK-like kinase"", ""hepatocyte progenitor kinase-like/germinal center kinase-like kinase"""	604666				9890973, 9734811, 9135144	Standard	NM_004834		Approved	HGK, NIK, FLH21957	uc002tbf.3	O95819	OTTHUMG00000155394	ENST00000347699.4:c.227A>T	2.37:g.102440436A>T	ENSP00000314363:p.Tyr76Phe					MAP4K4_uc002tbc.2_Missense_Mutation_p.Y76F|MAP4K4_uc002tbd.2_Missense_Mutation_p.Y76F|MAP4K4_uc002tbe.2_Missense_Mutation_p.Y76F|MAP4K4_uc002tbf.2_Missense_Mutation_p.Y76F|MAP4K4_uc010yvy.1_Missense_Mutation_p.Y76F|MAP4K4_uc002tbh.2_Missense_Mutation_p.Y76F|MAP4K4_uc002tbi.2_Missense_Mutation_p.Y76F|MAP4K4_uc010yvz.1_Missense_Mutation_p.Y56F|MAP4K4_uc010fiw.1_Intron|MAP4K4_uc002tbj.1_5'Flank	p.Y76F	NM_145687	NP_663720	O95819	M4K4_HUMAN			4	282	+			76			Protein kinase.		O75172|Q9NST7	Missense_Mutation	SNP	ENST00000347699.4	37	c.227A>T	CCDS56130.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.041107	0.75732	.	.	ENSG00000071054	ENST00000427603;ENST00000425019;ENST00000324219;ENST00000350198;ENST00000302217;ENST00000413150;ENST00000456652;ENST00000347699;ENST00000417294;ENST00000350878	T;T;T;T;T;T;T;T;T;T	0.64260	3.36;1.91;1.91;1.91;1.91;1.91;1.91;1.91;1.91;-0.09	5.78	5.78	0.91487	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.59128	0.2171	N	0.03016	-0.435	0.80722	D	1	P;P;D;P;D;D;B;D;D	0.59767	0.644;0.702;0.965;0.592;0.965;0.986;0.405;0.957;0.957	P;P;D;B;D;D;P;D;D	0.77004	0.766;0.647;0.984;0.399;0.984;0.989;0.654;0.973;0.973	T	0.69745	-0.5062	10	0.42905	T	0.14	.	16.1138	0.81283	1.0:0.0:0.0:0.0	.	56;76;76;76;76;76;76;76;76	B7Z388;B7Z3V5;C9J840;O95819-4;O95819;E7EN19;G3XAA2;O95819-2;G5E948	.;.;.;.;M4K4_HUMAN;.;.;.;.	F	76;76;76;76;76;76;76;76;38;56	ENSP00000403016:Y76F;ENSP00000392830:Y76F;ENSP00000313644:Y76F;ENSP00000281111:Y76F;ENSP00000303600:Y76F;ENSP00000389752:Y76F;ENSP00000387370:Y76F;ENSP00000314363:Y76F;ENSP00000409720:Y38F;ENSP00000343658:Y56F	ENSP00000303600:Y76F	Y	+	2	0	MAP4K4	101806868	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	9.287000	0.95975	2.220000	0.72140	0.533000	0.62120	TAC		0.368	MAP4K4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339839.1	NM_004834	
ST6GAL2	84620	broad.mit.edu	37	2	107460197	107460197	+	Silent	SNP	C	C	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr2:107460197C>T	ENST00000409382.3	-	2	847	c.237G>A	c.(235-237)gcG>gcA	p.A79A	AC016994.2_ENST00000425419.1_RNA|ST6GAL2_ENST00000361686.4_Silent_p.A79A|ST6GAL2_ENST00000409087.3_Silent_p.A79A	NM_001142351.1	NP_001135823.1	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 2	79					growth (GO:0040007)|multicellular organismal development (GO:0007275)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	beta-galactoside alpha-2,6-sialyltransferase activity (GO:0003835)	p.A79A(1)		autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(30)|ovary(5)|pancreas(6)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	65						CGCGGGGCAGCGCCTGGCGTG	0.657																																						uc002tdq.2																			1	Substitution - coding silent(1)	p.A79V(1)	prostate(1)	pancreas(6)|ovary(4)|skin(1)	11						c.(235-237)GCG>GCA		ST6 beta-galactosamide							18.0	23.0	22.0					2																	107460197		2153	4207	6360	SO:0001819	synonymous_variant	84620				growth|multicellular organismal development|oligosaccharide metabolic process|protein glycosylation	Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,6-sialyltransferase activity	g.chr2:107460197C>T	AB059555	CCDS2073.1, CCDS46380.1	2q11-q12	2008-02-05	2005-02-07	2005-02-07	ENSG00000144057	ENSG00000144057	2.4.99.2		10861	protein-coding gene	gene with protein product		608472	"""sialyltransferase 2 (monosialoganglioside sialyltransferase)"""	SIAT2			Standard	NM_032528		Approved	KIAA1877, St6gal2, St6GalII	uc002tdr.3	Q96JF0	OTTHUMG00000130923	ENST00000409382.3:c.237G>A	2.37:g.107460197C>T						ST6GAL2_uc002tdr.2_Silent_p.A79A|ST6GAL2_uc002tds.3_Silent_p.A79A	p.A79A	NM_001142351	NP_001135823	Q96JF0	SIAT2_HUMAN			2	356	-			79			Lumenal (Potential).		D3DVK3|Q53QP4|Q86Y44|Q8IUG7|Q96HE4	Silent	SNP	ENST00000409382.3	37	c.237G>A	CCDS2073.1																																																																																				0.657	ST6GAL2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330065.1	NM_032528	
GPR149	344758	broad.mit.edu	37	3	154139085	154139085	+	Missense_Mutation	SNP	T	T	C			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr3:154139085T>C	ENST00000389740.2	-	3	1465	c.1366A>G	c.(1366-1368)Atc>Gtc	p.I456V		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	456					antral ovarian follicle growth (GO:0001547)|estrous cycle phase (GO:0060206)|negative regulation of ovulation (GO:0060280)|preantral ovarian follicle growth (GO:0001546)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			GTGGTGCTGATTTCTACTTTT	0.393																																						uc003faa.2																			0				ovary(6)	6						c.(1366-1368)ATC>GTC		G protein-coupled receptor 149							254.0	244.0	247.0					3																	154139085		1965	4132	6097	SO:0001583	missense	344758					integral to membrane|plasma membrane	G-protein coupled receptor activity	g.chr3:154139085T>C	AY255534	CCDS43162.1	3q25.2	2012-08-21			ENSG00000174948	ENSG00000174948		"""GPCR / Class A : Orphans"""	23627	protein-coding gene	gene with protein product						12679517	Standard	NM_001038705		Approved	PGR10, IEDA	uc003faa.3	Q86SP6	OTTHUMG00000159131	ENST00000389740.2:c.1366A>G	3.37:g.154139085T>C	ENSP00000374390:p.Ile456Val						p.I456V	NM_001038705	NP_001033794	Q86SP6	GP149_HUMAN	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)		3	1466	-			456			Cytoplasmic (Potential).			Missense_Mutation	SNP	ENST00000389740.2	37	c.1366A>G	CCDS43162.1	.	.	.	.	.	.	.	.	.	.	T	12.33	1.906243	0.33628	.	.	ENSG00000174948	ENST00000389740	.	.	.	5.15	0.745	0.18359	.	0.209804	0.49305	D	0.000142	T	0.28466	0.0704	L	0.51422	1.61	0.24462	N	0.994431	B	0.09022	0.002	B	0.04013	0.001	T	0.27020	-1.0086	9	0.66056	D	0.02	-15.4784	0.4429	0.00489	0.3221:0.1833:0.1205:0.374	.	456	Q86SP6	GP149_HUMAN	V	456	.	ENSP00000374390:I456V	I	-	1	0	GPR149	155621779	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	2.593000	0.46180	0.390000	0.25115	0.372000	0.22366	ATC		0.393	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580	
SI	6476	broad.mit.edu	37	3	164716358	164716358	+	Nonsense_Mutation	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr3:164716358G>A	ENST00000264382.3	-	38	4572	c.4510C>T	c.(4510-4512)Cga>Tga	p.R1504*		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	1504	Sucrase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)			NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	TTGTCCCATCGTGCATAGTTG	0.403										HNSCC(35;0.089)																												uc003fei.2																			0				ovary(7)|upper_aerodigestive_tract(4)|skin(2)|pancreas(1)	14						c.(4510-4512)CGA>TGA		sucrase-isomaltase	Acarbose(DB00284)						203.0	179.0	187.0					3																	164716358		2203	4300	6503	SO:0001587	stop_gained	6476				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|brush border|Golgi apparatus|integral to membrane	carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity	g.chr3:164716358G>A	X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"""Oligosaccharide alpha-1,6-glucosidase"""	609845	"""sucrase-isomaltase"""			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.4510C>T	3.37:g.164716358G>A	ENSP00000264382:p.Arg1504*	HNSCC(35;0.089)					p.R1504*	NM_001041	NP_001032	P14410	SUIS_HUMAN			38	4572	-		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)	1504			Sucrase.|Lumenal.		A2RUC3|Q1JQ80|Q1RMC2	Nonsense_Mutation	SNP	ENST00000264382.3	37	c.4510C>T	CCDS3196.1	.	.	.	.	.	.	.	.	.	.	G	40	8.402375	0.98796	.	.	ENSG00000090402	ENST00000264382	.	.	.	4.76	-6.2	0.02072	.	2.336390	0.01527	N	0.018611	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.14252	T	0.57	.	12.35	0.55143	0.0:0.1777:0.1292:0.6931	.	.	.	.	X	1504	.	ENSP00000264382:R1504X	R	-	1	2	SI	166199052	0.000000	0.05858	0.001000	0.08648	0.670000	0.39368	-2.605000	0.00889	-0.915000	0.03823	0.650000	0.86243	CGA		0.403	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041	
