#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_filter	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
TNFRSF1B	7133	broad.mit.edu	37	1	12251959	12251959	+	Missense_Mutation	SNP	G	G	C			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr1:12251959G>C	ENST00000376259.3	+	4	525	c.436G>C	c.(436-438)Ggc>Cgc	p.G146R	TNFRSF1B_ENST00000536782.1_Missense_Mutation_p.G146R|TNFRSF1B_ENST00000492361.1_3'UTR|MIR4632_ENST00000584158.1_RNA	NM_001066.2	NP_001057.1	P20333	TNR1B_HUMAN	tumor necrosis factor receptor superfamily, member 1B	146					aging (GO:0007568)|cellular response to growth factor stimulus (GO:0071363)|cellular response to lipopolysaccharide (GO:0071222)|extrinsic apoptotic signaling pathway (GO:0097191)|immune response (GO:0006955)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of inflammatory response (GO:0050728)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|RNA destabilization (GO:0050779)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|varicosity (GO:0043196)	tumor necrosis factor-activated receptor activity (GO:0005031)|ubiquitin protein ligase binding (GO:0031625)	p.G146R(1)		central_nervous_system(1)|liver(1)|lung(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	Ovarian(185;0.249)	Lung NSC(185;8.72e-05)|all_lung(284;9.92e-05)|Renal(390;0.000147)|Colorectal(325;0.000584)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;5.52e-07)|COAD - Colon adenocarcinoma(227;0.000345)|BRCA - Breast invasive adenocarcinoma(304;0.000353)|Kidney(185;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00302)|STAD - Stomach adenocarcinoma(313;0.00815)|READ - Rectum adenocarcinoma(331;0.0284)	Etanercept(DB00005)	GTGCCGCCCGGGCTTCGGCGT	0.682																																						uc001att.2																			1	Substitution - Missense(1)		lung(1)	liver(1)|central_nervous_system(1)|skin(1)	3						c.(436-438)GGC>CGC		tumor necrosis factor receptor 2 precursor	Etanercept(DB00005)|Infliximab(DB00065)						16.0	19.0	18.0					1																	12251959		2197	4286	6483	SO:0001583	missense	7133				apoptosis	extracellular region|integral to membrane|membrane raft|plasma membrane	tumor necrosis factor receptor activity	g.chr1:12251959G>C	M32315	CCDS145.1	1p36.22	2008-02-05			ENSG00000028137	ENSG00000028137		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11917	protein-coding gene	gene with protein product		191191		TNFR2		2158863, 8702885	Standard	NM_001066		Approved	TNFBR, TNFR80, TNF-R75, TNF-R-II, p75, CD120b	uc001att.3	P20333	OTTHUMG00000001829	ENST00000376259.3:c.436G>C	1.37:g.12251959G>C	ENSP00000365435:p.Gly146Arg					TNFRSF1B_uc001atu.2_5'UTR|TNFRSF1B_uc009vnk.2_RNA	p.G146R	NM_001066	NP_001057	P20333	TNR1B_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;5.52e-07)|COAD - Colon adenocarcinoma(227;0.000345)|BRCA - Breast invasive adenocarcinoma(304;0.000353)|Kidney(185;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00302)|STAD - Stomach adenocarcinoma(313;0.00815)|READ - Rectum adenocarcinoma(331;0.0284)	4	525	+	Ovarian(185;0.249)	Lung NSC(185;8.72e-05)|all_lung(284;9.92e-05)|Renal(390;0.000147)|Colorectal(325;0.000584)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)	146			TNFR-Cys 3.|Extracellular (Potential).		B1AJZ3|Q16042|Q6YI29|Q9UIH1	Missense_Mutation	SNP	ENST00000376259.3	37	c.436G>C	CCDS145.1	.	.	.	.	.	.	.	.	.	.	G	19.23	3.788412	0.70337	.	.	ENSG00000028137	ENST00000376259;ENST00000400863;ENST00000536782	D;D	0.99722	-6.53;-4.67	3.91	3.91	0.45181	TNFR/CD27/30/40/95 cysteine-rich region (2);	0.000000	0.85682	D	0.000000	D	0.99677	0.9879	M	0.89715	3.055	0.46416	D	0.999036	D	0.89917	1.0	D	0.97110	1.0	D	0.97473	1.0042	10	0.87932	D	0	-39.3817	11.6276	0.51156	0.0:0.0:1.0:0.0	.	146	P20333	TNR1B_HUMAN	R	146	ENSP00000365435:G146R;ENSP00000440425:G146R	ENSP00000365435:G146R	G	+	1	0	TNFRSF1B	12174546	0.991000	0.36638	0.756000	0.31282	0.095000	0.18619	2.586000	0.46119	2.198000	0.70561	0.555000	0.69702	GGC		PASS	0.682	TNFRSF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005133.1	NM_001066		20	26	20	26	---	---	---	---
ZSWIM5	57643	broad.mit.edu	37	1	45484275	45484275	+	Missense_Mutation	SNP	C	C	G			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr1:45484275C>G	ENST00000359600.5	-	14	3614	c.3409G>C	c.(3409-3411)Gag>Cag	p.E1137Q		NM_020883.1	NP_065934.1	Q9P217	ZSWM5_HUMAN	zinc finger, SWIM-type containing 5	1137						extracellular space (GO:0005615)	zinc ion binding (GO:0008270)	p.E1137Q(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|liver(1)|lung(13)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Acute lymphoblastic leukemia(166;0.155)					TCAATGAACTCTCCATAGTGG	0.517											OREG0013450	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										uc001cnd.2																			1	Substitution - Missense(1)		lung(1)		0						c.(3409-3411)GAG>CAG		zinc finger, SWIM domain containing 5							189.0	184.0	186.0					1																	45484275		2102	4233	6335	SO:0001583	missense	57643						zinc ion binding	g.chr1:45484275C>G	AB040944	CCDS41319.1	1p34.1	2010-06-16			ENSG00000162415	ENSG00000162415		"""Zinc fingers, SWIM-type"""	29299	protein-coding gene	gene with protein product						10819331	Standard	NM_020883		Approved	KIAA1511	uc001cnd.2	Q9P217	OTTHUMG00000008950	ENST00000359600.5:c.3409G>C	1.37:g.45484275C>G	ENSP00000352614:p.Glu1137Gln		OREG0013450	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	932		p.E1137Q	NM_020883	NP_065934	Q9P217	ZSWM5_HUMAN			14	3637	-	Acute lymphoblastic leukemia(166;0.155)		1137					Q5SXQ9	Missense_Mutation	SNP	ENST00000359600.5	37	c.3409G>C	CCDS41319.1	.	.	.	.	.	.	.	.	.	.	C	19.51	3.841598	0.71488	.	.	ENSG00000162415	ENST00000359600	T	0.55052	0.54	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	T	0.57755	0.2075	M	0.75264	2.295	0.80722	D	1	P	0.40660	0.726	B	0.39258	0.295	T	0.66689	-0.5860	10	0.72032	D	0.01	-15.5224	19.058	0.93074	0.0:1.0:0.0:0.0	.	1137	Q9P217	ZSWM5_HUMAN	Q	1137	ENSP00000352614:E1137Q	ENSP00000352614:E1137Q	E	-	1	0	ZSWIM5	45256862	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.445000	0.80570	2.666000	0.90696	0.561000	0.74099	GAG		PASS	0.517	ZSWIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024823.2	XM_046581		123	164	123	164	---	---	---	---
COL11A1	1301	broad.mit.edu	37	1	103491792	103491792	+	Missense_Mutation	SNP	C	C	G			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr1:103491792C>G	ENST00000370096.3	-	6	1189	c.877G>C	c.(877-879)Gag>Cag	p.E293Q	COL11A1_ENST00000358392.2_Intron|COL11A1_ENST00000353414.4_Intron|COL11A1_ENST00000512756.1_Missense_Mutation_p.E293Q	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	293	Nonhelical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)	p.E293Q(1)		NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		GCTATTGTCTCCTCAGTTACA	0.448																																						uc001dul.2																			1	Substitution - Missense(1)		lung(1)	ovary(6)|breast(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	12						c.(877-879)GAG>CAG		alpha 1 type XI collagen isoform A							274.0	228.0	244.0					1																	103491792		2203	4300	6503	SO:0001583	missense	1301				collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging	g.chr1:103491792C>G	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"""Collagens"""	2186	protein-coding gene	gene with protein product	"""collagen XI, alpha-1 polypeptide"""	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.877G>C	1.37:g.103491792C>G	ENSP00000359114:p.Glu293Gln					COL11A1_uc001duk.2_5'UTR|COL11A1_uc001dum.2_Intron|COL11A1_uc001dun.2_Intron|COL11A1_uc009weh.2_Missense_Mutation_p.E293Q	p.E293Q	NM_001854	NP_001845	P12107	COBA1_HUMAN		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)	6	1195	-		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)	293			Nonhelical region.		B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	37	c.877G>C	CCDS778.1	.	.	.	.	.	.	.	.	.	.	C	16.14	3.039902	0.55003	.	.	ENSG00000060718	ENST00000370096;ENST00000512756	D;D	0.89123	-2.37;-2.47	5.39	5.39	0.77823	.	.	.	.	.	D	0.91150	0.7213	M	0.68952	2.095	0.80722	D	1	D;D	0.57899	0.981;0.981	D;D	0.65140	0.932;0.932	D	0.87977	0.2740	9	0.14252	T	0.57	.	19.1559	0.93510	0.0:1.0:0.0:0.0	.	293;293	E9PCU0;P12107	.;COBA1_HUMAN	Q	293	ENSP00000359114:E293Q;ENSP00000426533:E293Q	ENSP00000359114:E293Q	E	-	1	0	COL11A1	103264380	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.604000	0.67626	2.529000	0.85273	0.643000	0.83706	GAG		PASS	0.448	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		60	129	60	129	---	---	---	---
GON4L	54856	broad.mit.edu	37	1	155764901	155764901	+	Nonsense_Mutation	SNP	C	C	A			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr1:155764901C>A	ENST00000368331.1	-	12	1735	c.1687G>T	c.(1687-1689)Gaa>Taa	p.E563*	GON4L_ENST00000437809.1_Nonsense_Mutation_p.E563*|GON4L_ENST00000271883.5_Nonsense_Mutation_p.E563*|GON4L_ENST00000471341.1_5'UTR|GON4L_ENST00000361040.5_Nonsense_Mutation_p.E563*	NM_001282858.1|NM_001282860.1	NP_001269787.1|NP_001269789.1	Q3T8J9	GON4L_HUMAN	gon-4-like (C. elegans)	563	Asp-rich.				regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.E563*(3)		NS(2)|breast(4)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	45	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					TCGAGGTCTTCCAGGAAATTA	0.413																																						uc001flz.2																			3	Substitution - Nonsense(3)		lung(3)	ovary(3)	3						c.(1687-1689)GAA>TAA		gon-4-like isoform a							122.0	113.0	116.0					1																	155764901		2203	4300	6503	SO:0001587	stop_gained	54856				regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding	g.chr1:155764901C>A	AB046826	CCDS1121.1, CCDS44242.1, CCDS60296.1	1q22	2013-10-31	2006-11-08	2006-02-16	ENSG00000116580	ENSG00000116580			25973	protein-coding gene	gene with protein product		610393	"""gon-4 homolog (C.elegans)"""	GON4		16545939, 21454521	Standard	XM_005245283		Approved	FLJ20203, GON-4	uc001fly.1	Q3T8J9	OTTHUMG00000014106	ENST00000368331.1:c.1687G>T	1.37:g.155764901C>A	ENSP00000357315:p.Glu563*					GON4L_uc001fly.1_Nonsense_Mutation_p.E563*|GON4L_uc009wrh.1_Nonsense_Mutation_p.E563*|GON4L_uc001fma.1_Nonsense_Mutation_p.E563*|GON4L_uc001fmc.2_Nonsense_Mutation_p.E563*|GON4L_uc001fmd.3_Nonsense_Mutation_p.E563*|GON4L_uc009wri.2_Nonsense_Mutation_p.E149*|GON4L_uc009wrj.1_Nonsense_Mutation_p.E78*|GON4L_uc001fme.2_Nonsense_Mutation_p.E391*|GON4L_uc001fmf.2_Nonsense_Mutation_p.E257*	p.E563*	NM_001037533	NP_001032622	Q3T8J9	GON4L_HUMAN			12	1784	-	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)		563			Asp-rich.		B7ZBL4|Q14C93|Q3T8J8|Q5VYZ5|Q5W0D5|Q6AWA6|Q6P1Q6|Q7Z3L3|Q8IY79|Q9BQI1|Q9HCG6	Nonsense_Mutation	SNP	ENST00000368331.1	37	c.1687G>T		.	.	.	.	.	.	.	.	.	.	C	39	7.896327	0.98548	.	.	ENSG00000116580	ENST00000437809;ENST00000368331;ENST00000271883;ENST00000539959;ENST00000361040;ENST00000368327	.	.	.	5.11	5.11	0.69529	.	0.195583	0.44097	D	0.000493	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	18.6864	0.91565	0.0:1.0:0.0:0.0	.	.	.	.	X	563;563;563;563;563;42	.	ENSP00000271883:E563X	E	-	1	0	GON4L	154031525	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.195000	0.77798	2.807000	0.96579	0.591000	0.81541	GAA		PASS	0.413	GON4L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_032292		79	95	79	95	---	---	---	---
SPTA1	6708	broad.mit.edu	37	1	158597502	158597502	+	Missense_Mutation	SNP	C	C	T			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr1:158597502C>T	ENST00000368147.4	-	40	5757	c.5577G>A	c.(5575-5577)atG>atA	p.M1859I		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1859					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.M1859I(1)		NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					CTTCATGCTTCATTAGCAAGC	0.398																																						uc001fst.1																			1	Substitution - Missense(1)		lung(1)	ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8						c.(5575-5577)ATG>ATA		spectrin, alpha, erythrocytic 1							150.0	134.0	139.0					1																	158597502		1854	4095	5949	SO:0001583	missense	6708				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton	g.chr1:158597502C>T	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.5577G>A	1.37:g.158597502C>T	ENSP00000357129:p.Met1859Ile						p.M1859I	NM_003126	NP_003117	P02549	SPTA1_HUMAN			40	5776	-	all_hematologic(112;0.0378)		1859			Spectrin 18.		Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	c.5577G>A	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	C	14.68	2.609102	0.46527	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.49720	0.77;0.77	5.55	5.55	0.83447	.	0.500994	0.14895	N	0.292127	T	0.15219	0.0367	N	0.08118	0	0.29629	N	0.845592	B	0.12630	0.006	B	0.04013	0.001	T	0.12218	-1.0556	10	0.87932	D	0	.	11.6268	0.51151	0.0:0.9193:0.0:0.0807	.	1859	P02549	SPTA1_HUMAN	I	1859	ENSP00000357130:M1859I;ENSP00000357129:M1859I	ENSP00000357129:M1859I	M	-	3	0	SPTA1	156864126	1.000000	0.71417	1.000000	0.80357	0.727000	0.41649	1.074000	0.30703	2.885000	0.99019	0.655000	0.94253	ATG		PASS	0.398	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		21	188	21	188	---	---	---	---
IFI16	3428	broad.mit.edu	37	1	159002320	159002320	+	Nonsense_Mutation	SNP	A	A	T			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr1:159002320A>T	ENST00000295809.7	+	7	1423	c.1168A>T	c.(1168-1170)Aaa>Taa	p.K390*	IFI16_ENST00000359709.3_Nonsense_Mutation_p.K334*|IFI16_ENST00000340979.6_Nonsense_Mutation_p.K390*|IFI16_ENST00000448393.2_Nonsense_Mutation_p.K390*|IFI16_ENST00000368131.4_Nonsense_Mutation_p.K390*|IFI16_ENST00000430894.2_Nonsense_Mutation_p.K338*|IFI16_ENST00000368132.3_Nonsense_Mutation_p.K390*			Q16666	IF16_HUMAN	interferon, gamma-inducible protein 16	390	Interaction with TP53 C-terminus.				activation of cysteine-type endopeptidase activity (GO:0097202)|activation of innate immune response (GO:0002218)|autophagy (GO:0006914)|cell proliferation (GO:0008283)|cellular response to glucose starvation (GO:0042149)|cellular response to ionizing radiation (GO:0071479)|defense response to virus (GO:0051607)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|monocyte differentiation (GO:0030224)|myeloid cell differentiation (GO:0030099)|negative regulation of cysteine-type endopeptidase activity (GO:2000117)|negative regulation of DNA binding (GO:0043392)|negative regulation of innate immune response (GO:0045824)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|positive regulation of cytokine production (GO:0001819)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of autophagy (GO:0010506)|regulation of gene expression, epigenetic (GO:0040029)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)	p.K390*(1)		cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_hematologic(112;0.0429)					TCAGATAAAGAAAAAAACAAA	0.378																																						uc001ftg.2																			1	Substitution - Nonsense(1)		lung(1)	ovary(1)	1						c.(1168-1170)AAA>TAA		interferon, gamma-inducible protein 16							55.0	56.0	56.0					1																	159002320		2203	4300	6503	SO:0001587	stop_gained	3428				cell proliferation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|monocyte differentiation|negative regulation of transcription, DNA-dependent|response to virus|transcription, DNA-dependent	cytoplasm|nuclear speck|nucleolus	double-stranded DNA binding|protein binding	g.chr1:159002320A>T	M63838	CCDS1180.3, CCDS58039.1	1q22	2008-02-05			ENSG00000163565	ENSG00000163565			5395	protein-coding gene	gene with protein product		147586				1526658, 7959953	Standard	NM_005531		Approved	IFNGIP1, PYHIN2	uc010pis.2	Q16666	OTTHUMG00000037108	ENST00000295809.7:c.1168A>T	1.37:g.159002320A>T	ENSP00000295809:p.Lys390*					IFI16_uc010pis.1_Nonsense_Mutation_p.K334*|IFI16_uc001fth.2_5'UTR|IFI16_uc010pit.1_5'UTR	p.K390*	NM_005531	NP_005522	Q16666	IF16_HUMAN			7	1458	+	all_hematologic(112;0.0429)		390					B4DJT8|H3BLV7|Q59GX0|Q5T3W7|Q5T3W8|Q5T3X0|Q5T3X1|Q5T3X2|Q8N9E5|Q8NEQ7|Q96AJ5|Q9UH78	Nonsense_Mutation	SNP	ENST00000295809.7	37	c.1168A>T		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	39|39	7.689962|7.689962	0.98434|0.98434	.|.	.|.	ENSG00000163565|ENSG00000163565	ENST00000295809;ENST00000340979;ENST00000368131;ENST00000368132;ENST00000430894|ENST00000448393	.|.	.|.	.|.	1.9|1.9	-3.15|-3.15	0.05233|0.05233	.|.	.|.	.|.	.|.	.|.	.|T	.|0.12860	.|0.0312	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.26121	.|-1.0112	.|3	0.02654|.	T|.	1|.	.|.	6.0707|6.0707	0.19887|0.19887	0.5032:0.0:0.4968:0.0|0.5032:0.0:0.4968:0.0	.|.	.|.	.|.	.|.	X|S	390;390;390;390;338|210	.|.	ENSP00000295809:K390X|.	K|R	+|+	1|3	0|2	IFI16|IFI16	157268944|157268944	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.728000|0.728000	0.41692|0.41692	-0.267000|-0.267000	0.08619|0.08619	-0.753000|-0.753000	0.04721|0.04721	0.379000|0.379000	0.24179|0.24179	AAA|AGA		PASS	0.378	IFI16-013	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000421720.1	NM_005531		35	27	35	27	---	---	---	---
KLHDC9	126823	broad.mit.edu	37	1	161069480	161069480	+	Silent	SNP	G	G	C			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr1:161069480G>C	ENST00000368011.4	+	3	922	c.780G>C	c.(778-780)cgG>cgC	p.R260R	PFDN2_ENST00000468311.1_5'Flank|KLHDC9_ENST00000392192.2_Missense_Mutation_p.A267P|KLHDC9_ENST00000490724.2_3'UTR	NM_152366.4	NP_689579.3	Q8NEP7	KLDC9_HUMAN	kelch domain containing 9	260								p.A267P(1)|p.R260R(1)		lung(5)|upper_aerodigestive_tract(1)	6	all_cancers(52;1.28e-19)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			ATGGACTACGGCATCACTCAT	0.542																																						uc001fxr.2																			2	Substitution - Missense(1)|Substitution - coding silent(1)		lung(2)		0						c.(778-780)CGG>CGC		kelch/ankyrin repeat containing cyclin A1							151.0	155.0	154.0					1																	161069480		2203	4300	6503	SO:0001819	synonymous_variant	126823							g.chr1:161069480G>C	BC022077	CCDS30919.1, CCDS41425.1	1q23.3	2008-02-05			ENSG00000162755	ENSG00000162755			28489	protein-coding gene	gene with protein product	"""kelch/ankyrin repeat containing cyclin A1 interacting protein"""					15159402	Standard	NM_152366		Approved	KARCA1	uc001fxr.3	Q8NEP7	OTTHUMG00000031479	ENST00000368011.4:c.780G>C	1.37:g.161069480G>C						KLHDC9_uc001fxq.2_Silent_p.R22R|KLHDC9_uc001fxs.2_Missense_Mutation_p.A267P	p.R260R	NM_152366	NP_689579	Q8NEP7	KLDC9_HUMAN	BRCA - Breast invasive adenocarcinoma(70;0.00165)		3	952	+	all_cancers(52;1.28e-19)|Breast(13;0.00188)|all_hematologic(112;0.093)		260					Q5SY56|Q6NXT9|Q6PKN4|Q8N5E1|Q8NA16	Silent	SNP	ENST00000368011.4	37	c.780G>C	CCDS30919.1	.	.	.	.	.	.	.	.	.	.	G	17.73	3.462389	0.63513	.	.	ENSG00000162755	ENST00000392192	T	0.55588	0.51	4.75	0.627	0.17675	.	.	.	.	.	T	0.18923	0.0454	.	.	.	0.23657	N	0.997181	B	0.10296	0.003	B	0.11329	0.006	T	0.31052	-0.9957	8	0.87932	D	0	-34.6797	4.6424	0.12556	0.0814:0.2798:0.4946:0.1442	.	267	Q8NEP7-2	.	P	267	ENSP00000376030:A267P	ENSP00000376030:A267P	A	+	1	0	KLHDC9	159336104	1.000000	0.71417	0.984000	0.44739	0.992000	0.81027	0.531000	0.23052	-0.035000	0.13691	0.561000	0.74099	GCA		PASS	0.542	KLHDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077092.1	NM_152366		179	250	179	250	---	---	---	---
SMG7	9887	broad.mit.edu	37	1	183514079	183514079	+	Missense_Mutation	SNP	A	A	T			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr1:183514079A>T	ENST00000347615.2	+	16	2121	c.2002A>T	c.(2002-2004)Aca>Tca	p.T668S	SMG7_ENST00000515829.2_Missense_Mutation_p.T622S|SMG7_ENST00000367537.3_Missense_Mutation_p.T651S|SMG7_ENST00000456731.2_Missense_Mutation_p.T580S|SMG7_ENST00000508461.1_Missense_Mutation_p.T626S|SMG7_ENST00000507469.1_Missense_Mutation_p.T622S	NM_173156.2	NP_775179.1	Q92540	SMG7_HUMAN	SMG7 nonsense mediated mRNA decay factor	668	Gln/Pro-rich.				gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	protein phosphatase 2A binding (GO:0051721)	p.T668S(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(16)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	46						TCCGCCCCCAACATATGTTAT	0.433																																						uc001gqg.2																			1	Substitution - Missense(1)		lung(1)	upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						c.(2002-2004)ACA>TCA		SMG-7 homolog isoform 1							90.0	97.0	95.0					1																	183514079		2203	4300	6503	SO:0001583	missense	9887				mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation	cytoplasm|intermediate filament cytoskeleton|nucleus	protein phosphatase 2A binding	g.chr1:183514079A>T	D87437	CCDS1355.1, CCDS41445.1, CCDS41445.2, CCDS53444.1, CCDS53445.1	1q25	2013-07-02	2013-07-02	2006-02-16	ENSG00000116698	ENSG00000116698			16792	protein-coding gene	gene with protein product	"""EST1 telomerase component homolog C (S. cerevisiae)"""	610964	"""chromosome 1 open reading frame 16"", ""smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	C1orf16		14636577, 15721257	Standard	NM_173156		Approved	KIAA0250, EST1C, SGA56M, SMG-7	uc001gqf.3	Q92540	OTTHUMG00000035221	ENST00000347615.2:c.2002A>T	1.37:g.183514079A>T	ENSP00000340766:p.Thr668Ser					SMG7_uc010pob.1_Missense_Mutation_p.T651S|SMG7_uc001gqf.2_Missense_Mutation_p.T622S|SMG7_uc001gqh.2_Missense_Mutation_p.T622S|SMG7_uc001gqi.2_Missense_Mutation_p.T580S|SMG7_uc010poc.1_Missense_Mutation_p.T626S	p.T668S	NM_173156	NP_775179	Q92540	SMG7_HUMAN			16	2124	+			668			Gln/Pro-rich.		B4DRB2|E9PCI0|E9PEH2|Q5T1Q0|Q6PIE0|Q7Z7H9|Q8IXC1|Q8IXC2	Missense_Mutation	SNP	ENST00000347615.2	37	c.2002A>T	CCDS1355.1	.	.	.	.	.	.	.	.	.	.	A	13.69	2.313108	0.40895	.	.	ENSG00000116698	ENST00000456731;ENST00000367537;ENST00000508461;ENST00000419169;ENST00000347615;ENST00000507469;ENST00000515829	T;T;T;T;T;T;T	0.49720	0.77;0.77;0.77;0.77;0.77;0.77;0.77	5.67	3.24	0.37175	.	0.281842	0.41194	D	0.000926	T	0.25865	0.0630	N	0.14661	0.345	0.40542	D	0.981037	B;B;B;B;B;B	0.16603	0.009;0.009;0.001;0.002;0.012;0.018	B;B;B;B;B;B	0.18561	0.006;0.007;0.002;0.009;0.022;0.015	T	0.05750	-1.0866	10	0.20519	T	0.43	-2.5385	6.8655	0.24091	0.6126:0.0:0.3874:0.0	.	626;651;580;622;668;622	E9PCI0;E9PD50;E9PCE5;Q92540-2;Q92540;E9PEH2	.;.;.;.;SMG7_HUMAN;.	S	580;651;626;580;668;622;622	ENSP00000407629:T580S;ENSP00000356507:T651S;ENSP00000426915:T626S;ENSP00000388390:T580S;ENSP00000340766:T668S;ENSP00000425133:T622S;ENSP00000421358:T622S	ENSP00000340766:T668S	T	+	1	0	SMG7	181780702	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	2.451000	0.44952	0.917000	0.36895	0.459000	0.35465	ACA		PASS	0.433	SMG7-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000085432.1	NM_014837		115	146	115	146	---	---	---	---
SRGAP2	23380	broad.mit.edu	37	1	206619562	206619562	+	Silent	SNP	C	C	T			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr1:206619562C>T	ENST00000414007.1	+	14	1596	c.1596C>T	c.(1594-1596)atC>atT	p.I532I	SRGAP2_ENST00000471256.1_3'UTR|SRGAP2_ENST00000419187.2_5'UTR			O75044	SRGP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 2	672	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				actin filament severing (GO:0051014)|axon guidance (GO:0007411)|dendritic spine development (GO:0060996)|extension of a leading process involved in cell motility in cerebral cortex radial glia guided migration (GO:0021816)|filopodium assembly (GO:0046847)|lamellipodium assembly involved in ameboidal cell migration (GO:0003363)|negative regulation of neuron migration (GO:2001223)|neuron projection morphogenesis (GO:0048812)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|substrate adhesion-dependent cell spreading (GO:0034446)	cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic spine head (GO:0044327)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	protein homodimerization activity (GO:0042803)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)	p.I532I(1)		NS(1)|breast(1)|kidney(1)|lung(1)	4	Breast(84;0.137)					AAACCATCATCATCCAGCATG	0.587																																						uc001hdy.2																			1	Substitution - coding silent(1)		lung(1)		0						c.(1753-1755)ATC>ATT		SLIT-ROBO Rho GTPase activating protein 2							143.0	148.0	146.0					1																	206619562		2167	4286	6453	SO:0001819	synonymous_variant	23380				axon guidance|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding	g.chr1:206619562C>T	AB007925	CCDS73017.1	1q32.1	2014-08-13	2004-11-12	2004-11-12	ENSG00000163486	ENSG00000266028		"""Rho GTPase activating proteins"""	19751	protein-coding gene	gene with protein product		606524	"""formin binding protein 2"""	FNBP2		15046868, 11672528	Standard	XM_005277510		Approved	KIAA0456, ARHGAP34, SRGAP2A	uc001hdy.3	O75044	OTTHUMG00000184381	ENST00000414007.1:c.1596C>T	1.37:g.206619562C>T						SRGAP2_uc010prt.1_Silent_p.I508I|SRGAP2_uc001hdx.2_Silent_p.I585I|SRGAP2_uc010pru.1_Silent_p.I508I|SRGAP2_uc010prv.1_Silent_p.I509I	p.I585I	NM_015326	NP_056141	O75044	FNBP2_HUMAN			15	2088	+	Breast(84;0.137)		672			Rho-GAP.			Silent	SNP	ENST00000414007.1	37	c.1755C>T		.	.	.	.	.	.	.	.	.	.	C	10.67	1.414993	0.25552	.	.	ENSG00000163486	ENST00000295713	.	.	.	5.79	5.79	0.91817	.	.	.	.	.	T	0.80082	0.4558	.	.	.	0.30974	N	0.7227589999999999	.	.	.	.	.	.	T	0.77781	-0.2459	3	.	.	.	.	20.0236	0.97511	0.0:1.0:0.0:0.0	.	.	.	.	Y	586	.	.	H	+	1	0	SRGAP2	204686185	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.049000	0.71053	2.721000	0.93114	0.655000	0.94253	CAT		PASS	0.587	SRGAP2-201	KNOWN	basic	protein_coding	protein_coding		NM_015326		153	195	153	195	---	---	---	---
MARC1	64757	broad.mit.edu	37	1	220960480	220960480	+	Missense_Mutation	SNP	C	C	T			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr1:220960480C>T	ENST00000366910.5	+	1	380	c.194C>T	c.(193-195)cCt>cTt	p.P65L		NM_022746.3	NP_073583.3	Q5VT66	MARC1_HUMAN	mitochondrial amidoxime reducing component 1	65					detoxification of nitrogen compound (GO:0051410)|nitrate metabolic process (GO:0042126)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	molybdenum ion binding (GO:0030151)|molybdopterin cofactor binding (GO:0043546)|nitrate reductase activity (GO:0008940)|pyridoxal phosphate binding (GO:0030170)	p.P65L(1)									TGGATCTACCCTGTGAAATCC	0.741																																						uc001hms.2																			1	Substitution - Missense(1)		lung(1)		0						c.(193-195)CCT>CTT		MOCO sulphurase C-terminal domain containing 1							15.0	14.0	14.0					1																	220960480		2145	4220	6365	SO:0001583	missense	64757						molybdenum ion binding|oxidoreductase activity|pyridoxal phosphate binding	g.chr1:220960480C>T	AK026043	CCDS1526.1	1q41	2011-11-02	2011-11-02	2011-11-02	ENSG00000186205	ENSG00000186205			26189	protein-coding gene	gene with protein product		614126	"""MOCO sulphurase C-terminal domain containing 1"""	MOSC1		11886751	Standard	NM_022746		Approved	FLJ22390	uc001hms.3	Q5VT66	OTTHUMG00000037353	ENST00000366910.5:c.194C>T	1.37:g.220960480C>T	ENSP00000355877:p.Pro65Leu					MOSC1_uc001hmt.2_Missense_Mutation_p.P65L	p.P65L	NM_022746	NP_073583	Q5VT66	MOSC1_HUMAN		GBM - Glioblastoma multiforme(131;0.0358)	1	442	+			65					A8K447|B2D078|Q5VVS9|Q5VVT0|Q5VVT1|Q8N9P5|Q96FN8|Q9H6C7	Missense_Mutation	SNP	ENST00000366910.5	37	c.194C>T	CCDS1526.1	.	.	.	.	.	.	.	.	.	.	C	18.90	3.722308	0.68959	.	.	ENSG00000186205	ENST00000366910	T	0.79845	-1.31	4.14	1.1	0.20463	MOSC, N-terminal beta barrel (1);Pyruvate kinase-like, insert domain (1);	0.100353	0.42682	D	0.000667	D	0.89556	0.6749	M	0.92459	3.31	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.86547	0.1832	10	0.87932	D	0	-26.2662	6.6886	0.23158	0.0:0.6839:0.1459:0.1702	.	65;65	Q5VT66-2;Q5VT66	.;MOSC1_HUMAN	L	65	ENSP00000355877:P65L	ENSP00000355877:P65L	P	+	2	0	MOSC1	219027103	1.000000	0.71417	0.915000	0.36163	0.681000	0.39784	3.151000	0.50670	-0.075000	0.12798	0.313000	0.20887	CCT		PASS	0.741	MARC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090904.1	NM_022746		4	3	4	3	---	---	---	---
DNAH6	1768	broad.mit.edu	37	2	84804425	84804425	+	Missense_Mutation	SNP	C	C	T			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr2:84804425C>T	ENST00000237449.6	+	12	1977	c.1969C>T	c.(1969-1971)Cac>Tac	p.H657Y	DNAH6_ENST00000389394.3_Missense_Mutation_p.H657Y|DNAH6_ENST00000398278.2_Missense_Mutation_p.H657Y			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	657	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.H657Y(1)|p.H236Y(1)		NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						TCACAAACAGCACAAGGACGC	0.333																																						uc010fgb.2																			2	Substitution - Missense(2)		lung(2)	central_nervous_system(1)	1						c.(1969-1971)CAC>TAC		dynein, axonemal, heavy polypeptide 6							62.0	59.0	60.0					2																	84804425		2203	4300	6503	SO:0001583	missense	1768				microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity	g.chr2:84804425C>T	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"""Axonemal dyneins"""	2951	protein-coding gene	gene with protein product		603336	"""dynein, axonemal, heavy polypeptide 6"", ""dynein heavy chain-like 1"""	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.1969C>T	2.37:g.84804425C>T	ENSP00000237449:p.His657Tyr					DNAH6_uc002soo.2_Missense_Mutation_p.H236Y|DNAH6_uc002sop.2_Missense_Mutation_p.H236Y	p.H657Y	NM_001370	NP_001361	Q9C0G6	DYH6_HUMAN			13	2106	+			657			Stem (By similarity).		A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	37	c.1969C>T	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	C	8.826	0.938802	0.18281	.	.	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	T;T;T	0.24538	1.85;1.98;1.85	5.31	5.31	0.75309	.	0.000000	0.56097	D	0.000022	T	0.46034	0.1372	L	0.59436	1.845	0.41007	D	0.984974	P;D	0.76494	0.774;0.999	B;D	0.64776	0.326;0.929	T	0.19128	-1.0315	10	0.31617	T	0.26	.	18.1111	0.89536	0.0:1.0:0.0:0.0	.	657;236	Q9C0G6;Q9C0G6-3	DYH6_HUMAN;.	Y	657	ENSP00000374045:H657Y;ENSP00000381326:H657Y;ENSP00000237449:H657Y	ENSP00000237449:H657Y	H	+	1	0	DNAH6	84657936	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	5.681000	0.68175	2.642000	0.89623	0.561000	0.74099	CAC		PASS	0.333	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		27	33	27	33	---	---	---	---