TNIK	23043	broad.mit.edu	37	3	170800078	170800078	+	Missense_Mutation	SNP	T	T	G			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr3:170800078T>G	ENST00000436636.2	-	27	3619	c.3275A>C	c.(3274-3276)gAt>gCt	p.D1092A	TNIK_ENST00000341852.6_Missense_Mutation_p.D1008A|TNIK_ENST00000470834.1_Missense_Mutation_p.D1055A|TNIK_ENST00000460047.1_Missense_Mutation_p.D1029A|TNIK_ENST00000475336.1_Missense_Mutation_p.D1000A|TNIK_ENST00000369326.5_Missense_Mutation_p.D1070A|TNIK_ENST00000538048.1_Missense_Mutation_p.D1044A|TNIK_ENST00000357327.5_Missense_Mutation_p.D1063A|TNIK_ENST00000284483.8_Missense_Mutation_p.D1084A|TNIK_ENST00000488470.1_Missense_Mutation_p.D1037A	NM_015028.2	NP_055843.1	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase	1092	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				actin cytoskeleton reorganization (GO:0031532)|activation of JNKK activity (GO:0007256)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite morphogenesis (GO:0048814)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(22)|ovary(5)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)	62	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			CTCTAGCACATCCATCTGCTG	0.483																																						uc003fhh.2																			0				ovary(4)|large_intestine(1)	5						c.(3274-3276)GAT>GCT		TRAF2 and NCK interacting kinase isoform 1							76.0	75.0	75.0					3																	170800078		1972	4171	6143	SO:0001583	missense	23043				actin cytoskeleton reorganization|activation of JNKK activity|protein autophosphorylation|regulation of dendrite morphogenesis|Wnt receptor signaling pathway	cytoskeleton|nucleus|recycling endosome	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity	g.chr3:170800078T>G	AF172264	CCDS46956.1, CCDS54673.1, CCDS54674.1, CCDS54675.1, CCDS54676.1, CCDS54677.1, CCDS54678.1, CCDS54679.1	3q26.31	2008-01-23			ENSG00000154310	ENSG00000154310			30765	protein-coding gene	gene with protein product		610005				9628581, 10521462	Standard	NR_027767		Approved	KIAA0551	uc003fhh.2	Q9UKE5	OTTHUMG00000159036	ENST00000436636.2:c.3275A>C	3.37:g.170800078T>G	ENSP00000399511:p.Asp1092Ala					TNIK_uc003fhi.2_Missense_Mutation_p.D1037A|TNIK_uc003fhj.2_Missense_Mutation_p.D1063A|TNIK_uc003fhk.2_Missense_Mutation_p.D1084A|TNIK_uc003fhl.2_Missense_Mutation_p.D1008A|TNIK_uc003fhm.2_Missense_Mutation_p.D1029A|TNIK_uc003fhn.2_Missense_Mutation_p.D1055A|TNIK_uc003fho.2_Missense_Mutation_p.D1000A|TNIK_uc003fhg.2_Missense_Mutation_p.D270A|TNIK_uc003fhp.2_Missense_Mutation_p.D24A	p.D1092A	NM_015028	NP_055843	Q9UKE5	TNIK_HUMAN	LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		27	3620	-	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		1092			CNH.		A7E2A3|A8K4U1|D3DNQ6|O60298|Q8WUY7|Q9UKD8|Q9UKD9|Q9UKE0|Q9UKE1|Q9UKE2|Q9UKE3|Q9UKE4	Missense_Mutation	SNP	ENST00000436636.2	37	c.3275A>C	CCDS46956.1	.	.	.	.	.	.	.	.	.	.	T	24.4	4.523113	0.85600	.	.	ENSG00000154310	ENST00000436636;ENST00000369326;ENST00000538048;ENST00000341852;ENST00000284483;ENST00000475336;ENST00000357327;ENST00000460047;ENST00000488470;ENST00000470834	T;T;T;T;T;T;T;T;T;T	0.04156	3.69;3.69;3.69;3.69;3.69;3.69;3.69;3.69;3.69;3.69	5.79	5.79	0.91817	Citron-like (3);	0.000000	0.85682	D	0.000000	T	0.16938	0.0407	L	0.60455	1.87	0.80722	D	1	D;B;P;B;B;D;P;B;D	0.58970	0.984;0.221;0.76;0.221;0.221;0.965;0.76;0.221;0.972	P;B;B;B;B;P;P;B;P	0.61592	0.891;0.187;0.321;0.187;0.187;0.756;0.525;0.187;0.842	T	0.00061	-1.2160	10	0.87932	D	0	.	16.1278	0.81406	0.0:0.0:0.0:1.0	.	1044;1000;1055;1029;1008;1084;1063;1037;1092	F5H5M9;Q9UKE5-8;Q9UKE5-6;Q9UKE5-7;Q9UKE5-5;Q9UKE5-4;Q9UKE5-2;Q9UKE5-3;Q9UKE5	.;.;.;.;.;.;.;.;TNIK_HUMAN	A	1092;1070;1044;1008;1084;1000;1063;1029;1037;1055	ENSP00000399511:D1092A;ENSP00000358332:D1070A;ENSP00000443278:D1044A;ENSP00000345352:D1008A;ENSP00000284483:D1084A;ENSP00000418156:D1000A;ENSP00000349880:D1063A;ENSP00000418916:D1029A;ENSP00000418378:D1037A;ENSP00000419990:D1055A	ENSP00000284483:D1084A	D	-	2	0	TNIK	172282772	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.977000	0.88081	2.213000	0.71641	0.533000	0.62120	GAT		0.483	TNIK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352973.2	XM_039796	
FYB	2533	broad.mit.edu	37	5	39153687	39153687	+	Silent	SNP	C	C	T	rs375737931		TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr5:39153687C>T	ENST00000351578.6	-	3	1345	c.1155G>A	c.(1153-1155)acG>acA	p.T385T	FYB_ENST00000505428.1_Silent_p.T385T|FYB_ENST00000512982.1_Silent_p.T385T|FYB_ENST00000515010.1_Silent_p.T385T|FYB_ENST00000540520.1_Silent_p.T395T	NM_199335.3	NP_955367.1	O15117	FYB_HUMAN	FYN binding protein	385	Interaction with SKAP1.				immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|NLS-bearing protein import into nucleus (GO:0006607)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	receptor binding (GO:0005102)			endometrium(2)|kidney(4)|large_intestine(6)|liver(1)|lung(29)|ovary(2)|upper_aerodigestive_tract(1)	45	all_lung(31;0.000343)		Epithelial(62;0.235)			TTGAGTAAGACGTCTGGCCTT	0.468																																						uc003jls.2																			0				ovary(2)	2						c.(1153-1155)ACG>ACA		FYN binding protein (FYB-120/130) isoform 2		C	,	0,4112		0,0,2056	205.0	215.0	211.0		1155,1155	-9.3	0.0	5		211	2,8388		0,2,4193	no	coding-synonymous,coding-synonymous	FYB	NM_001465.4,NM_199335.3	,	0,2,6249	TT,TC,CC		0.0238,0.0,0.016	,	385/830,385/784	39153687	2,12500	2056	4195	6251	SO:0001819	synonymous_variant	2533				cell junction assembly|immune response|intracellular protein kinase cascade|NLS-bearing substrate import into nucleus|protein phosphorylation|T cell receptor signaling pathway	cytosol|nucleus	protein binding	g.chr5:39153687C>T	U93049	CCDS47200.1, CCDS54848.1	5p13.1	2012-05-04	2010-05-04		ENSG00000082074	ENSG00000082074			4036	protein-coding gene	gene with protein product		602731	"""FYN-binding protein (FYB-120/130)"""			9115214, 9207119	Standard	NM_001465		Approved	SLAP-130, FYB-120/130	uc011cpl.2	O15117	OTTHUMG00000162071	ENST00000351578.6:c.1155G>A	5.37:g.39153687C>T						FYB_uc003jlt.2_Silent_p.T385T|FYB_uc003jlu.2_Silent_p.T385T|FYB_uc011cpl.1_Silent_p.T395T	p.T385T	NM_199335	NP_955367	O15117	FYB_HUMAN	Epithelial(62;0.235)		2	1222	-	all_lung(31;0.000343)		385			Interaction with SKAP1.		A8K2Y8|B4DLN2|E9PBV9|O00359|Q9NZI9	Silent	SNP	ENST00000351578.6	37	c.1155G>A	CCDS47200.1																																																																																				0.468	FYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367098.1	NM_001465	
IQGAP2	10788	broad.mit.edu	37	5	75998408	75998408	+	Missense_Mutation	SNP	A	A	G	rs201167699		TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr5:75998408A>G	ENST00000274364.6	+	35	4904	c.4607A>G	c.(4606-4608)aAt>aGt	p.N1536S	CTD-2384B11.2_ENST00000507514.1_RNA|IQGAP2_ENST00000508410.1_3'UTR|IQGAP2_ENST00000379730.3_Missense_Mutation_p.N1038S|IQGAP2_ENST00000396234.3_Missense_Mutation_p.N1032S|IQGAP2_ENST00000502745.1_Missense_Mutation_p.N1032S	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	1536					negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		GTGCAACTCAATATTCAGGTA	0.353																																						uc003kek.2																			0				ovary(6)|central_nervous_system(1)	7						c.(4606-4608)AAT>AGT		IQ motif containing GTPase activating protein 2							104.0	101.0	102.0					5																	75998408		2203	4300	6503	SO:0001583	missense	10788				small GTPase mediated signal transduction	actin cytoskeleton	actin binding|calmodulin binding|GTPase inhibitor activity|Ras GTPase activator activity	g.chr5:75998408A>G	U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.4607A>G	5.37:g.75998408A>G	ENSP00000274364:p.Asn1536Ser					IQGAP2_uc011csv.1_Missense_Mutation_p.N1032S|IQGAP2_uc003kel.2_Missense_Mutation_p.N1032S	p.N1536S	NM_006633	NP_006624	Q13576	IQGA2_HUMAN		all cancers(79;1.38e-36)	35	4829	+		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)	1536					A8K4V1|B7Z8A4|J3KR91	Missense_Mutation	SNP	ENST00000274364.6	37	c.4607A>G	CCDS34188.1	.	.	.	.	.	.	.	.	.	.	A	16.63	3.176681	0.57692	.	.	ENSG00000145703	ENST00000274364;ENST00000379730;ENST00000396234;ENST00000502745	T;T;T;T	0.02525	4.42;4.26;4.26;4.27	5.41	5.41	0.78517	.	0.047625	0.85682	D	0.000000	T	0.02767	0.0083	N	0.20766	0.605	0.40523	D	0.980851	B;B;B	0.23735	0.09;0.09;0.017	B;B;B	0.28916	0.096;0.096;0.017	T	0.52837	-0.8522	10	0.10636	T	0.68	-23.4397	15.4411	0.75184	1.0:0.0:0.0:0.0	.	1038;1032;1536	F5H7S7;Q13576-2;Q13576	.;.;IQGA2_HUMAN	S	1536;1038;1032;1032	ENSP00000274364:N1536S;ENSP00000442313:N1038S;ENSP00000379535:N1032S;ENSP00000426027:N1032S	ENSP00000274364:N1536S	N	+	2	0	IQGAP2	76034164	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	9.287000	0.95975	2.060000	0.61445	0.533000	0.62120	AAT		0.353	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633	
CEP120	153241	broad.mit.edu	37	5	122754205	122754205	+	Silent	SNP	C	C	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr5:122754205C>T	ENST00000306467.5	-	2	358	c.54G>A	c.(52-54)cgG>cgA	p.R18R	CEP120_ENST00000328236.5_Silent_p.R18R|CEP120_ENST00000515110.1_Missense_Mutation_p.A55T|CEP120_ENST00000306481.6_5'UTR|CEP120_ENST00000395431.2_Silent_p.R18R			Q8N960	CE120_HUMAN	centrosomal protein 120kDa	18					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)|regulation of protein localization (GO:0032880)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	29						TGGGGAAATGCCGACCTGGAG	0.383																																						uc003ktk.2																			0				ovary(1)	1						c.(52-54)CGG>CGA		coiled-coil domain containing 100							95.0	86.0	89.0					5																	122754205		1861	4095	5956	SO:0001819	synonymous_variant	153241					centrosome		g.chr5:122754205C>T	AK095646	CCDS4134.2, CCDS54890.1	5q23.2	2014-02-20	2008-08-14	2008-08-14	ENSG00000168944	ENSG00000168944			26690	protein-coding gene	gene with protein product		613446	"""coiled-coil domain containing 100"""	CCDC100		17920017	Standard	NM_153223		Approved	FLJ36090	uc003ktk.3	Q8N960	OTTHUMG00000128922	ENST00000306467.5:c.54G>A	5.37:g.122754205C>T						CEP120_uc011cwq.1_5'UTR|CEP120_uc010jcz.1_5'UTR	p.R18R	NM_153223	NP_694955	Q8N960	CE120_HUMAN			3	136	-			18					Q6AI52|Q6AW89|Q8IWB5|Q8N9Y0|Q8NDE8	Silent	SNP	ENST00000306467.5	37	c.54G>A	CCDS4134.2	.	.	.	.	.	.	.	.	.	.	C	10.50	1.366987	0.24771	.	.	ENSG00000168944	ENST00000515110	.	.	.	5.18	-2.21	0.06973	.	.	.	.	.	T	0.47525	0.1450	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52373	-0.8584	5	0.87932	D	0	-4.8636	1.2262	0.01934	0.3503:0.1043:0.3403:0.205	.	.	.	.	T	55	.	ENSP00000428303:A55T	A	-	1	0	CEP120	122782104	0.255000	0.24002	0.992000	0.48379	0.712000	0.41017	-0.416000	0.07097	-0.297000	0.08934	-0.802000	0.03209	GCA		0.383	CEP120-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250899.2	NM_153223	
DSP	1832	broad.mit.edu	37	6	7565623	7565623	+	Missense_Mutation	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr6:7565623G>A	ENST00000379802.3	+	7	1150	c.809G>A	c.(808-810)cGa>cAa	p.R270Q	DSP_ENST00000418664.2_Missense_Mutation_p.R270Q	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	270	Globular 1.|Interacts with plakophilin 1 and junction plakoglobin.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		GATCACCTGCGACAGCTGCAG	0.502																																						uc003mxp.1																			0				central_nervous_system(6)|ovary(2)|skin(1)	9						c.(808-810)CGA>CAA		desmoplakin isoform I							131.0	109.0	116.0					6																	7565623		2203	4300	6503	SO:0001583	missense	1832				cellular component disassembly involved in apoptosis|keratinocyte differentiation|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural constituent of cytoskeleton	g.chr6:7565623G>A	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"""desmoplakin (DPI, DPII)"""			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.809G>A	6.37:g.7565623G>A	ENSP00000369129:p.Arg270Gln					DSP_uc003mxq.1_Missense_Mutation_p.R270Q	p.R270Q	NM_004415	NP_004406	P15924	DESP_HUMAN		OV - Ovarian serous cystadenocarcinoma(45;0.000508)	7	1088	+	Ovarian(93;0.0584)	all_hematologic(90;0.236)	270			Globular 1.|Interacts with plakophilin 1 and junction plakoglobin.		B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Missense_Mutation	SNP	ENST00000379802.3	37	c.809G>A	CCDS4501.1	.	.	.	.	.	.	.	.	.	.	G	34	5.319961	0.95682	.	.	ENSG00000096696	ENST00000379802;ENST00000418664;ENST00000397483	D;D	0.91351	-2.83;-2.83	5.42	5.42	0.78866	.	0.000000	0.53938	D	0.000041	D	0.85539	0.5720	N	0.17674	0.51	0.54753	D	0.999983	D;D	0.89917	0.999;1.0	P;P	0.54629	0.679;0.757	D	0.83601	0.0128	10	0.16420	T	0.52	.	19.2336	0.93849	0.0:0.0:1.0:0.0	.	317;270	Q4LE79;P15924	.;DESP_HUMAN	Q	270;270;75	ENSP00000369129:R270Q;ENSP00000396591:R270Q	ENSP00000369129:R270Q	R	+	2	0	DSP	7510622	1.000000	0.71417	0.986000	0.45419	0.997000	0.91878	6.686000	0.74548	2.534000	0.85438	0.563000	0.77884	CGA		0.502	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415	
DNAH8	1769	broad.mit.edu	37	6	38957817	38957817	+	Silent	SNP	G	G	A	rs143472136	byFrequency	TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr6:38957817G>A	ENST00000359357.3	+	86	12686	c.12432G>A	c.(12430-12432)ccG>ccA	p.P4144P	DNAH8_ENST00000441566.1_Silent_p.P4108P			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	4144					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						TGTTTGAACCGTCATTCTGCT	0.368																																						uc003ooe.1																			0				skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21						c.(12430-12432)CCG>CCA		dynein, axonemal, heavy polypeptide 8		G		2,4404	4.2+/-10.8	0,2,2201	155.0	146.0	149.0		13083	-5.6	0.4	6	dbSNP_134	149	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	DNAH8	NM_001206927.1		0,3,6500	AA,AG,GG		0.0116,0.0454,0.0231		4361/4708	38957817	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	1769							g.chr6:38957817G>A	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.12432G>A	6.37:g.38957817G>A							p.P4144P	NM_001371	NP_001362					86	13032	+								O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Silent	SNP	ENST00000359357.3	37	c.12432G>A																																																																																					0.368	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
GSTA1	2938	broad.mit.edu	37	6	52658945	52658945	+	Missense_Mutation	SNP	C	C	T	rs374431368		TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr6:52658945C>T	ENST00000334575.5	-	5	547	c.392G>A	c.(391-393)cGc>cAc	p.R131H	GSTA1_ENST00000493331.1_5'UTR	NM_145740.3	NP_665683.1	P08263	GSTA1_HUMAN	glutathione S-transferase alpha 1	131	GST C-terminal.				epithelial cell differentiation (GO:0030855)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|metabolic process (GO:0008152)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glutathione transferase activity (GO:0004364)			large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	12	Lung NSC(77;0.118)				Azathioprine(DB00993)|Busulfan(DB01008)|Glutathione(DB00143)	AGGGAAGTAGCGATTTTTTAT	0.438																																						uc003paz.2																			0				ovary(1)	1						c.(391-393)CGC>CAC		glutathione S-transferase alpha 1	Amsacrine(DB00276)|Busulfan(DB01008)|Glutathione(DB00143)	C	HIS/ARG	0,4406		0,0,2203	248.0	245.0	246.0		392	0.7	0.0	6		246	1,8599	1.2+/-3.3	0,1,4299	no	missense	GSTA1	NM_145740.3	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	131/223	52658945	1,13005	2203	4300	6503	SO:0001583	missense	2938				glutathione metabolic process|xenobiotic metabolic process	cytosol	glutathione transferase activity	g.chr6:52658945C>T		CCDS4945.1	6p12.2	2012-06-21	2008-11-26		ENSG00000243955	ENSG00000243955	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4626	protein-coding gene	gene with protein product		138359	"""glutathione S-transferase A1"""			9503014	Standard	NM_145740		Approved		uc003paz.3	P08263	OTTHUMG00000014861	ENST00000334575.5:c.392G>A	6.37:g.52658945C>T	ENSP00000335620:p.Arg131His						p.R131H	NM_145740	NP_665683	P08263	GSTA1_HUMAN			5	504	-	Lung NSC(77;0.118)		131			GST C-terminal.		Q14750|Q5GHF8|Q5SZC1	Missense_Mutation	SNP	ENST00000334575.5	37	c.392G>A	CCDS4945.1	.	.	.	.	.	.	.	.	.	.	c	10.52	1.374374	0.24857	0.0	1.16E-4	ENSG00000243955	ENST00000334575	T	0.02177	4.41	2.58	0.665	0.17896	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);Glutathione S-transferase, C-terminal (1);	0.064364	0.64402	N	0.000008	T	0.01287	0.0042	M	0.85777	2.775	0.09310	N	1	P	0.43024	0.798	B	0.35971	0.215	T	0.43376	-0.9395	10	0.51188	T	0.08	.	7.0109	0.24861	0.0:0.7509:0.0:0.2491	.	131	P08263	GSTA1_HUMAN	H	131	ENSP00000335620:R131H	ENSP00000335620:R131H	R	-	2	0	GSTA1	52766904	0.027000	0.19231	0.001000	0.08648	0.018000	0.09664	1.544000	0.36158	-0.177000	0.10690	0.195000	0.17529	CGC		0.438	GSTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040922.1		