REV1	51455	broad.mit.edu	37	2	100055628	100055628	+	Silent	SNP	C	C	T			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr2:100055628C>T	ENST00000258428.3	-	6	876	c.648G>A	c.(646-648)ccG>ccA	p.P216P	REV1_ENST00000393445.3_Silent_p.P216P|REV1_ENST00000465835.1_5'UTR	NM_001037872.1|NM_016316.2	NP_001032961.1|NP_057400.1	Q9UBZ9	REV1_HUMAN	REV1, polymerase (DNA directed)	216					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|error-prone translesion synthesis (GO:0042276)|response to UV (GO:0009411)	nucleoplasm (GO:0005654)	damaged DNA binding (GO:0003684)|deoxycytidyl transferase activity (GO:0017125)|DNA-directed DNA polymerase activity (GO:0003887)|magnesium ion binding (GO:0000287)	p.P216P(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(12)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CTCTGGGATGCGGAATTCCAT	0.448								Direct reversal of damage																														uc002tad.2																			1	Substitution - coding silent(1)		lung(1)	ovary(2)	2						c.(646-648)CCG>CCA	DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage	REV1-like isoform 1							82.0	75.0	77.0					2																	100055628		2203	4300	6503	SO:0001819	synonymous_variant	51455				DNA replication|error-prone translesion synthesis|response to UV	nucleoplasm	damaged DNA binding|DNA-directed DNA polymerase activity|magnesium ion binding|protein binding	g.chr2:100055628C>T	AF206019	CCDS2045.1, CCDS42722.1	2q11.1-q11.2	2012-05-18	2012-05-18	2006-11-07	ENSG00000135945	ENSG00000135945		"""DNA polymerases"""	14060	protein-coding gene	gene with protein product		606134	"""REV1 (yeast homolog)- like"", ""REV1-like (yeast)"", ""REV1 homolog (S. cerevisiae)"""	REV1L		10536157	Standard	XM_005263968		Approved		uc002tad.3	Q9UBZ9	OTTHUMG00000130636	ENST00000258428.3:c.648G>A	2.37:g.100055628C>T						REV1_uc002tac.2_Silent_p.P216P|REV1_uc002tae.1_Silent_p.P195P	p.P216P	NM_016316	NP_057400	Q9UBZ9	REV1_HUMAN			6	860	-			216					O95941|Q53SI7|Q9C0J4|Q9NUP2	Silent	SNP	ENST00000258428.3	37	c.648G>A	CCDS2045.1																																																																																				PASS	0.448	REV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253123.2	NM_016316		4	115	4	115	---	---	---	---
RAF1	5894	broad.mit.edu	37	3	12653511	12653511	+	Silent	SNP	G	G	C			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr3:12653511G>C	ENST00000251849.4	-	3	697	c.258C>G	c.(256-258)ctC>ctG	p.L86L	RAF1_ENST00000442415.2_Silent_p.L86L|RAF1_ENST00000534997.1_5'Flank|RAF1_ENST00000542177.1_Intron	NM_002880.3	NP_002871.1	P04049	RAF1_HUMAN	Raf-1 proto-oncogene, serine/threonine kinase	86	RBD. {ECO:0000255|PROSITE- ProRule:PRU00262}.				activation of adenylate cyclase activity (GO:0007190)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|death-inducing signaling complex assembly (GO:0071550)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intermediate filament cytoskeleton organization (GO:0045104)|ion transmembrane transport (GO:0034220)|MAPK cascade (GO:0000165)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of protein complex assembly (GO:0031333)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of cell differentiation (GO:0045595)|regulation of cell motility (GO:2000145)|regulation of Rho protein signal transduction (GO:0035023)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.L86L(1)	ESRP1/RAF1(4)|RAF1/DAZL(2)|SRGAP3/RAF1(6)	biliary_tract(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)	32					Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)	CCCTCACCTTGAGTGCTTTCA	0.483			T	SRGAP3	pilocytic astrocytoma				Noonan syndrome																													uc003bxf.3				Dom	yes		3	3p25	5894	T	v-raf-1 murine leukemia viral oncogene homolog 1			M	SRGAP3		pilocytic astrocytoma	ESRP1/RAF1(4)|SRGAP3/RAF1(4)	1	Substitution - coding silent(1)		lung(1)	central_nervous_system(4)|prostate(4)|lung(2)|upper_aerodigestive_tract(1)|stomach(1)|liver(1)|ovary(1)	14						c.(256-258)CTC>CTG		v-raf-1 murine leukemia viral oncogene homolog	Sorafenib(DB00398)						172.0	161.0	165.0					3																	12653511		2203	4300	6503	SO:0001819	synonymous_variant	5894	Noonan_syndrome	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	activation of MAPKK activity|apoptosis|axon guidance|cell proliferation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|negative regulation of apoptosis|negative regulation of cell proliferation|negative regulation of protein complex assembly|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of peptidyl-serine phosphorylation|Ras protein signal transduction|synaptic transmission	cytosol|mitochondrial outer membrane|plasma membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|receptor signaling protein activity	g.chr3:12653511G>C	X03484	CCDS2612.1	3p25	2014-09-17	2014-06-26		ENSG00000132155	ENSG00000132155			9829	protein-coding gene	gene with protein product	"""C-Raf proto-oncogene, serine/threonine kinase"""	164760	"""v-raf-1 murine leukemia viral oncogene homolog 1"""			1611909	Standard	NM_002880		Approved	Raf-1, c-Raf, CRAF	uc003bxf.4	P04049	OTTHUMG00000129789	ENST00000251849.4:c.258C>G	3.37:g.12653511G>C						RAF1_uc011aut.1_5'Flank|RAF1_uc011auu.1_Intron	p.L86L	NM_002880	NP_002871	P04049	RAF1_HUMAN			3	673	-			86			RBD.		B0LPH8|B2R5N3|Q15278|Q9UC20	Silent	SNP	ENST00000251849.4	37	c.258C>G	CCDS2612.1																																																																																				PASS	0.483	RAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252015.2	NM_002880		151	186	151	186	---	---	---	---
DHX30	22907	broad.mit.edu	37	3	47884701	47884701	+	Missense_Mutation	SNP	G	G	C			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr3:47884701G>C	ENST00000445061.1	+	9	1302	c.895G>C	c.(895-897)Gag>Cag	p.E299Q	DHX30_ENST00000348968.4_Missense_Mutation_p.E271Q|DHX30_ENST00000457607.1_Missense_Mutation_p.E327Q|DHX30_ENST00000446256.2_Missense_Mutation_p.E260Q	NM_138615.2	NP_619520.1	Q7L2E3	DHX30_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 30	299						cytoplasm (GO:0005737)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)	p.E299Q(1)		endometrium(3)|kidney(1)|large_intestine(11)|lung(13)|ovary(4)|pancreas(1)|prostate(1)|skin(3)	37				BRCA - Breast invasive adenocarcinoma(193;0.000696)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)		CCGCAAAGCAGAGGCTGAGAA	0.567																																						uc003cru.2																			1	Substitution - Missense(1)		lung(1)	ovary(2)|skin(2)	4						c.(895-897)GAG>CAG		DEAH (Asp-Glu-Ala-His) box polypeptide 30							87.0	79.0	82.0					3																	47884701		2203	4300	6503	SO:0001583	missense	22907					mitochondrial nucleoid	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding	g.chr3:47884701G>C	AB020697	CCDS2759.1	3p24.3-p22.1	2013-07-16	2013-07-16	2003-06-13	ENSG00000132153	ENSG00000132153		"""DEAH-boxes"""	16716	protein-coding gene	gene with protein product			"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 30"", ""DEAH (Asp-Glu-Ala-His) box polypeptide 30"""	DDX30		10048485, 18022663	Standard	NM_138615		Approved	KIAA0890, FLJ11214	uc003cru.3	Q7L2E3	OTTHUMG00000133522	ENST00000445061.1:c.895G>C	3.37:g.47884701G>C	ENSP00000405620:p.Glu299Gln					DHX30_uc003crt.2_Missense_Mutation_p.E260Q|DHX30_uc010hjr.1_Missense_Mutation_p.E327Q	p.E299Q	NM_138615	NP_619520	Q7L2E3	DHX30_HUMAN		BRCA - Breast invasive adenocarcinoma(193;0.000696)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)	9	1321	+			299					A8K5F1|O94965|Q7Z753|Q96CH4|Q9NUQ0	Missense_Mutation	SNP	ENST00000445061.1	37	c.895G>C	CCDS2759.1	.	.	.	.	.	.	.	.	.	.	G	17.37	3.372645	0.61624	.	.	ENSG00000132153	ENST00000446256;ENST00000445061;ENST00000348968;ENST00000457607	T;T;T;T	0.03607	3.9;3.88;3.89;3.87	5.4	4.47	0.54385	.	0.295763	0.35124	N	0.003423	T	0.06050	0.0157	L	0.48642	1.525	0.46028	D	0.99882	P;P	0.50528	0.894;0.936	B;P	0.45099	0.368;0.469	T	0.40608	-0.9554	10	0.40728	T	0.16	.	14.0156	0.64523	0.0:0.0:0.8484:0.1516	.	299;260	Q7L2E3;Q7L2E3-3	DHX30_HUMAN;.	Q	260;299;271;327	ENSP00000392601:E260Q;ENSP00000405620:E299Q;ENSP00000343442:E271Q;ENSP00000394682:E327Q	ENSP00000343442:E271Q	E	+	1	0	DHX30	47859705	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.535000	0.53575	2.539000	0.85634	0.591000	0.81541	GAG		PASS	0.567	DHX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257495.2	NM_138615		73	90	73	90	---	---	---	---
MAP4	4134	broad.mit.edu	37	3	47958284	47958284	+	Missense_Mutation	SNP	C	C	T			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr3:47958284C>T	ENST00000360240.6	-	7	1551	c.1033G>A	c.(1033-1035)Gcc>Acc	p.A345T	MAP4_ENST00000426837.2_Missense_Mutation_p.A362T|MAP4_ENST00000383737.4_Intron|MAP4_ENST00000395734.3_Missense_Mutation_p.A345T	NM_002375.4	NP_002366.2	P27816	MAP4_HUMAN	microtubule-associated protein 4	345	17 X 14 AA tandem repeats.				cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|microtubule sliding (GO:0051012)|mitotic spindle organization (GO:0007052)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|microtubule cytoskeleton (GO:0015630)|mitotic spindle (GO:0072686)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)	p.A345T(2)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(2)|pancreas(1)|skin(2)	32				BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)	Docetaxel(DB01248)|Paclitaxel(DB01229)	ACATCCTTGGCTGGGGCTACC	0.473																																						uc003csb.2																			2	Substitution - Missense(2)		lung(2)	ovary(2)|pancreas(1)	3						c.(1033-1035)GCC>ACC		microtubule-associated protein 4 isoform 1							230.0	219.0	222.0					3																	47958284		2203	4300	6503	SO:0001583	missense	4134				negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	protein binding|structural molecule activity	g.chr3:47958284C>T		CCDS33750.1, CCDS46818.1, CCDS46821.1	3p21	2008-07-18			ENSG00000047849	ENSG00000047849			6862	protein-coding gene	gene with protein product		157132				1905296	Standard	NM_002375		Approved		uc003csb.2	P27816	OTTHUMG00000156828	ENST00000360240.6:c.1033G>A	3.37:g.47958284C>T	ENSP00000353375:p.Ala345Thr					MAP4_uc003csc.3_Missense_Mutation_p.A345T|MAP4_uc011bbf.1_Missense_Mutation_p.A322T|MAP4_uc003csf.3_Missense_Mutation_p.A362T	p.A345T	NM_002375	NP_002366	P27816	MAP4_HUMAN		BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)	7	1559	-			345			7.|17 X 14 AA tandem repeats.		Q13082|Q59FT2|Q68D74|Q6ZUW9|Q86V26|Q96A76|Q96NS9	Missense_Mutation	SNP	ENST00000360240.6	37	c.1033G>A	CCDS33750.1	.	.	.	.	.	.	.	.	.	.	C	12.27	1.889004	0.33348	.	.	ENSG00000047849	ENST00000395734;ENST00000426837;ENST00000360240	T;T;T	0.07567	3.18;3.2;3.18	5.17	1.13	0.20643	.	.	.	.	.	T	0.15176	0.0366	M	0.76574	2.34	0.09310	N	1	P;D;P	0.54207	0.807;0.965;0.594	B;P;B	0.49887	0.256;0.625;0.164	T	0.13282	-1.0515	9	0.33141	T	0.24	-0.0695	8.2271	0.31575	0.411:0.3215:0.2675:0.0	.	322;345;345	C9JFC3;P27816-6;P27816	.;.;MAP4_HUMAN	T	345;362;345	ENSP00000379083:A345T;ENSP00000407602:A362T;ENSP00000353375:A345T	ENSP00000353375:A345T	A	-	1	0	MAP4	47933288	0.001000	0.12720	0.004000	0.12327	0.008000	0.06430	0.203000	0.17315	0.013000	0.14918	-1.014000	0.02459	GCC		PASS	0.473	MAP4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346085.1	NM_002375		216	275	216	275	---	---	---	---
BAP1	8314	broad.mit.edu	37	3	52440372	52440372	+	Missense_Mutation	SNP	C	C	T			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr3:52440372C>T	ENST00000460680.1	-	9	1151	c.680G>A	c.(679-681)cGc>cAc	p.R227H	BAP1_ENST00000296288.5_Intron	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	0					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R227H(2)		NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		CAGGTTGAAGCGGATGTCGTG	0.627			"""N, Mis, F, S, O"""		"""uveal melanoma, breast, NSCLC, RCC"""	"""mesothelioma, uveal melanoma"""																															GBM(101;493 1458 7992 21037 25532)	uc003ddx.2				Rec	yes		3	3p21.31-p21.2	8314	N|Mis|F|S|O	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)			E			uveal melanoma|breast|NSCLC		2	Substitution - Missense(2)	p.R227C(1)	lung(1)|prostate(1)	pleura(32)|eye(28)|lung(2)|ovary(2)|breast(1)	65						c.(679-681)CGC>CAC		BRCA1 associated protein-1							91.0	71.0	78.0					3																	52440372		2203	4300	6503	SO:0001583	missense	8314				monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|PR-DUB complex	chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity	g.chr3:52440372C>T	AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.680G>A	3.37:g.52440372C>T	ENSP00000417132:p.Arg227His					BAP1_uc003ddw.2_5'Flank|BAP1_uc010hmg.2_5'Flank|BAP1_uc010hmh.2_5'Flank	p.R227H	NM_004656	NP_004647	Q92560	BAP1_HUMAN		BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)	9	795	-			227					B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Missense_Mutation	SNP	ENST00000460680.1	37	c.680G>A	CCDS2853.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.640437	0.87859	.	.	ENSG00000163930	ENST00000460680	T	0.48201	0.82	6.04	6.04	0.98038	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (2);	0.000000	0.85682	D	0.000000	T	0.63343	0.2503	M	0.73217	2.22	0.80722	D	1	D	0.60160	0.987	P	0.53401	0.725	T	0.61787	-0.6991	10	0.48119	T	0.1	-4.619	20.5891	0.99427	0.0:1.0:0.0:0.0	.	227	Q92560	BAP1_HUMAN	H	227	ENSP00000417132:R227H	ENSP00000417132:R227H	R	-	2	0	BAP1	52415412	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.783000	0.85696	2.876000	0.98609	0.650000	0.86243	CGC		PASS	0.627	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			22	23	22	23	---	---	---	---
HLTF	6596	broad.mit.edu	37	3	148777580	148777580	+	Missense_Mutation	SNP	C	C	A	rs554357628		TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr3:148777580C>A	ENST00000310053.5	-	13	1493	c.1300G>T	c.(1300-1302)Gtt>Ttt	p.V434F	HLTF_ENST00000392912.2_Missense_Mutation_p.V434F|HLTF_ENST00000494055.1_Missense_Mutation_p.V434F|HLTF_ENST00000465259.1_Missense_Mutation_p.V433F	NM_003071.3|NM_139048.2	NP_003062.2|NP_620636.1	Q14527	HLTF_HUMAN	helicase-like transcription factor	434					chromatin modification (GO:0016568)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.V434F(1)		breast(2)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			TCTTCTATAACCTTAGAAGAT	0.318																																						uc003ewq.1																			1	Substitution - Missense(1)		lung(1)	ovary(1)	1						c.(1300-1302)GTT>TTT		helicase-like transcription factor							87.0	92.0	90.0					3																	148777580		2203	4286	6489	SO:0001583	missense	6596				chromatin modification|transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding	g.chr3:148777580C>A	L34673	CCDS33875.1	3q25.1-q26.1	2006-11-09	2006-11-09	2006-11-09	ENSG00000071794	ENSG00000071794		"""RING-type (C3HC4) zinc fingers"""	11099	protein-coding gene	gene with protein product		603257	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 3"""	SNF2L3, SMARCA3		7558014	Standard	NM_139048		Approved	HIP116A, HLTF1, RNF80	uc003ewr.1	Q14527	OTTHUMG00000159534	ENST00000310053.5:c.1300G>T	3.37:g.148777580C>A	ENSP00000308944:p.Val434Phe					HLTF_uc003ewr.1_Missense_Mutation_p.V434F|HLTF_uc003ews.1_Missense_Mutation_p.V433F|HLTF_uc010hve.1_Missense_Mutation_p.V433F	p.V434F	NM_139048	NP_620636	Q14527	HLTF_HUMAN	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		13	1518	-			434					D3DNH3|Q14536|Q16051|Q7KYJ6|Q86YA5|Q92652|Q96KM9	Missense_Mutation	SNP	ENST00000310053.5	37	c.1300G>T	CCDS33875.1	.	.	.	.	.	.	.	.	.	.	C	7.506	0.653572	0.14580	.	.	ENSG00000071794	ENST00000465259;ENST00000310053;ENST00000392912;ENST00000494055;ENST00000416117	D;D;D;D	0.89875	-2.58;-2.56;-2.56;-2.56	5.6	1.75	0.24633	DEAD-like helicase (1);	.	.	.	.	T	0.74076	0.3669	N	0.14661	0.345	0.23186	N	0.998153	P;P;P	0.38335	0.627;0.627;0.627	B;B;B	0.33799	0.17;0.17;0.17	T	0.61642	-0.7021	9	0.08599	T	0.76	-1.3098	8.7357	0.34528	0.0:0.628:0.0:0.372	.	434;434;434	Q59GQ7;A8K5B6;Q14527	.;.;HLTF_HUMAN	F	433;434;434;434;431	ENSP00000420745:V433F;ENSP00000308944:V434F;ENSP00000376644:V434F;ENSP00000420429:V434F	ENSP00000308944:V434F	V	-	1	0	HLTF	150260270	0.006000	0.16342	0.633000	0.29310	0.227000	0.25037	-0.002000	0.12924	0.027000	0.15297	0.655000	0.94253	GTT		PASS	0.318	HLTF-003	KNOWN	alternative_3_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356064.1			69	118	69	118	---	---	---	---
SLC33A1	9197	broad.mit.edu	37	3	155560270	155560270	+	Missense_Mutation	SNP	A	A	G			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr3:155560270A>G	ENST00000392845.3	-	2	1294	c.914T>C	c.(913-915)aTa>aCa	p.I305T	SLC33A1_ENST00000460729.1_5'Flank|SLC33A1_ENST00000359479.3_Missense_Mutation_p.I305T			O00400	ACATN_HUMAN	solute carrier family 33 (acetyl-CoA transporter), member 1	305					acetyl-CoA transport (GO:0015876)|cell death (GO:0008219)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	acetyl-CoA transporter activity (GO:0008521)	p.I305T(1)		endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	22			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			TGGCATTTTTATAATTGCAAA	0.313																																						uc003fan.3																			1	Substitution - Missense(1)		lung(1)	ovary(2)|large_intestine(1)|pancreas(1)	4						c.(913-915)ATA>ACA		acetyl-coenzyme A transporter							81.0	73.0	76.0					3																	155560270		2202	4299	6501	SO:0001583	missense	9197				cell death|transmembrane transport	endoplasmic reticulum membrane|Golgi membrane|integral to plasma membrane|membrane fraction	acetyl-CoA transporter activity	g.chr3:155560270A>G	D88152	CCDS3173.1	3q25.31	2013-05-22		2002-12-06	ENSG00000169359	ENSG00000169359		"""Solute carriers"""	95	protein-coding gene	gene with protein product		603690	"""acetyl-Coenzyme A transporter"", ""spastic paraplegia 42 (autosomal dominant)"""	ACATN, SPG42		9096318, 19061983	Standard	NM_004733		Approved	AT-1, AT1	uc003fao.2	O00400	OTTHUMG00000158481	ENST00000392845.3:c.914T>C	3.37:g.155560270A>G	ENSP00000376587:p.Ile305Thr					SLC33A1_uc003fao.1_Missense_Mutation_p.I305T	p.I305T	NM_004733	NP_004724	O00400	ACATN_HUMAN	Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)		2	1295	-			305			Helical; (Potential).		B2R5Q2|D3DNK4	Missense_Mutation	SNP	ENST00000392845.3	37	c.914T>C	CCDS3173.1	.	.	.	.	.	.	.	.	.	.	A	16.68	3.191031	0.58017	.	.	ENSG00000169359	ENST00000392845;ENST00000359479;ENST00000496772	T;T;T	0.81330	-1.48;-1.48;0.37	5.55	5.55	0.83447	Major facilitator superfamily domain, general substrate transporter (1);	0.315375	0.39274	N	0.001417	T	0.80523	0.4639	M	0.68317	2.08	0.58432	D	0.999992	B	0.17268	0.021	B	0.24848	0.056	T	0.76913	-0.2783	10	0.44086	T	0.13	-6.5037	15.7462	0.77944	1.0:0.0:0.0:0.0	.	305	O00400	ACATN_HUMAN	T	305;305;42	ENSP00000376587:I305T;ENSP00000352456:I305T;ENSP00000419165:I42T	ENSP00000352456:I305T	I	-	2	0	SLC33A1	157042964	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	8.832000	0.92079	2.122000	0.65172	0.374000	0.22700	ATA		PASS	0.313	SLC33A1-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351130.3	NM_004733		55	57	55	57	---	---	---	---
SI	6476	broad.mit.edu	37	3	164767660	164767660	+	Missense_Mutation	SNP	T	T	C			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr3:164767660T>C	ENST00000264382.3	-	14	1578	c.1516A>G	c.(1516-1518)Atg>Gtg	p.M506V		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	506	Isomaltase.				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)	p.M506V(1)		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)	ACTTCATTCATGTCCTGAATG	0.284										HNSCC(35;0.089)																												uc003fei.2																			1	Substitution - Missense(1)		lung(1)	ovary(7)|upper_aerodigestive_tract(4)|skin(2)|pancreas(1)	14						c.(1516-1518)ATG>GTG		sucrase-isomaltase	Acarbose(DB00284)						78.0	85.0	83.0					3																	164767660		2202	4281	6483	SO:0001583	missense	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.chr3:164767660T>C	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.1516A>G	3.37:g.164767660T>C	ENSP00000264382:p.Met506Val	HNSCC(35;0.089)					p.M506V	NM_001041	NP_001032	P14410	SUIS_HUMAN			14	1578	-		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)	506			Lumenal.|Isomaltase.		A2RUC3|Q1JQ80|Q1RMC2	Missense_Mutation	SNP	ENST00000264382.3	37	c.1516A>G	CCDS3196.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.941610	0.73557	.	.	ENSG00000090402	ENST00000264382	D	0.92545	-3.06	5.58	5.58	0.84498	Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	D	0.96100	0.8729	H	0.97158	3.95	0.53005	D	0.999968	P	0.46987	0.888	P	0.48795	0.59	D	0.97178	0.9849	10	0.87932	D	0	.	14.9328	0.70929	0.0:0.0:0.0:1.0	.	506	P14410	SUIS_HUMAN	V	506	ENSP00000264382:M506V	ENSP00000264382:M506V	M	-	1	0	SI	166250354	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.408000	0.80041	2.119000	0.64992	0.477000	0.44152	ATG		PASS	0.284	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041		59	82	59	82	---	---	---	---
PIK3CA	5290	broad.mit.edu	37	3	178936070	178936070	+	Missense_Mutation	SNP	G	G	A			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr3:178936070G>A	ENST00000263967.3	+	10	1769	c.1612G>A	c.(1612-1614)Gat>Aat	p.D538N		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	538	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.D538N(4)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TTCTACACGAGATCCTCTCTC	0.333		57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)	uc003fjk.2		57		Dom	yes		3	3q26.3	5290	Mis	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			"""E, O"""			colorectal|gastric|gliobastoma|breast		4	Substitution - Missense(4)	p.D538G(1)|p.D538N(1)	lung(2)|soft_tissue(1)|skin(1)	breast(1564)|large_intestine(776)|endometrium(246)|urinary_tract(195)|ovary(141)|skin(112)|stomach(98)|thyroid(77)|central_nervous_system(69)|lung(65)|upper_aerodigestive_tract(58)|haematopoietic_and_lymphoid_tissue(27)|cervix(25)|biliary_tract(22)|liver(20)|oesophagus(17)|pancreas(11)|penis(8)|pituitary(8)|autonomic_ganglia(4)|prostate(3)|kidney(2)|meninges(1)|eye(1)|NS(1)|soft_tissue(1)|bone(1)	3553						c.(1612-1614)GAT>AAT		phosphoinositide-3-kinase, catalytic, alpha							50.0	51.0	51.0					3																	178936070		1806	4068	5874	SO:0001583	missense	5290				epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway		1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity	g.chr3:178936070G>A		CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1612G>A	3.37:g.178936070G>A	ENSP00000263967:p.Asp538Asn	HNSCC(19;0.045)|TSP Lung(28;0.18)					p.D538N	NM_006218	NP_006209	P42336	PK3CA_HUMAN	OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		10	1769	+	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		538			PI3K helical.		Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	c.1612G>A	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	G	35	5.494593	0.96339	.	.	ENSG00000121879	ENST00000263967	T	0.71579	-0.58	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.85410	0.5690	M	0.78456	2.415	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85748	0.1341	10	0.62326	D	0.03	-7.9654	20.0024	0.97423	0.0:0.0:1.0:0.0	.	538	P42336	PK3CA_HUMAN	N	538	ENSP00000263967:D538N	ENSP00000263967:D538N	D	+	1	0	PIK3CA	180418764	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	9.476000	0.97823	2.722000	0.93159	0.467000	0.42956	GAT		PASS	0.333	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			45	53	45	53	---	---	---	---
PIK3CA	5290	broad.mit.edu	37	3	178936082	178936082	+	Missense_Mutation	SNP	G	G	A	rs121913273		TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr3:178936082G>A	ENST00000263967.3	+	10	1781	c.1624G>A	c.(1624-1626)Gaa>Aaa	p.E542K		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	542	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.		E -> K (in CLOVE, KERSEB, CRC and BC; also found in glioblastoma multiforme and endometrial carcinoma; shows an increase in lipid kinase activity; oncogenic in vivo; occurs in the interface between the PI3K helical domain and the nSH2 (N- terminal SH2) region of the p85 regulatory subunit and may reduce the inhibitory effect of p85; requires interaction with RAS to induce cellular transformation). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15924253, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22658544}.|E -> Q (found in an endometrial carcinoma sample; unknown pathological significance). {ECO:0000269|PubMed:16322209}.|E -> V (in BC; unknown pathological significance). {ECO:0000269|PubMed:16353168}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.E542K(545)|p.E542Q(10)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TCCTCTCTCTGAAATCACTGA	0.333	E542K(BT483_BREAST)|E542K(CAL51_BREAST)|E542K(HGC27_STOMACH)|E542K(IM95_STOMACH)|E542K(JHUEM1_ENDOMETRIUM)|E542K(NCIH1341_LUNG)|E542K(SW948_LARGE_INTESTINE)|E542K(T84_LARGE_INTESTINE)|E542K(VMCUB1_URINARY_TRACT)	57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)	uc003fjk.2	E542K(SW948_LARGE_INTESTINE)|E542K(T84_LARGE_INTESTINE)|E542K(CAL51_BREAST)|E542K(JHUEM1_ENDOMETRIUM)|E542K(NCIH1341_LUNG)|E542K(VMCUB1_URINARY_TRACT)|E542K(BT483_BREAST)|E542K(HGC27_STOMACH)|E542K(IM95_STOMACH)	57		Dom	yes		3	3q26.3	5290	Mis	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			"""E, O"""			colorectal|gastric|gliobastoma|breast		555	Substitution - Missense(555)	p.E542K(481)|p.E542V(8)|p.E542Q(6)|p.E542G(1)	breast(176)|large_intestine(166)|urinary_tract(45)|endometrium(37)|skin(19)|lung(18)|stomach(16)|ovary(16)|thyroid(14)|upper_aerodigestive_tract(9)|central_nervous_system(7)|cervix(6)|liver(6)|oesophagus(5)|penis(4)|kidney(3)|soft_tissue(2)|haematopoietic_and_lymphoid_tissue(2)|prostate(2)|biliary_tract(1)|pituitary(1)	breast(1564)|large_intestine(776)|endometrium(246)|urinary_tract(195)|ovary(141)|skin(112)|stomach(98)|thyroid(77)|central_nervous_system(69)|lung(65)|upper_aerodigestive_tract(58)|haematopoietic_and_lymphoid_tissue(27)|cervix(25)|biliary_tract(22)|liver(20)|oesophagus(17)|pancreas(11)|penis(8)|pituitary(8)|autonomic_ganglia(4)|prostate(3)|kidney(2)|meninges(1)|eye(1)|NS(1)|soft_tissue(1)|bone(1)	3553						c.(1624-1626)GAA>AAA		phosphoinositide-3-kinase, catalytic, alpha							56.0	56.0	56.0					3																	178936082		1809	4069	5878	SO:0001583	missense	5290				epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway		1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity	g.chr3:178936082G>A		CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1624G>A	3.37:g.178936082G>A	ENSP00000263967:p.Glu542Lys	HNSCC(19;0.045)|TSP Lung(28;0.18)					p.E542K	NM_006218	NP_006209	P42336	PK3CA_HUMAN	OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		10	1781	+	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		542		E -> V (in cancer).|E -> K (in KERSEB; shows an increase in lipid kinase activity; oncogenic in vivo; occurs in the interface between the PI3K helical domain and the nSH2 (N-terminal SH2) region of the p85 regulatory subunit and may reduce the inhibitory effect of p85; requires interaction with RAS to induce cellular transformation).|E -> Q (in cancer).	PI3K helical.		Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	c.1624G>A	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	G	34	5.360420	0.95877	.	.	ENSG00000121879	ENST00000263967	T	0.62105	0.05	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.69287	0.3094	L	0.41356	1.27	0.80722	D	1	D	0.65815	0.995	D	0.63192	0.912	T	0.60296	-0.7291	10	0.09843	T	0.71	-23.9623	20.0024	0.97423	0.0:0.0:1.0:0.0	.	542	P42336	PK3CA_HUMAN	K	542	ENSP00000263967:E542K	ENSP00000263967:E542K	E	+	1	0	PIK3CA	180418776	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.476000	0.97823	2.722000	0.93159	0.467000	0.42956	GAA		PASS	0.333	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			48	60	48	60	---	---	---	---
ATP13A5	344905	broad.mit.edu	37	3	193039551	193039551	+	Nonsense_Mutation	SNP	G	G	A	rs139981143		TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr3:193039551G>A	ENST00000342358.4	-	16	1951	c.1834C>T	c.(1834-1836)Cag>Tag	p.Q612*		NM_198505.2	NP_940907.2	Q4VNC0	AT135_HUMAN	ATPase type 13A5	612						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)	p.Q612*(1)		NS(1)|autonomic_ganglia(2)|breast(1)|endometrium(6)|kidney(4)|large_intestine(15)|liver(2)|lung(26)|ovary(5)|prostate(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)		CCAGCTAGCTGAGCGATCACG	0.502																																						uc011bsq.1																			1	Substitution - Nonsense(1)		lung(1)	ovary(5)|skin(4)|large_intestine(2)	11						c.(1834-1836)CAG>TAG		ATPase type 13A5		G	stop/GLN	1,4405	2.1+/-5.4	0,1,2202	97.0	92.0	93.0		1834	4.0	0.4	3	dbSNP_134	93	0,8600	1.2+/-3.3	0,0,4300	yes	stop-gained	ATP13A5	NM_198505.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		612/1219	193039551	1,13005	2203	4300	6503	SO:0001587	stop_gained	344905				ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding	g.chr3:193039551G>A	AK122613	CCDS33914.1	3q29	2010-04-20			ENSG00000187527	ENSG00000187527		"""ATPases / P-type"""	31789	protein-coding gene	gene with protein product							Standard	NM_198505		Approved	FLJ16025	uc011bsq.2	Q4VNC0	OTTHUMG00000156101	ENST00000342358.4:c.1834C>T	3.37:g.193039551G>A	ENSP00000341942:p.Gln612*						p.Q612*	NM_198505	NP_940907	Q4VNC0	AT135_HUMAN	OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)	16	1834	-	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		612					Q6UWS4|Q6ZWL0	Nonsense_Mutation	SNP	ENST00000342358.4	37	c.1834C>T	CCDS33914.1	.	.	.	.	.	.	.	.	.	.	G	36	5.851007	0.97023	2.27E-4	0.0	ENSG00000187527	ENST00000342358	.	.	.	5.82	4.03	0.46877	.	0.579783	0.17642	N	0.166987	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09590	T	0.72	0.4101	10.6355	0.45563	0.0721:0.133:0.7948:0.0	.	.	.	.	X	612	.	ENSP00000341942:Q612X	Q	-	1	0	ATP13A5	194522245	0.974000	0.33945	0.365000	0.25901	0.069000	0.16628	2.388000	0.44398	0.799000	0.34018	0.655000	0.94253	CAG		PASS	0.502	ATP13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343012.1	NM_198505		61	72	61	72	---	---	---	---
FGFR3	2261	broad.mit.edu	37	4	1803564	1803564	+	Missense_Mutation	SNP	C	C	T	rs121913482		TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr4:1803564C>T	ENST00000260795.2	+	6	844	c.742C>T	c.(742-744)Cgc>Tgc	p.R248C	FGFR3_ENST00000352904.1_Missense_Mutation_p.R248C|FGFR3_ENST00000474521.1_3'UTR|FGFR3_ENST00000481110.2_Missense_Mutation_p.R248C|FGFR3_ENST00000340107.4_Missense_Mutation_p.R248C|FGFR3_ENST00000412135.2_Missense_Mutation_p.R248C|FGFR3_ENST00000440486.2_Missense_Mutation_p.R248C			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	248			R -> C (in KERSEB, bladder cancer, keratinocytic non-epidermolytic nevus and TD1; severe and lethal; also found as somatic mutation in one patient with multiple myeloma; constitutive dimerization and kinase activation). {ECO:0000269|PubMed:10360402, ECO:0000269|PubMed:10471491, ECO:0000269|PubMed:11529856, ECO:0000269|PubMed:15772091, ECO:0000269|PubMed:16841094, ECO:0000269|PubMed:7773297, ECO:0000269|PubMed:8845844}.		alveolar secondary septum development (GO:0061144)|axonogenesis involved in innervation (GO:0060385)|bone maturation (GO:0070977)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cell-cell signaling (GO:0007267)|central nervous system myelination (GO:0022010)|chondrocyte differentiation (GO:0002062)|chondrocyte proliferation (GO:0035988)|cochlea development (GO:0090102)|digestive tract morphogenesis (GO:0048546)|endochondral bone growth (GO:0003416)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell fate commitment (GO:0072148)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor apoptotic signaling pathway (GO:1902178)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade (GO:0007259)|lens fiber cell development (GO:0070307)|lens morphogenesis in camera-type eye (GO:0002089)|MAPK cascade (GO:0000165)|morphogenesis of an epithelium (GO:0002009)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of developmental growth (GO:0048640)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|protein tyrosine kinase activity (GO:0004713)	p.R248C(241)|p.R248_S249del(1)|p.R248_S249insC(1)		NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607)	3091		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)|Pazopanib(DB06589)|Ponatinib(DB08901)	CCCCACAGAGCGCTCCCCGCA	0.741		1	"""Mis, T"""	"""IGH@, ETV6"""	"""bladder, MM, T-cell lymphoma"""		"""Hypochondroplasia, Thanatophoric dysplasia"""		Saethre-Chotzen syndrome;Muenke syndrome																													uc003gdr.3		1		Dom	yes		4	4p16.3	2261	Mis|T	fibroblast growth factor receptor 3	yes	Hypochondroplasia|Thanatophoric dysplasia	"""L, E"""	IGH@|ETV6		bladder|MM|T-cell lymphoma		243	Substitution - Missense(241)|Insertion - In frame(1)|Deletion - In frame(1)	p.R248C(291)|p.R248_S249insC(2)|p.R248_S249del(1)	urinary_tract(168)|skin(70)|haematopoietic_and_lymphoid_tissue(2)|lung(2)|upper_aerodigestive_tract(1)	urinary_tract(2177)|skin(314)|upper_aerodigestive_tract(57)|haematopoietic_and_lymphoid_tissue(24)|prostate(9)|cervix(6)|central_nervous_system(4)|large_intestine(3)|lung(3)|testis(2)|pancreas(1)	2600	GRCh37	CM950469	FGFR3	M	rs121913482	c.(742-744)CGC>TGC		fibroblast growth factor receptor 3 isoform 1	Palifermin(DB00039)						13.0	15.0	14.0					4																	1803564		2180	4268	6448	SO:0001583	missense	2261	Muenke_syndrome|Saethre-Chotzen_syndrome	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	bone maturation|cell growth|insulin receptor signaling pathway|JAK-STAT cascade|MAPKKK cascade|negative regulation of developmental growth|positive regulation of cell proliferation	integral to plasma membrane	ATP binding|fibroblast growth factor binding|fibroblast growth factor receptor activity|identical protein binding	g.chr4:1803564C>T	M64347	CCDS3353.1, CCDS3354.1, CCDS54706.1	4p16.3	2013-01-11	2008-08-01		ENSG00000068078	ENSG00000068078		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3690	protein-coding gene	gene with protein product		134934	"""achondroplasia, thanatophoric dwarfism"""	ACH		1847508	Standard	NM_000142		Approved	CEK2, JTK4, CD333	uc003gdu.2	P22607	OTTHUMG00000121148	ENST00000260795.2:c.742C>T	4.37:g.1803564C>T	ENSP00000260795:p.Arg248Cys					FGFR3_uc003gdu.2_Missense_Mutation_p.R248C|FGFR3_uc003gds.3_Missense_Mutation_p.R248C|FGFR3_uc003gdq.3_Missense_Mutation_p.R248C|FGFR3_uc010icb.1_Missense_Mutation_p.R90C|FGFR3_uc003gdt.1_Missense_Mutation_p.R90C	p.R248C	NM_000142	NP_000133	P22607	FGFR3_HUMAN	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		7	998	+		Breast(71;0.212)|all_epithelial(65;0.241)	248		R -> C (in KERSEB, bladder cancer, keratinocytic non-epidermolytic nevus and TD1; severe and lethal; also found as somatic mutation in one patient with multiple myeloma).	Extracellular (Potential).		D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Missense_Mutation	SNP	ENST00000260795.2	37	c.742C>T	CCDS3353.1	.	.	.	.	.	.	.	.	.	.	c	16.88	3.244004	0.58995	.	.	ENSG00000068078	ENST00000481110;ENST00000340107;ENST00000440486;ENST00000412135;ENST00000260795;ENST00000352904;ENST00000507588	D;T;T;T;T;T;T	0.83075	-1.68;-1.44;-1.44;-1.39;-1.44;-1.39;-1.37	3.93	3.0	0.34707	.	0.126462	0.53938	N	0.000041	D	0.93719	0.7993	H	0.97465	4.01	0.46499	A	0.999078	D;D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;1.0;1.0	P;D;D;D;D;D	0.91635	0.891;0.982;0.997;0.995;0.959;0.999	D	0.96515	0.9381	9	0.87932	D	0	.	13.5812	0.61905	0.236:0.764:0.0:0.0	.	211;248;248;248;248;248	Q8NI15;P22607-2;P22607-4;P22607-3;P22607;F8W9L4	.;.;.;.;FGFR3_HUMAN;.	C	248;248;248;248;248;248;68	ENSP00000420533:R248C;ENSP00000339824:R248C;ENSP00000414914:R248C;ENSP00000412903:R248C;ENSP00000260795:R248C;ENSP00000231803:R248C;ENSP00000427289:R68C	ENSP00000260795:R248C	R	+	1	0	FGFR3	1773362	1.000000	0.71417	1.000000	0.80357	0.453000	0.32348	2.239000	0.43079	1.898000	0.54952	0.430000	0.28490	CGC		PASS	0.741	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142		8	6	8	6	---	---	---	---
N4BP2	55728	broad.mit.edu	37	4	40122763	40122763	+	Missense_Mutation	SNP	T	T	C			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr4:40122763T>C	ENST00000261435.6	+	9	3448	c.3032T>C	c.(3031-3033)gTa>gCa	p.V1011A		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	1011					nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|endonuclease activity (GO:0004519)	p.V1011A(1)		breast(4)|endometrium(3)|kidney(12)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	60						GGAAAAGAAGTAGGCATGTGC	0.378																																						uc003guy.3																			1	Substitution - Missense(1)		lung(1)	lung(3)|breast(2)|kidney(2)|ovary(1)	8						c.(3031-3033)GTA>GCA		Nedd4 binding protein 2							57.0	57.0	57.0					4																	40122763		2203	4300	6503	SO:0001583	missense	55728					cytoplasm	ATP binding|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity|endonuclease activity|protein binding	g.chr4:40122763T>C	AB037834	CCDS3457.1	4p14	2008-01-18			ENSG00000078177	ENSG00000078177			29851	protein-coding gene	gene with protein product	"""BCL-3 binding protein"""					10718198, 11717310	Standard	NM_018177		Approved	B3BP	uc003guy.4	Q86UW6	OTTHUMG00000128599	ENST00000261435.6:c.3032T>C	4.37:g.40122763T>C	ENSP00000261435:p.Val1011Ala					N4BP2_uc010ifq.2_Missense_Mutation_p.V931A|N4BP2_uc010ifr.2_Missense_Mutation_p.V931A	p.V1011A	NM_018177	NP_060647	Q86UW6	N4BP2_HUMAN			9	3370	+			1011					A0AVR3|Q9NVK2|Q9P2D4	Missense_Mutation	SNP	ENST00000261435.6	37	c.3032T>C	CCDS3457.1	.	.	.	.	.	.	.	.	.	.	T	0.491	-0.875518	0.02550	.	.	ENSG00000078177	ENST00000261435;ENST00000381804	T	0.18810	2.19	6.02	-3.94	0.04130	.	1.957170	0.02089	N	0.053012	T	0.12518	0.0304	L	0.34521	1.04	0.09310	N	1	B;B	0.11235	0.004;0.003	B;B	0.10450	0.005;0.002	T	0.14035	-1.0487	10	0.16420	T	0.52	-0.7984	1.0898	0.01661	0.2177:0.3212:0.2086:0.2525	.	1011;1011	Q86UW6-2;Q86UW6	.;N4BP2_HUMAN	A	1011;931	ENSP00000261435:V1011A	ENSP00000261435:V1011A	V	+	2	0	N4BP2	39799158	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.035000	0.13797	-0.646000	0.05452	-0.313000	0.08912	GTA		PASS	0.378	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177		75	76	75	76	---	---	---	---
ANKRD50	57182	broad.mit.edu	37	4	125593004	125593004	+	Missense_Mutation	SNP	T	T	C			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr4:125593004T>C	ENST00000504087.1	-	4	2465	c.1428A>G	c.(1426-1428)atA>atG	p.I476M	ANKRD50_ENST00000515641.1_Missense_Mutation_p.I297M	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	476								p.I476M(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(14)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	55						TACCATTCCATATCATCCACA	0.413																																						uc003ifg.3																			1	Substitution - Missense(1)		lung(1)	central_nervous_system(1)	1						c.(1426-1428)ATA>ATG		ankyrin repeat domain 50							105.0	104.0	105.0					4																	125593004		2203	4300	6503	SO:0001583	missense	57182							g.chr4:125593004T>C	AB033049	CCDS34060.1, CCDS54802.1	4q28.1	2013-01-10			ENSG00000151458	ENSG00000151458		"""Ankyrin repeat domain containing"""	29223	protein-coding gene	gene with protein product							Standard	NM_020337		Approved	KIAA1223	uc010inw.3	Q9ULJ7	OTTHUMG00000161398	ENST00000504087.1:c.1428A>G	4.37:g.125593004T>C	ENSP00000425658:p.Ile476Met					ANKRD50_uc011cgo.1_Missense_Mutation_p.I297M|ANKRD50_uc010inw.2_Missense_Mutation_p.I476M	p.I476M	NM_020337	NP_065070	Q9ULJ7	ANR50_HUMAN			3	1694	-			476					A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	Missense_Mutation	SNP	ENST00000504087.1	37	c.1428A>G	CCDS34060.1	.	.	.	.	.	.	.	.	.	.	T	11.41	1.631323	0.28978	.	.	ENSG00000151458	ENST00000504087;ENST00000515641	T;T	0.67865	-0.29;-0.25	5.39	-0.0904	0.13665	.	0.168499	0.51477	D	0.000093	T	0.56514	0.1990	L	0.45470	1.425	0.36171	D	0.848744	P	0.45396	0.857	P	0.46758	0.526	T	0.56727	-0.7931	10	0.49607	T	0.09	.	2.8362	0.05516	0.2326:0.0672:0.36:0.3401	.	476	Q9ULJ7	ANR50_HUMAN	M	476;297	ENSP00000425658:I476M;ENSP00000425355:I297M	ENSP00000425658:I476M	I	-	3	3	ANKRD50	125812454	0.599000	0.26891	0.997000	0.53966	0.996000	0.88848	-0.289000	0.08365	-0.114000	0.11936	0.454000	0.30748	ATA		PASS	0.413	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337		129	133	129	133	---	---	---	---
FBXW7	55294	broad.mit.edu	37	4	153249384	153249384	+	Missense_Mutation	SNP	C	C	T			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr4:153249384C>T	ENST00000281708.4	-	9	2623	c.1394G>A	c.(1393-1395)cGt>cAt	p.R465H	FBXW7_ENST00000263981.5_Missense_Mutation_p.R385H|FBXW7_ENST00000296555.5_Missense_Mutation_p.R347H|FBXW7_ENST00000393956.3_Missense_Mutation_p.R289H|FBXW7_ENST00000603548.1_Missense_Mutation_p.R465H|FBXW7_ENST00000603841.1_Missense_Mutation_p.R465H	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	465			R -> C (in a acute lymphoblastic leukemia cell line). {ECO:0000269|PubMed:11565033}.|R -> H (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.R465H(69)|p.R385H(16)|p.R226H(16)|p.R465L(4)|p.R347H(4)|p.R465Y(2)|p.?(1)|p.R385L(1)|p.R226L(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				ATGCATACAACGCACAGTGGA	0.408			"""Mis, N, D, F"""		"""colorectal, endometrial, T-ALL"""																																	uc003ims.2				Rec	yes		4	4q31.3	55294	Mis|N|D|F	"""F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"""			"""E, L"""			colorectal|endometrial|T-ALL		114	Substitution - Missense(113)|Unknown(1)	p.R465C(52)|p.R465H(36)|p.R465L(2)	haematopoietic_and_lymphoid_tissue(40)|large_intestine(39)|endometrium(24)|lung(5)|ovary(4)|cervix(1)|biliary_tract(1)	haematopoietic_and_lymphoid_tissue(125)|large_intestine(99)|stomach(16)|lung(14)|endometrium(13)|ovary(9)|biliary_tract(8)|upper_aerodigestive_tract(5)|central_nervous_system(3)|kidney(3)|skin(3)|pancreas(3)|breast(2)|prostate(2)|cervix(1)|NS(1)|bone(1)	308						c.(1393-1395)CGT>CAT		F-box and WD repeat domain containing 7 isoform							253.0	218.0	230.0					4																	153249384		2203	4300	6503	SO:0001583	missense	55294				interspecies interaction between organisms|lipid homeostasis|negative regulation of DNA endoreduplication|negative regulation of hepatocyte proliferation|negative regulation of Notch signaling pathway|negative regulation of triglyceride biosynthetic process|positive regulation of epidermal growth factor receptor activity|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|protein stabilization|protein ubiquitination|regulation of lipid storage|regulation of protein localization|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|sister chromatid cohesion|vasculature development	nucleolus|nucleolus|nucleoplasm|nucleoplasm|SCF ubiquitin ligase complex	protein binding|protein binding	g.chr4:153249384C>T	AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	16712	protein-coding gene	gene with protein product	"""archipelago homolog (Drosophila)"""	606278	"""F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"", ""F-box and WD repeat domain containing 7"""			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1394G>A	4.37:g.153249384C>T	ENSP00000281708:p.Arg465His					FBXW7_uc011cii.1_Missense_Mutation_p.R465H|FBXW7_uc003imt.2_Missense_Mutation_p.R465H|FBXW7_uc011cih.1_Missense_Mutation_p.R289H|FBXW7_uc003imq.2_Missense_Mutation_p.R385H|FBXW7_uc003imr.2_Missense_Mutation_p.R347H	p.R465H	NM_033632	NP_361014	Q969H0	FBXW7_HUMAN			9	1543	-	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)	465		R -> H (in a colorectal cancer sample; somatic mutation).|R -> C (in a acute lymphoblastic leukemia cell line).	WD 3.		B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	c.1394G>A	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	C	32	5.178201	0.94846	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	6.05	6.05	0.98169	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.63827	0.2544	L	0.56124	1.755	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;1.0;1.0	T	0.62469	-0.6848	10	0.87932	D	0	-17.2313	20.6013	0.99457	0.0:1.0:0.0:0.0	.	289;465;347;385	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	H	465;347;385;289	ENSP00000281708:R465H;ENSP00000296555:R347H;ENSP00000263981:R385H;ENSP00000377528:R289H	ENSP00000263981:R385H	R	-	2	0	FBXW7	153468834	1.000000	0.71417	0.960000	0.40013	0.996000	0.88848	7.818000	0.86416	2.878000	0.98634	0.650000	0.86243	CGT		PASS	0.408	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1			168	235	168	235	---	---	---	---
PCDHA8	56140	broad.mit.edu	37	5	140221266	140221266	+	Silent	SNP	C	C	T			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr5:140221266C>T	ENST00000531613.1	+	1	360	c.360C>T	c.(358-360)gaC>gaT	p.D120D	PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA8_ENST00000378123.3_Silent_p.D120D|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA3_ENST00000522353.2_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	120	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.D120D(2)		NS(2)|breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(31)|ovary(2)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(6)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCATGTGGACGTGGAGGTGA	0.567																																						uc003lhs.2																			2	Substitution - coding silent(2)		lung(2)	upper_aerodigestive_tract(1)|ovary(1)	2						c.(358-360)GAC>GAT		protocadherin alpha 8 isoform 1 precursor							90.0	104.0	99.0					5																	140221266		2203	4300	6503	SO:0001819	synonymous_variant	56140				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding	g.chr5:140221266C>T	AF152486	CCDS54919.1	5q31	2010-11-26				ENSG00000204962		"""Cadherins / Protocadherins : Clustered"""	8674	other	complex locus constituent	"""KIAA0345-like 6"""	606314				10380929	Standard	NM_018911		Approved			Q9Y5H6		ENST00000531613.1:c.360C>T	5.37:g.140221266C>T						PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhr.1_Silent_p.D120D	p.D120D	NM_018911	NP_061734	Q9Y5H6	PCDA8_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		1	360	+			120			Cadherin 1.|Extracellular (Potential).		B9EGT7|O75281	Silent	SNP	ENST00000531613.1	37	c.360C>T	CCDS54919.1																																																																																				PASS	0.567	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911		9	249	9	249	---	---	---	---
NCR2	9436	broad.mit.edu	37	6	41304003	41304003	+	Missense_Mutation	SNP	G	G	C			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr6:41304003G>C	ENST00000373089.5	+	2	319	c.231G>C	c.(229-231)tgG>tgC	p.W77C	NCR2_ENST00000373083.4_Missense_Mutation_p.W77C|NCR2_ENST00000373086.3_Missense_Mutation_p.W77C	NM_004828.3	NP_004819.2	O95944	NCTR2_HUMAN	natural cytotoxicity triggering receptor 2	77	Ig-like.				cellular defense response (GO:0006968)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)	p.W77C(1)		NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	14	Ovarian(28;0.0327)|Colorectal(47;0.196)					CGATGGCTTGGACCTCTCGAT	0.527																																						uc003oqh.2																			1	Substitution - Missense(1)		lung(1)	ovary(1)	1						c.(229-231)TGG>TGC		natural cytotoxicity triggering receptor 2							72.0	69.0	70.0					6																	41304003		2203	4300	6503	SO:0001583	missense	9436				cellular defense response	integral to plasma membrane	transmembrane receptor activity	g.chr6:41304003G>C	AJ225109	CCDS4855.1, CCDS56428.1, CCDS56429.1	6p21.1	2013-01-11	2002-11-13	2002-11-15	ENSG00000096264	ENSG00000096264		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	6732	protein-coding gene	gene with protein product		604531	"""lymphocyte antigen 95 (activating NK-receptor; NK-p44)"""	LY95		10049942	Standard	NM_004828		Approved	NK-p44, CD336	uc003oqh.2	O95944	OTTHUMG00000014678	ENST00000373089.5:c.231G>C	6.37:g.41304003G>C	ENSP00000362181:p.Trp77Cys					NCR2_uc003oqi.2_Missense_Mutation_p.W77C|NCR2_uc003oqj.2_Missense_Mutation_p.W77C	p.W77C	NM_004828	NP_004819	O95944	NCTR2_HUMAN			2	318	+	Ovarian(28;0.0327)|Colorectal(47;0.196)		77			Extracellular (Potential).|Ig-like.		Q9H562|Q9H563|Q9H564|Q9UMT1|Q9UMT2	Missense_Mutation	SNP	ENST00000373089.5	37	c.231G>C	CCDS4855.1	.	.	.	.	.	.	.	.	.	.	G	3.512	-0.099620	0.07010	.	.	ENSG00000096264	ENST00000373083;ENST00000373089;ENST00000373086	T;T;T	0.63913	-0.07;-0.07;-0.07	3.72	-0.239	0.13050	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.18425	0.0442	N	0.19112	0.55	0.09310	N	1	P;P;B	0.35908	0.527;0.527;0.069	B;B;B	0.29598	0.072;0.104;0.017	T	0.08493	-1.0719	9	0.66056	D	0.02	.	3.5983	0.08014	0.3423:0.1916:0.4662:0.0	.	77;77;77	O95944-3;O95944-2;O95944	.;.;NCTR2_HUMAN	C	77	ENSP00000362175:W77C;ENSP00000362181:W77C;ENSP00000362178:W77C	ENSP00000362175:W77C	W	+	3	0	NCR2	41411981	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.108000	0.10857	-0.289000	0.09038	-0.122000	0.15005	TGG		PASS	0.527	NCR2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040511.3			63	57	63	57	---	---	---	---
CUL9	23113	broad.mit.edu	37	6	43189468	43189468	+	Silent	SNP	C	C	G			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr6:43189468C>G	ENST00000252050.4	+	35	6882	c.6798C>G	c.(6796-6798)ctC>ctG	p.L2266L	CUL9_ENST00000372647.2_Silent_p.L2238L|CUL9_ENST00000354495.3_Silent_p.L2156L|RP3-330M21.5_ENST00000500590.1_RNA	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	2266					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)	p.L2266L(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						GGCGCTGCCTCAAGTCCTGGA	0.597																																						uc003ouk.2																			1	Substitution - coding silent(1)		lung(1)	ovary(5)|lung(3)|skin(2)|breast(1)|central_nervous_system(1)	12						c.(6796-6798)CTC>CTG		p53-associated parkin-like cytoplasmic protein							69.0	58.0	62.0					6																	43189468		2203	4300	6503	SO:0001819	synonymous_variant	23113				ubiquitin-dependent protein catabolic process	cullin-RING ubiquitin ligase complex|cytoplasm	ATP binding|ubiquitin protein ligase binding|zinc ion binding	g.chr6:43189468C>G	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"""parkin-like cytoplasmic p53 binding protein"", ""p53-associated parkin-like cytoplasmic protein"""	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.6798C>G	6.37:g.43189468C>G						CUL9_uc003oul.2_Silent_p.L2238L|CUL9_uc010jyk.2_Silent_p.L1418L|CUL9_uc003oun.2_Silent_p.L61L	p.L2266L	NM_015089	NP_055904	Q8IWT3	CUL9_HUMAN			35	6873	+			2266					O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Silent	SNP	ENST00000252050.4	37	c.6798C>G	CCDS4890.1																																																																																				PASS	0.597	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		30	41	30	41	---	---	---	---
DOPEY1	23033	broad.mit.edu	37	6	83863335	83863335	+	Missense_Mutation	SNP	C	C	G			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr6:83863335C>G	ENST00000349129.2	+	31	6495	c.6235C>G	c.(6235-6237)Cac>Gac	p.H2079D	DOPEY1_ENST00000484282.1_3'UTR|DOPEY1_ENST00000369739.3_Missense_Mutation_p.H2070D|DOPEY1_ENST00000237163.5_Missense_Mutation_p.H2009D	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	2079					protein transport (GO:0015031)			p.H2079D(1)		breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(16)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	67		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		CCTCAGAAATCACAGGTACTA	0.308																																						uc003pjs.1																			1	Substitution - Missense(1)		lung(1)	ovary(2)|breast(1)|central_nervous_system(1)	4						c.(6235-6237)CAC>GAC		dopey family member 1							121.0	121.0	121.0					6																	83863335		2203	4300	6503	SO:0001583	missense	23033				protein transport			g.chr6:83863335C>G	AK027030	CCDS4996.1, CCDS64467.1	6q15	2013-03-05	2006-02-02	2006-02-02	ENSG00000083097	ENSG00000083097			21194	protein-coding gene	gene with protein product			"""KIAA1117"""	KIAA1117		16301316, 16303751, 10931277	Standard	NM_015018		Approved	dJ202D23.2	uc011dyy.2	Q5JWR5	OTTHUMG00000016365	ENST00000349129.2:c.6235C>G	6.37:g.83863335C>G	ENSP00000195654:p.His2079Asp					DOPEY1_uc011dyy.1_Missense_Mutation_p.H2070D|DOPEY1_uc010kbl.1_Missense_Mutation_p.H2070D|DOPEY1_uc003pjt.2_RNA	p.H2079D	NM_015018	NP_055833	Q5JWR5	DOP1_HUMAN		BRCA - Breast invasive adenocarcinoma(397;0.053)	31	6495	+		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)	2079					Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Missense_Mutation	SNP	ENST00000349129.2	37	c.6235C>G	CCDS4996.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.507367	0.85282	.	.	ENSG00000083097	ENST00000349129;ENST00000237163;ENST00000369739	T;T	0.26518	1.73;1.86	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	T	0.45054	0.1323	M	0.69523	2.12	0.80722	D	1	D;D;D	0.65815	0.995;0.993;0.995	D;D;D	0.70487	0.969;0.958;0.969	T	0.42275	-0.9461	10	0.72032	D	0.01	.	18.8557	0.92251	0.0:1.0:0.0:0.0	.	1970;2070;2079	E1P545;B2RWN9;Q5JWR5	.;.;DOP1_HUMAN	D	2079;2009;2009	ENSP00000195654:H2079D;ENSP00000237163:H2009D	ENSP00000237163:H2009D	H	+	1	0	DOPEY1	83920054	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.268000	0.78473	2.688000	0.91661	0.650000	0.86243	CAC		PASS	0.308	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018		51	89	51	89	---	---	---	---
MOXD1	26002	broad.mit.edu	37	6	132693969	132693969	+	Splice_Site	SNP	G	G	A	rs373772503		TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr6:132693969G>A	ENST00000367963.3	-	3	697	c.579C>T	c.(577-579)gaC>gaT	p.D193D	MOXD1_ENST00000336749.3_Splice_Site_p.D125D	NM_015529.2	NP_056344.2	Q6UVY6	MOXD1_HUMAN	monooxygenase, DBH-like 1	193						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)	p.D193D(1)|p.D125D(1)		breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(3)|skin(1)	37	Breast(56;0.0495)			OV - Ovarian serous cystadenocarcinoma(155;0.0132)|GBM - Glioblastoma multiforme(226;0.0191)		AAACACTTACGTCCTGATTTA	0.383																																						uc003qdf.2																			2	Substitution - coding silent(2)		lung(2)	ovary(1)	1						c.(577-579)GAC>GAT		monooxygenase, DBH-like 1 isoform 2		G		1,4405	2.1+/-5.4	0,1,2202	102.0	92.0	96.0		579	4.2	1.0	6		96	0,8600		0,0,4300	no	coding-synonymous-near-splice	MOXD1	NM_015529.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		193/614	132693969	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	26002				catecholamine metabolic process	endoplasmic reticulum membrane|integral to membrane	copper ion binding|dopamine beta-monooxygenase activity	g.chr6:132693969G>A	AY007239	CCDS5152.2	6q23.2	2010-09-24			ENSG00000079931	ENSG00000079931			21063	protein-coding gene	gene with protein product		609000				9751809	Standard	XM_006715456		Approved	DKFZP564G202, MOX, dJ248E1.1	uc003qdf.3	Q6UVY6	OTTHUMG00000055853	ENST00000367963.3:c.579+1C>T	6.37:g.132693969G>A						MOXD1_uc003qde.2_Silent_p.D125D	p.D193D	NM_015529	NP_056344	Q6UVY6	MOXD1_HUMAN		OV - Ovarian serous cystadenocarcinoma(155;0.0132)|GBM - Glioblastoma multiforme(226;0.0191)	3	678	-	Breast(56;0.0495)		193			Lumenal (Potential).		Q5THU6|Q8NC97|Q8WV49|Q9H4M6|Q9Y4U3	Silent	SNP	ENST00000367963.3	37	c.579C>T	CCDS5152.2																																																																																				PASS	0.383	MOXD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000125837.1	NM_015529	Silent	97	125	97	125	---	---	---	---
TIAM2	26230	broad.mit.edu	37	6	155577835	155577835	+	Silent	SNP	C	C	T			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr6:155577835C>T	ENST00000461783.3	+	29	5959	c.4686C>T	c.(4684-4686)atC>atT	p.I1562I	TIAM2_ENST00000529824.2_Silent_p.I1591I|TIAM2_ENST00000275246.7_Silent_p.I487I|TIAM2_ENST00000528391.2_Silent_p.I906I|TIAM2_ENST00000456144.1_Silent_p.I1591I|TIAM2_ENST00000367174.2_Silent_p.I938I|TIAM2_ENST00000456877.2_Silent_p.I874I|TIAM2_ENST00000360366.4_Silent_p.I1586I|RP11-477D19.2_ENST00000435295.1_RNA|TIAM2_ENST00000318981.5_Silent_p.I1562I			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	1562					apoptotic signaling pathway (GO:0097190)|cellular lipid metabolic process (GO:0044255)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.I1562I(1)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(20)|lung(21)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	65		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		ACAATCTCATCAAAGAGAGTG	0.552																																						uc003qqb.2																			1	Substitution - coding silent(1)		lung(1)	ovary(3)|breast(1)	4						c.(4684-4686)ATC>ATT		T-cell lymphoma invasion and metastasis 2							54.0	55.0	54.0					6																	155577835		2203	4300	6503	SO:0001819	synonymous_variant	26230				apoptosis|cellular lipid metabolic process|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|filopodium|growth cone|lamellipodium	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity	g.chr6:155577835C>T		CCDS34558.1, CCDS34559.1	6q25	2013-01-10			ENSG00000146426	ENSG00000146426		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11806	protein-coding gene	gene with protein product		604709				10512681	Standard	NM_012454		Approved	STEF	uc003qqe.3	Q8IVF5	OTTHUMG00000015880	ENST00000461783.3:c.4686C>T	6.37:g.155577835C>T						TIAM2_uc003qqe.2_Silent_p.I1562I|TIAM2_uc010kjj.2_Silent_p.I1124I|TIAM2_uc003qqf.2_Silent_p.I938I|TIAM2_uc011efl.1_Silent_p.I906I|TIAM2_uc003qqg.2_Silent_p.I874I|TIAM2_uc003qqh.2_Silent_p.I487I|uc003qqi.1_RNA	p.I1562I	NM_012454	NP_036586	Q8IVF5	TIAM2_HUMAN		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)	29	5959	+		Ovarian(120;0.196)	1562					B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Silent	SNP	ENST00000461783.3	37	c.4686C>T	CCDS34558.1																																																																																				PASS	0.552	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454		43	53	43	53	---	---	---	---
THBS2	7058	broad.mit.edu	37	6	169634881	169634881	+	Nonsense_Mutation	SNP	G	G	T	rs139787473		TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr6:169634881G>T	ENST00000366787.3	-	11	1848	c.1599C>A	c.(1597-1599)tgC>tgA	p.C533*	XXyac-YX65C7_A.2_ENST00000444188.1_RNA	NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	533	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.C533*(1)		NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		CATCCCCCACGCAGGCCTTCC	0.662																																					Esophageal Squamous(91;219 1934 18562 44706)	uc003qwt.2																			1	Substitution - Nonsense(1)		lung(1)	ovary(5)	5						c.(1597-1599)TGC>TGA		thrombospondin 2 precursor							57.0	54.0	55.0					6																	169634881		2203	4300	6503	SO:0001587	stop_gained	7058				cell adhesion	extracellular region	calcium ion binding|heparin binding|protein binding|structural molecule activity	g.chr6:169634881G>T		CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.1599C>A	6.37:g.169634881G>T	ENSP00000355751:p.Cys533*						p.C533*	NM_003247	NP_003238	P35442	TSP2_HUMAN		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)	11	1847	-		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)	533			TSP type-1 3.		A6H8N1|A7E232|Q5RI52	Nonsense_Mutation	SNP	ENST00000366787.3	37	c.1599C>A	CCDS34574.1	.	.	.	.	.	.	.	.	.	.	G	39	7.450168	0.98292	.	.	ENSG00000186340	ENST00000366787	.	.	.	4.38	-1.54	0.08584	.	0.000000	0.44902	U	0.000417	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-40.5579	9.913	0.41417	0.797:0.0:0.203:0.0	.	.	.	.	X	533	.	ENSP00000355751:C533X	C	-	3	2	THBS2	169376806	0.631000	0.27164	0.441000	0.26858	0.911000	0.54048	0.396000	0.20867	-0.165000	0.10908	0.590000	0.80494	TGC		PASS	0.662	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247		41	70	41	70	---	---	---	---