AK9	221264	broad.mit.edu	37	6	109827537	109827537	+	Missense_Mutation	SNP	T	T	C			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr6:109827537T>C	ENST00000424296.2	-	35	4918	c.4842A>G	c.(4840-4842)atA>atG	p.I1614M	AL109947.2_ENST00000517228.1_RNA|RP5-919F19.5_ENST00000423747.2_RNA	NM_001145128.2	NP_001138600.2	Q5TCS8	KAD9_HUMAN	adenylate kinase 9	1614					ADP phosphorylation (GO:0006757)|AMP phosphorylation (GO:0006756)|CDP phosphorylation (GO:0061508)|CMP phosphorylation (GO:0061566)|dADP phosphorylation (GO:0006174)|dAMP phosphorylation (GO:0061565)|dCDP phosphorylation (GO:0061570)|dCMP phosphorylation (GO:0061567)|dGDP phosphorylation (GO:0006186)|GDP phosphorylation (GO:0061568)|TDP phosphorylation (GO:0061571)|UDP phosphorylation (GO:0061569)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside phosphate kinase activity (GO:0050145)										TACCTGCTTTTATTCTTTCCA	0.323																																						uc003ptn.2																			0				ovary(1)	1						c.(4840-4842)ATA>ATG		adenylate kinase domain containing 1 isoform 1							117.0	113.0	114.0					6																	109827537		2203	4299	6502	SO:0001583	missense	221264				nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|nucleoside-triphosphatase activity	g.chr6:109827537T>C	AK131244, BC146443, BC087860	CCDS5077.1, CCDS55048.1	6q21	2013-04-29	2013-04-29	2013-04-29			2.7.4.3		33814	protein-coding gene	gene with protein product		615358	"""chromosome 6 open reading frame 224"", ""adenylate kinase domain containing 2"", ""chromosome 6 open reading frame 199"", ""adenylate kinase domain containing 1"""	C6orf224, AKD2, C6orf199, AKD1		23416111	Standard	NM_145025		Approved	FLJ42177, FLJ25791, dJ70A9.1, MGC26954		Q5TCS8		ENST00000424296.2:c.4842A>G	6.37:g.109827537T>C	ENSP00000410186:p.Ile1614Met					AKD1_uc011eas.1_Missense_Mutation_p.I13M	p.I1614M	NM_001145128	NP_001138600	Q5TCS8	AKD1_HUMAN			35	4919	-			1614					A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4	Missense_Mutation	SNP	ENST00000424296.2	37	c.4842A>G	CCDS55048.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.49|13.49	2.251712|2.251712	0.39797|0.39797	.|.	.|.	ENSG00000155085|ENSG00000155085	ENST00000424296|ENST00000490722	T|.	0.68181|.	-0.31|.	5.01|5.01	2.33|2.33	0.28932|0.28932	.|.	0.147566|.	0.64402|.	D|.	0.000019|.	T|T	0.58935|0.58935	0.2157|0.2157	M|M	0.70275|0.70275	2.135|2.135	0.80722|0.80722	D|D	1|1	D;D|.	0.60575|.	0.963;0.988|.	P;P|.	0.54664|.	0.755;0.758|.	T|T	0.60125|0.60125	-0.7324|-0.7324	9|5	.|.	.|.	.|.	.|.	11.4438|11.4438	0.50112|0.50112	0.0:0.0:0.286:0.714|0.0:0.0:0.286:0.714	.|.	13;1614|.	B7ZL24;Q5TCS8|.	.;AKD1_HUMAN|.	M|E	1614|29	ENSP00000410186:I1614M|.	.|.	I|K	-|-	3|1	3|0	AKD1|AKD1	109934230|109934230	0.806000|0.806000	0.28996|0.28996	1.000000|1.000000	0.80357|0.80357	0.787000|0.787000	0.44495|0.44495	0.864000|0.864000	0.27926|0.27926	0.812000|0.812000	0.34326|0.34326	0.533000|0.533000	0.62120|0.62120	ATA|AAA		0.323	AK9-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001145128	
MIOS	54468	broad.mit.edu	37	7	7612689	7612689	+	Nonsense_Mutation	SNP	C	C	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr7:7612689C>T	ENST00000340080.4	+	4	1004	c.583C>T	c.(583-585)Cga>Tga	p.R195*	MIOS_ENST00000405785.1_Nonsense_Mutation_p.R195*	NM_019005.3	NP_061878.3	Q9NXC5	MIO_HUMAN	missing oocyte, meiosis regulator, homolog (Drosophila)	195						lysosomal membrane (GO:0005765)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(15)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TTGGCTTCCACGAGACCAGAA	0.383																																						uc003srf.2																			0					0						c.(583-585)CGA>TGA		missing oocyte, meiosis regulator, homolog							51.0	47.0	48.0					7																	7612689		1902	4127	6029	SO:0001587	stop_gained	54468							g.chr7:7612689C>T		CCDS43554.1	7p21.3	2011-09-12			ENSG00000164654	ENSG00000164654			21905	protein-coding gene	gene with protein product	"""WD repeat-containing protein mio"""	615359				14973288	Standard	NM_019005		Approved	FLJ20323	uc003srf.3	Q9NXC5	OTTHUMG00000152440	ENST00000340080.4:c.583C>T	7.37:g.7612689C>T	ENSP00000339881:p.Arg195*					MIOS_uc010ktp.1_Nonsense_Mutation_p.R195*	p.R195*	NM_019005	NP_061878	Q9NXC5	MIO_HUMAN			4	891	+			195			WD 3.		B2RTV6|O75216|Q7L551|Q9H092	Nonsense_Mutation	SNP	ENST00000340080.4	37	c.583C>T	CCDS43554.1	.	.	.	.	.	.	.	.	.	.	C	37	6.064515	0.97251	.	.	ENSG00000164654	ENST00000340080;ENST00000405785	.	.	.	5.85	4.0	0.46444	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	-9.9939	14.2093	0.65755	0.3924:0.6076:0.0:0.0	.	.	.	.	X	195	.	ENSP00000339881:R195X	R	+	1	2	MIOS	7579214	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	2.267000	0.43329	0.887000	0.36136	0.655000	0.94253	CGA		0.383	MIOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326218.1	NM_019005	
ABCA13	154664	broad.mit.edu	37	7	48450229	48450229	+	Silent	SNP	G	G	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr7:48450229G>T	ENST00000435803.1	+	40	12207	c.12183G>T	c.(12181-12183)ctG>ctT	p.L4061L		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	4061	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						CCTTCTGCCTGAAGGAGGCAT	0.582																																						uc003toq.2																			0				ovary(5)|central_nervous_system(4)|skin(1)	10						c.(12181-12183)CTG>CTT		ATP binding cassette, sub-family A (ABC1),							116.0	116.0	116.0					7																	48450229		2056	4201	6257	SO:0001819	synonymous_variant	154664				transport	integral to membrane	ATP binding|ATPase activity	g.chr7:48450229G>T	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"""ATP binding cassette transporters / subfamily A"""	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.12183G>T	7.37:g.48450229G>T						ABCA13_uc010kys.1_Silent_p.L1135L|ABCA13_uc010kyt.1_RNA	p.L4061L	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN			40	12208	+			4061			ABC transporter 1.		K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	37	c.12183G>T	CCDS47584.1																																																																																				0.582	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
POM121L12	285877	broad.mit.edu	37	7	53104048	53104048	+	Silent	SNP	C	C	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr7:53104048C>A	ENST00000408890.4	+	1	700	c.684C>A	c.(682-684)tcC>tcA	p.S228S		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	228										endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						CGGTTGCTTCCTTCGTGCCCA	0.637																																						uc003tpz.2																			0					0						c.(682-684)TCC>TCA		POM121 membrane glycoprotein-like 12							45.0	53.0	50.0					7																	53104048		1963	4132	6095	SO:0001819	synonymous_variant	285877							g.chr7:53104048C>A		CCDS43584.1	7p12.1	2012-03-13	2012-03-13		ENSG00000221900	ENSG00000221900			25369	protein-coding gene	gene with protein product			"""POM121 membrane glycoprotein-like 12"""				Standard	NM_182595		Approved	DKFZp564N2472	uc003tpz.3	Q8N7R1	OTTHUMG00000155995	ENST00000408890.4:c.684C>A	7.37:g.53104048C>A							p.S228S	NM_182595	NP_872401	Q8N7R1	P1L12_HUMAN			1	700	+			228					Q8NDI9	Silent	SNP	ENST00000408890.4	37	c.684C>A	CCDS43584.1																																																																																				0.637	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595	
NSUN5	55695	broad.mit.edu	37	7	72717906	72717906	+	Silent	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr7:72717906G>A	ENST00000252594.6	-	8	1077	c.1062C>T	c.(1060-1062)ctC>ctT	p.L354L	NSUN5_ENST00000428206.1_Silent_p.L316L|NSUN5_ENST00000438747.2_Silent_p.L354L|NSUN5_ENST00000310326.8_Silent_p.L354L			Q96P11	NSUN5_HUMAN	NOP2/Sun domain family, member 5	354					rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)	methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|large_intestine(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	8		Lung NSC(55;0.163)				TGGAGTAGACGAGCCGCTGCA	0.677																																						uc003txw.2																			0					0						c.(1060-1062)CTC>CTT		NOL1/NOP2/Sun domain family, member 5 isoform 2							32.0	35.0	34.0					7																	72717906		2203	4300	6503	SO:0001819	synonymous_variant	55695						methyltransferase activity	g.chr7:72717906G>A	AF420249	CCDS5546.1, CCDS5547.1, CCDS55118.1, CCDS55119.1	7q11.23	2010-04-08	2009-11-23	2005-01-14	ENSG00000130305	ENSG00000130305		"""NOP2/Sun domain containing"""	16385	protein-coding gene	gene with protein product	"""NOP2/Sun domain family, member 5A"""	615732	"""Williams Beuren syndrome chromosome region 20A"", ""NOL1/NOP2/Sun domain family, member 5"""	WBSCR20, WBSCR20A		11978965, 12073013	Standard	NM_148956		Approved	NOL1R, p120, (NOL1), FLJ10267, NSUN5A, Ynl022cL	uc011kev.2	Q96P11	OTTHUMG00000129869	ENST00000252594.6:c.1062C>T	7.37:g.72717906G>A						FKBP6_uc003twz.2_Intron|NSUN5_uc003txv.2_Silent_p.L354L|NSUN5_uc003txx.2_Silent_p.L316L|NSUN5_uc011kev.1_Silent_p.L354L	p.L354L	NM_018044	NP_060514	Q96P11	NSUN5_HUMAN			8	1098	-		Lung NSC(55;0.163)	354					B3KX04|B4DP79|G3V0G9|Q6ZUI8|Q96HT9|Q9NW70	Silent	SNP	ENST00000252594.6	37	c.1062C>T	CCDS5547.1																																																																																				0.677	NSUN5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252113.1	NM_148956	