MDH2	4191	broad.mit.edu	37	7	75689711	75689711	+	Silent	SNP	C	C	A			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr7:75689711C>A	ENST00000315758.5	+	5	544	c.450C>A	c.(448-450)atC>atA	p.I150I	MDH2_ENST00000443006.1_Silent_p.I43I|MDH2_ENST00000432020.2_Intron	NM_005918.2	NP_005909.2	P40926	MDHM_HUMAN	malate dehydrogenase 2, NAD (mitochondrial)	150					carbohydrate metabolic process (GO:0005975)|cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|internal protein amino acid acetylation (GO:0006475)|malate metabolic process (GO:0006108)|NADH metabolic process (GO:0006734)|oxaloacetate metabolic process (GO:0006107)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	L-malate dehydrogenase activity (GO:0030060)|malate dehydrogenase (NADP+) activity (GO:0046554)|poly(A) RNA binding (GO:0044822)	p.I150I(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|skin(2)	14						CCATCCCCATCACAGCAGAAG	0.527																																						uc003ueo.2																			1	Substitution - coding silent(1)		lung(1)	ovary(1)|central_nervous_system(1)|skin(1)	3						c.(448-450)ATC>ATA		mitochondrial malate dehydrogenase precursor	NADH(DB00157)						145.0	113.0	124.0					7																	75689711		2203	4300	6503	SO:0001819	synonymous_variant	4191				gluconeogenesis|malate metabolic process|tricarboxylic acid cycle	mitochondrial matrix|nucleus|plasma membrane	binding|L-malate dehydrogenase activity	g.chr7:75689711C>A		CCDS5581.1, CCDS64691.1, CCDS75622.1	7q11.23	2013-09-20			ENSG00000146701	ENSG00000146701	1.1.1.37		6971	protein-coding gene	gene with protein product		154100					Standard	NM_005918		Approved		uc003ueo.3	P40926	OTTHUMG00000023827	ENST00000315758.5:c.450C>A	7.37:g.75689711C>A						MDH2_uc003uep.2_Silent_p.I43I|MDH2_uc011kgh.1_Intron	p.I150I	NM_005918	NP_005909	P40926	MDHM_HUMAN			5	536	+			150					A8K414|B2RE78|B4DE44|E9PDB2|O43682	Silent	SNP	ENST00000315758.5	37	c.450C>A	CCDS5581.1																																																																																				PASS	0.527	MDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252851.1			40	63	40	63	---	---	---	---
CSGALNACT1	55790	broad.mit.edu	37	8	19362750	19362750	+	Missense_Mutation	SNP	G	G	A			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr8:19362750G>A	ENST00000454498.2	-	4	1609	c.596C>T	c.(595-597)cCc>cTc	p.P199L	CSGALNACT1_ENST00000544602.1_Missense_Mutation_p.P199L|CSGALNACT1_ENST00000522854.1_Missense_Mutation_p.P199L|CSGALNACT1_ENST00000332246.6_Missense_Mutation_p.P199L|CSGALNACT1_ENST00000311540.4_Missense_Mutation_p.P199L	NM_001130518.1	NP_001123990.1	Q8TDX6	CGAT1_HUMAN	chondroitin sulfate N-acetylgalactosaminyltransferase 1	199					anatomical structure morphogenesis (GO:0009653)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050653)|dermatan sulfate proteoglycan biosynthetic process (GO:0050651)|endochondral ossification (GO:0001958)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0015014)|heparin biosynthetic process (GO:0030210)|nervous system development (GO:0007399)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)|UDP-glucuronate metabolic process (GO:0046398)|UDP-N-acetylgalactosamine metabolic process (GO:0019276)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|intracellular (GO:0005622)	acetylgalactosaminyltransferase activity (GO:0008376)|glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|glucuronosyltransferase activity (GO:0015020)|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047237)|metal ion binding (GO:0046872)|peptidoglycan glycosyltransferase activity (GO:0008955)	p.P199L(1)		NS(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				Colorectal(111;0.182)		ACGGTGATTGGGGCTGTTCTC	0.527																																						uc011kyn.1																			1	Substitution - Missense(1)		lung(1)	central_nervous_system(2)|ovary(1)	3						c.(595-597)CCC>CTC		chondroitin sulfate							133.0	118.0	123.0					8																	19362750		2203	4300	6503	SO:0001583	missense	55790				anatomical structure morphogenesis|cell proliferation|cell recognition|chondroitin sulfate biosynthetic process|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|dermatan sulfate proteoglycan biosynthetic process|extracellular matrix organization|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|heparin biosynthetic process|nervous system development|UDP-glucuronate metabolic process|UDP-N-acetylgalactosamine metabolic process	Golgi cisterna membrane|integral to Golgi membrane|soluble fraction	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|glucuronosyltransferase activity|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|peptidoglycan glycosyltransferase activity	g.chr8:19362750G>A	AK002126	CCDS6010.1	8p21.3	2013-02-19				ENSG00000147408		"""Beta 4-glycosyltransferases"""	24290	protein-coding gene	gene with protein product	"""chondroitin beta1,4 N-acetylgalactosaminyltransferase"""					17145758, 12446672	Standard	NM_018371		Approved	CSGalNAcT-1, FLJ11264, ChGn	uc011kyo.2	Q8TDX6		ENST00000454498.2:c.596C>T	8.37:g.19362750G>A	ENSP00000411816:p.Pro199Leu					CSGALNACT1_uc011kyo.1_Missense_Mutation_p.P199L|CSGALNACT1_uc003wzg.2_RNA|CSGALNACT1_uc011kyp.1_Missense_Mutation_p.P198L|CSGALNACT1_uc003wzh.2_RNA	p.P199L	NM_001130518	NP_001123990	Q8TDX6	CGAT1_HUMAN		Colorectal(111;0.182)	4	1660	-			199			Lumenal (Potential).		B2RBE4|Q6P9G6|Q8IUF9|Q9NSQ7|Q9NUM9	Missense_Mutation	SNP	ENST00000454498.2	37	c.596C>T	CCDS6010.1	.	.	.	.	.	.	.	.	.	.	G	4.483	0.089491	0.08632	.	.	ENSG00000147408	ENST00000454498;ENST00000332246;ENST00000311540;ENST00000522854;ENST00000544602	T;T;T;T;T	0.22743	1.94;1.94;1.94;1.94;1.94	5.74	2.69	0.31865	.	0.836317	0.11262	N	0.582470	T	0.15132	0.0365	N	0.25647	0.755	0.25362	N	0.988778	B	0.02656	0.0	B	0.06405	0.002	T	0.23833	-1.0177	10	0.27082	T	0.32	-9.9658	11.1131	0.48246	0.0:0.2598:0.6059:0.1344	.	199	Q8TDX6	CGAT1_HUMAN	L	199	ENSP00000411816:P199L;ENSP00000330805:P199L;ENSP00000310891:P199L;ENSP00000429809:P199L;ENSP00000442155:P199L	ENSP00000310891:P199L	P	-	2	0	CSGALNACT1	19407030	0.091000	0.21658	0.374000	0.26016	0.058000	0.15608	2.273000	0.43381	0.822000	0.34565	0.563000	0.77884	CCC		PASS	0.527	CSGALNACT1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375204.1	NM_018371		65	89	65	89	---	---	---	---
PREX2	80243	broad.mit.edu	37	8	68968100	68968100	+	Missense_Mutation	SNP	A	A	G			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr8:68968100A>G	ENST00000288368.4	+	10	1406	c.1129A>G	c.(1129-1131)Atg>Gtg	p.M377V	PREX2_ENST00000529398.1_3'UTR	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	377					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)	p.M377V(2)		NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						TACCTGGGTCATGATCTCTGA	0.363																																						uc003xxv.1																			2	Substitution - Missense(2)		lung(2)	skin(6)|large_intestine(4)|pancreas(3)|lung(2)|ovary(1)|kidney(1)	17						c.(1129-1131)ATG>GTG		DEP domain containing 2 isoform a							83.0	91.0	88.0					8																	68968100		2203	4300	6503	SO:0001583	missense	80243				G-protein coupled receptor protein signaling pathway|intracellular signal transduction	intracellular	protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity	g.chr8:68968100A>G	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"""Rho guanine nucleotide exchange factors"""	22950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 129"""	612139	"""DEP domain containing 2"""	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.1129A>G	8.37:g.68968100A>G	ENSP00000288368:p.Met377Val					PREX2_uc003xxu.1_Missense_Mutation_p.M377V|PREX2_uc011lez.1_Missense_Mutation_p.M312V	p.M377V	NM_024870	NP_079146	Q70Z35	PREX2_HUMAN			10	1156	+			377					B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	37	c.1129A>G	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	A	19.77	3.888569	0.72524	.	.	ENSG00000046889	ENST00000288368;ENST00000396539;ENST00000354677	T	0.59772	0.24	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.60495	0.2273	N	0.20685	0.6	0.58432	D	0.999997	D;B;B	0.54397	0.966;0.434;0.383	P;B;B	0.60682	0.878;0.325;0.219	T	0.63462	-0.6632	10	0.48119	T	0.1	.	15.9708	0.80019	1.0:0.0:0.0:0.0	.	377;377;377	Q70Z35-2;Q70Z35;Q70Z35-3	.;PREX2_HUMAN;.	V	377	ENSP00000288368:M377V	ENSP00000288368:M377V	M	+	1	0	PREX2	69130654	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.256000	0.78350	2.231000	0.72958	0.533000	0.62120	ATG		PASS	0.363	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		57	96	57	96	---	---	---	---
PARP10	84875	broad.mit.edu	37	8	145059449	145059449	+	Silent	SNP	G	G	A			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr8:145059449G>A	ENST00000313028.7	-	5	815	c.721C>T	c.(721-723)Ctg>Ttg	p.L241L	PARP10_ENST00000524918.1_Silent_p.L241L|PARP10_ENST00000533665.1_5'UTR|PARP10_ENST00000525773.1_Silent_p.L253L	NM_032789.3	NP_116178.2	Q53GL7	PAR10_HUMAN	poly (ADP-ribose) polymerase family, member 10	241					negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of gene expression (GO:0010629)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein import into nucleus, translocation (GO:0033159)|negative regulation of protein K63-linked ubiquitination (GO:1900045)|negative regulation of viral genome replication (GO:0045071)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein poly-ADP-ribosylation (GO:0070212)|regulation of chromatin assembly (GO:0010847)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	K63-linked polyubiquitin binding (GO:0070530)|NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.L241L(1)		NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(4)|pancreas(1)|upper_aerodigestive_tract(2)	27	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.31e-40)|Epithelial(56;1.16e-39)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			acaaggctcagctctgagccc	0.612																																						uc003zal.3																			1	Substitution - coding silent(1)		lung(1)	ovary(2)|upper_aerodigestive_tract(1)|lung(1)|breast(1)|pancreas(1)	6						c.(721-723)CTG>TTG		poly (ADP-ribose) polymerase family, member 10							32.0	35.0	34.0					8																	145059449		2203	4299	6502	SO:0001819	synonymous_variant	84875					Golgi apparatus|nucleolus	NAD+ ADP-ribosyltransferase activity|nucleotide binding	g.chr8:145059449G>A	AK027370	CCDS34960.1	8q24	2010-02-16				ENSG00000178685		"""Poly (ADP-ribose) polymerases"""	25895	protein-coding gene	gene with protein product		609564				15273990	Standard	NM_032789		Approved	FLJ14464	uc003zal.4	Q53GL7		ENST00000313028.7:c.721C>T	8.37:g.145059449G>A						PARP10_uc003zak.3_5'UTR|PARP10_uc011lku.1_Silent_p.L253L|PARP10_uc011lkv.1_RNA|PARP10_uc003zam.2_Silent_p.L241L|PARP10_uc010mfn.1_Silent_p.L156L|PARP10_uc010mfo.1_Silent_p.S133S	p.L241L	NM_032789	NP_116178	Q53GL7	PAR10_HUMAN	OV - Ovarian serous cystadenocarcinoma(54;1.31e-40)|Epithelial(56;1.16e-39)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)		5	829	-	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		241					Q8N2I0|Q8WV05|Q96CH7|Q96K72	Silent	SNP	ENST00000313028.7	37	c.721C>T	CCDS34960.1																																																																																				PASS	0.612	PARP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383866.1	NM_032789		28	32	28	32	---	---	---	---
FOCAD	54914	broad.mit.edu	37	9	20862683	20862683	+	Missense_Mutation	SNP	C	C	A			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr9:20862683C>A	ENST00000380249.1	+	18	2391	c.2027C>A	c.(2026-2028)tCc>tAc	p.S676Y	FOCAD_ENST00000605086.1_Missense_Mutation_p.S112Y|FOCAD_ENST00000338382.6_Missense_Mutation_p.S676Y	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	676						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)		p.S676Y(1)									CTAGTTCCTTCCTTAACGGTC	0.413																																						uc003zog.1																			1	Substitution - Missense(1)		lung(1)	ovary(8)|breast(1)|kidney(1)	10						c.(2026-2028)TCC>TAC		hypothetical protein LOC54914							184.0	158.0	166.0					9																	20862683		2203	4300	6503	SO:0001583	missense	54914					integral to membrane	binding	g.chr9:20862683C>A	AB058700	CCDS34993.1	9p21	2012-03-23	2012-03-23	2012-03-23	ENSG00000188352	ENSG00000188352			23377	protein-coding gene	gene with protein product		614606	"""KIAA1797"""	KIAA1797		22427331	Standard	XM_006716794		Approved	FLJ20375	uc003zog.1	Q5VW36	OTTHUMG00000066930	ENST00000380249.1:c.2027C>A	9.37:g.20862683C>A	ENSP00000369599:p.Ser676Tyr					KIAA1797_uc003zoh.1_Missense_Mutation_p.S112Y	p.S676Y	NM_017794	NP_060264	Q5VW36	K1797_HUMAN		GBM - Glioblastoma multiforme(3;2.1e-125)|Lung(42;2.76e-14)|LUSC - Lung squamous cell carcinoma(42;1.99e-11)	18	2390	+			676					D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Missense_Mutation	SNP	ENST00000380249.1	37	c.2027C>A	CCDS34993.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.319996	0.81469	.	.	ENSG00000188352	ENST00000380249;ENST00000338382	T;T	0.23552	1.9;1.9	5.9	5.9	0.94986	Armadillo-type fold (1);Domain of unknown function DUF3730 (1);	0.225146	0.47852	D	0.000202	T	0.47322	0.1439	L	0.43152	1.355	0.53005	D	0.999969	D	0.89917	1.0	D	0.91635	0.999	T	0.31081	-0.9956	10	0.66056	D	0.02	-0.0649	20.2787	0.98501	0.0:1.0:0.0:0.0	.	676	Q5VW36	K1797_HUMAN	Y	676	ENSP00000369599:S676Y;ENSP00000344307:S676Y	ENSP00000344307:S676Y	S	+	2	0	KIAA1797	20852683	0.987000	0.35691	1.000000	0.80357	0.945000	0.59286	3.175000	0.50855	2.798000	0.96311	0.650000	0.86243	TCC		PASS	0.413	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794		93	14	93	14	---	---	---	---
FOCAD	54914	broad.mit.edu	37	9	20862693	20862693	+	Silent	SNP	C	C	A			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr9:20862693C>A	ENST00000380249.1	+	18	2401	c.2037C>A	c.(2035-2037)gtC>gtA	p.V679V	FOCAD_ENST00000605086.1_Silent_p.V115V|FOCAD_ENST00000338382.6_Silent_p.V679V	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	679						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)		p.V679V(1)									CCTTAACGGTCAATACAACTG	0.398																																						uc003zog.1																			1	Substitution - coding silent(1)		lung(1)	ovary(8)|breast(1)|kidney(1)	10						c.(2035-2037)GTC>GTA		hypothetical protein LOC54914							173.0	150.0	158.0					9																	20862693		2203	4300	6503	SO:0001819	synonymous_variant	54914					integral to membrane	binding	g.chr9:20862693C>A	AB058700	CCDS34993.1	9p21	2012-03-23	2012-03-23	2012-03-23	ENSG00000188352	ENSG00000188352			23377	protein-coding gene	gene with protein product		614606	"""KIAA1797"""	KIAA1797		22427331	Standard	XM_006716794		Approved	FLJ20375	uc003zog.1	Q5VW36	OTTHUMG00000066930	ENST00000380249.1:c.2037C>A	9.37:g.20862693C>A						KIAA1797_uc003zoh.1_Silent_p.V115V	p.V679V	NM_017794	NP_060264	Q5VW36	K1797_HUMAN		GBM - Glioblastoma multiforme(3;2.1e-125)|Lung(42;2.76e-14)|LUSC - Lung squamous cell carcinoma(42;1.99e-11)	18	2400	+			679					D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Silent	SNP	ENST00000380249.1	37	c.2037C>A	CCDS34993.1																																																																																				PASS	0.398	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794		86	14	86	14	---	---	---	---
RUSC2	9853	broad.mit.edu	37	9	35561252	35561252	+	Missense_Mutation	SNP	G	G	A			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr9:35561252G>A	ENST00000455600.1	+	12	4993	c.4424G>A	c.(4423-4425)cGa>cAa	p.R1475Q	FAM166B_ENST00000492890.1_5'Flank	NM_001135999.1	NP_001129471	Q8N2Y8	RUSC2_HUMAN	RUN and SH3 domain containing 2	1475	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.					cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)	Rab GTPase binding (GO:0017137)	p.R1475Q(1)		NS(1)|breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|lung(4)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32			Lung(28;0.000837)|LUSC - Lung squamous cell carcinoma(32;0.00109)|STAD - Stomach adenocarcinoma(86;0.194)			GACATCCTACGAGTGCTGGGG	0.642																																						uc003zww.2																			1	Substitution - Missense(1)		lung(1)	ovary(1)	1						c.(4423-4425)CGA>CAA		RUN and SH3 domain containing 2							54.0	63.0	60.0					9																	35561252		2203	4300	6503	SO:0001583	missense	9853					cytosol		g.chr9:35561252G>A	AB002373	CCDS35008.1	9p13.2	2003-12-02			ENSG00000198853	ENSG00000198853			23625	protein-coding gene	gene with protein product		611053				9205841	Standard	NM_001135999		Approved	KIAA0375	uc003zww.3	Q8N2Y8	OTTHUMG00000019861	ENST00000455600.1:c.4424G>A	9.37:g.35561252G>A	ENSP00000393922:p.Arg1475Gln					RUSC2_uc010mkq.2_RNA|RUSC2_uc003zwx.3_Missense_Mutation_p.R1475Q	p.R1475Q	NM_014806	NP_055621	Q8N2Y8	RUSC2_HUMAN	Lung(28;0.000837)|LUSC - Lung squamous cell carcinoma(32;0.00109)|STAD - Stomach adenocarcinoma(86;0.194)		12	4679	+			1475			SH3.		A2RU62|A7E2A9|O15080|Q5W134|Q641Q6|Q6P1W7	Missense_Mutation	SNP	ENST00000455600.1	37	c.4424G>A	CCDS35008.1	.	.	.	.	.	.	.	.	.	.	G	14.16	2.451854	0.43531	.	.	ENSG00000198853	ENST00000361226;ENST00000455600	T;T	0.08546	3.08;3.08	5.39	5.39	0.77823	Src homology-3 domain (3);Variant SH3 (1);	0.204155	0.44483	D	0.000448	T	0.03564	0.0102	N	0.05554	-0.025	0.38066	D	0.936228	P	0.40398	0.716	B	0.28385	0.089	T	0.51228	-0.8732	10	0.39692	T	0.17	-17.9221	10.2042	0.43103	0.1535:0.0:0.8465:0.0	.	1475	Q8N2Y8	RUSC2_HUMAN	Q	1475	ENSP00000355177:R1475Q;ENSP00000393922:R1475Q	ENSP00000355177:R1475Q	R	+	2	0	RUSC2	35551252	0.830000	0.29337	0.908000	0.35775	0.897000	0.52465	1.482000	0.35486	2.679000	0.91253	0.650000	0.86243	CGA		PASS	0.642	RUSC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052309.1	XM_048462		4	120	4	120	---	---	---	---
ANKRD20A2	441430	broad.mit.edu	37	9	42368547	42368547	+	Missense_Mutation	SNP	G	G	A			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr9:42368547G>A	ENST00000377601.2	+	1	245	c.133G>A	c.(133-135)Gac>Aac	p.D45N	RP11-216M21.7_ENST00000450520.1_RNA	NM_001012421.1	NP_001012421.1	Q5SQ80	A20A2_HUMAN	ankyrin repeat domain 20 family, member A2	45								p.D45N(2)		large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	4						TGTCAAAGGCGACGCCGCGGA	0.677																																						uc004acd.2																			2	Substitution - Missense(2)		urinary_tract(1)|lung(1)		0						c.(133-135)GAC>AAC		ankyrin repeat domain 20 family, member A3							7.0	7.0	7.0					9																	42368547		2120	4092	6212	SO:0001583	missense	441425							g.chr9:42368547G>A		CCDS35028.1	9p12	2013-01-10			ENSG00000183148	ENSG00000183148		"""Ankyrin repeat domain containing"""	31979	protein-coding gene	gene with protein product							Standard	XM_005272519		Approved			Q5SQ80	OTTHUMG00000058641	ENST00000377601.2:c.133G>A	9.37:g.42368547G>A	ENSP00000366826:p.Asp45Asn					ANKRD20A3_uc010mmv.2_Missense_Mutation_p.D45N	p.D45N	NM_001012419	NP_001012419	Q5VUR7	A20A3_HUMAN			1	245	+			45						Missense_Mutation	SNP	ENST00000377601.2	37	c.133G>A	CCDS35028.1	.	.	.	.	.	.	.	.	.	.	G	10.33	1.321736	0.23994	.	.	ENSG00000183148	ENST00000377601	T	0.63580	-0.05	1.23	-1.0	0.10196	Ankyrin repeat-containing domain (8);	.	.	.	.	T	0.50633	0.1627	N	0.17474	0.49	0.09310	N	1	D;D	0.62365	0.991;0.979	D;B	0.65443	0.935;0.301	T	0.46119	-0.9214	9	0.02654	T	1	.	4.104	0.10028	0.451:0.0:0.549:0.0	.	45;45	Q5CZ79;Q5SQ80	AN20B_HUMAN;A20A2_HUMAN	N	45	ENSP00000366826:D45N	ENSP00000366826:D45N	D	+	1	0	ANKRD20A2	42358543	0.000000	0.05858	0.000000	0.03702	0.050000	0.14768	-0.719000	0.04974	-0.312000	0.08741	0.121000	0.15741	GAC		PASS	0.677	ANKRD20A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129794.1	NM_001012421		25	103	25	103	---	---	---	---
KIAA0368	23392	broad.mit.edu	37	9	114176211	114176211	+	Silent	SNP	C	C	T			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr9:114176211C>T	ENST00000338205.5	-	19	2262	c.2043G>A	c.(2041-2043)ctG>ctA	p.L681L	KIAA0368_ENST00000259335.4_Silent_p.L859L|RNA5SP294_ENST00000411306.1_RNA			Q5VYK3	ECM29_HUMAN	KIAA0368	687					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)		p.L859L(1)		NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						ATTTGGTAGCCAGCTTTTCTG	0.323																																						uc004bfe.1																			1	Substitution - coding silent(1)		lung(1)		0						c.(2575-2577)CTG>CTA		KIAA0368 protein							69.0	60.0	63.0					9																	114176211		1828	4092	5920	SO:0001819	synonymous_variant	23392							g.chr9:114176211C>T	AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"""ECM29 homolog (S. cerevisiae)"""					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.2043G>A	9.37:g.114176211C>T						KIAA0368_uc010muc.1_Silent_p.L681L	p.L859L	NM_001080398	NP_001073867					21	2577	-								O15074|Q8WU82	Silent	SNP	ENST00000338205.5	37	c.2577G>A																																																																																					PASS	0.323	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686		6	13	6	13	---	---	---	---
RGS3	5998	broad.mit.edu	37	9	116356725	116356725	+	Missense_Mutation	SNP	G	G	C			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr9:116356725G>C	ENST00000374140.2	+	23	3305	c.3096G>C	c.(3094-3096)aaG>aaC	p.K1032N	RGS3_ENST00000462403.1_Missense_Mutation_p.K145N|RGS3_ENST00000342620.5_Missense_Mutation_p.K2N|RGS3_ENST00000394646.3_Missense_Mutation_p.K425N|RGS3_ENST00000343817.5_Missense_Mutation_p.K751N|RGS3_ENST00000462143.1_Missense_Mutation_p.K353N|RGS3_ENST00000374134.3_Missense_Mutation_p.K353N|RGS3_ENST00000350696.5_Missense_Mutation_p.K1032N	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3	1032					inactivation of MAPK activity (GO:0000188)|positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)	p.K145N(1)|p.K928N(1)|p.K1032N(1)		cervix(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	48						AGGACATGAAGAACAAGCTGG	0.592																																						uc004bhq.2																			3	Substitution - Missense(3)		lung(3)	ovary(1)|lung(1)|skin(1)	3						c.(3094-3096)AAG>AAC		regulator of G-protein signalling 3 isoform 6							63.0	73.0	69.0					9																	116356725		2203	4300	6503	SO:0001583	missense	5998				inactivation of MAPK activity|regulation of G-protein coupled receptor protein signaling pathway	cytosol|nucleus|plasma membrane	GTPase activator activity|signal transducer activity	g.chr9:116356725G>C	AF006610	CCDS6797.1, CCDS6798.1, CCDS35113.1, CCDS35114.1, CCDS43869.1, CCDS65111.1	9q32	2008-02-05	2007-08-14		ENSG00000138835	ENSG00000138835		"""Regulators of G-protein signaling"""	9999	protein-coding gene	gene with protein product		602189	"""regulator of G-protein signalling 3"""			8602223, 11034339	Standard	NM_001276260		Approved	C2PA, FLJ20370, PDZ-RGS3	uc004bhq.4	P49796	OTTHUMG00000021048	ENST00000374140.2:c.3096G>C	9.37:g.116356725G>C	ENSP00000363255:p.Lys1032Asn					RGS3_uc004bhs.2_Missense_Mutation_p.K922N|RGS3_uc004bht.2_Missense_Mutation_p.K751N|RGS3_uc010muy.2_Missense_Mutation_p.K425N|RGS3_uc004bhv.2_Missense_Mutation_p.K353N|RGS3_uc004bhw.2_Missense_Mutation_p.K2N|RGS3_uc011lxh.1_Missense_Mutation_p.K342N|RGS3_uc004bhx.2_Missense_Mutation_p.K353N|RGS3_uc004bhz.2_Missense_Mutation_p.K374N|RGS3_uc004bia.2_Missense_Mutation_p.K145N	p.K1032N	NM_144488	NP_652759	P49796	RGS3_HUMAN			23	3305	+			1032					A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Missense_Mutation	SNP	ENST00000374140.2	37	c.3096G>C	CCDS43869.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.683524	0.88639	.	.	ENSG00000138835	ENST00000374140;ENST00000350696;ENST00000343817;ENST00000394646;ENST00000474719;ENST00000462143;ENST00000342620;ENST00000374134;ENST00000467805;ENST00000462403	T;T;T;T;T;T;T;D;T	0.83914	0.46;0.46;-0.04;2.58;-0.18;0.13;-0.18;-1.78;-0.18	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	D	0.90528	0.7032	M	0.79258	2.445	0.58432	D	0.999998	D;D;D;D;D;D	0.71674	0.974;0.997;0.995;0.995;0.996;0.998	P;D;P;P;P;P	0.68765	0.617;0.96;0.903;0.903;0.802;0.883	D	0.91652	0.5335	10	0.87932	D	0	.	15.733	0.77819	0.0:0.0:1.0:0.0	.	425;145;928;751;922;1032	B3KUB2;Q5VZ06;P49796-6;P49796-4;B3KWG8;P49796	.;.;.;.;.;RGS3_HUMAN	N	1032;1032;751;425;200;353;2;353;198;145	ENSP00000363255:K1032N;ENSP00000259406:K1032N;ENSP00000340284:K751N;ENSP00000378141:K425N;ENSP00000420356:K353N;ENSP00000343359:K2N;ENSP00000363249:K353N;ENSP00000417994:K198N;ENSP00000436168:K145N	ENSP00000343359:K2N	K	+	3	2	RGS3	115396546	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	6.266000	0.72540	2.478000	0.83669	0.558000	0.71614	AAG		PASS	0.592	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790		66	71	66	71	---	---	---	---
SFMBT2	57713	broad.mit.edu	37	10	7409620	7409620	+	Missense_Mutation	SNP	G	G	A			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr10:7409620G>A	ENST00000361972.4	-	4	517	c.427C>T	c.(427-429)Ccg>Tcg	p.P143S	SFMBT2_ENST00000379713.3_Missense_Mutation_p.P143S|SFMBT2_ENST00000397160.3_Missense_Mutation_p.P143S|SFMBT2_ENST00000379711.2_Missense_Mutation_p.P143S|SFMBT2_ENST00000397167.1_Missense_Mutation_p.P143S	NM_001018039.1	NP_001018049.1	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	143					negative regulation of gene expression (GO:0010629)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	histone binding (GO:0042393)	p.P143S(1)		NS(2)|breast(3)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(26)|lung(34)|ovary(5)|pancreas(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	99						CCGTCCGGCGGCATCAACACC	0.572																																						uc009xio.1																			1	Substitution - Missense(1)		lung(1)	ovary(4)|upper_aerodigestive_tract(2)|large_intestine(1)|central_nervous_system(1)	8						c.(427-429)CCG>TCG		Scm-like with four mbt domains 2							79.0	72.0	74.0					10																	7409620		2203	4300	6503	SO:0001583	missense	57713				regulation of transcription, DNA-dependent	nucleus		g.chr10:7409620G>A	AB046837	CCDS31138.1	10p15.1	2013-01-10	2003-11-14		ENSG00000198879	ENSG00000198879		"""Sterile alpha motif (SAM) domain containing"""	20256	protein-coding gene	gene with protein product		615392	"""Scm-related gene containing four mbt domains 2"""			10997877	Standard	NM_001029880		Approved	KIAA1617	uc009xio.2	Q5VUG0	OTTHUMG00000017630	ENST00000361972.4:c.427C>T	10.37:g.7409620G>A	ENSP00000355109:p.Pro143Ser					SFMBT2_uc001ijn.1_Missense_Mutation_p.P143S|SFMBT2_uc010qay.1_Missense_Mutation_p.P143S|SFMBT2_uc001ijo.1_Missense_Mutation_p.P143S	p.P143S	NM_001029880	NP_001025051	Q5VUG0	SMBT2_HUMAN			4	518	-			143			MBT 1.		A7MD09|Q9HCF5	Missense_Mutation	SNP	ENST00000361972.4	37	c.427C>T	CCDS31138.1	.	.	.	.	.	.	.	.	.	.	G	17.44	3.390425	0.62066	.	.	ENSG00000198879	ENST00000361972;ENST00000397167;ENST00000379713;ENST00000379711;ENST00000397160	T;T;T;T;T	0.39592	1.07;1.07;1.07;1.07;1.07	4.79	4.79	0.61399	.	0.230699	0.45361	D	0.000365	T	0.69780	0.3149	M	0.87758	2.905	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.80764	0.98;0.994	T	0.76402	-0.2972	10	0.66056	D	0.02	.	17.8186	0.88643	0.0:0.0:1.0:0.0	.	143;143	Q5T981;Q5VUG0	.;SMBT2_HUMAN	S	143	ENSP00000355109:P143S;ENSP00000380353:P143S;ENSP00000369035:P143S;ENSP00000369033:P143S;ENSP00000380346:P143S	ENSP00000355109:P143S	P	-	1	0	SFMBT2	7449626	1.000000	0.71417	1.000000	0.80357	0.140000	0.21249	9.634000	0.98435	2.371000	0.80710	0.305000	0.20034	CCG		PASS	0.572	SFMBT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046673.1	NM_001029880		4	82	4	82	---	---	---	---
ARHGAP22	58504	broad.mit.edu	37	10	49661458	49661458	+	Missense_Mutation	SNP	C	C	T			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr10:49661458C>T	ENST00000249601.4	-	8	1173	c.877G>A	c.(877-879)Gaa>Aaa	p.E293K	ARHGAP22_ENST00000417912.2_Missense_Mutation_p.E309K|ARHGAP22_ENST00000435790.2_Missense_Mutation_p.E299K|ARHGAP22_ENST00000374172.1_Missense_Mutation_p.E184K|ARHGAP22_ENST00000477708.2_5'Flank|ARHGAP22_ENST00000374170.1_Missense_Mutation_p.E134K|ARHGAP22_ENST00000417247.2_Missense_Mutation_p.E203K	NM_001256024.1|NM_021226.3	NP_001242953.1|NP_067049.2	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 22	293	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)	p.E293K(1)		endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						GCCTGAACTTCATCCAGAAAC	0.517																																						uc001jgt.2																			1	Substitution - Missense(1)		lung(1)	ovary(1)	1						c.(877-879)GAA>AAA		Rho GTPase activating protein 2							143.0	133.0	136.0					10																	49661458		2203	4300	6503	SO:0001583	missense	58504				angiogenesis|cell differentiation|regulation of small GTPase mediated signal transduction|regulation of transcription, DNA-dependent|small GTPase mediated signal transduction|transcription, DNA-dependent	cytosol|nucleus	GTPase activator activity	g.chr10:49661458C>T	AY324801	CCDS7227.1, CCDS58079.1, CCDS58080.1, CCDS58081.1	10q11.23	2013-01-10			ENSG00000128805	ENSG00000128805		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	30320	protein-coding gene	gene with protein product		610585				8619474	Standard	NM_021226		Approved	RhoGAP2	uc010qgm.3	Q7Z5H3	OTTHUMG00000018176	ENST00000249601.4:c.877G>A	10.37:g.49661458C>T	ENSP00000249601:p.Glu293Lys					ARHGAP22_uc001jgs.2_Missense_Mutation_p.E203K|ARHGAP22_uc001jgu.2_Missense_Mutation_p.E309K|ARHGAP22_uc010qgl.1_Missense_Mutation_p.E250K|ARHGAP22_uc010qgm.1_Missense_Mutation_p.E299K|ARHGAP22_uc001jgv.2_5'UTR|ARHGAP22_uc001jgr.2_5'Flank	p.E293K	NM_021226	NP_067049	Q7Z5H3	RHG22_HUMAN			8	1174	-			293			Rho-GAP.		A0AVP7|A5YM75|B4DED8|B9EGA0|C9JDM2|O00152|Q6ZSB0	Missense_Mutation	SNP	ENST00000249601.4	37	c.877G>A	CCDS7227.1	.	.	.	.	.	.	.	.	.	.	C	33	5.236252	0.95240	.	.	ENSG00000128805	ENST00000249601;ENST00000374172;ENST00000374170;ENST00000417247;ENST00000435790;ENST00000417912	T;T;T;T;T;T	0.17213	2.29;2.29;2.29;2.29;2.29;2.29	5.37	4.47	0.54385	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.28995	0.0720	L	0.35723	1.085	0.80722	D	1	P;D;D;D;B	0.71674	0.747;0.997;0.998;0.997;0.29	P;D;D;D;P	0.78314	0.78;0.982;0.991;0.982;0.699	T	0.01951	-1.1241	10	0.22706	T	0.39	.	13.2537	0.60066	0.0:0.9234:0.0:0.0766	.	299;293;309;293;203	B4DED8;A6NDI7;Q7Z5H3-2;Q7Z5H3;Q7Z5H3-3	.;.;.;RHG22_HUMAN;.	K	293;184;134;203;299;309	ENSP00000249601:E293K;ENSP00000363287:E184K;ENSP00000363285:E134K;ENSP00000410054:E203K;ENSP00000416701:E299K;ENSP00000412461:E309K	ENSP00000249601:E293K	E	-	1	0	ARHGAP22	49331464	1.000000	0.71417	0.999000	0.59377	0.961000	0.63080	5.936000	0.70153	1.268000	0.44264	0.637000	0.83480	GAA		PASS	0.517	ARHGAP22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358767.1	NM_021226		41	68	41	68	---	---	---	---
CSTF2T	23283	broad.mit.edu	37	10	53458869	53458869	+	Missense_Mutation	SNP	C	C	T			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr10:53458869C>T	ENST00000331173.4	-	1	486	c.441G>A	c.(439-441)atG>atA	p.M147I	PRKG1_ENST00000373985.1_Intron|PRKG1_ENST00000373980.4_Intron|PRKG1_ENST00000401604.2_Intron	NM_015235.2	NP_056050.1	Q9H0L4	CSTFT_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant	147					mRNA processing (GO:0006397)	intracellular (GO:0005622)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.M147I(1)		NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	30				COAD - Colon adenocarcinoma(2;0.00736)|Colorectal(2;0.00898)|all cancers(4;0.0188)|GBM - Glioblastoma multiforme(4;0.0778)|Epithelial(53;0.122)		CACAGAGCTTCATCTGCTTCA	0.498																																						uc001jjp.2																			1	Substitution - Missense(1)		lung(1)	ovary(1)	1						c.(439-441)ATG>ATA		cleavage stimulation factor, 3' pre-RNA, subunit							184.0	175.0	178.0					10																	53458869		2203	4300	6503	SO:0001583	missense	23283				mRNA processing	nucleus	nucleotide binding|RNA binding	g.chr10:53458869C>T	AB014589	CCDS7245.1	10q11	2013-02-12			ENSG00000177613	ENSG00000177613		"""RNA binding motif (RRM) containing"""	17086	protein-coding gene	gene with protein product		611968				12408968, 11113135	Standard	NM_015235		Approved	DKFZp434C1013, KIAA0689, CstF-64T	uc001jjp.3	Q9H0L4	OTTHUMG00000018246	ENST00000331173.4:c.441G>A	10.37:g.53458869C>T	ENSP00000332444:p.Met147Ile					PRKG1_uc001jjm.2_Intron|PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron	p.M147I	NM_015235	NP_056050	Q9H0L4	CSTFT_HUMAN		COAD - Colon adenocarcinoma(2;0.00736)|Colorectal(2;0.00898)|all cancers(4;0.0188)|GBM - Glioblastoma multiforme(4;0.0778)|Epithelial(53;0.122)	1	487	-			147					B2RAR9|O75174|Q53HK6|Q7LGE8|Q8N6T1	Missense_Mutation	SNP	ENST00000331173.4	37	c.441G>A	CCDS7245.1	.	.	.	.	.	.	.	.	.	.	C	18.81	3.703209	0.68501	.	.	ENSG00000177613	ENST00000331173	T	0.30182	1.54	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	T	0.64972	0.2647	H	0.94264	3.515	0.80722	D	1	P	0.50819	0.939	P	0.62740	0.906	T	0.73833	-0.3858	10	0.59425	D	0.04	-15.178	16.1846	0.81942	0.0:1.0:0.0:0.0	.	147	Q9H0L4	CSTFT_HUMAN	I	147	ENSP00000332444:M147I	ENSP00000332444:M147I	M	-	3	0	CSTF2T	53128875	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.443000	0.66581	2.767000	0.95098	0.655000	0.94253	ATG		PASS	0.498	CSTF2T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048097.1	NM_015235		111	164	111	164	---	---	---	---
OR10A3	26496	broad.mit.edu	37	11	7960244	7960244	+	Missense_Mutation	SNP	G	G	A			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr11:7960244G>A	ENST00000360759.3	-	1	897	c.824C>T	c.(823-825)tCa>tTa	p.S275L		NM_001003745.1	NP_001003745.1	P58181	O10A3_HUMAN	olfactory receptor, family 10, subfamily A, member 3	275					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S275L(1)		endometrium(1)|large_intestine(5)|lung(12)|pancreas(1)|skin(2)	21				Epithelial(150;1.38e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		GTAAGCCAATGAGATCAGTTT	0.443																																						uc010rbi.1																			1	Substitution - Missense(1)		lung(1)	pancreas(1)	1						c.(823-825)TCA>TTA		olfactory receptor, family 10, subfamily A,							205.0	185.0	192.0					11																	7960244		2201	4296	6497	SO:0001583	missense	26496				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:7960244G>A	BK004404	CCDS31421.1	11p15.4	2012-08-09			ENSG00000170683	ENSG00000170683		"""GPCR / Class A : Olfactory receptors"""	8162	protein-coding gene	gene with protein product						1370859	Standard	NM_001003745		Approved	HTPCRX12, HSHTPCRX12	uc010rbi.2	P58181	OTTHUMG00000165672	ENST00000360759.3:c.824C>T	11.37:g.7960244G>A	ENSP00000353988:p.Ser275Leu						p.S275L	NM_001003745	NP_001003745	P58181	O10A3_HUMAN		Epithelial(150;1.38e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)	1	824	-			275			Helical; Name=7; (Potential).		B9EH39|Q6IF58|Q96R11	Missense_Mutation	SNP	ENST00000360759.3	37	c.824C>T	CCDS31421.1	.	.	.	.	.	.	.	.	.	.	g	10.79	1.450176	0.26074	.	.	ENSG00000170683	ENST00000360759	T	0.00265	8.39	4.65	3.74	0.42951	GPCR, rhodopsin-like superfamily (1);	0.246918	0.21058	U	0.080872	T	0.00666	0.0022	M	0.88842	2.985	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.24012	-1.0172	10	0.87932	D	0	.	12.3808	0.55305	0.0:0.0:0.8301:0.1699	.	275	P58181	O10A3_HUMAN	L	275	ENSP00000353988:S275L	ENSP00000353988:S275L	S	-	2	0	OR10A3	7916820	0.003000	0.15002	0.758000	0.31321	0.049000	0.14656	1.368000	0.34216	1.338000	0.45544	-0.196000	0.12772	TCA		PASS	0.443	OR10A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385704.1	NM_001003745		74	74	74	74	---	---	---	---
ALX4	60529	broad.mit.edu	37	11	44289129	44289129	+	Missense_Mutation	SNP	C	C	T	rs368050443		TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr11:44289129C>T	ENST00000329255.3	-	3	924	c.821G>A	c.(820-822)cGt>cAt	p.R274H		NM_021926.3	NP_068745.2	Q9H161	ALX4_HUMAN	ALX homeobox 4	274					anterior/posterior pattern specification (GO:0009952)|digestive tract development (GO:0048565)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal system morphogenesis (GO:0048704)|hair follicle development (GO:0001942)|muscle organ development (GO:0007517)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of apoptotic process (GO:0042981)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R274H(1)		central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	16						CTGCCCAAAACGCTCCCGCTT	0.597																																						uc001myb.2																			1	Substitution - Missense(1)		lung(1)		0						c.(820-822)CGT>CAT		aristaless-like homeobox 4		C	HIS/ARG	0,4406		0,0,2203	179.0	146.0	157.0		821	4.9	1.0	11		157	1,8597	1.2+/-3.3	0,1,4298	no	missense	ALX4	NM_021926.3	29	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	274/412	44289129	1,13003	2203	4299	6502	SO:0001583	missense	60529				hair follicle development			g.chr11:44289129C>T	AF294629	CCDS31468.1	11p11.2	2011-06-20	2008-11-04		ENSG00000052850	ENSG00000052850		"""Homeoboxes / PRD class"""	450	protein-coding gene	gene with protein product		605420	"""parietal foramina 2"", ""aristaless-like homeobox 4"""	PFM2		11017806, 8644736	Standard	NM_021926		Approved	FPP, PFM, KIAA1788	uc001myb.3	Q9H161	OTTHUMG00000166557	ENST00000329255.3:c.821G>A	11.37:g.44289129C>T	ENSP00000332744:p.Arg274His						p.R274H	NM_021926	NP_068745	Q9H161	ALX4_HUMAN			3	925	-			274					Q96JN7|Q9H198|Q9HAY9	Missense_Mutation	SNP	ENST00000329255.3	37	c.821G>A	CCDS31468.1	.	.	.	.	.	.	.	.	.	.	C	36	5.646267	0.96704	0.0	1.16E-4	ENSG00000052850	ENST00000329255	D	0.92965	-3.14	4.88	4.88	0.63580	Homeobox (1);Homeodomain-like (1);	0.116529	0.64402	D	0.000018	D	0.95853	0.8650	M	0.75777	2.31	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	D	0.96120	0.9084	10	0.87932	D	0	.	18.578	0.91162	0.0:1.0:0.0:0.0	.	274	Q9H161	ALX4_HUMAN	H	274	ENSP00000332744:R274H	ENSP00000332744:R274H	R	-	2	0	ALX4	44245705	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	5.817000	0.69229	2.700000	0.92200	0.462000	0.41574	CGT		PASS	0.597	ALX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390399.1			84	100	84	100	---	---	---	---
PPFIA1	8500	broad.mit.edu	37	11	70171633	70171633	+	Missense_Mutation	SNP	G	G	C			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr11:70171633G>C	ENST00000253925.7	+	5	774	c.559G>C	c.(559-561)Gaa>Caa	p.E187Q	AP000487.6_ENST00000528607.1_RNA|PPFIA1_ENST00000389547.3_Missense_Mutation_p.E187Q|CTA-797E19.2_ENST00000526017.1_RNA	NM_003626.3	NP_003617.1	Q13136	LIPA1_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1	187					cell-matrix adhesion (GO:0007160)|negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of stress fiber assembly (GO:0051497)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|presynaptic active zone (GO:0048786)	signal transducer activity (GO:0004871)	p.E187Q(1)		breast(3)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	65			BRCA - Breast invasive adenocarcinoma(2;1.04e-44)|LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)			AGTAGCACTTGAAAGATGTAG	0.368																																						uc001opo.2																			1	Substitution - Missense(1)		lung(1)	lung(2)|ovary(1)	3						c.(559-561)GAA>CAA		PTPRF interacting protein alpha 1 isoform b							114.0	112.0	112.0					11																	70171633		2200	4294	6494	SO:0001583	missense	8500				cell-matrix adhesion	cytoplasm	protein binding|signal transducer activity	g.chr11:70171633G>C	U22816	CCDS31627.1, CCDS31628.1	11q13.3	2013-01-10			ENSG00000131626	ENSG00000131626		"""Sterile alpha motif (SAM) domain containing"""	9245	protein-coding gene	gene with protein product	"""Liprin-alpha1"""	611054				7796809, 9624153	Standard	NM_003626		Approved	LIP.1, LIPRIN	uc001opo.3	Q13136	OTTHUMG00000167266	ENST00000253925.7:c.559G>C	11.37:g.70171633G>C	ENSP00000253925:p.Glu187Gln					PPFIA1_uc001opn.1_Missense_Mutation_p.E187Q|PPFIA1_uc001opp.2_RNA|PPFIA1_uc001opq.1_5'Flank	p.E187Q	NM_003626	NP_003617	Q13136	LIPA1_HUMAN	BRCA - Breast invasive adenocarcinoma(2;1.04e-44)|LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)		5	757	+			187			Potential.		A6NLE3|Q13135|Q14567|Q8N4I2	Missense_Mutation	SNP	ENST00000253925.7	37	c.559G>C	CCDS31627.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.246036	0.80024	.	.	ENSG00000131626	ENST00000253925;ENST00000389547	T;T	0.46063	0.88;0.88	5.12	5.12	0.69794	.	0.133460	0.48767	U	0.000174	T	0.54581	0.1867	M	0.74467	2.265	0.53688	D	0.999973	B;P	0.50943	0.198;0.94	B;P	0.47981	0.247;0.563	T	0.63256	-0.6678	10	0.87932	D	0	.	18.6421	0.91399	0.0:0.0:1.0:0.0	.	187;187	Q13136;Q13136-2	LIPA1_HUMAN;.	Q	187	ENSP00000253925:E187Q;ENSP00000374198:E187Q	ENSP00000253925:E187Q	E	+	1	0	PPFIA1	69849281	1.000000	0.71417	0.537000	0.28052	0.987000	0.75469	9.381000	0.97205	2.392000	0.81423	0.558000	0.71614	GAA		PASS	0.368	PPFIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393905.1	NM_003626		61	81	61	81	---	---	---	---
PPFIA1	8500	broad.mit.edu	37	11	70172894	70172894	+	Missense_Mutation	SNP	G	G	T			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr11:70172894G>T	ENST00000253925.7	+	7	1115	c.900G>T	c.(898-900)atG>atT	p.M300I	AP000487.6_ENST00000528607.1_RNA|PPFIA1_ENST00000389547.3_Missense_Mutation_p.M300I|CTA-797E19.2_ENST00000526017.1_RNA	NM_003626.3	NP_003617.1	Q13136	LIPA1_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1	300					cell-matrix adhesion (GO:0007160)|negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of stress fiber assembly (GO:0051497)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|presynaptic active zone (GO:0048786)	signal transducer activity (GO:0004871)	p.M300I(1)		breast(3)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	65			BRCA - Breast invasive adenocarcinoma(2;1.04e-44)|LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)			CTGAAGAAATGAACACAAAAT	0.398																																						uc001opo.2																			1	Substitution - Missense(1)		lung(1)	lung(2)|ovary(1)	3						c.(898-900)ATG>ATT		PTPRF interacting protein alpha 1 isoform b							119.0	116.0	117.0					11																	70172894		2200	4294	6494	SO:0001583	missense	8500				cell-matrix adhesion	cytoplasm	protein binding|signal transducer activity	g.chr11:70172894G>T	U22816	CCDS31627.1, CCDS31628.1	11q13.3	2013-01-10			ENSG00000131626	ENSG00000131626		"""Sterile alpha motif (SAM) domain containing"""	9245	protein-coding gene	gene with protein product	"""Liprin-alpha1"""	611054				7796809, 9624153	Standard	NM_003626		Approved	LIP.1, LIPRIN	uc001opo.3	Q13136	OTTHUMG00000167266	ENST00000253925.7:c.900G>T	11.37:g.70172894G>T	ENSP00000253925:p.Met300Ile					PPFIA1_uc001opn.1_Missense_Mutation_p.M300I|PPFIA1_uc001opp.2_RNA|PPFIA1_uc001opq.1_RNA	p.M300I	NM_003626	NP_003617	Q13136	LIPA1_HUMAN	BRCA - Breast invasive adenocarcinoma(2;1.04e-44)|LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)		7	1098	+			300			Potential.		A6NLE3|Q13135|Q14567|Q8N4I2	Missense_Mutation	SNP	ENST00000253925.7	37	c.900G>T	CCDS31627.1	.	.	.	.	.	.	.	.	.	.	G	13.00	2.106683	0.37145	.	.	ENSG00000131626	ENST00000253925;ENST00000389547	T;T	0.77620	-1.11;-1.11	4.58	2.62	0.31277	.	0.176147	0.46758	U	0.000279	T	0.64735	0.2625	L	0.36672	1.1	0.42647	D	0.993435	B;B	0.02656	0.0;0.0	B;B	0.08055	0.001;0.003	T	0.58555	-0.7616	10	0.32370	T	0.25	.	8.5911	0.33688	0.085:0.1557:0.7593:0.0	.	300;300	Q13136;Q13136-2	LIPA1_HUMAN;.	I	300	ENSP00000253925:M300I;ENSP00000374198:M300I	ENSP00000253925:M300I	M	+	3	0	PPFIA1	69850542	1.000000	0.71417	0.726000	0.30738	0.987000	0.75469	3.260000	0.51523	1.024000	0.39682	0.655000	0.94253	ATG		PASS	0.398	PPFIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393905.1	NM_003626		100	148	100	148	---	---	---	---
GUCY1A2	2977	broad.mit.edu	37	11	106849404	106849404	+	Missense_Mutation	SNP	G	G	C			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr11:106849404G>C	ENST00000526355.2	-	3	896	c.428C>G	c.(427-429)tCc>tGc	p.S143C	GUCY1A2_ENST00000347596.2_Missense_Mutation_p.S143C|GUCY1A2_ENST00000282249.2_Missense_Mutation_p.S143C	NM_000855.2	NP_000846.1	P33402	GCYA2_HUMAN	guanylate cyclase 1, soluble, alpha 2	143					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|positive regulation of cGMP biosynthetic process (GO:0030828)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)	p.S143C(1)		breast(5)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(18)|liver(1)|lung(32)|ovary(1)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	74		all_epithelial(67;3.66e-05)|Melanoma(852;0.000382)|Acute lymphoblastic leukemia(157;0.001)|all_hematologic(158;0.0017)|Breast(348;0.026)|all_neural(303;0.068)		BRCA - Breast invasive adenocarcinoma(274;8.04e-05)|Epithelial(105;0.0036)|all cancers(92;0.0476)	Isosorbide Mononitrate(DB01020)|Nitric Oxide(DB00435)	TTCTTTGTTGGAGTGGTCTGC	0.323																																						uc001pjg.1																			1	Substitution - Missense(1)		lung(1)	large_intestine(3)|lung(2)|pancreas(2)|ovary(1)	8						c.(427-429)TCC>TGC		guanylate cyclase 1, soluble, alpha 2							123.0	120.0	121.0					11																	106849404		2201	4298	6499	SO:0001583	missense	2977				intracellular signal transduction|platelet activation	cytoplasm	GTP binding|guanylate cyclase activity|heme binding	g.chr11:106849404G>C	X63282	CCDS8335.1, CCDS58170.1	11q21-q22	2008-03-18			ENSG00000152402	ENSG00000152402	4.6.1.2		4684	protein-coding gene	gene with protein product		601244		GUC1A2		1683630	Standard	NM_000855		Approved	GC-SA2	uc001pjg.2	P33402	OTTHUMG00000166296	ENST00000526355.2:c.428C>G	11.37:g.106849404G>C	ENSP00000431245:p.Ser143Cys					GUCY1A2_uc010rvo.1_Missense_Mutation_p.S143C|GUCY1A2_uc009yxn.1_Missense_Mutation_p.S143C	p.S143C	NM_000855	NP_000846	P33402	GCYA2_HUMAN		BRCA - Breast invasive adenocarcinoma(274;8.04e-05)|Epithelial(105;0.0036)|all cancers(92;0.0476)	3	818	-		all_epithelial(67;3.66e-05)|Melanoma(852;0.000382)|Acute lymphoblastic leukemia(157;0.001)|all_hematologic(158;0.0017)|Breast(348;0.026)|all_neural(303;0.068)	143					A1L4C4|B7ZLT5	Missense_Mutation	SNP	ENST00000526355.2	37	c.428C>G	CCDS8335.1	.	.	.	.	.	.	.	.	.	.	G	19.01	3.744571	0.69418	.	.	ENSG00000152402	ENST00000526355;ENST00000282249;ENST00000347596	D;D;D	0.88046	-2.0;-2.33;-2.01	5.73	5.73	0.89815	.	0.184175	0.25916	U	0.027465	D	0.89153	0.6634	L	0.36672	1.1	0.48830	D	0.999715	P;P;P	0.51537	0.928;0.946;0.928	P;P;P	0.56398	0.797;0.716;0.701	D	0.89218	0.3569	10	0.59425	D	0.04	.	18.8659	0.92292	0.0:0.0:1.0:0.0	.	143;143;143	B7ZLT5;P33402-2;P33402	.;.;GCYA2_HUMAN	C	143	ENSP00000431245:S143C;ENSP00000282249:S143C;ENSP00000344874:S143C	ENSP00000282249:S143C	S	-	2	0	GUCY1A2	106354614	1.000000	0.71417	1.000000	0.80357	0.640000	0.38277	5.316000	0.65815	2.882000	0.98803	0.655000	0.94253	TCC		PASS	0.323	GUCY1A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389003.2			58	66	58	66	---	---	---	---
WNK1	65125	broad.mit.edu	37	12	1017901	1017901	+	Silent	SNP	C	C	T			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr12:1017901C>T	ENST00000315939.6	+	28	7735	c.7092C>T	c.(7090-7092)atC>atT	p.I2364I	WNK1_ENST00000537687.1_Silent_p.I2624I|WNK1_ENST00000530271.2_Silent_p.I2862I|WNK1_ENST00000535572.1_Silent_p.I2116I|WNK1_ENST00000340908.4_Silent_p.I1957I	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	2364					intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)	p.I2624I(1)|p.I2364I(1)		breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			ATTTCAACATCAGCAATTTGC	0.547																																					Colon(19;451 567 6672 12618 28860)	uc001qio.3																			2	Substitution - coding silent(2)		lung(2)	stomach(6)|breast(6)|ovary(5)|lung(4)|large_intestine(1)|central_nervous_system(1)	23						c.(7090-7092)ATC>ATT		WNK lysine deficient protein kinase 1							65.0	67.0	66.0					12																	1017901		2203	4300	6503	SO:0001819	synonymous_variant	65125				intracellular protein kinase cascade|ion transport|neuron development	cytoplasm	ATP binding|protein binding|protein kinase inhibitor activity|protein serine/threonine kinase activity	g.chr12:1017901C>T	AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 167"""	605232	"""protein kinase, lysine deficient 1"", ""hereditary sensory neuropathy, type II"""	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.7092C>T	12.37:g.1017901C>T						WNK1_uc001qip.3_Silent_p.I2116I|WNK1_uc001qir.3_Silent_p.I1537I	p.I2364I	NM_018979	NP_061852	Q9H4A3	WNK1_HUMAN	Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)		28	7599	+	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		2364					A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Silent	SNP	ENST00000315939.6	37	c.7092C>T	CCDS8506.1																																																																																				PASS	0.547	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979		33	56	33	56	---	---	---	---
FAM90A1	55138	broad.mit.edu	37	12	8376647	8376647	+	Silent	SNP	C	C	T			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr12:8376647C>T	ENST00000538603.1	-	5	846	c.288G>A	c.(286-288)ttG>ttA	p.L96L	FAM90A1_ENST00000307435.6_Silent_p.L96L	NM_018088.3	NP_060558.3	Q86YD7	F90A1_HUMAN	family with sequence similarity 90, member A1	96							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.L96L(1)		endometrium(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	25				Kidney(36;0.0866)		TATCCTTGTTCAAGGGCCCAG	0.542																																						uc001qui.2																			1	Substitution - coding silent(1)		lung(1)	ovary(1)	1						c.(286-288)TTG>TTA		hypothetical protein LOC55138							97.0	119.0	111.0					12																	8376647		2203	4300	6503	SO:0001819	synonymous_variant	55138						nucleic acid binding|zinc ion binding	g.chr12:8376647C>T	AK001270	CCDS31738.1	12p13.31	2011-08-31		2005-11-20	ENSG00000171847	ENSG00000171847			25526	protein-coding gene	gene with protein product		613041					Standard	NM_018088		Approved	FLJ10408	uc001qui.2	Q86YD7	OTTHUMG00000168641	ENST00000538603.1:c.288G>A	12.37:g.8376647C>T						FAM90A1_uc001quh.2_Silent_p.L96L	p.L96L	NM_018088	NP_060558	Q86YD7	F90A1_HUMAN		Kidney(36;0.0866)	5	847	-			96					D3DUU9|Q9NVZ6	Silent	SNP	ENST00000538603.1	37	c.288G>A	CCDS31738.1																																																																																				PASS	0.542	FAM90A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400468.1	NM_018088		148	159	148	159	---	---	---	---
STYK1	55359	broad.mit.edu	37	12	10772780	10772780	+	Missense_Mutation	SNP	C	C	G			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr12:10772780C>G	ENST00000075503.3	-	11	1752	c.1232G>C	c.(1231-1233)aGa>aCa	p.R411T		NM_018423.2	NP_060893.2	Q6J9G0	STYK1_HUMAN	serine/threonine/tyrosine kinase 1	411						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)	p.R411T(1)		breast(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|liver(1)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	26						GCTCTCCACTCTGATGCCGGC	0.458										HNSCC(73;0.22)																												uc001qys.2																			1	Substitution - Missense(1)		lung(1)	central_nervous_system(3)|ovary(2)|lung(2)|breast(1)	8						c.(1231-1233)AGA>ACA		serine/threonine/tyrosine kinase 1							160.0	154.0	156.0					12																	10772780		2203	4300	6503	SO:0001583	missense	55359					integral to membrane|plasma membrane	ATP binding|non-membrane spanning protein tyrosine kinase activity	g.chr12:10772780C>G	AF251059	CCDS8629.1	12p13.2	2005-01-21							18889	protein-coding gene	gene with protein product		611433				12841579	Standard	NM_018423		Approved	SuRTK106, DKFZp761P1010, NOK	uc001qys.2	Q6J9G0		ENST00000075503.3:c.1232G>C	12.37:g.10772780C>G	ENSP00000075503:p.Arg411Thr	HNSCC(73;0.22)					p.R411T	NM_018423	NP_060893	Q6J9G0	STYK1_HUMAN			11	1753	-			411					B2R9T2|Q52LR3|Q9BXY2|Q9NSH1	Missense_Mutation	SNP	ENST00000075503.3	37	c.1232G>C	CCDS8629.1	.	.	.	.	.	.	.	.	.	.	C	8.412	0.844307	0.16963	.	.	ENSG00000060140	ENST00000075503	T	0.77620	-1.11	4.96	4.0	0.46444	.	0.636602	0.15583	N	0.254802	T	0.64757	0.2627	L	0.36672	1.1	0.09310	N	0.99999	B	0.15473	0.013	B	0.14023	0.01	T	0.48768	-0.9006	10	0.30078	T	0.28	-1.2267	6.2127	0.20638	0.0:0.7088:0.1909:0.1004	.	411	Q6J9G0	STYK1_HUMAN	T	411	ENSP00000075503:R411T	ENSP00000075503:R411T	R	-	2	0	STYK1	10664047	0.014000	0.17966	0.841000	0.33234	0.795000	0.44927	0.235000	0.17948	2.279000	0.76181	0.563000	0.77884	AGA		PASS	0.458	STYK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399622.1	NM_018423		200	250	200	250	---	---	---	---
KRAS	3845	broad.mit.edu	37	12	25378645	25378645	+	Missense_Mutation	SNP	C	C	G			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr12:25378645C>G	ENST00000256078.4	-	4	416	c.353G>C	c.(352-354)tGt>tCt	p.C118S	KRAS_ENST00000311936.3_Missense_Mutation_p.C118S|KRAS_ENST00000557334.1_Intron|AC087239.1_ENST00000594112.1_5'Flank	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	118					actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.C118S(2)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			AGGCAAATCACATTTATTTCC	0.353		119	Mis		"""pancreatic, colorectal, lung, thyroid, AML, others"""				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	uc001rgp.1		119		Dom	yes		12	12p12.1	3845	Mis	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog			"""L, E, M, O"""			pancreatic|colorectal|lung|thyroid|AML|others		2	Substitution - Missense(2)		lung(2)	large_intestine(12391)|pancreas(3285)|lung(2847)|biliary_tract(521)|ovary(443)|endometrium(339)|haematopoietic_and_lymphoid_tissue(318)|stomach(203)|thyroid(149)|prostate(85)|soft_tissue(77)|small_intestine(62)|upper_aerodigestive_tract(59)|cervix(49)|urinary_tract(48)|skin(38)|liver(31)|breast(28)|testis(17)|oesophagus(15)|central_nervous_system(9)|peritoneum(6)|salivary_gland(6)|kidney(5)|gastrointestinal_tract_(site_indeterminate)(5)|thymus(5)|eye(4)|autonomic_ganglia(2)|bone(2)|genital_tract(1)|penis(1)|adrenal_gland(1)	21052						c.(352-354)TGT>TCT		c-K-ras2 protein isoform a precursor							167.0	151.0	157.0					12																	25378645		2202	4300	6502	SO:0001583	missense	3845	Cardiofaciocutaneous_syndrome|Noonan_syndrome	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	plasma membrane	GTP binding|GTPase activity|protein binding	g.chr12:25378645C>G	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"""v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog"", ""v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"""	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.353G>C	12.37:g.25378645C>G	ENSP00000256078:p.Cys118Ser	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)				KRAS_uc001rgq.1_Missense_Mutation_p.C118S	p.C118S	NM_033360	NP_203524	P01116	RASK_HUMAN	OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)		4	534	-	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		118			GTP.		A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	c.353G>C	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	17.39	3.378752	0.61735	.	.	ENSG00000133703	ENST00000311936;ENST00000256078	T;T	0.79352	-1.26;-0.35	5.52	5.52	0.82312	Small GTP-binding protein domain (1);	0.082023	0.85682	D	0.000000	T	0.66684	0.2814	N	0.13235	0.315	0.80722	D	1	B;B	0.19817	0.038;0.039	B;B	0.17979	0.01;0.02	T	0.62854	-0.6766	10	0.56958	D	0.05	.	18.7849	0.91951	0.0:1.0:0.0:0.0	.	118;118	P01116-2;P01116	.;RASK_HUMAN	S	118	ENSP00000308495:C118S;ENSP00000256078:C118S	ENSP00000256078:C118S	C	-	2	0	KRAS	25269912	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.762000	0.85270	2.757000	0.94681	0.585000	0.79938	TGT		PASS	0.353	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		103	109	103	109	---	---	---	---
KMT2D	8085	broad.mit.edu	37	12	49427255	49427255	+	Nonsense_Mutation	SNP	G	G	A			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr12:49427255G>A	ENST00000301067.7	-	39	11232	c.11233C>T	c.(11233-11235)Cag>Tag	p.Q3745*	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	3745	Gln-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.Q3475*(1)|p.Q3745*(1)									AGAAGGtgctgctgctgctgt	0.577																																						uc001rta.3										N|F|Mis							medulloblastoma|renal		2	Substitution - Nonsense(2)		lung(2)	kidney(16)|central_nervous_system(12)|lung(4)|skin(4)|ovary(3)|pancreas(2)	41						c.(11233-11235)CAG>TAG		myeloid/lymphoid or mixed-lineage leukemia 2							15.0	18.0	17.0					12																	49427255		2196	4292	6488	SO:0001587	stop_gained	8085				chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent	histone methyltransferase complex	histone-lysine N-methyltransferase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding	g.chr12:49427255G>A	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7133	protein-coding gene	gene with protein product		602113	"""trinucleotide repeat containing 21"", ""myeloid/lymphoid or mixed-lineage leukemia 2"""	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.11233C>T	12.37:g.49427255G>A	ENSP00000301067:p.Gln3745*	HNSCC(34;0.089)					p.Q3745*	NM_003482	NP_003473	O14686	MLL2_HUMAN			39	11233	-			3745			Potential.|Gln-rich.		O14687	Nonsense_Mutation	SNP	ENST00000301067.7	37	c.11233C>T	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	G	50	17.028974	0.99877	.	.	ENSG00000167548	ENST00000301067	.	.	.	4.17	4.17	0.49024	.	0.000000	0.33180	N	0.005189	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	16.1063	0.81225	0.0:0.0:1.0:0.0	.	.	.	.	X	3745	.	ENSP00000301067:Q3745X	Q	-	1	0	MLL2	47713522	1.000000	0.71417	1.000000	0.80357	0.433000	0.31745	8.815000	0.91973	2.243000	0.73865	0.462000	0.41574	CAG		PASS	0.577	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			6	7	6	7	---	---	---	---
KCNH3	23416	broad.mit.edu	37	12	49951431	49951431	+	Nonsense_Mutation	SNP	C	C	T			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr12:49951431C>T	ENST00000257981.6	+	15	3207	c.2947C>T	c.(2947-2949)Cag>Tag	p.Q983*	MCRS1_ENST00000547182.1_5'Flank	NM_012284.1	NP_036416.1	Q9ULD8	KCNH3_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 3	983	Pro-rich.				potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)	p.Q983*(1)		NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(20)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36						CCCAGCGTCTCAGAGCTCCCC	0.692																																						uc001ruh.1																			1	Substitution - Nonsense(1)		lung(1)		0						c.(2947-2949)CAG>TAG		potassium voltage-gated channel, subfamily H							40.0	44.0	43.0					12																	49951431		2203	4300	6503	SO:0001587	stop_gained	23416				regulation of transcription, DNA-dependent	integral to membrane	two-component sensor activity|voltage-gated potassium channel activity	g.chr12:49951431C>T	AB022696	CCDS8786.1	12q13	2012-07-05				ENSG00000135519		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6252	protein-coding gene	gene with protein product		604527				10455180, 16382104	Standard	NM_012284		Approved	Kv12.2, BEC1, elk2	uc001ruh.1	Q9ULD8	OTTHUMG00000169517	ENST00000257981.6:c.2947C>T	12.37:g.49951431C>T	ENSP00000257981:p.Gln983*					KCNH3_uc010smj.1_Nonsense_Mutation_p.Q923*	p.Q983*	NM_012284	NP_036416	Q9ULD8	KCNH3_HUMAN			15	3207	+			983			Pro-rich.|Cytoplasmic (Potential).		Q9UQ06	Nonsense_Mutation	SNP	ENST00000257981.6	37	c.2947C>T	CCDS8786.1	.	.	.	.	.	.	.	.	.	.	C	39	7.865063	0.98531	.	.	ENSG00000135519	ENST00000257981	.	.	.	5.02	5.02	0.67125	.	0.000000	0.39475	N	0.001347	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07175	T	0.84	.	13.7179	0.62710	0.0:1.0:0.0:0.0	.	.	.	.	X	983	.	ENSP00000257981:Q983X	Q	+	1	0	KCNH3	48237698	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.154000	0.64894	2.607000	0.88179	0.561000	0.74099	CAG		PASS	0.692	KCNH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404571.2	NM_012284		44	69	44	69	---	---	---	---