EPHB6	2051	broad.mit.edu	37	7	142566033	142566033	+	Silent	SNP	C	C	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr7:142566033C>T	ENST00000392957.2	+	14	2740	c.1953C>T	c.(1951-1953)taC>taT	p.Y651Y	EPHB6_ENST00000411471.2_Silent_p.Y374Y|EPHB6_ENST00000442129.1_Silent_p.Y651Y	NM_004445.3	NP_004436.3	O15197	EPHB6_HUMAN	EPH receptor B6	651						extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(46)|ovary(2)|pancreas(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	87	Melanoma(164;0.059)					CCTCCACCTACGAGGACCCCT	0.577																																						uc011kst.1																			0				lung(8)|large_intestine(4)|central_nervous_system(3)|stomach(1)|skin(1)|ovary(1)|pancreas(1)	19						c.(1951-1953)TAC>TAT		ephrin receptor EphB6 precursor							108.0	101.0	104.0					7																	142566033		2203	4300	6503	SO:0001819	synonymous_variant	2051					extracellular region|integral to plasma membrane	ATP binding|ephrin receptor activity	g.chr7:142566033C>T	D83492	CCDS5873.2, CCDS75672.1	7q33-q35	2013-02-11	2004-10-28		ENSG00000106123	ENSG00000106123		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3396	protein-coding gene	gene with protein product		602757	"""EphB6"""				Standard	XM_006715881		Approved	HEP	uc011kst.2	O15197	OTTHUMG00000155707	ENST00000392957.2:c.1953C>T	7.37:g.142566033C>T						EPHB6_uc011ksu.1_Silent_p.Y651Y|EPHB6_uc003wbs.2_Silent_p.Y359Y|EPHB6_uc003wbt.2_Silent_p.Y125Y|EPHB6_uc003wbu.2_Silent_p.Y359Y|EPHB6_uc003wbv.2_Silent_p.Y35Y	p.Y651Y	NM_004445	NP_004436	O15197	EPHB6_HUMAN			14	2740	+	Melanoma(164;0.059)		651			Cytoplasmic (Potential).		A4D2I7|A8CDT5|D3DXD3|Q2TB23|Q2TB24	Silent	SNP	ENST00000392957.2	37	c.1953C>T	CCDS5873.2																																																																																				0.577	EPHB6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341329.1		
FAM110B	90362	broad.mit.edu	37	8	59059474	59059474	+	Missense_Mutation	SNP	A	A	C			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr8:59059474A>C	ENST00000361488.3	+	5	1565	c.685A>C	c.(685-687)Aaa>Caa	p.K229Q	FAM110B_ENST00000520369.1_Intron	NM_147189.2	NP_671722.1	Q8TC76	F110B_HUMAN	family with sequence similarity 110, member B	229						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(9)|skin(2)	26		all_epithelial(80;0.025)|all_lung(136;0.0274)|Lung NSC(129;0.0355)				TCCCAAGCCCAAAATCGCAGC	0.632																																						uc003xtj.1																			0				large_intestine(1)	1						c.(685-687)AAA>CAA		hypothetical protein LOC90362							78.0	84.0	82.0					8																	59059474		2203	4300	6503	SO:0001583	missense	90362					microtubule organizing center|mitochondrion|nucleus		g.chr8:59059474A>C	U79298	CCDS6170.1	8q12.1	2007-06-21	2007-03-21	2007-03-21		ENSG00000169122			28587	protein-coding gene	gene with protein product		611394	"""chromosome 8 open reading frame 72"""	C8orf72		8619474, 9110174, 17499476	Standard	XM_005251324		Approved	MGC39325	uc003xtj.1	Q8TC76		ENST00000361488.3:c.685A>C	8.37:g.59059474A>C	ENSP00000355204:p.Lys229Gln						p.K229Q	NM_147189	NP_671722	Q8TC76	F110B_HUMAN			5	1565	+		all_epithelial(80;0.025)|all_lung(136;0.0274)|Lung NSC(129;0.0355)	229					Q5BM08|Q9Y4K2	Missense_Mutation	SNP	ENST00000361488.3	37	c.685A>C	CCDS6170.1	.	.	.	.	.	.	.	.	.	.	A	12.29	1.894274	0.33442	.	.	ENSG00000169122	ENST00000361488	T	0.31247	1.5	5.39	5.39	0.77823	.	0.098189	0.64402	D	0.000002	T	0.23171	0.0560	L	0.27053	0.805	0.49687	D	0.999818	P	0.43477	0.808	B	0.39119	0.291	T	0.02617	-1.1133	9	.	.	.	-22.1023	15.3808	0.74654	1.0:0.0:0.0:0.0	.	229	Q8TC76	F110B_HUMAN	Q	229	ENSP00000355204:K229Q	.	K	+	1	0	FAM110B	59222028	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	3.828000	0.55753	2.019000	0.59389	0.459000	0.35465	AAA		0.632	FAM110B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378095.2	NM_147189	
MYBL1	4603	broad.mit.edu	37	8	67507922	67507922	+	Nonsense_Mutation	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr8:67507922G>A	ENST00000522677.3	-	6	993	c.583C>T	c.(583-585)Caa>Taa	p.Q195*	MYBL1_ENST00000524176.2_Nonsense_Mutation_p.Q195*|MYBL1_ENST00000517885.1_Intron	NM_001080416.2|NM_001144755.1	NP_001073885.1|NP_001138227.1	P10243	MYBA_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 1	195					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|pancreas(1)|skin(1)	25			Epithelial(68;0.00211)|all cancers(69;0.00726)|OV - Ovarian serous cystadenocarcinoma(28;0.00989)|BRCA - Breast invasive adenocarcinoma(89;0.0938)			ATTCCATCTTGTAAATAGCCC	0.343																																						uc003xwj.2																			0				ovary(2)|pancreas(1)	3						c.(583-585)CAA>TAA		v-myb myeloblastosis viral oncogene homolog							182.0	165.0	170.0					8																	67507922		1847	4082	5929	SO:0001587	stop_gained	4603				positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding	g.chr8:67507922G>A	X13294	CCDS47867.1, CCDS55241.1	8q22	2013-07-09	2013-07-09		ENSG00000185697	ENSG00000185697			7547	protein-coding gene	gene with protein product		159405					Standard	XM_005251251		Approved	AMYB, A-myb	uc003xwj.3	P10243	OTTHUMG00000164559	ENST00000522677.3:c.583C>T	8.37:g.67507922G>A	ENSP00000429633:p.Gln195*					MYBL1_uc003xwl.2_Nonsense_Mutation_p.Q195*|MYBL1_uc003xwk.2_Nonsense_Mutation_p.Q195*	p.Q195*	NM_001080416	NP_001073885	P10243	MYBA_HUMAN	Epithelial(68;0.00211)|all cancers(69;0.00726)|OV - Ovarian serous cystadenocarcinoma(28;0.00989)|BRCA - Breast invasive adenocarcinoma(89;0.0938)		6	990	-			195					E7EW29|Q495F9	Nonsense_Mutation	SNP	ENST00000522677.3	37	c.583C>T	CCDS47867.1	.	.	.	.	.	.	.	.	.	.	G	40	8.362113	0.98777	.	.	ENSG00000185697	ENST00000522677;ENST00000524176	.	.	.	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	-12.6774	19.7654	0.96337	0.0:0.0:1.0:0.0	.	.	.	.	X	195	.	ENSP00000429633:Q195X	Q	-	1	0	MYBL1	67670476	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.767000	0.98960	2.750000	0.94351	0.655000	0.94253	CAA		0.343	MYBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379221.3	XM_034274	
NOL8	55035	broad.mit.edu	37	9	95077750	95077750	+	Missense_Mutation	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr9:95077750G>A	ENST00000535387.1	-	6	1156	c.1157C>T	c.(1156-1158)gCg>gTg	p.A386V	NOL8_ENST00000545558.1_Missense_Mutation_p.A386V|NOL8_ENST00000442668.2_Missense_Mutation_p.A386V|NOL8_ENST00000358855.4_Missense_Mutation_p.A318V|NOL8_ENST00000542053.1_Missense_Mutation_p.A318V					nucleolar protein 8											endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	16						TTTTTTCATCGCAATAATTTC	0.323																																						uc004arv.2																			0				ovary(1)	1						c.(1156-1158)GCG>GTG		nucleolar protein 8							53.0	44.0	47.0					9																	95077750		1843	4085	5928	SO:0001583	missense	55035				DNA replication|positive regulation of cell growth	nucleolus	nucleotide binding|protein binding|RNA binding	g.chr9:95077750G>A	AB109030	CCDS47993.1, CCDS59135.1	9q22.32	2013-02-12	2004-01-12	2004-01-14	ENSG00000198000	ENSG00000198000		"""RNA binding motif (RRM) containing"""	23387	protein-coding gene	gene with protein product		611534	"""chromosome 9 open reading frame 34"""	C9orf34		12477932	Standard	NM_017948		Approved	FLJ20736, Nop132	uc022bjx.1	Q76FK4	OTTHUMG00000020221	ENST00000535387.1:c.1157C>T	9.37:g.95077750G>A	ENSP00000441300:p.Ala386Val					NOL8_uc010mqw.2_RNA|NOL8_uc004arw.2_Intron|NOL8_uc011ltw.1_Missense_Mutation_p.A318V	p.A386V	NM_017948	NP_060418	Q76FK4	NOL8_HUMAN			7	1494	-			386						Missense_Mutation	SNP	ENST00000535387.1	37	c.1157C>T	CCDS47993.1	.	.	.	.	.	.	.	.	.	.	G	15.80	2.939182	0.52972	.	.	ENSG00000198000	ENST00000442668;ENST00000375594;ENST00000358855;ENST00000545558;ENST00000535387;ENST00000542053;ENST00000432670;ENST00000433029	T;T;T;T;T;T;T	0.60171	1.7;1.73;1.7;1.88;1.73;1.39;0.21	5.63	4.74	0.60224	.	0.226352	0.45867	N	0.000325	T	0.63082	0.2481	L	0.43923	1.385	0.36187	D	0.849808	D	0.71674	0.998	P	0.55345	0.774	T	0.72880	-0.4158	10	0.62326	D	0.03	-6.815	14.8263	0.70117	0.0691:0.0:0.9309:0.0	.	386	Q76FK4	NOL8_HUMAN	V	386;388;318;386;386;318;386;386	ENSP00000401177:A386V;ENSP00000351723:A318V;ENSP00000441140:A386V;ENSP00000441300:A386V;ENSP00000440709:A318V;ENSP00000414112:A386V;ENSP00000412471:A386V	ENSP00000351723:A318V	A	-	2	0	NOL8	94117571	1.000000	0.71417	0.825000	0.32803	0.664000	0.39144	5.387000	0.66243	1.387000	0.46486	-0.173000	0.13275	GCG		0.323	NOL8-010	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053082.2	NM_017948	