BBS10	79738	broad.mit.edu	37	12	76741254	76741254	+	Missense_Mutation	SNP	C	C	G			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr12:76741254C>G	ENST00000393262.3	-	2	594	c.511G>C	c.(511-513)Gag>Cag	p.E171Q		NM_024685.3	NP_078961.3	Q8TAM1	BBS10_HUMAN	Bardet-Biedl syndrome 10	171					cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|regulation of protein complex assembly (GO:0043254)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	cell projection (GO:0042995)	ATP binding (GO:0005524)|RNA polymerase II repressing transcription factor binding (GO:0001103)	p.E171Q(1)		endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)	19						AAGAGCAACTCTAAAGAGCTC	0.353									Bardet-Biedl syndrome																													uc001syd.1																			1	Substitution - Missense(1)		lung(1)	ovary(1)|skin(1)	2						c.(511-513)GAG>CAG		Bardet-Biedl syndrome 10							64.0	59.0	61.0					12																	76741254		2203	4300	6503	SO:0001583	missense	79738	Bardet-Biedl_syndrome	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	cellular protein metabolic process|nonmotile primary cilium assembly|photoreceptor cell maintenance|response to stimulus|retina homeostasis	cilium	ATP binding	g.chr12:76741254C>G	BC026355	CCDS9014.2	12q21.2	2014-06-17	2006-04-28	2006-04-28	ENSG00000179941	ENSG00000179941		"""Heat Shock Proteins / Chaperonins"""	26291	protein-coding gene	gene with protein product		610148	"""chromosome 12 open reading frame 58"""	C12orf58		16582908	Standard	NM_024685		Approved	FLJ23560	uc001syd.1	Q8TAM1	OTTHUMG00000147352	ENST00000393262.3:c.511G>C	12.37:g.76741254C>G	ENSP00000376946:p.Glu171Gln						p.E171Q	NM_024685	NP_078961	Q8TAM1	BBS10_HUMAN			2	595	-			171					Q96CW2|Q9H5D2	Missense_Mutation	SNP	ENST00000393262.3	37	c.511G>C	CCDS9014.2	.	.	.	.	.	.	.	.	.	.	C	6.996	0.553934	0.13374	.	.	ENSG00000179941	ENST00000393262	T	0.78924	-1.22	5.13	2.17	0.27698	.	0.453160	0.21628	N	0.071535	T	0.68622	0.3021	L	0.50333	1.59	0.19300	N	0.999972	B	0.17465	0.022	B	0.17433	0.018	T	0.53844	-0.8381	10	0.24483	T	0.36	-1.7177	9.8819	0.41238	0.1451:0.3925:0.4625:0.0	.	171	Q8TAM1	BBS10_HUMAN	Q	171	ENSP00000376946:E171Q	ENSP00000376946:E171Q	E	-	1	0	BBS10	75265385	0.238000	0.23825	0.176000	0.23000	0.932000	0.56968	0.097000	0.15168	0.356000	0.24157	0.650000	0.86243	GAG		PASS	0.353	BBS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303983.2	NM_024685		67	71	67	71	---	---	---	---
CCDC60	160777	broad.mit.edu	37	12	119909929	119909929	+	Missense_Mutation	SNP	G	G	A			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr12:119909929G>A	ENST00000327554.2	+	3	766	c.301G>A	c.(301-303)Gaa>Aaa	p.E101K	RP11-768F21.1_ENST00000509470.2_lincRNA|CCDC60_ENST00000546345.1_3'UTR	NM_178499.3	NP_848594.2	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60	101								p.E101K(2)		endometrium(4)|kidney(3)|large_intestine(8)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)		CCAGCCAGCCGAAAAGATCTC	0.423																																						uc001txe.2																			2	Substitution - Missense(2)		lung(1)|skin(1)	ovary(2)|upper_aerodigestive_tract(1)	3						c.(301-303)GAA>AAA		coiled-coil domain containing 60							160.0	166.0	164.0					12																	119909929		2203	4300	6503	SO:0001583	missense	160777							g.chr12:119909929G>A	BC040553	CCDS9190.1	12q24.23	2006-02-03			ENSG00000183273	ENSG00000183273			28610	protein-coding gene	gene with protein product						12477932	Standard	NM_178499		Approved	MGC39827	uc001txe.3	Q8IWA6	OTTHUMG00000168943	ENST00000327554.2:c.301G>A	12.37:g.119909929G>A	ENSP00000333374:p.Glu101Lys					uc001txf.2_Intron	p.E101K	NM_178499	NP_848594	Q8IWA6	CCD60_HUMAN		BRCA - Breast invasive adenocarcinoma(302;0.207)	3	766	+	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)		101						Missense_Mutation	SNP	ENST00000327554.2	37	c.301G>A	CCDS9190.1	.	.	.	.	.	.	.	.	.	.	G	1.545	-0.540681	0.04053	.	.	ENSG00000183273	ENST00000327554	T	0.21361	2.01	5.22	2.8	0.32819	.	0.477213	0.19451	N	0.113928	T	0.06325	0.0163	N	0.01705	-0.755	0.33283	D	0.562555	B	0.09022	0.002	B	0.04013	0.001	T	0.26780	-1.0093	9	.	.	.	-6.4841	4.9568	0.14046	0.715:0.1871:0.0978:0.0	.	101	Q8IWA6	CCD60_HUMAN	K	101	ENSP00000333374:E101K	.	E	+	1	0	CCDC60	118394312	0.704000	0.27836	0.569000	0.28460	0.315000	0.28087	1.025000	0.30090	0.289000	0.22422	-0.481000	0.04817	GAA		PASS	0.423	CCDC60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401680.1	NM_178499		180	244	180	244	---	---	---	---
ANKLE2	23141	broad.mit.edu	37	12	133324434	133324434	+	Missense_Mutation	SNP	T	T	G			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr12:133324434T>G	ENST00000357997.5	-	5	1303	c.1214A>C	c.(1213-1215)aAc>aCc	p.N405T	ANKLE2_ENST00000337516.5_Missense_Mutation_p.N405T|ANKLE2_ENST00000539605.1_Missense_Mutation_p.N343T	NM_015114.1	NP_055929.1	Q86XL3	ANKL2_HUMAN	ankyrin repeat and LEM domain containing 2	405					mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope reassembly (GO:0007084)|negative regulation of phosphorylation (GO:0042326)|positive regulation of protein dephosphorylation (GO:0035307)|regulation of catalytic activity (GO:0050790)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	protein phosphatase 2A binding (GO:0051721)|protein phosphatase type 2A regulator activity (GO:0008601)	p.N405T(1)		NS(2)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|lung(20)|ovary(1)|urinary_tract(2)	45	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.3e-08)|Epithelial(86;1.56e-07)|all cancers(50;4.94e-06)		GTCGGGGGTGTTGAGGTACAG	0.498																																						uc001ukx.2																			1	Substitution - Missense(1)		lung(1)		0						c.(1213-1215)AAC>ACC		ankyrin repeat and LEM domain containing 2							112.0	115.0	114.0					12																	133324434		2155	4255	6410	SO:0001583	missense	23141					cytoplasm|integral to membrane|nuclear envelope		g.chr12:133324434T>G	AB014592	CCDS41869.1	12q24.33	2013-01-11	2008-03-25	2008-03-25	ENSG00000176915	ENSG00000176915		"""Ankyrin repeat domain containing"""	29101	protein-coding gene	gene with protein product	"""LEM domain containing 7"""		"""KIAA0692"""	KIAA0692		9734811	Standard	XM_005266159		Approved	LEMD7, Lem4	uc001ukx.2	Q86XL3	OTTHUMG00000168046	ENST00000357997.5:c.1214A>C	12.37:g.133324434T>G	ENSP00000350686:p.Asn405Thr					ANKLE2_uc001uky.3_Missense_Mutation_p.N343T	p.N405T	NM_015114	NP_055929	Q86XL3	ANKL2_HUMAN		OV - Ovarian serous cystadenocarcinoma(86;2.3e-08)|Epithelial(86;1.56e-07)|all cancers(50;4.94e-06)	5	1281	-	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)	405					A8KAG3|B3KN97|B3KSF8|O75176|Q6P6A5|Q8TAZ9|Q96DH4	Missense_Mutation	SNP	ENST00000357997.5	37	c.1214A>C	CCDS41869.1	.	.	.	.	.	.	.	.	.	.	t	15.90	2.968618	0.53614	.	.	ENSG00000176915	ENST00000539605;ENST00000357997;ENST00000337516;ENST00000545623;ENST00000546061	T;T;T;T;T	0.71222	0.91;0.91;-0.55;-0.55;0.91	5.7	5.7	0.88788	Ankyrin repeat-containing domain (2);	0.000000	0.85682	D	0.000000	D	0.86632	0.5979	M	0.89095	3.005	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.89235	0.3580	10	0.87932	D	0	-22.7689	15.9735	0.80040	0.0:0.0:0.0:1.0	.	405;405	Q86XL3-2;Q86XL3	.;ANKL2_HUMAN	T	343;405;405;175;51	ENSP00000446268:N343T;ENSP00000350686:N405T;ENSP00000337651:N405T;ENSP00000438515:N175T;ENSP00000445718:N51T	ENSP00000337651:N405T	N	-	2	0	ANKLE2	131834507	1.000000	0.71417	0.886000	0.34754	0.010000	0.07245	7.567000	0.82357	2.159000	0.67721	0.533000	0.62120	AAC		PASS	0.498	ANKLE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397712.1			52	73	52	73	---	---	---	---
PARP4	143	broad.mit.edu	37	13	25049640	25049640	+	Silent	SNP	G	G	A			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr13:25049640G>A	ENST00000381989.3	-	15	1989	c.1884C>T	c.(1882-1884)atC>atT	p.I628I		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	628	VIT. {ECO:0000255|PROSITE- ProRule:PRU00801}.				cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.I628I(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		TTCTCCCTTTGATGTGGACAT	0.463																																						uc001upl.2																			1	Substitution - coding silent(1)		lung(1)	ovary(3)|skin(1)	4						c.(1882-1884)ATC>ATT		poly (ADP-ribose) polymerase family, member 4							115.0	113.0	114.0					13																	25049640		2203	4300	6503	SO:0001819	synonymous_variant	143				cell death|DNA repair|inflammatory response|protein ADP-ribosylation|response to drug|transport	cytoplasm|nucleus|ribonucleoprotein complex|spindle microtubule	DNA binding|enzyme binding|NAD+ ADP-ribosyltransferase activity	g.chr13:25049640G>A	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.1884C>T	13.37:g.25049640G>A						PARP4_uc010tdc.1_Silent_p.I628I	p.I628I	NM_006437	NP_006428	Q9UKK3	PARP4_HUMAN		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)	15	1990	-		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)	628			VIT.		O75903|Q14682|Q5QNZ9|Q9H1M6	Silent	SNP	ENST00000381989.3	37	c.1884C>T	CCDS9307.1																																																																																				PASS	0.463	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437		98	152	98	152	---	---	---	---
BRCA2	675	broad.mit.edu	37	13	32944665	32944665	+	Missense_Mutation	SNP	G	G	A	rs80359095		TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr13:32944665G>A	ENST00000380152.3	+	19	8691	c.8458G>A	c.(8458-8460)Gta>Ata	p.V2820I	BRCA2_ENST00000544455.1_Missense_Mutation_p.V2820I			P51587	BRCA2_HUMAN	breast cancer 2, early onset	2820					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)	p.V2820I(2)		NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		TTGTGTTGATGTAATTATTCA	0.353			"""D, Mis, N, F, S"""		"""breast, ovarian, pancreatic"""	"""breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"""		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	uc001uub.1			yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	D|Mis|N|F|S	familial breast/ovarian cancer gene 2			"""L, E"""		breast|ovarian|pancreatic|leukemia  (FANCB|FANCD1)	breast|ovarian|pancreatic		2	Substitution - Missense(2)		lung(2)	ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1)	64						c.(8458-8460)GTA>ATA	Direct_reversal_of_damage|Homologous_recombination	breast cancer 2, early onset							146.0	130.0	136.0					13																	32944665		2203	4300	6503	SO:0001583	missense	675	Fanconi_Anemia_type_D1_bi-allelic_BRCA2_mutations|Fanconi_Anemia|Pancreatic_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_BRCA2_type|Hereditary_Prostate_Cancer|Li-Fraumeni_syndrome	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle	BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule	gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding	g.chr13:32944665G>A	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"""Fanconi anemia, complementation groups"""	1101	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 2"""	600185	"""Fanconi anemia, complementation group D1"""	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.8458G>A	13.37:g.32944665G>A	ENSP00000369497:p.Val2820Ile	TCGA Ovarian(8;0.087)					p.V2820I	NM_000059	NP_000050	P51587	BRCA2_HUMAN		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)	19	8685	+		Lung SC(185;0.0262)	2820					O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	c.8458G>A	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	G	13.95	2.391090	0.42410	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.73681	-0.77;-0.77	5.19	1.33	0.21861	Nucleic acid-binding, OB-fold-like (1);	0.365877	0.27932	N	0.017271	T	0.51160	0.1658	N	0.11756	0.17	0.30311	N	0.788568	B	0.23591	0.088	B	0.15870	0.014	T	0.42616	-0.9441	10	0.24483	T	0.36	.	9.7185	0.40289	0.2988:0.0:0.7012:0.0	.	2820	P51587	BRCA2_HUMAN	I	2820	ENSP00000369497:V2820I;ENSP00000439902:V2820I	ENSP00000369497:V2820I	V	+	1	0	BRCA2	31842665	0.992000	0.36948	0.012000	0.15200	0.945000	0.59286	0.403000	0.20982	0.171000	0.19730	-0.266000	0.10368	GTA		PASS	0.353	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		72	106	72	106	---	---	---	---
KL	9365	broad.mit.edu	37	13	33590885	33590885	+	Missense_Mutation	SNP	G	G	A	rs548833535		TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr13:33590885G>A	ENST00000380099.3	+	1	315	c.307G>A	c.(307-309)Gac>Aac	p.D103N	KL_ENST00000426690.2_Intron|KL_ENST00000487852.1_3'UTR	NM_004795.3	NP_004786.2	Q9UEF7	KLOT_HUMAN	klotho	103	Glycosyl hydrolase-1 1.				acute inflammatory response (GO:0002526)|aging (GO:0007568)|calcium ion homeostasis (GO:0055074)|carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-glucosidase activity (GO:0008422)|beta-glucuronidase activity (GO:0004566)|fibroblast growth factor binding (GO:0017134)|signal transducer activity (GO:0004871)|vitamin D binding (GO:0005499)	p.D103N(1)		breast(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|skin(5)	41	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		ACCCCCGGGAGACTCCCGGAA	0.711																																						uc001uus.2																			1	Substitution - Missense(1)		lung(1)	large_intestine(1)|ovary(1)|skin(1)	3						c.(307-309)GAC>AAC		klotho precursor							10.0	13.0	12.0					13																	33590885		2119	4181	6300	SO:0001583	missense	9365				aging|carbohydrate metabolic process|insulin receptor signaling pathway|positive regulation of bone mineralization	extracellular space|extracellular space|integral to membrane|integral to plasma membrane|membrane fraction|soluble fraction	beta-glucosidase activity|beta-glucuronidase activity|cation binding|fibroblast growth factor binding|hormone activity|signal transducer activity|vitamin D binding	g.chr13:33590885G>A	AB005142	CCDS9347.1	13q12	2008-02-05			ENSG00000133116	ENSG00000133116			6344	protein-coding gene	gene with protein product		604824				9464267	Standard	NM_004795		Approved		uc001uus.3	Q9UEF7	OTTHUMG00000017408	ENST00000380099.3:c.307G>A	13.37:g.33590885G>A	ENSP00000369442:p.Asp103Asn					KL_uc001uur.1_Intron	p.D103N	NM_004795	NP_004786	Q9UEF7	KLOT_HUMAN		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)	1	315	+	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)	103			Glycosyl hydrolase-1 1.|Extracellular (Potential).		Q5VZ95|Q96KV5|Q96KW5|Q9UEI9|Q9Y4F0	Missense_Mutation	SNP	ENST00000380099.3	37	c.307G>A	CCDS9347.1	.	.	.	.	.	.	.	.	.	.	G	0.540	-0.854068	0.02630	.	.	ENSG00000133116	ENST00000380099	T	0.32753	1.44	3.73	2.88	0.33553	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	1.254550	0.05570	N	0.571023	T	0.23965	0.0580	N	0.22421	0.69	0.09310	N	1	B	0.31413	0.322	B	0.31686	0.134	T	0.30327	-0.9982	10	0.41790	T	0.15	-4.746	9.3655	0.38221	0.1041:0.0:0.8959:0.0	.	103	Q9UEF7	KLOT_HUMAN	N	103	ENSP00000369442:D103N	ENSP00000369442:D103N	D	+	1	0	KL	32488885	0.372000	0.25064	0.001000	0.08648	0.005000	0.04900	1.364000	0.34171	0.792000	0.33850	-0.448000	0.05591	GAC		PASS	0.711	KL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045987.1			20	28	20	28	---	---	---	---
YLPM1	56252	broad.mit.edu	37	14	75287820	75287820	+	Missense_Mutation	SNP	G	G	C			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr14:75287820G>C	ENST00000552421.1	+	16	4097	c.3973G>C	c.(3973-3975)Gag>Cag	p.E1325Q	YLPM1_ENST00000238571.3_Missense_Mutation_p.E1796Q|YLPM1_ENST00000325680.7_Missense_Mutation_p.E2031Q|YLPM1_ENST00000546901.1_3'UTR			P49750	YLPM1_HUMAN	YLP motif containing 1	1836					regulation of telomere maintenance (GO:0032204)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)	p.E1796Q(1)|p.E2031Q(1)		breast(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	62			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		GAAAGATGCAGAGGAAGAGGA	0.333																																						uc001xqj.3																			2	Substitution - Missense(2)		lung(2)	ovary(2)|pancreas(1)	3						c.(6091-6093)GAG>CAG		YLP motif containing 1							58.0	73.0	68.0					14																	75287820		1820	4038	5858	SO:0001583	missense	56252				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck		g.chr14:75287820G>C	AK090435	CCDS45135.1	14q24.3	2014-06-13	2004-07-15	2004-07-15	ENSG00000119596	ENSG00000119596			17798	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 169"""		"""chromosome 14 open reading frame 170"""	C14orf170		7596406	Standard	NM_019589		Approved	ZAP, PPP1R169	uc001xqj.4	P49750	OTTHUMG00000172503	ENST00000552421.1:c.3973G>C	14.37:g.75287820G>C	ENSP00000447921:p.Glu1325Gln					YLPM1_uc001xql.3_RNA|YLPM1_uc001xqm.1_Missense_Mutation_p.E514Q	p.E2031Q	NM_019589	NP_062535	P49750	YLPM1_HUMAN	KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)	17	6215	+			1836					P49752|Q96I64|Q9P1V7	Missense_Mutation	SNP	ENST00000552421.1	37	c.6091G>C		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.20|17.20	3.329300|3.329300	0.60743|0.60743	.|.	.|.	ENSG00000119596|ENSG00000119596	ENST00000552421;ENST00000325680;ENST00000238571;ENST00000423680;ENST00000547879|ENST00000554107	.|.	.|.	.|.	5.76|5.76	5.76|5.76	0.90799|0.90799	.|.	0.000000|.	0.64402|.	D|.	0.000006|.	T|T	0.58337|0.58337	0.2115|0.2115	L|L	0.36672|0.36672	1.1|1.1	0.46279|0.46279	D|D	0.998966|0.998966	P;D|.	0.67145|.	0.827;0.996|.	P;D|.	0.71656|.	0.526;0.974|.	T|T	0.52571|0.52571	-0.8558|-0.8558	9|5	0.18276|.	T|.	0.48|.	-13.6594|-13.6594	15.141|15.141	0.72609|0.72609	0.0695:0.0:0.9305:0.0|0.0695:0.0:0.9305:0.0	.|.	1836;2031|.	P49750-3;P49750-4|.	.;.|.	Q|T	1325;2031;1796;1744;440|62	.|.	ENSP00000238571:E1796Q|.	E|R	+|+	1|2	0|0	YLPM1|YLPM1	74357573|74357573	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	7.444000|7.444000	0.80532|0.80532	2.726000|2.726000	0.93360|0.93360	0.655000|0.655000	0.94253|0.94253	GAG|AGA		PASS	0.333	YLPM1-008	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404450.1	NM_019589		4	4	4	4	---	---	---	---
ZNF839	55778	broad.mit.edu	37	14	102792953	102792953	+	Missense_Mutation	SNP	C	C	T			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr14:102792953C>T	ENST00000558850.1	+	2	922	c.572C>T	c.(571-573)tCc>tTc	p.S191F	ZNF839_ENST00000559185.1_Missense_Mutation_p.S191F|ZNF839_ENST00000262236.5_Missense_Mutation_p.S191F|ZNF839_ENST00000442396.2_Missense_Mutation_p.S307F	NM_001267827.1	NP_001254756.1	A8K0R7	ZN839_HUMAN	zinc finger protein 839	191							metal ion binding (GO:0046872)	p.S307F(1)		breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						TCGAGCTGCTCCCTGAGGCCC	0.483																																						uc001ylo.2																			1	Substitution - Missense(1)		lung(1)	ovary(1)|central_nervous_system(1)	2						c.(571-573)TCC>TTC		zinc finger protein 839							35.0	34.0	34.0					14																	102792953		1896	4119	6015	SO:0001583	missense	55778					intracellular	zinc ion binding	g.chr14:102792953C>T	AK093342	CCDS45164.1, CCDS58336.1	14q32.32	2010-05-06	2008-06-23	2008-06-23	ENSG00000022976	ENSG00000022976			20345	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 131"""	C14orf131			Standard	NM_018335		Approved		uc010awk.2	A8K0R7		ENST00000558850.1:c.572C>T	14.37:g.102792953C>T	ENSP00000453363:p.Ser191Phe					ZNF839_uc010awk.1_Missense_Mutation_p.S307F|ZNF839_uc001ylp.2_RNA|ZNF839_uc001ylq.1_Missense_Mutation_p.S191F|ZNF839_uc001ylr.2_Missense_Mutation_p.S191F	p.S191F	NM_018335	NP_060805	A8K0R7	ZN839_HUMAN			2	922	+			191					B3KSD2|Q53FH5|Q6GPI5|Q86TU1|Q9BQ86|Q9NUU3	Missense_Mutation	SNP	ENST00000558850.1	37	c.572C>T	CCDS58336.1	.	.	.	.	.	.	.	.	.	.	C	11.90	1.776459	0.31411	.	.	ENSG00000022976	ENST00000442396;ENST00000262236	T;T	0.48522	0.81;0.81	4.79	2.76	0.32466	.	.	.	.	.	T	0.48333	0.1494	L	0.55481	1.735	0.09310	N	1	P;P;P;P	0.50528	0.936;0.878;0.878;0.878	P;P;P;P	0.49477	0.612;0.458;0.458;0.458	T	0.31668	-0.9935	9	0.49607	T	0.09	.	7.4929	0.27473	0.2528:0.6488:0.0:0.0984	.	307;191;70;191	A8K0R7-5;A8K0R7-2;Q9NT83;A8K0R7	.;.;.;ZN839_HUMAN	F	307;191	ENSP00000399863:S307F;ENSP00000262236:S191F	ENSP00000262236:S191F	S	+	2	0	ZNF839	101862706	0.825000	0.29262	0.442000	0.26870	0.769000	0.43574	2.644000	0.46613	1.029000	0.39812	0.650000	0.86243	TCC		PASS	0.483	ZNF839-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000415492.2	NM_018335		20	23	20	23	---	---	---	---
AHNAK2	113146	broad.mit.edu	37	14	105409053	105409053	+	Silent	SNP	C	C	G	rs574649015	byFrequency	TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr14:105409053C>G	ENST00000333244.5	-	7	12854	c.12735G>C	c.(12733-12735)ctG>ctC	p.L4245L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4245						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)		p.L4245L(2)		cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			TGGGGCCTTTCAGGTCCAGCT	0.637																																						uc010axc.1																			2	Substitution - coding silent(2)		lung(2)	ovary(1)	1						c.(12733-12735)CTG>CTC		AHNAK nucleoprotein 2							114.0	125.0	121.0					14																	105409053		1880	4106	5986	SO:0001819	synonymous_variant	113146					nucleus		g.chr14:105409053C>G	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.12735G>C	14.37:g.105409053C>G						AHNAK2_uc001ypx.2_Silent_p.L4145L	p.L4245L	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)		7	12855	-		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	4245					Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	c.12735G>C	CCDS45177.1																																																																																				PASS	0.637	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		157	186	157	186	---	---	---	---
AHNAK2	113146	broad.mit.edu	37	14	105409191	105409191	+	Silent	SNP	C	C	T			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr14:105409191C>T	ENST00000333244.5	-	7	12716	c.12597G>A	c.(12595-12597)gtG>gtA	p.V4199V	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4199						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)		p.V4199V(1)		cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CCGGGAGTTTCACGTCCACTT	0.642																																						uc010axc.1																			1	Substitution - coding silent(1)		lung(1)	ovary(1)	1						c.(12595-12597)GTG>GTA		AHNAK nucleoprotein 2							107.0	112.0	110.0					14																	105409191		1893	4118	6011	SO:0001819	synonymous_variant	113146					nucleus		g.chr14:105409191C>T	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.12597G>A	14.37:g.105409191C>T						AHNAK2_uc001ypx.2_Silent_p.V4099V	p.V4199V	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)		7	12717	-		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	4199					Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	c.12597G>A	CCDS45177.1																																																																																				PASS	0.642	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		118	181	118	181	---	---	---	---
IGHV2-26	28455	broad.mit.edu	37	14	106757880	106757880	+	RNA	SNP	C	C	T	rs146488407	byFrequency	TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr14:106757880C>T	ENST00000390611.2	-	0	150									immunoglobulin heavy variable 2-26																		AACCCAGAGACGGTGCAGGTC	0.552													c|||	10	0.00199681	0.0068	0.0	5008	,	,		14914	0.0		0.001	False		,,,				2504	0.0					uc010tyt.1																			0					0								Parts of antibodies, mostly variable regions.		T		27,3959		0,27,1966	48.0	46.0	47.0			-5.4	0.0	14	dbSNP_134	47	3,8325		1,1,4162	no	intergenic				1,28,6128	TT,TC,CC		0.036,0.6774,0.2436			106757880	30,12284	1993	4164	6157			8755							g.chr14:106757880C>T	M99648		14q32.33	2012-02-08			ENSG00000211951	ENSG00000211951		"""Immunoglobulins / IGH locus"""	5575	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000152100		14.37:g.106757880C>T														472		-									RNA	SNP	ENST00000390611.2	37	c.16185G>A																																																																																					PASS	0.552	IGHV2-26-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene	OTTHUMT00000325197.1	NG_001019		47	64	47	64	---	---	---	---
CD276	80381	broad.mit.edu	37	15	73994714	73994714	+	Missense_Mutation	SNP	C	C	G			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr15:73994714C>G	ENST00000318443.5	+	3	500	c.198C>G	c.(196-198)atC>atG	p.I66M	CD276_ENST00000318424.5_Missense_Mutation_p.I66M|CD276_ENST00000564751.1_Missense_Mutation_p.I66M|CD276_ENST00000561213.1_Missense_Mutation_p.I66M|CD276_ENST00000537340.2_5'UTR	NM_001024736.1	NP_001019907.1	Q5ZPR3	CD276_HUMAN	CD276 molecule	66	Ig-like V-type 1.				cell proliferation (GO:0008283)|immune response (GO:0006955)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of bone mineralization (GO:0030501)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|regulation of immune response (GO:0050776)|T cell activation (GO:0042110)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)	p.I66M(1)		endometrium(3)|lung(5)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	13						TCAACCTCATCTGGCAGCTGA	0.637																																						uc002avv.1																			1	Substitution - Missense(1)		lung(1)	skin(1)	1						c.(196-198)ATC>ATG		CD276 antigen isoform a							48.0	42.0	44.0					15																	73994714		2198	4297	6495	SO:0001583	missense	80381				cell proliferation|immune response|positive regulation of interferon-gamma biosynthetic process|positive regulation of T cell proliferation|regulation of immune response|T cell activation	external side of plasma membrane|integral to membrane	receptor binding	g.chr15:73994714C>G	AF302102	CCDS10251.1, CCDS32288.1	15q23-q24	2013-01-11	2006-03-28		ENSG00000103855	ENSG00000103855		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	19137	protein-coding gene	gene with protein product		605715	"""CD276 antigen"""			11224528, 12055244	Standard	XM_005254699		Approved	B7-H3, B7H3, B7RP-2	uc002avv.1	Q5ZPR3	OTTHUMG00000137585	ENST00000318443.5:c.198C>G	15.37:g.73994714C>G	ENSP00000320084:p.Ile66Met					CD276_uc010bjd.1_Translation_Start_Site|CD276_uc002avu.1_Missense_Mutation_p.I66M|CD276_uc002avw.1_Missense_Mutation_p.I66M|CD276_uc010ulb.1_Intron|CD276_uc002avx.2_5'Flank	p.I66M	NM_001024736	NP_001019907	Q5ZPR3	CD276_HUMAN			3	432	+			66			Ig-like V-type 1.|Extracellular (Potential).		Q6P5Y4|Q6UXI2|Q8NBI8|Q8NC34|Q8NCB6|Q9BXR1	Missense_Mutation	SNP	ENST00000318443.5	37	c.198C>G	CCDS32288.1	.	.	.	.	.	.	.	.	.	.	C	13.85	2.358894	0.41801	.	.	ENSG00000103855	ENST00000318424;ENST00000318443;ENST00000379823;ENST00000543481	T;T	0.66280	-0.2;-0.2	2.84	2.84	0.33178	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.59500	0.2198	L	0.31476	0.935	0.38415	D	0.946024	D;B;B	0.61080	0.989;0.246;0.207	P;B;B	0.56278	0.795;0.121;0.118	T	0.62291	-0.6885	9	0.51188	T	0.08	-14.0073	8.5839	0.33646	0.0:0.8847:0.0:0.1153	.	66;66;66	Q5ZPR3-2;Q5ZPR3;Q5ZPR3-4	.;CD276_HUMAN;.	M	66	ENSP00000320058:I66M;ENSP00000320084:I66M	ENSP00000320058:I66M	I	+	3	3	CD276	71781767	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	2.641000	0.46587	1.888000	0.54679	0.313000	0.20887	ATC		PASS	0.637	CD276-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268979.1	NM_025240		39	36	39	36	---	---	---	---
CREBBP	1387	broad.mit.edu	37	16	3788618	3788618	+	Missense_Mutation	SNP	G	G	A	rs398124146		TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr16:3788618G>A	ENST00000262367.5	-	26	5145	c.4336C>T	c.(4336-4338)Cgc>Tgc	p.R1446C	CREBBP_ENST00000382070.3_Missense_Mutation_p.R1408C	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1446	Acetyl-CoA binding. {ECO:0000250|UniProtKB:Q09472}.|CBP/p300-type HAT. {ECO:0000255|PROSITE- ProRule:PRU01065}.|Cys/His-rich.				cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.R1446C(6)|p.R1446G(1)		NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		ACGGCTGTGCGGAGGCAACGT	0.413			"""T, N, F, Mis, O"""	"""MLL, MORF, RUNXBP2"""	"""ALL, AML, DLBCL, B-NHL """		Rubinstein-Taybi syndrome																															uc002cvv.2				Dom/Rec	yes		16	16p13.3	1387	T|N|F|Mis|O	CREB binding protein (CBP)	yes	Rubinstein-Taybi syndrome	L	MLL|MORF|RUNXBP2		ALL|AML|DLBCL|B-NHL 		7	Substitution - Missense(7)	p.R1446H(3)|p.R1446L(2)|p.R1446C(2)	haematopoietic_and_lymphoid_tissue(4)|urinary_tract(1)|lung(1)|central_nervous_system(1)	haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1)	127						c.(4336-4338)CGC>TGC		CREB binding protein isoform a							75.0	68.0	71.0					16																	3788618		2197	4300	6497	SO:0001583	missense	1387	Rubinstein-Taybi_syndrome			cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia	cytoplasm|nuclear body	histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding	g.chr16:3788618G>A	U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"""Chromatin-modifying enzymes / K-acetyltransferases"""	2348	protein-coding gene	gene with protein product		600140	"""Rubinstein-Taybi syndrome"""	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.4336C>T	16.37:g.3788618G>A	ENSP00000262367:p.Arg1446Cys					CREBBP_uc002cvw.2_Missense_Mutation_p.R1408C	p.R1446C	NM_004380	NP_004371	Q92793	CBP_HUMAN		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)	26	4540	-		Ovarian(90;0.0266)	1446			Cys/His-rich.		D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	37	c.4336C>T	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	g	17.20	3.329498	0.60743	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070;ENST00000323508	D;D	0.94330	-3.4;-3.4	5.28	4.29	0.51040	.	0.000000	0.64402	D	0.000004	D	0.97739	0.9258	H	0.96080	3.765	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98988	1.0807	10	0.87932	D	0	-29.6499	15.2916	0.73870	0.0:0.0:0.8588:0.1412	.	1476;1446	Q4LE28;Q92793	.;CBP_HUMAN	C	1446;1476;1408;35	ENSP00000262367:R1446C;ENSP00000371502:R1408C	ENSP00000262367:R1446C	R	-	1	0	CREBBP	3728619	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	4.937000	0.63513	1.303000	0.44873	0.561000	0.74099	CGC		PASS	0.413	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		32	28	32	28	---	---	---	---
TSNAXIP1	55815	broad.mit.edu	37	16	67858617	67858617	+	Missense_Mutation	SNP	G	G	C			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr16:67858617G>C	ENST00000388833.3	+	6	828	c.451G>C	c.(451-453)Gag>Cag	p.E151Q	TSNAXIP1_ENST00000562321.1_Intron|TSNAXIP1_ENST00000415766.3_Missense_Mutation_p.E136Q|TSNAXIP1_ENST00000561639.1_Missense_Mutation_p.E205Q	NM_018430.2	NP_060900.2			translin-associated factor X interacting protein 1									p.E151Q(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(8)|prostate(1)|soft_tissue(1)|urinary_tract(1)	22		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00432)|Epithelial(162;0.0192)|all cancers(182;0.125)		GCTCAAGAAAGAGAAGATGAA	0.468																																						uc002euj.2																			1	Substitution - Missense(1)		lung(1)		0						c.(451-453)GAG>CAG		translin-associated factor X interacting protein							69.0	68.0	68.0					16																	67858617		1968	4152	6120	SO:0001583	missense	55815				cell differentiation|multicellular organismal development|spermatogenesis	perinuclear region of cytoplasm		g.chr16:67858617G>C	AF132730	CCDS10846.2, CCDS73903.1, CCDS73904.1	16q22.2	2008-02-05			ENSG00000102904	ENSG00000102904			18586	protein-coding gene	gene with protein product		607720				12036294	Standard	XM_005256051		Approved	TXI1	uc002euj.3	Q2TAA8	OTTHUMG00000137545	ENST00000388833.3:c.451G>C	16.37:g.67858617G>C	ENSP00000373485:p.Glu151Gln					TSNAXIP1_uc010cep.2_Missense_Mutation_p.E15Q|TSNAXIP1_uc010vjz.1_Intron|TSNAXIP1_uc002euf.3_Intron|TSNAXIP1_uc010vka.1_Missense_Mutation_p.E205Q|TSNAXIP1_uc010vkb.1_Missense_Mutation_p.E136Q|TSNAXIP1_uc002eug.3_5'UTR|TSNAXIP1_uc002euh.3_5'UTR|TSNAXIP1_uc002eui.3_Intron|TSNAXIP1_uc002euk.2_5'UTR	p.E151Q	NM_018430	NP_060900	Q2TAA8	TXIP1_HUMAN		OV - Ovarian serous cystadenocarcinoma(108;0.00432)|Epithelial(162;0.0192)|all cancers(182;0.125)	6	845	+		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)	151			Potential.			Missense_Mutation	SNP	ENST00000388833.3	37	c.451G>C	CCDS10846.2	.	.	.	.	.	.	.	.	.	.	G	22.9	4.356028	0.82243	.	.	ENSG00000102904	ENST00000415766;ENST00000388833	T;T	0.01025	5.43;5.43	6.17	6.17	0.99709	.	0.000000	0.64402	D	0.000002	T	0.05823	0.0152	M	0.70275	2.135	0.44985	D	0.998006	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77004	0.989;0.982;0.982	T	0.03051	-1.1078	10	0.72032	D	0.01	-32.0121	18.6524	0.91435	0.0:0.0:1.0:0.0	.	136;205;151	E7ENJ7;B4DXD0;Q2TAA8	.;.;TXIP1_HUMAN	Q	136;151	ENSP00000411472:E136Q;ENSP00000373485:E151Q	ENSP00000373485:E151Q	E	+	1	0	TSNAXIP1	66416118	1.000000	0.71417	1.000000	0.80357	0.798000	0.45092	6.163000	0.71880	2.941000	0.99782	0.655000	0.94253	GAG		PASS	0.468	TSNAXIP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268876.2	NM_018430		36	53	36	53	---	---	---	---
KIAA0753	9851	broad.mit.edu	37	17	6483097	6483097	+	Silent	SNP	G	G	A			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr17:6483097G>A	ENST00000361413.3	-	19	3232	c.2874C>T	c.(2872-2874)ttC>ttT	p.F958F	KIAA0753_ENST00000542606.1_Silent_p.F659F|KIAA0753_ENST00000589033.1_Silent_p.F414F|KIAA0753_ENST00000572370.1_Silent_p.F659F	NM_014804.2	NP_055619.2	Q2KHM9	K0753_HUMAN	KIAA0753	958						centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.F958F(1)		endometrium(4)|large_intestine(11)|lung(5)|prostate(4)	24				COAD - Colon adenocarcinoma(228;0.157)		ATTCTGAGGTGAACACAGCTT	0.498																																						uc002gde.3																			1	Substitution - coding silent(1)		lung(1)		0						c.(2872-2874)TTC>TTT		hypothetical protein LOC9851							127.0	124.0	125.0					17																	6483097		1981	4180	6161	SO:0001819	synonymous_variant	9851					centrosome		g.chr17:6483097G>A		CCDS42247.1	17p13.1	2014-04-04			ENSG00000198920	ENSG00000198920			29110	protein-coding gene	gene with protein product						24613305	Standard	NM_014804		Approved		uc002gde.4	Q2KHM9	OTTHUMG00000177928	ENST00000361413.3:c.2874C>T	17.37:g.6483097G>A						KIAA0753_uc010vtd.1_Silent_p.F414F|KIAA0753_uc010clo.2_Silent_p.F659F|KIAA0753_uc010vte.1_Silent_p.F659F	p.F958F	NM_014804	NP_055619	Q2KHM9	K0753_HUMAN		COAD - Colon adenocarcinoma(228;0.157)	19	3233	-			958					A8KA11|B7Z479|O94853|Q05D97|Q2KHN0|Q9UG45	Silent	SNP	ENST00000361413.3	37	c.2874C>T	CCDS42247.1																																																																																				PASS	0.498	KIAA0753-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439769.3	NM_014804		108	112	108	112	---	---	---	---
SHBG	6462	broad.mit.edu	37	17	7534110	7534110	+	Missense_Mutation	SNP	G	G	C			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr17:7534110G>C	ENST00000380450.4	+	3	347	c.316G>C	c.(316-318)Gag>Cag	p.E106Q	SHBG_ENST00000576478.1_Missense_Mutation_p.E48Q|SAT2_ENST00000269298.5_5'Flank|SHBG_ENST00000340624.5_Missense_Mutation_p.E48Q|SHBG_ENST00000416273.3_Missense_Mutation_p.E106Q|SHBG_ENST00000441599.2_Missense_Mutation_p.E106Q|SHBG_ENST00000575903.1_Missense_Mutation_p.E106Q|SHBG_ENST00000572182.1_Missense_Mutation_p.E48Q|SAT2_ENST00000380466.2_5'Flank|SHBG_ENST00000575314.1_Missense_Mutation_p.E48Q|SHBG_ENST00000572262.1_Missense_Mutation_p.E48Q|SHBG_ENST00000570547.1_Missense_Mutation_p.E48Q|SHBG_ENST00000574539.1_Missense_Mutation_p.E48Q|SAT2_ENST00000573566.1_5'Flank|SHBG_ENST00000576728.1_Missense_Mutation_p.E48Q	NM_001040.3	NP_001031.2	P04278	SHBG_HUMAN	sex hormone-binding globulin	106	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				primary spermatocyte growth (GO:0007285)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	androgen binding (GO:0005497)	p.E106Q(1)|p.?(1)		cervix(1)|endometrium(2)|large_intestine(4)|lung(2)|skin(1)	10		all_cancers(10;0.0867)		READ - Rectum adenocarcinoma(115;0.168)	Danazol(DB01406)|Drostanolone(DB00858)|Estradiol(DB00783)|Estropipate(DB04574)|Fluoxymesterone(DB01185)|Hydrocortisone(DB00741)|Methyltestosterone(DB06710)|Mitotane(DB00648)|Norethindrone(DB00717)|Spironolactone(DB00421)|Testosterone(DB00624)|transdermal testosterone gel(DB05275)	CGGCAGGCCTGAGATCCAACT	0.557																																						uc002gie.2																			2	Substitution - Missense(1)|Unknown(1)	p.?(1)	haematopoietic_and_lymphoid_tissue(1)|lung(1)		0						c.(316-318)GAG>CAG		sex hormone-binding globulin isoform 1	Danazol(DB01406)|Dromostanolone(DB00858)|Estradiol(DB00783)|Estrone(DB00655)|Fluoxymesterone(DB01185)|Hydrocortisone(DB00741)|Mitotane(DB00648)|Norethindrone(DB00717)|Testosterone(DB00624)						85.0	81.0	82.0					17																	7534110		2203	4300	6503	SO:0001583	missense	6462				hormone transport	extracellular region	androgen binding|protein homodimerization activity	g.chr17:7534110G>C		CCDS11117.1, CCDS54082.1, CCDS54083.1, CCDS58513.1, CCDS73961.1, CCDS73962.1	17p13.1	2013-09-19			ENSG00000129214	ENSG00000129214			10839	protein-coding gene	gene with protein product	"""androgen binding protein"""	182205				2587256	Standard	NM_001146279		Approved	ABP, TEBG, MGC126834, MGC138391	uc002gie.2	P04278	OTTHUMG00000108153	ENST00000380450.4:c.316G>C	17.37:g.7534110G>C	ENSP00000369816:p.Glu106Gln					SHBG_uc010cmo.2_Missense_Mutation_p.E48Q|SHBG_uc010cmp.2_Missense_Mutation_p.E48Q|SHBG_uc010cmq.2_Missense_Mutation_p.E48Q|SHBG_uc010cmr.2_Missense_Mutation_p.E48Q|SHBG_uc010cms.2_Missense_Mutation_p.E48Q|SHBG_uc010cmt.2_Missense_Mutation_p.E48Q|SHBG_uc010cmu.2_Missense_Mutation_p.E48Q|SAT2_uc002gib.1_5'Flank|SAT2_uc002gic.2_5'Flank|SHBG_uc010cmz.2_Missense_Mutation_p.E48Q|SHBG_uc010cmv.2_Missense_Mutation_p.E48Q|SHBG_uc010cmw.2_Missense_Mutation_p.E48Q|SHBG_uc010cmx.2_Missense_Mutation_p.E48Q|SHBG_uc010cmy.2_Missense_Mutation_p.E48Q|SHBG_uc002gid.3_Missense_Mutation_p.E48Q|SHBG_uc010cnd.2_Missense_Mutation_p.E106Q|SHBG_uc010cna.2_Missense_Mutation_p.E106Q|SHBG_uc010vue.1_Missense_Mutation_p.E106Q|SHBG_uc010vuf.1_Missense_Mutation_p.E106Q|SHBG_uc010cnb.2_Missense_Mutation_p.E106Q|SHBG_uc010cnc.2_Missense_Mutation_p.E106Q	p.E106Q	NM_001040	NP_001031	P04278	SHBG_HUMAN		READ - Rectum adenocarcinoma(115;0.168)	3	354	+		all_cancers(10;0.0867)	106			Laminin G-like 1.		B0FWH4|E9PGW1|F5H5Z8|I3L1N7|P14689|Q16616|Q3MIL0|Q6ISD2	Missense_Mutation	SNP	ENST00000380450.4	37	c.316G>C	CCDS11117.1	.	.	.	.	.	.	.	.	.	.	G	19.69	3.874686	0.72180	.	.	ENSG00000129214	ENST00000340624;ENST00000441599;ENST00000416273;ENST00000441313;ENST00000452698;ENST00000380450	T;T;T;T	0.77229	-1.08;-1.08;-1.08;-1.08	5.04	5.04	0.67666	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 1 (1);	0.142722	0.45126	D	0.000394	D	0.87857	0.6283	M	0.77820	2.39	0.38104	D	0.937348	D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.984;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D	0.97110	0.999;0.999;0.998;0.981;0.999;0.998;0.998;0.999;0.998;1.0;1.0	D	0.90154	0.4223	10	0.59425	D	0.04	-21.4818	15.8751	0.79156	0.0:0.0:1.0:0.0	.	106;101;79;106;106;106;79;79;79;106;48	F5H5Z8;P04278-2;B0FWH6;E9PH59;E9PGW1;E9PGQ3;B0FWH7;B0FWH5;B0FWH4;P04278;B4DYU0	.;.;.;.;.;.;.;.;.;SHBG_HUMAN;.	Q	48;106;106;106;106;106	ENSP00000345675:E48Q;ENSP00000393426:E106Q;ENSP00000388867:E106Q;ENSP00000369816:E106Q	ENSP00000345675:E48Q	E	+	1	0	SHBG	7474835	1.000000	0.71417	0.989000	0.46669	0.877000	0.50540	4.812000	0.62613	2.355000	0.79922	0.561000	0.74099	GAG		PASS	0.557	SHBG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226957.2	NM_001040		75	61	75	61	---	---	---	---
PIGL	9487	broad.mit.edu	37	17	16120682	16120682	+	Missense_Mutation	SNP	G	G	C			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr17:16120682G>C	ENST00000225609.5	+	1	159	c.142G>C	c.(142-144)Gcg>Ccg	p.A48P	PIGL_ENST00000581006.1_Missense_Mutation_p.A48P|PIGL_ENST00000395844.4_Missense_Mutation_p.A48P|NCOR1_ENST00000268712.3_5'Flank|PIGL_ENST00000463810.1_3'UTR|PIGL_ENST00000498772.2_Missense_Mutation_p.A48P	NM_004278.3	NP_004269.1	Q9Y2B2	PIGL_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class L	48					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	N-acetylglucosaminylphosphatidylinositol deacetylase activity (GO:0000225)	p.A48P(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|skin(1)	11				UCEC - Uterine corpus endometrioid carcinoma (92;0.0934)		GCTGGTCATAGCGCACCCTGA	0.597																																						uc002gpv.2																			1	Substitution - Missense(1)		lung(1)		0						c.(142-144)GCG>CCG		phosphatidylinositol glycan anchor biosynthesis,							126.0	114.0	118.0					17																	16120682		2203	4300	6503	SO:0001583	missense	9487				C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	N-acetylglucosaminylphosphatidylinositol deacetylase activity	g.chr17:16120682G>C	AB017165	CCDS11176.1	17p12-p11.2	2013-02-26	2006-06-28		ENSG00000108474	ENSG00000108474	3.5.1.89	"""Phosphatidylinositol glycan anchor biosynthesis"""	8966	protein-coding gene	gene with protein product	"""N-acetylglucosaminylphosphatidylinositol deacetylase"""	605947	"""phosphatidylinositol glycan, class L"""			10085243	Standard	NM_004278		Approved		uc002gpv.3	Q9Y2B2	OTTHUMG00000059346	ENST00000225609.5:c.142G>C	17.37:g.16120682G>C	ENSP00000225609:p.Ala48Pro					NCOR1_uc002gpo.2_5'Flank|PIGL_uc010vwd.1_Missense_Mutation_p.A48P|NCOR1_uc002gps.1_5'Flank|NCOR1_uc010coz.1_5'Flank|NCOR1_uc010cpb.1_5'Flank|NCOR1_uc010cpa.1_5'Flank|NCOR1_uc002gpu.2_5'Flank	p.A48P	NM_004278	NP_004269	Q9Y2B2	PIGL_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (92;0.0934)	1	174	+			48			Cytoplasmic (Potential).		A8KA67|B4DYN4	Missense_Mutation	SNP	ENST00000225609.5	37	c.142G>C	CCDS11176.1	.	.	.	.	.	.	.	.	.	.	G	10.49	1.365819	0.24684	.	.	ENSG00000108474	ENST00000225609;ENST00000395844	D;D	0.81579	-1.51;-1.51	5.49	5.49	0.81192	Putative deacetylase LmbE-like domain (2);	0.000000	0.85682	D	0.000000	D	0.89033	0.6600	M	0.77313	2.365	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.88140	0.2844	10	0.38643	T	0.18	-25.5022	14.8862	0.70570	0.0:0.0:1.0:0.0	.	48;48	B4DYN4;Q9Y2B2	.;PIGL_HUMAN	P	48	ENSP00000225609:A48P;ENSP00000379185:A48P	ENSP00000225609:A48P	A	+	1	0	PIGL	16061407	1.000000	0.71417	0.991000	0.47740	0.007000	0.05969	4.971000	0.63749	2.565000	0.86533	0.655000	0.94253	GCG		PASS	0.597	PIGL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131881.1			59	78	59	78	---	---	---	---
RAD51D	5892	broad.mit.edu	37	17	33434099	33434099	+	Missense_Mutation	SNP	G	G	C			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr17:33434099G>C	ENST00000345365.6	-	5	643	c.388C>G	c.(388-390)Caa>Gaa	p.Q130E	RAD51D_ENST00000590016.1_Missense_Mutation_p.Q150E|RAD51D_ENST00000394589.4_Missense_Mutation_p.Q130E|RAD51L3-RFFL_ENST00000593039.1_Intron|RAD51D_ENST00000590380.1_Intron|RAD51D_ENST00000360276.3_Intron|RAD51D_ENST00000460118.2_Missense_Mutation_p.Q11E|RAD51D_ENST00000335858.7_Intron	NM_002878.3	NP_002869.3	O75771	RA51D_HUMAN	RAD51 paralog D	130					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|reciprocal meiotic recombination (GO:0007131)|strand invasion (GO:0042148)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Rad51B-Rad51C-Rad51D-XRCC2 complex (GO:0033063)|replication fork (GO:0005657)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|gamma-tubulin binding (GO:0043015)|single-stranded DNA binding (GO:0003697)	p.Q130E(1)|p.Q150E(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|liver(1)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						AGGACGTTTTGCTGCAGGCCA	0.552								Direct reversal of damage																														uc002hir.2																			2	Substitution - Missense(2)		lung(2)		0						c.(388-390)CAA>GAA	Direct_reversal_of_damage|Homologous_recombination	RAD51-like 3 isoform 1							98.0	92.0	94.0					17																	33434099		2203	4300	6503	SO:0001583	missense	5892				DNA repair|reciprocal meiotic recombination	nucleus	ATP binding|DNA binding|DNA-dependent ATPase activity|protein binding	g.chr17:33434099G>C	AF034956	CCDS11287.1, CCDS11288.1, CCDS45646.1	17q11	2014-09-17	2013-07-02	2011-07-01	ENSG00000185379	ENSG00000185379			9823	protein-coding gene	gene with protein product	"""recombination repair protein"", ""DNA repair protein RAD51 homolog 4"""	602954	"""RAD51 (S. cerevisiae)-like 3"", ""RAD51-like 3 (S. cerevisiae)"", ""RAD51 homolog D (S. cerevisiae)"""	RAD51L3		9570954	Standard	NM_001142571		Approved	R51H3, Trad, HsTRAD	uc010ctj.2	O75771	OTTHUMG00000132930	ENST00000345365.6:c.388C>G	17.37:g.33434099G>C	ENSP00000338790:p.Gln130Glu					RFFL_uc002hiq.2_Intron|RAD51L3_uc010ctj.2_5'Flank|RAD51L3_uc010wcd.1_Missense_Mutation_p.Q150E|RAD51L3_uc002his.2_Intron|RAD51L3_uc010ctk.2_Missense_Mutation_p.Q11E|RAD51L3_uc010wce.1_Missense_Mutation_p.Q11E|RAD51L3_uc002hit.2_Missense_Mutation_p.Q11E|RAD51L3_uc002hiu.2_Intron|RAD51L3_uc010wcf.1_RNA|RAD51L3_uc002hiw.1_RNA|RAD51L3_uc002hiv.1_Intron|RAD51L3_uc010ctl.1_Intron|RAD51L3_uc010ctm.1_Intron	p.Q130E	NM_002878	NP_002869	O75771	RA51D_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)	5	644	-		Ovarian(249;0.17)	130					B4DJU7|E1P637|O43537|O60355|O75196|O75847|O75848|O76073|O76085|O94908|Q9UFU5	Missense_Mutation	SNP	ENST00000345365.6	37	c.388C>G	CCDS11287.1	.	.	.	.	.	.	.	.	.	.	G	12.32	1.903673	0.33628	.	.	ENSG00000185379	ENST00000345365;ENST00000394589;ENST00000335858;ENST00000418935;ENST00000415064	T	0.38401	1.14	4.56	4.56	0.56223	DNA recombination/repair protein RecA/RadB, ATP-binding domain (1);ATPase, AAA+ type, core (1);DNA recombination and repair protein Rad51, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.47801	0.1465	L	0.27944	0.81	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.83275	0.996;0.983	T	0.52403	-0.8580	10	0.72032	D	0.01	-11.0856	16.0526	0.80774	0.0:0.0:1.0:0.0	.	150;130	B4DJU7;O75771	.;RA51D_HUMAN	E	130;150;130;130;133	ENSP00000338790:Q130E	ENSP00000338408:Q130E	Q	-	1	0	RAD51D	30458212	1.000000	0.71417	0.998000	0.56505	0.823000	0.46562	7.239000	0.78182	2.355000	0.79922	0.484000	0.47621	CAA		PASS	0.552	RAD51D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256446.1	NM_002878		76	95	76	95	---	---	---	---
CCL16	6360	broad.mit.edu	37	17	34305249	34305249	+	Missense_Mutation	SNP	C	C	T			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr17:34305249C>T	ENST00000293275.3	-	2	202	c.127G>A	c.(127-129)Gag>Aag	p.E43K		NM_004590.2	NP_004581.1	O15467	CCL16_HUMAN	chemokine (C-C motif) ligand 16	43					cell chemotaxis (GO:0060326)|cell communication (GO:0007154)|cell-cell signaling (GO:0007267)|chemotaxis (GO:0006935)|immune response (GO:0006955)|inflammatory response (GO:0006954)|positive chemotaxis (GO:0050918)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemoattractant activity (GO:0042056)|chemokine activity (GO:0008009)	p.E43K(1)		endometrium(1)|lung(2)	3		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		AACACTTTCTCATAATACTTC	0.502																																						uc002hkl.2																			1	Substitution - Missense(1)		lung(1)		0						c.(127-129)GAG>AAG		small inducible cytokine A16 precursor							215.0	202.0	206.0					17																	34305249		2203	4300	6503	SO:0001583	missense	6360				cell-cell signaling|immune response|inflammatory response	extracellular space	chemoattractant activity|chemokine activity	g.chr17:34305249C>T	AB007454	CCDS11303.1	17q11.2	2014-05-06	2002-08-22	2002-08-23	ENSG00000161573	ENSG00000275152		"""Chemokine ligands"", ""Endogenous ligands"""	10614	protein-coding gene	gene with protein product		601394	"""small inducible cytokine subfamily A (Cys-Cys), member 16"""	SCYA16		8661057	Standard	NM_004590		Approved	NCC-4, SCYL4, LEC, HCC-4, LMC, LCC-1, CKb12, Mtn-1	uc002hkl.3	O15467	OTTHUMG00000188402	ENST00000293275.3:c.127G>A	17.37:g.34305249C>T	ENSP00000293275:p.Glu43Lys					CCL16_uc002hkm.2_RNA	p.E43K	NM_004590	NP_004581	O15467	CCL16_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)	2	194	-		Ovarian(249;0.17)	43					Q4KKU0	Missense_Mutation	SNP	ENST00000293275.3	37	c.127G>A	CCDS11303.1	.	.	.	.	.	.	.	.	.	.	C	12.34	1.908931	0.33721	.	.	ENSG00000161573	ENST00000293275	T	0.03717	3.83	5.13	-0.869	0.10649	CC chemokine, conserved site (1);Chemokine interleukin-8-like domain (3);	0.493428	0.17233	N	0.181888	T	0.02455	0.0075	N	0.25825	0.765	0.09310	N	1	B	0.25904	0.137	B	0.31290	0.127	T	0.47222	-0.9134	10	0.17832	T	0.49	.	4.1168	0.10086	0.0:0.3632:0.338:0.2988	.	43	O15467	CCL16_HUMAN	K	43	ENSP00000293275:E43K	ENSP00000293275:E43K	E	-	1	0	CCL16	31329362	0.044000	0.20184	0.000000	0.03702	0.343000	0.28985	0.005000	0.13129	0.073000	0.16731	0.563000	0.77884	GAG		PASS	0.502	CCL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256579.1	NM_004590		162	227	162	227	---	---	---	---
ZNF236	7776	broad.mit.edu	37	18	74620297	74620297	+	Silent	SNP	C	C	G			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr18:74620297C>G	ENST00000253159.8	+	14	2511	c.2313C>G	c.(2311-2313)ctC>ctG	p.L771L	ZNF236_ENST00000320610.9_Silent_p.L773L	NM_007345.3	NP_031371.3	Q9UL36	ZN236_HUMAN	zinc finger protein 236	771					cellular response to glucose stimulus (GO:0071333)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L771L(2)		NS(1)|breast(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(43)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	94		Prostate(75;0.0405)|Esophageal squamous(42;0.129)|Melanoma(33;0.132)		OV - Ovarian serous cystadenocarcinoma(15;4.36e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0686)		CCCAGCAGCTCCAACAGCATC	0.493																																						uc002lmi.2																			2	Substitution - coding silent(2)		lung(2)	ovary(4)	4						c.(2311-2313)CTC>CTG		zinc finger protein 236							123.0	131.0	129.0					18																	74620297		2066	4209	6275	SO:0001819	synonymous_variant	7776				cellular response to glucose stimulus	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr18:74620297C>G	AF085243	CCDS42447.1	18q22-q23	2013-01-08				ENSG00000130856		"""Zinc fingers, C2H2-type"""	13028	protein-coding gene	gene with protein product		604760				10458916	Standard	NM_007345		Approved		uc002lmi.3	Q9UL36		ENST00000253159.8:c.2313C>G	18.37:g.74620297C>G						ZNF236_uc002lmj.2_RNA	p.L771L	NM_007345	NP_031371	Q9UL36	ZN236_HUMAN		OV - Ovarian serous cystadenocarcinoma(15;4.36e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0686)	14	2511	+		Prostate(75;0.0405)|Esophageal squamous(42;0.129)|Melanoma(33;0.132)	771					B2RTX9|Q9UL37	Silent	SNP	ENST00000253159.8	37	c.2313C>G	CCDS42447.1																																																																																				PASS	0.493	ZNF236-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000445776.1			87	168	87	168	---	---	---	---
APC2	10297	broad.mit.edu	37	19	1470100	1470100	+	Missense_Mutation	SNP	C	C	T			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr19:1470100C>T	ENST00000535453.1	+	14	8513	c.6800C>T	c.(6799-6801)tCg>tTg	p.S2267L	APC2_ENST00000238483.4_Missense_Mutation_p.S1993L|C19orf25_ENST00000588427.1_Intron|APC2_ENST00000233607.2_Missense_Mutation_p.S2267L			P02655	APOC2_HUMAN	adenomatosis polyposis coli 2	0					cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|chylomicron remnant clearance (GO:0034382)|chylomicron remodeling (GO:0034371)|high-density lipoprotein particle clearance (GO:0034384)|lipid catabolic process (GO:0016042)|lipoprotein metabolic process (GO:0042157)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of lipid metabolic process (GO:0045833)|negative regulation of receptor-mediated endocytosis (GO:0048261)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipid catabolic process (GO:0060697)|positive regulation of triglyceride catabolic process (GO:0010898)|positive regulation of very-low-density lipoprotein particle remodeling (GO:0010902)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)|triglyceride-rich lipoprotein particle remodeling (GO:0034370)|very-low-density lipoprotein particle remodeling (GO:0034372)	chylomicron (GO:0042627)|early endosome (GO:0005769)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate-density lipoprotein particle (GO:0034363)|low-density lipoprotein particle (GO:0034362)|spherical high-density lipoprotein particle (GO:0034366)|very-low-density lipoprotein particle (GO:0034361)	lipase inhibitor activity (GO:0055102)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|protein homodimerization activity (GO:0042803)	p.S2267L(1)		breast(3)|cervix(1)|kidney(4)|large_intestine(2)|lung(5)|pancreas(1)|skin(2)	18		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCCAGCCGCTCGGCCCGAGTA	0.736																																						uc002lsr.1																			1	Substitution - Missense(1)		lung(1)	breast(3)|pancreas(1)	4						c.(6799-6801)TCG>TTG		adenomatosis polyposis coli 2							5.0	7.0	6.0					19																	1470100		1668	3743	5411	SO:0001583	missense	10297				negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|Wnt receptor signaling pathway	actin filament|catenin complex|cytoplasmic microtubule|Golgi membrane|lamellipodium membrane|perinuclear region of cytoplasm	beta-catenin binding|microtubule binding	g.chr19:1470100C>T		CCDS12068.1	19p13.3	2013-02-14			ENSG00000115266	ENSG00000115266		"""Armadillo repeat containing"""	24036	protein-coding gene	gene with protein product	"""adenomatous polyposis coli like"""	612034				9823329, 10021369	Standard	XM_005259475		Approved	APCL	uc002lsr.1	O95996		ENST00000535453.1:c.6800C>T	19.37:g.1470100C>T	ENSP00000442954:p.Ser2267Leu					APC2_uc002lss.1_Missense_Mutation_p.S1849L|APC2_uc002lst.1_Missense_Mutation_p.S2267L|APC2_uc002lsu.1_Missense_Mutation_p.S2266L|C19orf25_uc010xgn.1_Intron	p.S2267L	NM_005883	NP_005874	O95996	APC2_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	15	7008	+		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)	2267					C0JYY4|Q9BS39|Q9UDE3|Q9UNK3	Missense_Mutation	SNP	ENST00000535453.1	37	c.6800C>T	CCDS12068.1	.	.	.	.	.	.	.	.	.	.	C	18.56	3.651272	0.67472	.	.	ENSG00000115266	ENST00000233607;ENST00000238483;ENST00000535453	D;D;D	0.93019	-3.15;-2.82;-3.15	4.05	4.05	0.47172	.	0.322331	0.27143	N	0.020725	D	0.85314	0.5668	N	0.14661	0.345	0.80722	D	1	P;P	0.39022	0.655;0.524	B;B	0.31751	0.135;0.064	D	0.87505	0.2436	10	0.72032	D	0.01	-5.2513	13.7397	0.62840	0.0:1.0:0.0:0.0	.	2266;2267	O95996-3;O95996	.;APC2_HUMAN	L	2267;1993;2267	ENSP00000233607:S2267L;ENSP00000238483:S1993L;ENSP00000442954:S2267L	ENSP00000233607:S2267L	S	+	2	0	APC2	1421100	0.945000	0.32115	0.216000	0.23742	0.969000	0.65631	4.964000	0.63701	1.813000	0.52934	0.555000	0.69702	TCG		PASS	0.736	APC2-004	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449539.2	NM_005883		4	12	4	12	---	---	---	---
PLIN3	10226	broad.mit.edu	37	19	4839538	4839538	+	Missense_Mutation	SNP	G	G	A			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr19:4839538G>A	ENST00000221957.4	-	8	1147	c.971C>T	c.(970-972)tCc>tTc	p.S324F	PLIN3_ENST00000585479.1_Missense_Mutation_p.S323F|CTC-518P12.6_ENST00000591657.1_RNA|PLIN3_ENST00000592528.1_Missense_Mutation_p.S312F	NM_001164189.1|NM_001164194.1|NM_005817.4	NP_001157661.1|NP_001157666.1|NP_005808.3	O60664	PLIN3_HUMAN	perilipin 3	324					vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|membrane (GO:0016020)		p.S324F(1)		cervix(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	9					Galsulfase(DB01279)|Idursulfase(DB01271)	GAGCGCCCGGGACTCGACCTG	0.597																																						uc002mbj.2																			1	Substitution - Missense(1)		lung(1)		0						c.(970-972)TCC>TTC		mannose 6 phosphate receptor binding protein 1	Galsulfase(DB01279)|Idursulfase(DB01271)						22.0	19.0	20.0					19																	4839538		2202	4298	6500	SO:0001583	missense	10226				vesicle-mediated transport	endosome membrane|Golgi apparatus|lipid particle	protein binding	g.chr19:4839538G>A	AF051314	CCDS12137.1, CCDS59337.1, CCDS59338.1	19p13.3	2009-08-12	2009-08-12	2009-08-12		ENSG00000105355		"""Perilipins"""	16893	protein-coding gene	gene with protein product	"""cargo selection protein (mannose 6 phosphate receptor binding protein)"", ""placental protein 17"", ""MPR-BINDING PROTEIN, 47-KD"""	602702	"""mannose-6-phosphate receptor binding protein 1"""	M6PRBP1		9590177, 6856484, 19638644	Standard	NM_005817		Approved	TIP47, PP17	uc002mbj.2	O60664		ENST00000221957.4:c.971C>T	19.37:g.4839538G>A	ENSP00000221957:p.Ser324Phe					PLIN3_uc002mbk.2_Missense_Mutation_p.S312F|PLIN3_uc002mbl.3_Missense_Mutation_p.S323F	p.S324F	NM_005817	NP_005808	O60664	PLIN3_HUMAN			8	1148	-			324					A8K4Y9|K7EQF4|Q53G77|Q9BS03|Q9UBD7|Q9UP92	Missense_Mutation	SNP	ENST00000221957.4	37	c.971C>T	CCDS12137.1	.	.	.	.	.	.	.	.	.	.	G	10.39	1.338178	0.24253	.	.	ENSG00000105355	ENST00000221957	T	0.06768	3.26	4.85	2.72	0.32119	.	1.377330	0.04422	U	0.367776	T	0.15262	0.0368	M	0.82056	2.57	0.25458	N	0.98795	B;B;B	0.17038	0.02;0.007;0.02	B;B;B	0.17433	0.014;0.006;0.018	T	0.34625	-0.9821	10	0.62326	D	0.03	-25.4633	5.7639	0.18215	0.162:0.0:0.6827:0.1553	.	323;141;324	O60664-3;O60664-2;O60664	.;.;PLIN3_HUMAN	F	324	ENSP00000221957:S324F	ENSP00000221957:S324F	S	-	2	0	PLIN3	4790538	0.969000	0.33509	0.053000	0.19242	0.519000	0.34347	1.776000	0.38594	0.470000	0.27294	0.555000	0.69702	TCC		PASS	0.597	PLIN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450436.1	NM_005817		25	13	25	13	---	---	---	---
MUC16	94025	broad.mit.edu	37	19	9069097	9069097	+	Missense_Mutation	SNP	C	C	A			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr19:9069097C>A	ENST00000397910.4	-	3	18552	c.18349G>T	c.(18349-18351)Gat>Tat	p.D6117Y		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	6119	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.D6117Y(2)|p.D1750Y(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AATGTAGGATCATAGTAGGTG	0.493																																						uc002mkp.2																			3	Substitution - Missense(3)		lung(3)	lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						c.(18349-18351)GAT>TAT		mucin 16							61.0	65.0	64.0					19																	9069097		2053	4213	6266	SO:0001583	missense	94025				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding	g.chr19:9069097C>A	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.18349G>T	19.37:g.9069097C>A	ENSP00000381008:p.Asp6117Tyr						p.D6117Y	NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN			3	18553	-			6119			Thr-rich.|Extracellular (Potential).		Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	c.18349G>T	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	1.730	-0.494475	0.04322	.	.	ENSG00000181143	ENST00000397910	T	0.03124	4.04	1.35	-0.0925	0.13656	.	.	.	.	.	T	0.02193	0.0068	N	0.08118	0	.	.	.	D	0.58268	0.982	P	0.44518	0.452	T	0.44283	-0.9338	8	0.87932	D	0	.	3.3745	0.07233	0.0:0.5896:0.0:0.4104	.	6117	B5ME49	.	Y	6117	ENSP00000381008:D6117Y	ENSP00000381008:D6117Y	D	-	1	0	MUC16	8930097	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-3.447000	0.00467	-0.002000	0.14469	0.163000	0.16589	GAT		PASS	0.493	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		22	37	22	37	---	---	---	---