PALM2	114299	broad.mit.edu	37	9	112687347	112687347	+	Missense_Mutation	SNP	T	T	C			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr9:112687347T>C	ENST00000374531.2	+	6	459	c.385T>C	c.(385-387)Tcc>Ccc	p.S129P	PALM2-AKAP2_ENST00000302798.7_Missense_Mutation_p.S127P|PALM2_ENST00000448454.2_Missense_Mutation_p.S129P|AKAP2_ENST00000555236.1_Missense_Mutation_p.S127P|PALM2-AKAP2_ENST00000374530.3_Missense_Mutation_p.S127P|AKAP2_ENST00000510514.5_Missense_Mutation_p.S127P|PALM2_ENST00000314527.4_Missense_Mutation_p.S127P|PALM2_ENST00000483909.1_Missense_Mutation_p.S127P	NM_001037293.2	NP_001032370.1	Q8IXS6	PALM2_HUMAN	paralemmin 2	129					regulation of cell shape (GO:0008360)	plasma membrane (GO:0005886)				breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(2)|skin(3)|upper_aerodigestive_tract(1)	18						ACAGGGTTTCTCCAGTACGGA	0.463																																						uc004bei.2																			0		p.S127Y(1)		ovary(3)|central_nervous_system(2)|skin(1)	6						c.(379-381)TCC>CCC		A kinase (PRKA) anchor protein 2 isoform 2							231.0	197.0	208.0					9																	112687347		2203	4300	6503	SO:0001583	missense	445815						enzyme binding	g.chr9:112687347T>C	AJ312216	CCDS35099.1, CCDS48002.1, CCDS48002.2	9q31.3	2009-10-16			ENSG00000243444	ENSG00000243444			15845	protein-coding gene	gene with protein product						11478809	Standard	NM_001037293		Approved			Q8IXS6	OTTHUMG00000020479	ENST00000374531.2:c.385T>C	9.37:g.112687347T>C	ENSP00000363656:p.Ser129Pro					PALM2_uc004bef.2_Missense_Mutation_p.S129P|PALM2_uc004beg.2_Missense_Mutation_p.S129P|PALM2_uc004beh.3_Missense_Mutation_p.S127P|PALM2-AKAP2_uc004bek.3_Missense_Mutation_p.S127P|PALM2-AKAP2_uc004bej.3_Missense_Mutation_p.S127P|PALM2-AKAP2_uc004bel.1_5'UTR	p.S127P	NM_001136562	NP_001130034	Q9Y2D5	AKAP2_HUMAN			5	571	+			Error:Variant_position_missing_in_Q9Y2D5_after_alignment					A9Z1X9|Q8N9D5|Q96DU1	Missense_Mutation	SNP	ENST00000374531.2	37	c.379T>C	CCDS35099.1	.	.	.	.	.	.	.	.	.	.	T	16.66	3.185983	0.57909	.	.	ENSG00000243444;ENSG00000243444;ENSG00000243444;ENSG00000243444;ENSG00000243444;ENSG00000157654;ENSG00000157654;ENSG00000157654;ENSG00000241978;ENSG00000241978	ENST00000374531;ENST00000448454;ENST00000483909;ENST00000314527;ENST00000497711;ENST00000374530;ENST00000413420;ENST00000302798;ENST00000555236;ENST00000510514	T;T;T;T;T;T;T;T;T;T	0.32515	2.27;2.3;2.27;2.3;1.45;2.13;2.3;2.13;2.13;2.13	5.42	4.26	0.50523	.	0.865894	0.09880	N	0.743803	T	0.37839	0.1018	L	0.29908	0.895	0.31971	N	0.607136	D;D;P;P	0.55385	0.971;0.971;0.566;0.917	P;P;P;P	0.55455	0.776;0.776;0.478;0.569	T	0.40136	-0.9579	10	0.87932	D	0	-0.1798	10.8561	0.46800	0.0:0.0:0.158:0.842	.	127;127;129;129	Q9Y2D5-6;Q9Y2D5-4;Q8IXS6;D3YTA4	.;.;PALM2_HUMAN;.	P	129;129;127;127;113;127;127;127;127;127	ENSP00000363656:S129P;ENSP00000400206:S129P;ENSP00000417525:S127P;ENSP00000323805:S127P;ENSP00000419747:S113P;ENSP00000363654:S127P;ENSP00000397839:S127P;ENSP00000305861:S127P;ENSP00000451476:S127P;ENSP00000421522:S127P	ENSP00000305861:S127P	S	+	1	0	PALM2-AKAP2;PALM2;AKAP2	111727168	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	2.760000	0.47581	0.973000	0.38340	0.533000	0.62120	TCC		0.463	PALM2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053604.1	NM_001037293	
CEL	1056	broad.mit.edu	37	9	135945919	135945919	+	Missense_Mutation	SNP	C	C	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr9:135945919C>T	ENST00000372080.4	+	10	1383	c.1367C>T	c.(1366-1368)gCc>gTc	p.A456V	CEL_ENST00000351304.7_Intron	NM_001807.3	NP_001798.2	P19835	CEL_HUMAN	carboxyl ester lipase	453					cholesterol catabolic process (GO:0006707)|fatty acid catabolic process (GO:0009062)|intestinal cholesterol absorption (GO:0030299)|intestinal lipid catabolic process (GO:0044258)|lipid digestion (GO:0044241)|lipid metabolic process (GO:0006629)|pancreatic juice secretion (GO:0030157)|protein esterification (GO:0018350)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	acylglycerol lipase activity (GO:0047372)|catalytic activity (GO:0003824)|heparin binding (GO:0008201)|hydrolase activity (GO:0016787)|sterol esterase activity (GO:0004771)|triglyceride lipase activity (GO:0004806)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(9)|pancreas(2)|skin(1)	20				OV - Ovarian serous cystadenocarcinoma(145;1.03e-40)|Epithelial(140;3.58e-37)|GBM - Glioblastoma multiforme(294;0.00164)|READ - Rectum adenocarcinoma(205;0.196)		TGGGTGGGGGCCGACCATGCA	0.607																																						uc010naa.1																			0				pancreas(1)	1						c.(1366-1368)GCC>GTC		carboxyl ester lipase precursor							80.0	86.0	84.0					9																	135945919		1931	4124	6055	SO:0001583	missense	1056				cholesterol catabolic process|fatty acid catabolic process|intestinal cholesterol absorption|intestinal lipid catabolic process|pancreatic juice secretion|protein esterification	cytosol|extracellular space	acylglycerol lipase activity|carboxylesterase activity|heparin binding|sterol esterase activity|triglyceride lipase activity	g.chr9:135945919C>T	M54994	CCDS43896.1	9q34.3	2013-03-13	2013-03-13		ENSG00000170835	ENSG00000170835	3.1.1.3, 3.1.1.13		1848	protein-coding gene	gene with protein product	"""bile salt-stimulated lipase"""	114840				1676983	Standard	NM_001807		Approved	BSSL, MODY8	uc010naa.2	P19835	OTTHUMG00000020855	ENST00000372080.4:c.1367C>T	9.37:g.135945919C>T	ENSP00000361151:p.Ala456Val						p.A456V	NM_001807	NP_001798	P19835	CEL_HUMAN		OV - Ovarian serous cystadenocarcinoma(145;1.03e-40)|Epithelial(140;3.58e-37)|GBM - Glioblastoma multiforme(294;0.00164)|READ - Rectum adenocarcinoma(205;0.196)	10	1383	+			453					Q16398|Q5T7U7|Q9UCH1|Q9UP41	Missense_Mutation	SNP	ENST00000372080.4	37	c.1367C>T	CCDS43896.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.432891	0.83776	.	.	ENSG00000170835	ENST00000372080;ENST00000303626	T	0.59502	0.26	5.72	5.72	0.89469	Carboxylesterase, type B (1);	0.000000	0.85682	D	0.000000	T	0.69824	0.3154	L	0.46157	1.445	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.61724	-0.7004	10	0.17369	T	0.5	.	18.8638	0.92283	0.0:1.0:0.0:0.0	.	453	P19835	CEL_HUMAN	V	456;455	ENSP00000361151:A456V	ENSP00000304021:A455V	A	+	2	0	CEL	134935740	1.000000	0.71417	0.958000	0.39756	0.139000	0.21198	7.414000	0.80117	2.703000	0.92315	0.478000	0.44815	GCC		0.607	CEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054823.1		
MAP7D2	256714	broad.mit.edu	37	X	20074865	20074865	+	Silent	SNP	C	C	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chrX:20074865C>T	ENST00000379651.3	-	4	435	c.417G>A	c.(415-417)caG>caA	p.Q139Q	MAP7D2_ENST00000452324.3_Silent_p.Q95Q|MAP7D2_ENST00000379643.5_Silent_p.Q139Q|MAP7D2_ENST00000543767.1_Silent_p.Q10Q|MAP7D2_ENST00000443379.3_Silent_p.Q139Q	NM_152780.3	NP_689993.2	Q96T17	MA7D2_HUMAN	MAP7 domain containing 2	139					microtubule cytoskeleton organization (GO:0000226)	microtubule (GO:0005874)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(13)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	37						GCTCCAGCTGCTGTGTGCGCT	0.557																																						uc004czr.1																			0				ovary(2)|breast(1)	3						c.(415-417)CAG>CAA		MAP7 domain containing 2							111.0	77.0	88.0					X																	20074865		2203	4300	6503	SO:0001819	synonymous_variant	256714							g.chrX:20074865C>T	BC089400	CCDS14195.1, CCDS55384.1, CCDS55385.1, CCDS55386.1	Xp22.12	2008-02-05			ENSG00000184368	ENSG00000184368			25899	protein-coding gene	gene with protein product						12477932	Standard	NM_152780		Approved	FLJ14503	uc010nfo.2	Q96T17	OTTHUMG00000021228	ENST00000379651.3:c.417G>A	X.37:g.20074865C>T						MAP7D2_uc004czq.1_Silent_p.Q10Q|MAP7D2_uc011mji.1_Silent_p.Q95Q|MAP7D2_uc010nfo.1_Silent_p.Q139Q|MAP7D2_uc011mjj.1_Silent_p.Q139Q|MAP7D2_uc004czs.1_Silent_p.Q95Q	p.Q139Q	NM_152780	NP_689993	Q96T17	MA7D2_HUMAN			4	436	-			139			Potential.		B7Z2J8|B7Z3S7|B9EGC7|C9JMA4|C9JYW0|Q5EBN1|Q5JPS7|Q6PIC7|Q8N792	Silent	SNP	ENST00000379651.3	37	c.417G>A	CCDS14195.1																																																																																				0.557	MAP7D2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056001.1	NM_152780	
BCOR	54880	broad.mit.edu	37	X	39933293	39933293	+	Missense_Mutation	SNP	C	C	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chrX:39933293C>T	ENST00000378444.4	-	4	1534	c.1306G>A	c.(1306-1308)Gtc>Atc	p.V436I	BCOR_ENST00000378455.4_Missense_Mutation_p.V436I|BCOR_ENST00000397354.3_Missense_Mutation_p.V436I|BCOR_ENST00000342274.4_Missense_Mutation_p.V436I	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	436					heart development (GO:0007507)|histone H2A monoubiquitination (GO:0035518)|negative regulation of bone mineralization (GO:0030502)|negative regulation of histone H3-K36 methylation (GO:0000415)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|palate development (GO:0060021)|specification of axis polarity (GO:0065001)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	heat shock protein binding (GO:0031072)|histone deacetylase binding (GO:0042826)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(4)|central_nervous_system(11)|cervix(1)|endometrium(24)|eye(6)|haematopoietic_and_lymphoid_tissue(33)|kidney(2)|large_intestine(11)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	126						TTATCTGTGACGTCTTTGGTA	0.527			"""F, N, S, T"""	RARA	"""retinoblastoma, AML, APL(translocation)"""		oculo-facio-cardio-dental genetic																															uc004den.3				Rec	yes		X	Xp11.4	54880		BCL6 corepressor	yes							0				ovary(2)|kidney(1)|central_nervous_system(1)	4						c.(1306-1308)GTC>ATC		BCL-6 interacting corepressor isoform c							76.0	55.0	62.0					X																	39933293		2202	4300	6502	SO:0001583	missense	54880				heart development|histone H2A monoubiquitination|negative regulation of bone mineralization|negative regulation of histone H3-K36 methylation|negative regulation of histone H3-K4 methylation|negative regulation of tooth mineralization|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|palate development|specification of axis polarity|transcription, DNA-dependent	nucleus	heat shock protein binding|histone deacetylase binding|transcription corepressor activity|transcription factor binding|transcription regulatory region DNA binding	g.chrX:39933293C>T	AF317391	CCDS14250.1, CCDS48092.1, CCDS48093.1	Xp11.4	2014-09-17	2010-06-10		ENSG00000183337	ENSG00000183337		"""Ankyrin repeat domain containing"""	20893	protein-coding gene	gene with protein product		300485	"""BCL6 co-repressor"""			10898795	Standard	NM_017745		Approved	FLJ20285, KIAA1575	uc004den.4	Q6W2J9	OTTHUMG00000024100	ENST00000378444.4:c.1306G>A	X.37:g.39933293C>T	ENSP00000367705:p.Val436Ile					BCOR_uc004dep.3_Missense_Mutation_p.V436I|BCOR_uc004deo.3_Missense_Mutation_p.V436I|BCOR_uc004dem.3_Missense_Mutation_p.V436I|BCOR_uc004deq.3_Missense_Mutation_p.V436I	p.V436I	NM_001123385	NP_001116857	Q6W2J9	BCOR_HUMAN			4	1598	-			436					D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Missense_Mutation	SNP	ENST00000378444.4	37	c.1306G>A	CCDS48093.1	.	.	.	.	.	.	.	.	.	.	C	10.34	1.324465	0.24080	.	.	ENSG00000183337	ENST00000378455;ENST00000397354;ENST00000378444;ENST00000342274;ENST00000406200	T;T;T;T;T	0.12984	2.63;2.63;2.63;2.63;2.63	5.56	3.8	0.43715	.	.	.	.	.	T	0.09949	0.0244	N	0.24115	0.695	0.25338	N	0.988971	B;B;B;B	0.19706	0.011;0.038;0.023;0.038	B;B;B;B	0.15052	0.007;0.012;0.005;0.012	T	0.27536	-1.0071	9	0.41790	T	0.15	-11.6674	9.5889	0.39534	0.0:0.7695:0.0:0.2305	.	436;436;436;436	Q6W2J9-3;Q6W2J9-4;Q6W2J9;Q6W2J9-2	.;.;BCOR_HUMAN;.	I	436	ENSP00000367716:V436I;ENSP00000380512:V436I;ENSP00000367705:V436I;ENSP00000345923:V436I;ENSP00000384485:V436I	ENSP00000345923:V436I	V	-	1	0	BCOR	39818237	0.942000	0.31987	0.974000	0.42286	0.951000	0.60555	1.522000	0.35921	0.532000	0.28657	0.600000	0.82982	GTC		0.527	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745	
ITIH6	347365	broad.mit.edu	37	X	54783873	54783873	+	Missense_Mutation	SNP	G	G	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chrX:54783873G>T	ENST00000218436.6	-	8	2663	c.2634C>A	c.(2632-2634)aaC>aaA	p.N878K		NM_198510.2	NP_940912.1	Q6UXX5	ITIH6_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 6	878	Pro-rich.				hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)										GCATATGGGGGTTTGGGGTCT	0.483																																						uc004dtj.2																			0				lung(2)|skin(2)|ovary(1)|breast(1)	6						c.(2632-2634)AAC>AAA		inter-alpha (globulin) inhibitor H5-like							75.0	70.0	72.0					X																	54783873		2203	4300	6503	SO:0001583	missense	347365				hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity	g.chrX:54783873G>T	AY358170	CCDS14361.1	Xp11.22-p11.21	2011-10-26	2011-10-26	2011-10-26	ENSG00000102313	ENSG00000102313			28907	protein-coding gene	gene with protein product			"""inter-alpha (globulin) inhibitor H5-like"""	ITIH5L		12975309	Standard	NM_198510		Approved	UNQ6369	uc004dtj.2	Q6UXX5	OTTHUMG00000021634	ENST00000218436.6:c.2634C>A	X.37:g.54783873G>T	ENSP00000218436:p.Asn878Lys						p.N878K	NM_198510	NP_940912	Q6UXX5	ITH5L_HUMAN			8	2664	-			878			Pro-rich.		A6NN03	Missense_Mutation	SNP	ENST00000218436.6	37	c.2634C>A	CCDS14361.1	.	.	.	.	.	.	.	.	.	.	G	0.030	-1.337892	0.01287	.	.	ENSG00000102313	ENST00000218436	T	0.02032	4.49	4.1	-5.63	0.02474	.	6.303450	0.00481	U	0.000123	T	0.01320	0.0043	N	0.08118	0	0.09310	N	1	B	0.14012	0.009	B	0.10450	0.005	T	0.44174	-0.9345	10	0.52906	T	0.07	.	0.7325	0.00959	0.2866:0.1949:0.3212:0.1973	.	878	Q6UXX5	ITH5L_HUMAN	K	878	ENSP00000218436:N878K	ENSP00000218436:N878K	N	-	3	2	ITIH5L	54800598	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.401000	0.07232	-2.367000	0.00605	-2.835000	0.00106	AAC		0.483	ITIH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056814.2	NM_198510	
ZXDA	7789	broad.mit.edu	37	X	57935325	57935325	+	Silent	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chrX:57935325G>A	ENST00000358697.4	-	1	1742	c.1530C>T	c.(1528-1530)ttC>ttT	p.F510F		NM_007156.4	NP_009087.1	P98168	ZXDA_HUMAN	zinc finger, X-linked, duplicated A	510	Required for interaction with ZXDC.				positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F510F(1)		breast(2)|endometrium(9)|kidney(1)|large_intestine(7)|lung(13)|ovary(2)|prostate(2)|skin(1)	37						CAGGACACACGAAAGGCTTTG	0.552																																						uc004dve.2																			1	Substitution - coding silent(1)		large_intestine(1)	ovary(1)	1						c.(1528-1530)TTC>TTT		zinc finger, X-linked, duplicated A							51.0	46.0	48.0					X																	57935325		2203	4300	6503	SO:0001819	synonymous_variant	7789				positive regulation of transcription, DNA-dependent	nucleus	C2H2 zinc finger domain binding|identical protein binding|nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chrX:57935325G>A	L14787	CCDS14376.1	Xp11.21	2013-01-08			ENSG00000198205	ENSG00000198205		"""Zinc fingers, C2H2-type"""	13198	protein-coding gene	gene with protein product	"""zinc finger protein 896"""	300235				8268913	Standard	NM_007156		Approved	ZNF896	uc004dve.3	P98168	OTTHUMG00000021688	ENST00000358697.4:c.1530C>T	X.37:g.57935325G>A							p.F510F	NM_007156	NP_009087	P98168	ZXDA_HUMAN			1	1743	-			510			Required for interaction with ZXDC.|C2H2-type 9.		Q9UJP7	Silent	SNP	ENST00000358697.4	37	c.1530C>T	CCDS14376.1																																																																																				0.552	ZXDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056925.1	NM_007156	
MAGT1	84061	broad.mit.edu	37	X	77112989	77112989	+	Missense_Mutation	SNP	G	G	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chrX:77112989G>T	ENST00000358075.6	-	4	578	c.492C>A	c.(490-492)aaC>aaA	p.N164K		NM_032121.5	NP_115497.4	Q9H0U3	MAGT1_HUMAN	magnesium transporter 1	132	Thioredoxin.				cellular protein metabolic process (GO:0044267)|cognition (GO:0050890)|magnesium ion transport (GO:0015693)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	magnesium ion transmembrane transporter activity (GO:0015095)			cervix(1)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	17						CTGAATTCATGTTTAGCTGAA	0.368																																						uc004fof.2																			0				upper_aerodigestive_tract(1)	1						c.(490-492)AAC>AAA		magnesium transporter 1							85.0	82.0	83.0					X																	77112989		2203	4296	6499	SO:0001583	missense	84061				protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex		g.chrX:77112989G>T		CCDS14436.2	Xq21.1	2014-09-17			ENSG00000102158	ENSG00000102158			28880	protein-coding gene	gene with protein product	"""oligosaccharyltransferase 3 homolog B (S. cerevisiae)"""	300715				15804357	Standard	NM_032121		Approved	DKFZp564K142, IAP, OST3B, MRX95	uc004fof.3	Q9H0U3	OTTHUMG00000021882	ENST00000358075.6:c.492C>A	X.37:g.77112989G>T	ENSP00000354649:p.Asn164Lys					MAGT1_uc004fog.3_RNA	p.N164K	NM_032121	NP_115497	Q9H0U3	MAGT1_HUMAN			4	554	-			132					B2RAR4|D3DTE3|Q53G00|Q6P577|Q8NBN6	Missense_Mutation	SNP	ENST00000358075.6	37	c.492C>A	CCDS14436.2	.	.	.	.	.	.	.	.	.	.	G	10.66	1.413988	0.25465	.	.	ENSG00000102158	ENST00000358075;ENST00000453109	T	0.22539	1.95	4.85	3.98	0.46160	Thioredoxin-like fold (2);	0.052185	0.64402	U	0.000001	T	0.12944	0.0314	L	0.39020	1.185	0.80722	D	1	B	0.16396	0.017	B	0.15484	0.013	T	0.09530	-1.0670	10	0.02654	T	1	-8.6114	8.6158	0.33831	0.1847:0.0:0.8153:0.0	.	132	Q9H0U3	MAGT1_HUMAN	K	164;15	ENSP00000354649:N164K	ENSP00000354649:N164K	N	-	3	2	MAGT1	76999645	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.389000	0.34453	0.821000	0.34540	0.513000	0.50165	AAC		0.368	MAGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057301.2	NM_032121	