CSNK2A1	1457	broad.mit.edu	37	20	472947	472947	+	Missense_Mutation	SNP	C	C	T			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr20:472947C>T	ENST00000217244.3	-	9	947	c.572G>A	c.(571-573)cGa>cAa	p.R191Q	CSNK2A1_ENST00000400227.3_Missense_Mutation_p.R191Q|CSNK2A1_ENST00000349736.5_Missense_Mutation_p.R191Q|CSNK2A1_ENST00000400217.2_Missense_Mutation_p.R55Q	NM_177559.2	NP_808227.1	P68400	CSK21_HUMAN	casein kinase 2, alpha 1 polypeptide	191	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|chaperone-mediated protein folding (GO:0061077)|mitotic cell cycle (GO:0000278)|mitotic spindle checkpoint (GO:0071174)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway (GO:0030177)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|plasma membrane (GO:0005886)|Sin3 complex (GO:0016580)	ATP binding (GO:0005524)|Hsp90 protein binding (GO:0051879)|protein N-terminus binding (GO:0047485)|protein phosphatase regulator activity (GO:0019888)|protein serine/threonine kinase activity (GO:0004674)	p.R191Q(1)		autonomic_ganglia(1)|central_nervous_system(2)|endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|urinary_tract(1)	17		Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.0969)			GGAAGCAACTCGGACATTATA	0.413																																						uc002wdw.1																			1	Substitution - Missense(1)		lung(1)	ovary(1)	1						c.(571-573)CGA>CAA		casein kinase II alpha 1 subunit isoform a							87.0	81.0	83.0					20																	472947		2203	4297	6500	SO:0001583	missense	1457				axon guidance|Wnt receptor signaling pathway	cytosol|NuRD complex|plasma membrane|Sin3 complex	ATP binding|protein N-terminus binding|protein serine/threonine kinase activity	g.chr20:472947C>T	M55265	CCDS13003.1, CCDS13004.1	20p13	2013-01-17			ENSG00000101266	ENSG00000101266			2457	protein-coding gene	gene with protein product		115440				2174700, 1766873	Standard	NM_177559		Approved		uc002wdx.1	P68400	OTTHUMG00000031636	ENST00000217244.3:c.572G>A	20.37:g.472947C>T	ENSP00000217244:p.Arg191Gln					CSNK2A1_uc002wdx.1_Missense_Mutation_p.R191Q|CSNK2A1_uc002wdy.1_Missense_Mutation_p.R55Q	p.R191Q	NM_177559	NP_808227	P68400	CSK21_HUMAN	OV - Ovarian serous cystadenocarcinoma(29;0.0969)		9	965	-		Breast(17;0.231)	191			Protein kinase.		B4DYS6|D3DVV8|P19138|P20426|Q14013|Q5U065	Missense_Mutation	SNP	ENST00000217244.3	37	c.572G>A	CCDS13003.1	.	.	.	.	.	.	.	.	.	.	C	36	5.606366	0.96626	.	.	ENSG00000101266	ENST00000400227;ENST00000349736;ENST00000217244;ENST00000381973;ENST00000400217	T;T;T;T	0.43688	3.28;3.28;3.28;0.94	4.84	4.84	0.62591	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.049668	0.85682	D	0.000000	T	0.61640	0.2363	M	0.62154	1.92	0.80722	D	1	D	0.76494	0.999	D	0.67231	0.95	T	0.64795	-0.6323	10	0.87932	D	0	-4.8796	17.471	0.87646	0.0:1.0:0.0:0.0	.	191	P68400	CSK21_HUMAN	Q	191;191;191;191;55	ENSP00000383086:R191Q;ENSP00000339247:R191Q;ENSP00000217244:R191Q;ENSP00000383076:R55Q	ENSP00000217244:R191Q	R	-	2	0	CSNK2A1	420947	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.580000	0.82523	2.679000	0.91253	0.655000	0.94253	CGA		PASS	0.413	CSNK2A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077466.1	NM_001895		4	47	4	47	---	---	---	---
JPH2	57158	broad.mit.edu	37	20	42744725	42744725	+	Silent	SNP	C	C	A			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr20:42744725C>A	ENST00000372980.3	-	4	2462	c.1590G>T	c.(1588-1590)gcG>gcT	p.A530A		NM_020433.4	NP_065166.2	Q9BR39	JPH2_HUMAN	junctophilin 2	530	Pro-rich.				calcium ion homeostasis (GO:0055074)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport into cytosol (GO:0060402)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle tissue development (GO:0055024)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	calcium-release channel activity (GO:0015278)|phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)|phosphatidylserine binding (GO:0001786)	p.A530A(1)		NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(19)|prostate(1)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			TGCGGCGGCCCGCGCCCTCGG	0.761																																						uc002xli.1																			1	Substitution - coding silent(1)		lung(1)		0						c.(1588-1590)GCG>GCT		junctophilin 2 isoform 1							3.0	3.0	3.0					20																	42744725		1282	2992	4274	SO:0001819	synonymous_variant	57158				calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional sarcoplasmic reticulum membrane|plasma membrane		g.chr20:42744725C>A	AL034419	CCDS13325.1, CCDS13326.1	20q12-q13.11	2014-09-17			ENSG00000149596	ENSG00000149596			14202	protein-coding gene	gene with protein product		605267				10891348, 10949023	Standard	XM_006723832		Approved	JP-2	uc002xli.1	Q9BR39	OTTHUMG00000033037	ENST00000372980.3:c.1590G>T	20.37:g.42744725C>A							p.A530A	NM_020433	NP_065166	Q9BR39	JPH2_HUMAN	COAD - Colon adenocarcinoma(18;0.00189)		4	2463	-		Myeloproliferative disorder(115;0.0122)	530			Pro-rich.|Cytoplasmic (Potential).		E1P5X1|O95913|Q5JY74|Q9UJN4	Silent	SNP	ENST00000372980.3	37	c.1590G>T	CCDS13325.1																																																																																				PASS	0.761	JPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080307.1			5	2	5	2	---	---	---	---
LAMA5	3911	broad.mit.edu	37	20	60908748	60908748	+	Nonsense_Mutation	SNP	G	G	A			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr20:60908748G>A	ENST00000252999.3	-	24	2959	c.2893C>T	c.(2893-2895)Cag>Tag	p.Q965*	MIR4758_ENST00000577688.1_RNA	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	965	Domain IV 1 (domain IV B).				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)	p.Q965*(1)		breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			GCCACGGGCTGACTCTGTGCT	0.692																																						uc002ycq.2																			1	Substitution - Nonsense(1)		lung(1)	ovary(1)|pancreas(1)|skin(1)	3						c.(2893-2895)CAG>TAG		laminin alpha 5 precursor	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)						12.0	11.0	11.0					20																	60908748		2187	4274	6461	SO:0001587	stop_gained	3911				angiogenesis|cell proliferation|cell recognition|cytoskeleton organization|endothelial cell differentiation|focal adhesion assembly|integrin-mediated signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	integrin binding	g.chr20:60908748G>A	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.2893C>T	20.37:g.60908748G>A	ENSP00000252999:p.Gln965*						p.Q965*	NM_005560	NP_005551	O15230	LAMA5_HUMAN	BRCA - Breast invasive adenocarcinoma(19;4.36e-06)		24	2960	-	Breast(26;1.57e-08)		965			Domain IV 1 (domain IV B).		Q8TDF8|Q8WZA7|Q9H1P1	Nonsense_Mutation	SNP	ENST00000252999.3	37	c.2893C>T	CCDS33502.1	.	.	.	.	.	.	.	.	.	.	g	37	6.350542	0.97498	.	.	ENSG00000130702	ENST00000252999	.	.	.	4.24	3.2	0.36748	.	0.107759	0.64402	D	0.000010	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.7697	0.40582	0.0:0.0:0.5539:0.4461	.	.	.	.	X	965	.	ENSP00000252999:Q965X	Q	-	1	0	LAMA5	60342143	1.000000	0.71417	0.999000	0.59377	0.087000	0.18053	6.001000	0.70685	1.900000	0.55004	0.550000	0.68814	CAG		PASS	0.692	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		4	1	4	1	---	---	---	---
MCM3AP	8888	broad.mit.edu	37	21	47666692	47666692	+	Missense_Mutation	SNP	C	C	T			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr21:47666692C>T	ENST00000397708.1	-	22	4653	c.4399G>A	c.(4399-4401)Gag>Aag	p.E1467K	MCM3AP_ENST00000467026.1_5'UTR|MCM3AP-AS1_ENST00000414659.1_RNA|AP001469.7_ENST00000444966.1_RNA|MCM3AP-AS1_ENST00000590829.1_RNA|MCM3AP-AS1_ENST00000588753.1_RNA|MCM3AP-AS1_ENST00000455567.1_RNA|MCM3AP_ENST00000291688.1_Missense_Mutation_p.E1467K			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	1467					DNA replication (GO:0006260)|immune system process (GO:0002376)|mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transferase activity, transferring acyl groups (GO:0016746)	p.E1467K(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(5)|large_intestine(17)|lung(24)|ovary(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	72	Breast(49;0.112)					GCCATGTCCTCACTCTTCATT	0.602																																						uc002zir.1																			1	Substitution - Missense(1)		lung(1)	large_intestine(2)|lung(1)|ovary(1)|skin(1)	5						c.(4399-4401)GAG>AAG		minichromosome maintenance complex component 3							167.0	161.0	163.0					21																	47666692		2203	4300	6503	SO:0001583	missense	8888				DNA replication|protein import into nucleus	cytosol|nucleus	DNA binding|nucleotide binding	g.chr21:47666692C>T	AB005543	CCDS13734.1	21q22.3	2012-12-19	2007-04-04		ENSG00000160294	ENSG00000160294			6946	protein-coding gene	gene with protein product	"""germinal-centre associated nuclear protein"""	603294	"""minichromosome maintenance deficient (S. cerevisiae) 3-associated protein"", ""MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) associated protein"""			9712829, 16914116, 21195085	Standard	XM_005261205		Approved	Map80, KIAA0572, GANP, SAC3	uc002zir.1	O60318	OTTHUMG00000090630	ENST00000397708.1:c.4399G>A	21.37:g.47666692C>T	ENSP00000380820:p.Glu1467Lys					MCM3APAS_uc002zim.2_Intron|MCM3APAS_uc002zin.2_Intron|MCM3AP_uc002zio.1_5'UTR|MCM3AP_uc002zip.1_Missense_Mutation_p.E208K|MCM3AP_uc002ziq.1_Missense_Mutation_p.E394K|MCM3APAS_uc002zis.1_Intron	p.E1467K	NM_003906	NP_003897	O60318	MCM3A_HUMAN			21	4435	-	Breast(49;0.112)		1467					C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Missense_Mutation	SNP	ENST00000397708.1	37	c.4399G>A	CCDS13734.1	.	.	.	.	.	.	.	.	.	.	C	16.55	3.153573	0.57259	.	.	ENSG00000160294	ENST00000397708;ENST00000291688	T;T	0.04194	3.68;3.68	5.68	5.68	0.88126	.	0.412983	0.28072	N	0.016703	T	0.08626	0.0214	L	0.60455	1.87	0.36661	D	0.877938	B	0.32245	0.361	B	0.30646	0.118	T	0.08973	-1.0696	10	0.51188	T	0.08	-17.7588	17.9711	0.89113	0.0:1.0:0.0:0.0	.	1467	O60318	MCM3A_HUMAN	K	1467	ENSP00000380820:E1467K;ENSP00000291688:E1467K	ENSP00000291688:E1467K	E	-	1	0	MCM3AP	46491120	0.221000	0.23642	0.553000	0.28255	0.111000	0.19643	3.864000	0.56024	2.691000	0.91804	0.650000	0.86243	GAG		PASS	0.602	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906		140	214	140	214	---	---	---	---
HUWE1	10075	broad.mit.edu	37	X	53581603	53581603	+	Missense_Mutation	SNP	G	G	C			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chrX:53581603G>C	ENST00000342160.3	-	60	8942	c.8485C>G	c.(8485-8487)Ccc>Gcc	p.P2829A	MIRLET7F2_ENST00000385277.1_RNA|HUWE1_ENST00000262854.6_Missense_Mutation_p.P2829A|MIR98_ENST00000606724.1_RNA			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	2829					base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)	p.P2829A(1)|p.P2707A(1)		NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						CTTATAGTGGGAGCTGGGGAT	0.458																																						uc004dsp.2																			2	Substitution - Missense(2)		lung(2)	ovary(8)|large_intestine(4)|breast(4)|kidney(1)	17						c.(8485-8487)CCC>GCC		HECT, UBA and WWE domain containing 1							76.0	68.0	71.0					X																	53581603		2203	4300	6503	SO:0001583	missense	10075				base-excision repair|cell differentiation|histone ubiquitination|protein monoubiquitination|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	DNA binding|protein binding|ubiquitin-protein ligase activity	g.chrX:53581603G>C	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"""HECT, UBA and WWE domain containing 1"""			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.8485C>G	X.37:g.53581603G>C	ENSP00000340648:p.Pro2829Ala					HUWE1_uc004dsn.2_Missense_Mutation_p.P1653A	p.P2829A	NM_031407	NP_113584	Q7Z6Z7	HUWE1_HUMAN			61	8887	-			2829					O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	37	c.8485C>G	CCDS35301.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.84|17.84	3.488900|3.488900	0.64074|0.64074	.|.	.|.	ENSG00000086758|ENSG00000086758	ENST00000342160;ENST00000262854|ENST00000427052	T;T|.	0.46451|.	0.87;0.87|.	5.84|5.84	5.84|5.84	0.93424|0.93424	.|.	0.135528|.	0.50627|.	D|.	0.000111|.	T|T	0.57755|0.57755	0.2075|0.2075	L|L	0.29908|0.29908	0.895|0.895	0.80722|0.80722	D|D	1|1	D;D|.	0.67145|.	0.993;0.996|.	D;D|.	0.76071|.	0.971;0.987|.	T|T	0.52510|0.52510	-0.8566|-0.8566	10|5	0.30854|.	T|.	0.27|.	.|.	17.7627|17.7627	0.88469|0.88469	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	2829;2829|.	Q7Z6Z7;Q7Z6Z7-2|.	HUWE1_HUMAN;.|.	A|C	2829|1862	ENSP00000340648:P2829A;ENSP00000262854:P2829A|.	ENSP00000262854:P2829A|.	P|S	-|-	1|2	0|0	HUWE1|HUWE1	53598328|53598328	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	8.569000|8.569000	0.90744|0.90744	2.467000|2.467000	0.83353|0.83353	0.600000|0.600000	0.82982|0.82982	CCC|TCC		PASS	0.458	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		41	2	41	2	---	---	---	---
DRP2	1821	broad.mit.edu	37	X	100494030	100494030	+	Missense_Mutation	SNP	C	C	A			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chrX:100494030C>A	ENST00000395209.3	+	6	1026	c.499C>A	c.(499-501)Cag>Aag	p.Q167K	DRP2_ENST00000538510.1_Missense_Mutation_p.Q167K|DRP2_ENST00000402866.1_Missense_Mutation_p.Q167K|DRP2_ENST00000541709.1_Missense_Mutation_p.Q89K	NM_001939.2	NP_001930.2	Q13474	DRP2_HUMAN	dystrophin related protein 2	167					central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)	p.Q164K(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(10)|ovary(3)|prostate(1)|skin(2)|urinary_tract(2)	31						GGAGTCAGCTCAGGCCTTCCT	0.473																																						uc004egz.2																			1	Substitution - Missense(1)		lung(1)	ovary(2)	2						c.(499-501)CAG>AAG		dystrophin related protein 2							158.0	134.0	142.0					X																	100494030		2203	4300	6503	SO:0001583	missense	1821				central nervous system development	cytoplasm|cytoskeleton	zinc ion binding	g.chrX:100494030C>A	U43519	CCDS14480.2, CCDS55465.1	Xq22	2008-02-05			ENSG00000102385	ENSG00000102385			3032	protein-coding gene	gene with protein product		300052				8640231	Standard	NM_001939		Approved		uc004egz.2	Q13474	OTTHUMG00000022020	ENST00000395209.3:c.499C>A	X.37:g.100494030C>A	ENSP00000378635:p.Gln167Lys					DRP2_uc011mrh.1_Missense_Mutation_p.Q89K	p.Q167K	NM_001939	NP_001930	Q13474	DRP2_HUMAN			6	868	+			167			Spectrin 1.		A6ZKI5|A8K1B0|B1B1F3|B4DIZ0	Missense_Mutation	SNP	ENST00000395209.3	37	c.499C>A	CCDS14480.2	.	.	.	.	.	.	.	.	.	.	C	25.7	4.661570	0.88154	.	.	ENSG00000102385	ENST00000402866;ENST00000395209;ENST00000541709;ENST00000538510	T;T;T;T	0.36699	1.24;1.24;1.24;1.24	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.53916	0.1826	L	0.52364	1.645	0.58432	D	0.999997	P	0.49447	0.924	P	0.62298	0.9	T	0.50171	-0.8859	10	0.44086	T	0.13	-13.3455	18.2643	0.90048	0.0:1.0:0.0:0.0	.	167	Q13474	DRP2_HUMAN	K	167;167;89;167	ENSP00000385038:Q167K;ENSP00000378635:Q167K;ENSP00000444752:Q89K;ENSP00000441051:Q167K	ENSP00000362007:Q167K	Q	+	1	0	DRP2	100380686	1.000000	0.71417	0.997000	0.53966	0.893000	0.52053	7.257000	0.78362	2.251000	0.74343	0.499000	0.49734	CAG		PASS	0.473	DRP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057522.3	NM_001939		130	12	130	12	---	---	---	---
ARID1A	8289	broad.mit.edu	37	1	27056345	27056346	+	Frame_Shift_Ins	INS	-	-	AC			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr1:27056345_27056346insAC	ENST00000324856.7	+	2	1712_1713	c.1341_1342insAC	c.(1342-1344)acafs	p.T448fs	ARID1A_ENST00000374152.2_Frame_Shift_Ins_p.T65fs|ARID1A_ENST00000457599.2_Frame_Shift_Ins_p.T448fs	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	448					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)	p.Y447*(1)	ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		GCCTCTCTTATACACAGCAGGT	0.554			"""Mis, N, F, S, D"""		"""clear cell ovarian carcinoma, RCC"""																																	uc001bmv.1				Rec	yes		1	1p35.3	8289	Mis|N|F|S|D	AT rich interactive domain 1A (SWI-like)			E			clear cell ovarian carcinoma|RCC		1	Substitution - Nonsense(1)	p.Y447*(1)	ovary(1)	ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	142						c.(1339-1344)TATACAfs		AT rich interactive domain 1A isoform a																																				SO:0001589	frameshift_variant	8289				androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent	nBAF complex|npBAF complex|SWI/SNF complex	DNA binding|protein binding	g.chr1:27056345_27056346insAC	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"""-"""	11110	protein-coding gene	gene with protein product		603024	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1"", ""AT rich interactive domain 1A (SWI- like)"""	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.1344_1345dupAC	1.37:g.27056348_27056349dupAC	ENSP00000320485:p.Thr448fs					ARID1A_uc001bmt.1_Frame_Shift_Ins_p.Y447fs|ARID1A_uc001bmu.1_Frame_Shift_Ins_p.Y447fs|ARID1A_uc001bmw.1_Frame_Shift_Ins_p.Y64fs	p.Y447fs	NM_006015	NP_006006	O14497	ARI1A_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)	2	1714_1715	+		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)	447_448					D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Ins	INS	ENST00000324856.7	37	c.1341_1342insAC	CCDS285.1																																																																																					0.554	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		66	38	66	38	---	---	---	---
CTBS	1486	broad.mit.edu	37	1	85040032	85040033	+	Frame_Shift_Ins	INS	-	-	CA	rs201734152	byFrequency	TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr1:85040032_85040033insCA	ENST00000370630.5	-	1	114_115	c.66_67insTG	c.(64-69)ctagcgfs	p.A23fs	CTBS_ENST00000477677.1_5'UTR	NM_004388.2	NP_004379.1	Q01459	DIAC_HUMAN	chitobiase, di-N-acetyl-	23					chitin catabolic process (GO:0006032)|oligosaccharide catabolic process (GO:0009313)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	chitinase activity (GO:0004568)			breast(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)	9				all cancers(265;0.00727)|Epithelial(280;0.0192)|OV - Ovarian serous cystadenocarcinoma(397;0.166)		gccagcagcgcTAGACCCGGGA	0.733																																						uc001dka.2																			0					0						c.(64-69)CTAGCGfs		chitobiase, di-N-acetyl- precursor																																				SO:0001589	frameshift_variant	1486					lysosome	cation binding	g.chr1:85040032_85040033insCA	M95767	CCDS698.1	1p22	2010-05-04			ENSG00000117151	ENSG00000117151	3.2.1.-		2496	protein-coding gene	gene with protein product		600873		CTB		1549114, 7606925	Standard	NM_004388		Approved		uc001dka.2	Q01459	OTTHUMG00000009922	ENST00000370630.5:c.66_67insTG	1.37:g.85040032_85040033insCA	ENSP00000359664:p.Ala23fs					CTBS_uc001dkc.2_Translation_Start_Site|CTBS_uc001dkd.2_Translation_Start_Site|CTBS_uc001dkb.2_Translation_Start_Site	p.L22fs	NM_004388	NP_004379	Q01459	DIAC_HUMAN		all cancers(265;0.00727)|Epithelial(280;0.0192)|OV - Ovarian serous cystadenocarcinoma(397;0.166)	1	131_132	-			22_23					Q5VX50	Frame_Shift_Ins	INS	ENST00000370630.5	37	c.66_67insTG	CCDS698.1																																																																																					0.733	CTBS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027457.2	NM_004388		6	5	6	5	---	---	---	---
Unknown	0	broad.mit.edu	37	6	28185336	28185337	+	IGR	INS	-	-	T	rs199720838|rs113483443|rs565354205		TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr6:28185336_28185337insT								ZNF192P1 (47964 upstream) : ZSCAN9 (7704 downstream)																							tccttttcctcttttttttttt	0.436																																						uc011dla.1																			0					0								Homo sapiens pp14762 mRNA, complete cds.																																				SO:0001628	intergenic_variant	222699							g.chr6:28185336_28185337insT																													6.37:g.28185347_28185347dupT								NR_002936						1		-									RNA	INS		37	c.1371_1372insA																																																																																				0		0.436									5	3	5	3	---	---	---	---
KMT2C	58508	broad.mit.edu	37	7	151875059	151875060	+	Frame_Shift_Ins	INS	-	-	T			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr7:151875059_151875060insT	ENST00000262189.6	-	38	7696_7697	c.7478_7479insA	c.(7477-7479)ccgfs	p.P2493fs	KMT2C_ENST00000355193.2_Frame_Shift_Ins_p.P2493fs	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	2493	Pro-rich.				histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										GCTCTTGACTCGGCATGGTACC	0.361																																						uc003wla.2										N							medulloblastoma		0				large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63						c.(7477-7479)CCGfs		myeloid/lymphoid or mixed-lineage leukemia 3																																				SO:0001589	frameshift_variant	58508				intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding	g.chr7:151875059_151875060insT	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.7478_7479insA	7.37:g.151875059_151875060insT	ENSP00000262189:p.Pro2493fs					MLL3_uc003wkz.2_Frame_Shift_Ins_p.P1554fs|MLL3_uc003wky.2_Frame_Shift_Ins_p.P2fs	p.P2493fs	NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)	38	7697_7698	-	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	2493			Pro-rich.		Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Frame_Shift_Ins	INS	ENST00000262189.6	37	c.7478_7479insA	CCDS5931.1																																																																																					0.361	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			122	87	122	87	---	---	---	---
FOCAD	54914	broad.mit.edu	37	9	20862670	20862671	+	Frame_Shift_Del	DEL	TC	TC	-			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr9:20862670_20862671delTC	ENST00000380249.1	+	18	2378_2379	c.2014_2015delTC	c.(2014-2016)tctfs	p.S672fs	FOCAD_ENST00000605086.1_Frame_Shift_Del_p.S108fs|FOCAD_ENST00000338382.6_Frame_Shift_Del_p.S672fs	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	672						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)											TGAACTATTTTCTCTAGTTCCT	0.421																																						uc003zog.1																			0				ovary(8)|breast(1)|kidney(1)	10						c.(2014-2016)TCTfs		hypothetical protein LOC54914																																				SO:0001589	frameshift_variant	54914					integral to membrane	binding	g.chr9:20862670_20862671delTC	AB058700	CCDS34993.1	9p21	2012-03-23	2012-03-23	2012-03-23	ENSG00000188352	ENSG00000188352			23377	protein-coding gene	gene with protein product		614606	"""KIAA1797"""	KIAA1797		22427331	Standard	XM_006716794		Approved	FLJ20375	uc003zog.1	Q5VW36	OTTHUMG00000066930	ENST00000380249.1:c.2014_2015delTC	9.37:g.20862672_20862673delTC	ENSP00000369599:p.Ser672fs					KIAA1797_uc003zoh.1_Frame_Shift_Del_p.S108fs	p.S672fs	NM_017794	NP_060264	Q5VW36	K1797_HUMAN		GBM - Glioblastoma multiforme(3;2.1e-125)|Lung(42;2.76e-14)|LUSC - Lung squamous cell carcinoma(42;1.99e-11)	18	2377_2378	+			672					D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Frame_Shift_Del	DEL	ENST00000380249.1	37	c.2014_2015delTC	CCDS34993.1																																																																																					0.421	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794		54	116	54	116	---	---	---	---
SMCHD1	23347	broad.mit.edu	37	18	2688481	2688483	+	In_Frame_Del	DEL	TCT	TCT	-			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr18:2688481_2688483delTCT	ENST00000320876.6	+	6	1066_1068	c.728_730delTCT	c.(727-732)gtcttc>gtc	p.F245del	SMCHD1_ENST00000261598.8_In_Frame_Del_p.F245del|RP11-703M24.5_ENST00000583546.1_RNA	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	245					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						AAGCAAGCTGTCTTCTTTGTTGG	0.35																																						uc002klm.3																			0					0						c.(727-732)GTCTTC>GTC		structural maintenance of chromosomes flexible																																				SO:0001651	inframe_deletion	23347				chromosome organization		ATP binding	g.chr18:2688481_2688483delTCT	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.728_730delTCT	18.37:g.2688484_2688486delTCT	ENSP00000326603:p.Phe245del						p.F245del	NM_015295	NP_056110	A6NHR9	SMHD1_HUMAN			6	917_919	+			245					O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	In_Frame_Del	DEL	ENST00000320876.6	37	c.728_730delTCT	CCDS45822.1																																																																																					0.350	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			117	82	117	82	---	---	---	---
SPTBN4	57731	broad.mit.edu	37	19	41076449	41076450	+	Frame_Shift_Ins	INS	-	-	A	rs376707355		TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr19:41076449_41076450insA	ENST00000352632.3	+	33	7220_7221	c.7134_7135insA	c.(7135-7137)aagfs	p.K2379fs	SPTBN4_ENST00000392025.1_Frame_Shift_Ins_p.K1122fs|SPTBN4_ENST00000598249.1_Frame_Shift_Ins_p.K2379fs			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	2379					actin filament capping (GO:0051693)|adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cardiac conduction (GO:0061337)|central nervous system projection neuron axonogenesis (GO:0021952)|clustering of voltage-gated sodium channels (GO:0045162)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization to plasma membrane (GO:0090002)|fertilization (GO:0009566)|negative regulation of heart rate (GO:0010459)|positive regulation of multicellular organism growth (GO:0040018)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of sodium ion transport (GO:0002028)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|axon hillock (GO:0043203)|axon initial segment (GO:0043194)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|nuclear matrix (GO:0016363)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|PML body (GO:0016605)|spectrin (GO:0008091)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phosphatase binding (GO:0019902)|phospholipid binding (GO:0005543)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			breast(4)|central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	73			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			gggaccggcccaagccgcgacg	0.812																																						uc002ony.2																			0				ovary(3)|central_nervous_system(1)|skin(1)	5						c.(7132-7137)CCCAAGfs		spectrin, beta, non-erythrocytic 4 isoform				40,912		11,18,447						4.4	1.0			2	142,2212		44,54,1079	no	frameshift	SPTBN4	NM_020971.2		55,72,1526	A1A1,A1R,RR		6.0323,4.2017,5.5051				182,3124				SO:0001589	frameshift_variant	57731				actin filament capping|axon guidance|cytoskeletal anchoring at plasma membrane|vesicle-mediated transport	cytosol|nuclear matrix|PML body|spectrin	actin binding|ankyrin binding|structural constituent of cytoskeleton	g.chr19:41076449_41076450insA	AF082075	CCDS12559.1, CCDS42569.1	19q13.13	2013-01-10				ENSG00000160460		"""Pleckstrin homology (PH) domain containing"""	14896	protein-coding gene	gene with protein product		606214				11086001	Standard	NM_020971		Approved	SPTBN3, KIAA1642	uc002onz.3	Q9H254		ENST00000352632.3:c.7136dupA	19.37:g.41076451_41076451dupA	ENSP00000263373:p.Lys2379fs					SPTBN4_uc002onz.2_Frame_Shift_Ins_p.P2378fs|SPTBN4_uc010egx.2_Frame_Shift_Ins_p.P1121fs	p.P2378fs	NM_020971	NP_066022	Q9H254	SPTN4_HUMAN	Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)		33	7220_7221	+			2378_2379					E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Frame_Shift_Ins	INS	ENST00000352632.3	37	c.7134_7135insA	CCDS12559.1																																																																																					0.812	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2			5	3	5	3	---	---	---	---
SHANK3	85358	broad.mit.edu	37	22	51159932	51159933	+	Frame_Shift_Ins	INS	-	-	G			TCGA-21-1078-01A-01D-1521-08	TCGA-21-1078-11A-01D-1521-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8cf9b32d-3d6f-4898-8c7a-89511b754021	59ed3755-0b09-4a75-81bf-0994e7a2d11a	g.chr22:51159932_51159933insG	ENST00000414786.2	+	21	3856_3857	c.3629_3630insG	c.(3628-3633)ctggggfs	p.LG1210fs	SHANK3_ENST00000262795.3_Frame_Shift_Ins_p.LG1240fs|SHANK3_ENST00000445220.2_Frame_Shift_Ins_p.LG1226fs			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	1224					adult behavior (GO:0030534)|alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|brain morphogenesis (GO:0048854)|dendritic spine morphogenesis (GO:0060997)|guanylate kinase-associated protein clustering (GO:0097117)|learning (GO:0007612)|MAPK cascade (GO:0000165)|memory (GO:0007613)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell volume (GO:0045794)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glutamate receptor signaling pathway (GO:1900451)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse structural plasticity (GO:0051835)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density assembly (GO:0097107)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of long term synaptic depression (GO:1900452)|regulation of long-term synaptic potentiation (GO:1900271)|social behavior (GO:0035176)|striatal medium spiny neuron differentiation (GO:0021773)|synapse assembly (GO:0007416)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(5)	8		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)		CCCAGCAGGCTGGGGGGGGCCG	0.718																																						uc003bne.1																			0				central_nervous_system(1)	1						c.(3718-3720)CTGfs		SH3 and multiple ankyrin repeat domains 3																																				SO:0001589	frameshift_variant	85358							g.chr22:51159932_51159933insG	AB051437		22q13.3	2013-11-14			ENSG00000251322	ENSG00000251322		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	14294	protein-coding gene	gene with protein product	"""proline rich synapse associated protein 2"", ""shank postsynaptic density protein"""	606230				11258795, 11431708, 10806096, 17173049	Standard	NM_033517		Approved	SPANK-2, prosap2, KIAA1650, PSAP2	uc031ryd.1	Q9BYB0	OTTHUMG00000150169	ENST00000414786.2:c.3637dupG	22.37:g.51159940_51159940dupG	ENSP00000464552:p.Leu1210fs					SHANK3_uc003bnf.1_Frame_Shift_Ins_p.L687fs|SHANK3_uc010hbg.1_Frame_Shift_Ins_p.L422fs	p.L1240fs	NM_001080420	NP_001073889	F2Z3L0	F2Z3L0_HUMAN		BRCA - Breast invasive adenocarcinoma(115;0.22)	22	3719_3720	+		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)	1240					D7UT47|Q8TET3	Frame_Shift_Ins	INS	ENST00000414786.2	37	c.3719_3720insG																																																																																						0.718	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420		4	2	4	2	---	---	---	---