RHOXF1	158800	broad.mit.edu	37	X	119243159	119243159	+	Silent	SNP	G	G	A	rs145568775		TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chrX:119243159G>A	ENST00000217999.2	-	3	620	c.546C>T	c.(544-546)gtC>gtT	p.V182V	RP4-755D9.1_ENST00000553843.1_RNA	NM_139282.1	NP_644811.1	Q8NHV9	RHXF1_HUMAN	Rhox homeobox family, member 1	182					gamete generation (GO:0007276)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|sexual reproduction (GO:0019953)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)	10						GCTAGTCCACGACGATGTAGA	0.507																																						uc004esk.1																			0					0						c.(544-546)GTC>GTT		Rhox homeobox family, member 1		G		1,3834		0,1,1631,571	106.0	82.0	90.0		546	-6.3	0.0	X	dbSNP_134	90	0,6728		0,0,2428,1872	no	coding-synonymous	RHOXF1	NM_139282.1		0,1,4059,2443	AA,AG,GG,G		0.0,0.0261,0.0095		182/185	119243159	1,10562	2203	4300	6503	SO:0001819	synonymous_variant	158800				gamete generation|multicellular organismal development|steroid hormone receptor signaling pathway	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chrX:119243159G>A		CCDS14593.1	Xq24	2011-06-20			ENSG00000101883	ENSG00000101883		"""Homeoboxes / PRD class"""	29993	protein-coding gene	gene with protein product		300446				11980563, 12490318	Standard	NM_139282		Approved	OTEX, PEPP1	uc004esk.2	Q8NHV9	OTTHUMG00000022290	ENST00000217999.2:c.546C>T	X.37:g.119243159G>A						uc004esi.1_Intron	p.V182V	NM_139282	NP_644811	Q8NHV9	RHXF1_HUMAN			3	621	-			182					O95030|Q3SYE0	Silent	SNP	ENST00000217999.2	37	c.546C>T	CCDS14593.1																																																																																				0.507	RHOXF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058083.2	NM_139282	
RAP2C	57826	broad.mit.edu	37	X	131348336	131348336	+	Missense_Mutation	SNP	A	A	C			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chrX:131348336A>C	ENST00000342983.2	-	3	1158	c.412T>G	c.(412-414)Tgg>Ggg	p.W138G	RAP2C_ENST00000370874.1_Missense_Mutation_p.W138G|RAP2C-AS1_ENST00000421483.2_RNA|RAP2C_ENST00000460462.1_5'UTR	NM_001271187.1|NM_021183.4	NP_001258116.1|NP_067006.3	Q9Y3L5	RAP2C_HUMAN	RAP2C, member of RAS oncogene family	138					GTP catabolic process (GO:0006184)|negative regulation of cell migration (GO:0030336)|positive regulation of protein autophosphorylation (GO:0031954)|Rap protein signal transduction (GO:0032486)|regulation of protein tyrosine kinase activity (GO:0061097)|regulation of RNA biosynthetic process (GO:2001141)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|transcription coactivator activity (GO:0003713)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1)|upper_aerodigestive_tract(2)	8	Acute lymphoblastic leukemia(192;0.000127)					GGACAGCCCCATTCTTGAGCC	0.438																																						uc004ewp.2																			0				ovary(1)	1						c.(412-414)TGG>GGG		RAP2C, member of RAS oncogene family precursor							152.0	124.0	134.0					X																	131348336		2203	4300	6503	SO:0001583	missense	57826				negative regulation of cell migration|positive regulation of protein autophosphorylation|Rap protein signal transduction|regulation of protein tyrosine kinase activity	recycling endosome membrane	GTP binding|GTPase activity	g.chrX:131348336A>C	BC051467	CCDS14632.1, CCDS76024.1	Xq25	2014-05-09			ENSG00000123728	ENSG00000123728			21165	protein-coding gene	gene with protein product							Standard	NM_001271186		Approved	DKFZp313B211	uc004ewp.4	Q9Y3L5	OTTHUMG00000022424	ENST00000342983.2:c.412T>G	X.37:g.131348336A>C	ENSP00000340274:p.Trp138Gly					RAP2C_uc004ewo.2_Missense_Mutation_p.W72G|RAP2C_uc010nrk.2_RNA|RAP2C_uc004ewq.3_Missense_Mutation_p.W138G	p.W138G	NM_021183	NP_067006	Q9Y3L5	RAP2C_HUMAN			3	1196	-	Acute lymphoblastic leukemia(192;0.000127)		138					B3KWD6|Q5H9H9|Q9BTS0	Missense_Mutation	SNP	ENST00000342983.2	37	c.412T>G	CCDS14632.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.018239	0.75275	.	.	ENSG00000123728	ENST00000342983;ENST00000370874	T;T	0.79749	-1.3;-1.3	5.62	5.62	0.85841	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.89420	0.6710	M	0.77406	2.37	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.90331	0.4352	10	0.59425	D	0.04	.	14.8537	0.70319	1.0:0.0:0.0:0.0	.	138	Q9Y3L5	RAP2C_HUMAN	G	138	ENSP00000340274:W138G;ENSP00000359911:W138G	ENSP00000340274:W138G	W	-	1	0	RAP2C	131176017	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.913000	0.92730	1.890000	0.54733	0.451000	0.29950	TGG		0.438	RAP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058312.1	NM_021183	
F9	2158	broad.mit.edu	37	X	138643011	138643011	+	Missense_Mutation	SNP	G	G	A	rs137852247		TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chrX:138643011G>A	ENST00000218099.2	+	7	842	c.835G>A	c.(835-837)Gca>Aca	p.A279T	F9_ENST00000394090.2_Missense_Mutation_p.A241T	NM_000133.3	NP_000124.1	P00740	FA9_HUMAN	coagulation factor IX	279	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		A -> T (in HEMB; mild). {ECO:0000269|PubMed:2773937, ECO:0000269|PubMed:8076946}.		blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|blood coagulation, intrinsic pathway (GO:0007597)|cellular protein metabolic process (GO:0044267)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|lung(19)|ovary(1)|skin(1)	35	Acute lymphoblastic leukemia(192;0.000127)				Antihemophilic Factor(DB00025)|Menadione(DB00170)	TACAGTTGTCGCAGGTAAATA	0.353																																						uc004fas.1																			0				lung(2)|ovary(1)	3	GRCh37	CM940587	F9	M	rs137852247	c.(835-837)GCA>ACA		coagulation factor IX preproprotein	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Heparin(DB01109)|Menadione(DB00170)						162.0	145.0	151.0					X																	138643011		2203	4300	6503	SO:0001583	missense	2158				blood coagulation, extrinsic pathway|blood coagulation, intrinsic pathway|peptidyl-glutamic acid carboxylation|post-translational protein modification|proteolysis	endoplasmic reticulum lumen|extracellular region|Golgi lumen|plasma membrane	calcium ion binding|serine-type endopeptidase activity	g.chrX:138643011G>A	M11309	CCDS14666.1	Xq26.3-q27.1	2014-09-17	2008-08-01		ENSG00000101981	ENSG00000101981	3.4.21.22		3551	protein-coding gene	gene with protein product	"""Factor IX"", ""plasma thromboplastic component"", ""Christmas disease"", ""hemophilia B"""	300746					Standard	NM_000133		Approved	FIX	uc004fas.1	P00740	OTTHUMG00000022536	ENST00000218099.2:c.835G>A	X.37:g.138643011G>A	ENSP00000218099:p.Ala279Thr					F9_uc004fat.1_Missense_Mutation_p.A241T	p.A279T	NM_000133	NP_000124	P00740	FA9_HUMAN			7	864	+	Acute lymphoblastic leukemia(192;0.000127)		279		A -> T (in HEMB; mild).	Peptidase S1.		A8K9N4|F2RM36|Q5FBE1|Q5JYJ8	Missense_Mutation	SNP	ENST00000218099.2	37	c.835G>A	CCDS14666.1	.	.	.	.	.	.	.	.	.	.	G	16.95	3.264663	0.59431	.	.	ENSG00000101981	ENST00000218099;ENST00000394090	D;D	0.88896	-2.44;-2.44	5.84	5.84	0.93424	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.106822	0.64402	D	0.000005	D	0.92961	0.7760	L	0.60455	1.87	0.47341	D	0.999392	D;D	0.71674	0.998;0.959	D;P	0.68353	0.957;0.633	D	0.93242	0.6627	10	0.62326	D	0.03	.	16.3112	0.82872	0.0:0.0:1.0:0.0	.	241;279	Q5FBE1;P00740	.;FA9_HUMAN	T	279;241	ENSP00000218099:A279T;ENSP00000377650:A241T	ENSP00000218099:A279T	A	+	1	0	F9	138470677	1.000000	0.71417	0.949000	0.38748	0.199000	0.23934	6.978000	0.76147	2.457000	0.83068	0.544000	0.68410	GCA		0.353	F9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058557.1		
FATE1	89885	broad.mit.edu	37	X	150891145	150891145	+	Missense_Mutation	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chrX:150891145G>A	ENST00000370350.3	+	5	551	c.466G>A	c.(466-468)Gcc>Acc	p.A156T		NM_033085.2	NP_149076.1	Q969F0	FATE1_HUMAN	fetal and adult testis expressed 1	156						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(2)|lung(6)|ovary(1)	15	Acute lymphoblastic leukemia(192;6.56e-05)					GGAACAGGGCGCCACCTGGCG	0.652																																						uc004fex.2																			0				ovary(1)	1						c.(466-468)GCC>ACC		fetal and adult testis expressed transcript							51.0	56.0	54.0					X																	150891145		2202	4299	6501	SO:0001583	missense	89885					endoplasmic reticulum|integral to membrane		g.chrX:150891145G>A	AF249872	CCDS14700.1	Xq28	2009-03-25			ENSG00000147378	ENSG00000147378			24683	protein-coding gene	gene with protein product	"""cancer/testis antigen 43"""	300450				11694338	Standard	NM_033085		Approved	FATE, CT43	uc004fex.3	Q969F0	OTTHUMG00000024172	ENST00000370350.3:c.466G>A	X.37:g.150891145G>A	ENSP00000359375:p.Ala156Thr						p.A156T	NM_033085	NP_149076	Q969F0	FATE1_HUMAN			5	550	+	Acute lymphoblastic leukemia(192;6.56e-05)		156						Missense_Mutation	SNP	ENST00000370350.3	37	c.466G>A	CCDS14700.1	.	.	.	.	.	.	.	.	.	.	G	13.10	2.135168	0.37728	.	.	ENSG00000147378	ENST00000370350	T	0.49139	0.79	4.39	-0.512	0.11966	.	0.873850	0.09694	N	0.768003	T	0.29190	0.0726	L	0.34521	1.04	0.09310	N	1	P	0.35575	0.51	B	0.27715	0.082	T	0.10428	-1.0630	10	0.27785	T	0.31	-1.0276	7.3704	0.26798	0.6257:0.0:0.3743:0.0	.	156	Q969F0	FATE1_HUMAN	T	156	ENSP00000359375:A156T	ENSP00000359375:A156T	A	+	1	0	FATE1	150641801	0.000000	0.05858	0.000000	0.03702	0.054000	0.15201	-0.685000	0.05167	-0.172000	0.10779	-0.380000	0.06706	GCC		0.652	FATE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060885.1	NM_033085	
